Instrumentation and methods for analysis of nucleic acids

Abstract

The present disclosure provides various systems, diagnostic devices, and methods for nucleic acid analysis. The systems, devices, and methods allow for the analysis of nucleic acids, in a sample, via programmable nuclease-based assays. Provided are systems comprising an instrument and a cartridge allowing for point of care use. The systems, devices, and methods described herein can be configured for multiplexed detection of nucleic acids in a single sample.

Description

INSTRUMENTATION AND METHODS FOR ANALYSIS OF NUCLEIC ACIDSCROSS-REFERENCE

[0001] This application claims priority to U.S. Provisional Application Serial No. 63 / 517,870 filed August 4, 2023, which is incorporated herein in its entirety for all purposes.BACKGROUND

[0002] Nucleic acid tests can be used to detect and identify nucleic acid sequences associated with disease-causing organisms, such as influenza. Diagnostic tests that detect the presence or absence of disease-associated nucleic acids often have an advantage in sensitivity and specificity over other test methods, such as those based on protein detection (e.g., antigens of a pathogenic organism). Currently, existing lower cost, easy-to-use nucleic acid-based test systems are limited in their ability to perform multiplexing due at least in part to difficulties in signal differentiation while trying to maintain a high reliability at lower cost and greater ease of use.

[0003] Detection of ailments, especially at the early stages of disease or infection, can provide guidance on treatment or intervention to reduce the progression or transmission of said ailments. Unfortunately, there is currently a lack of low cost and easy to use systems capable of such detection assays. Existing systems, due at least in part to the cost and / or ease of use hurdles, may be less than ideal as a candidate for widespread decentralization.SUMMARY

[0004] In view of the foregoing, it would be desirable to provide an easy to use, low cost, decentralized nucleic acid test system capable of multiplexing samples and / or detected targets. Systems, methods, and compositions described herein address this need, and provide other advantages as well. Not necessarily all such aspects or advantages are achieved by any particular embodiment. Thus, various embodiments may be carried out in a manner that achieves or optimizes one advantage or group of advantages taught herein without necessarily achieving other aspects or advantages as may also be taught or suggested herein.

[0005] In various aspects, the present disclosure provides cartridges and devices for detecting nucleic acids, systems comprising the same, and methods of use thereof. The systems or components thereof may be configured for one or more of initial sample processing (e.g., nucleic acid extraction), nucleic acid amplification, and / or nucleic acid detection. In someembodiments, the system or a component thereof (e.g., a cartridge) is configured for nucleic acid amplification. In some embodiments, the system or a component thereof is configured for nucleic acid amplification and detection. A non-limiting example of a nucleic acid detection comprises methodologies using a programmable nuclease.

[0006] An aspect of the present disclosure provides a system for detecting a target nucleic acid, the system comprising: an instrument configured to interface with a cartridge; wherein: (a) the instrument includes: (i) one or more pumps; (ii) at least one valve actuator; (iii) a light source configured to illuminate a detection region of the cartridge; and (iv) an optical sensor configured to detect one or more signals from the detection region; (b) the cartridge includes: (i) a sample interface configured to receive a sample including one or more nucleic acids; (ii) one or more reagent capsules; (iii) a sample preparation region; (iv) a detection region; (iv) and a plurality of pump interfaces fluidically connected to the sample interface, the one or more reagent capsules, the sample preparation region, and the detection region via a plurality of valves; (c) the one or more pumps is configured to apply positive and / or negative pressure through the plurality of pump interfaces; (d) the at least one valve actuator is configured to actuate the plurality of valves; (e) one or more pumps and at least one valve actuator are operable to move fluid between the sample interface, the one or more reagent capsules, the sample preparation region, and the detection region; and (f) the detection region includes a plurality of chambers that are fluidically connected to one another.

[0007] In some embodiments, each chamber of the plurality of chambers further includes detection reagents including a guide nucleic acid and a reporter, and further wherein: (a) each guide nucleic acid (i) includes a targeting sequence that hybridizes with a target nucleic acid of a plurality of different target nucleic acids or an amplicon thereof, and (ii) is effective to form a complex with a programmable nuclease that is activated upon binding the corresponding target nucleic acid or amplicon thereof; (b) the guide nucleic acid of a first chamber in the plurality of chambers includes a different targeting sequence from the guide nucleic acid of a second chamber in the plurality of chambers; and (c) each reporter (i) includes a cleavable nucleic acid and a detection moiety, and (ii) is configured to be cleaved to form a detectable cleavage product in response to activation of the complex in the respective chamber.

[0008] In some embodiments, (a) the one or more reagent capsules comprises dried reagents; (b) the cartridge comprises one or more fluid reservoirs; and (c) a pump of the one or more pumps is configured to move fluid from the fluid reservoir to the one or more reagent capsules. In some embodiments, (a) the instrument comprises one or more heaters; and (b) at least one of the one ormore heaters is configured to interface with the detection region and heat contents thereof. In some embodiments, (a) the sample preparation region comprises a lysis region for the lysis one or more components of the sample; and optionally (b) at least one of the one or more reagent capsules comprises lysis reagents. In some embodiments, at least one of the one or more heaters, is configured to interface with the sample preparation region and heat the contents thereof. In some embodiments, (a) the cartridge further comprises a nucleic acid capture region; (b) the one or more pumps comprises an actuator operable to move a sample preparation fluid through the nucleic acid capture region to capture the one or more nucleic acids; and (c) the one or more pumps comprises an actuator operable to move an elution fluid from one of the one or more fluid reservoirs through the nucleic acid capture region to release the captured nucleic acids.

[0009] In some embodiments, at least one of the one or more reagent capsules or the plurality of chambers comprises a programmable nuclease. In some embodiments, (a) the programmable nuclease comprises a Cas protein; and optionally (b) the Cas protein comprises Casl2, Casl3, Cast 4, CasPhi, a thermostable Cas, or any combination thereof. In some embodiments, (a) the detection reagents further comprise amplification reagents; and optionally (b) the amplification reagents in each chamber of the plurality of chambers comprises one or more primers for amplifying the target nucleic acid bound by the respective targeting sequence. In some embodiments, (a) the detection reagents are in a lyophilized form, and / or (b) the guide nucleic acid and / or the reporter in each chamber are immobilized to a surface of the respective chamber.

[0010] In some embodiments, the system further comprises a gear that translates the cartridge between two or more positions in the instrument. In some embodiments, the two or more positions comprise positions in which (a) one of the one or more pumps aligns with one or more of the plurality of pump interfaces; (b) one of the at least one valve actuator aligns with one or more of the plurality of valves; (c) the optical sensor aligns with the detection region; or (d) any combination thereof. In some embodiments, the two or more positions comprise a position in which at least one of the one or more heaters aligns with the sample preparation region or the detection region.

[0011] In some embodiments, the system further comprises a user interface for receiving instructions from a user. In some embodiments, the system further comprises a non-transitory computer-readable medium with instructions stored thereon, that when executed by one or more processors, (a) activates the one or more pumps and the at least one valve actuator to move fluid between the sample interface, the one or more reagent capsules, the sample preparation region, and the detection region; (b) activates the light source; (c) stores detection results from theoptical sensor; and (d) reports results to a user.

[0012] In one aspect, the present disclosure provides methods for detecting one or more of a plurality of different target nucleic acids. In some embodiments, the detecting is performed using any of the systems described herein. In some embodiments, the method comprises: (a) flowing a liquid comprising one or more of the different target nucleic acids or amplicons thereof into the plurality of chambers; (b) in one or more of the plurality of chambers, forming the activated complex and cleaving the reporters; and (c) detecting the detectable cleavage products in one or more of the plurality of chambers, wherein the location of a chamber comprising a detectable cleavage product identifies the target nucleic acid or amplicon thereof present in the chamber.INCORPORATION BY REFERENCE

[0013] All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference.BRIEF DESCRIPTION OF THE DRAWINGS

[0014] The novel features of the present disclosure are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present disclosure may be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the present disclosure are utilized, and the accompanying drawings of which:

[0015] FIGS. 1A-1C show representations of exemplary cartridge embodiments and instrument structure. FIG. 1A and FIG. 1C show representations of exemplary cartridges described herein. FIG. IB shows a representation of an exemplary instrument for use with cartridges described herein. Illustrative dimensions are shown in inches.

[0016] FIGS. 2A-2C show illustrative views and schematic representations of a cartridge and operations thereof, according to some embodiments. FIG. 2A shows a schematic representation of a process workflow. FIG. 2B shows a representation of an exemplary cartridge (top view). Elements illustrated in FIG. 2B include dried reagents (enzyme (E), activator (A), extra reagent (ER), proteinase K (PK), and lysis (L)), vents (v), and pumps to transfer / mix (P). FIG. 2C shows a representation of an exemplary cartridge (perspective view).

[0017] FIG. 3 shows a schematic representation of a process workflow in a cartridge of FIGS. 2A-2C, with components used during a sample lysis step indicated by outline.

[0018] FIG. 4 shows a schematic representation of a process workflow in a cartridge of FIGS. 2A-2C, with components used during a nucleic acid binding / capture step indicated by outline.

[0019] FIG. 5 shows a schematic representation of a process workflow in a cartridge of FIGS. 2A-2C, with components used during one or more washing steps indicated by an outline.

[0020] FIG. 6 shows a schematic representation of a process workflow in a cartridge of FIGS. 2A-2C, with components used during an elution step and a detection step indicated by an outline.

[0021] FIG. 7 shows an illustrative schematic representation for the operation of a two-pump, two-valve cartridge, in accordance with some embodiments. Illustrated elements include dried tRNA (R), dried lysis reagent (L), neutralizer (N), activator (A), and LAMP + CRISPR reagents (L / C).

[0022] FIGS. 8A-8B show side (FIG. 8A) and top (FIG. 8B) view representations of an exemplary cartridge housing, including dimensions indicated in millimeters and inches.

[0023] FIG. 9 shows a perspective view representation of an exemplary cartridge housing.

[0024] FIGS. 10A-10B shows views of internal components of an exemplary cartridge with housing removed, according to some embodiments. FIG. 10A shows a perspective view of the cartridge. FIG. 10B shows: (a) a perspective view of a dry reagent capsule body, perspective view with transparent body housing, and cross-sectional view along YZ plane of the dry reagent capsule body (top row, left to right); and (b) an exploded view of a dry reagent capsule assembly, and cross-sectional view of assembled dry reagent capsule along YZ plane including connections to fluid channels below the dry reagent capsule (bottom row, left to right).

[0025] FIG. 10C shows an exploded view of an exemplary cartridge assembly, in accordance with embodiments.

[0026] FIG. 11 shows an exploded view of a cartridge rotary valve, according to some embodiments. Part A includes the fluid holes that act as the valve inlet and outlet ports. Part B is an elastomeric sealing gasket that prevents leaking. During manufacture, Part B is affixed to Part C by over-molding adhesion of the Part B and Part C plastics. Part D compresses the combined Parts B and C to Part A. Part D is joined to Part A by laser welding or ultrasonic welding or the like. The joining of Part D to Part A also forms fluid paths on the cartridge bottom. A similar joining of another plastic part to the top of Part A also provides fluidic chambers and channels(now shown).

[0027] FIG. 12 shows a perspective view representation of dry reagent chambers of an exemplary cartridge and a detection region (e.g., for a DETECTR reaction).

[0028] FIG. 13 shows a layout diagram of an exemplary detection region (e.g., for a DETECTR reaction).

[0029] FIG. 14 shows cartridge positions in various zones within an exemplary instrument described herein.

[0030] FIG. 15 shows cartridge working zones with optical interfaces highlighted.

[0031] FIG. 16 is an illustration of an exemplary instrument (with housing and display removed) comprising four instrument modules shown that directly interface with a cartridge as it is moved through the exemplary instrument by a cartridge mover module.

[0032] FIG. 17 is an illustration of an exemplary instrument showing an exemplary cartridge for insertion into an instrument described herein.

[0033] FIG. 18 is an illustration of an isometric frontal view of an exemplary instrument showing an exemplary cartridge in an instrument described herein.

[0034] FIG. 19 is an illustration of an instrument module contacting an exemplary cartridge.

[0035] FIG. 20 is an illustration of a cartridge mover module, with a gear that translates a cartridge between two or more positions in an instrument described herein.

[0036] FIG. 21 is an illustration of a layout of optical components in an instrument’s optical module, in accordance with some embodiments.

[0037] FIG. 22 is an illustration of an exemplary thermal module for heating portions of a cartridge described herein.

[0038] FIG. 23 is an exploded view of an exemplary thermal module, according to some embodiments.

[0039] FIG. 24 is an illustration of an isometric view of a thermal module in an instrument described herein.

[0040] FIG. 25 is an illustration of a pump module including reagent capsule pushers and actuators, according to some embodiments.

[0041] FIG. 26 is an illustration of a pump module viewed from within the cartridge housing, according to some embodiments.

[0042] FIG. 27 is a side view illustration of a cartridge interfacing with a pump module and rotary valve actuator, according to some embodiments.

[0043] FIG. 28 is an illustration of a rotary valve actuator, according to some embodiments.

[0044] FIGS. 29A-29B are illustrations of a rotary valve actuator contacting a cartridge, according to some embodiments. FIG. 29A is an illustration of an external view of a rotary valve actuator contacting a cartridge. FIG. 29B is an illustration of a perspective view of a rotary valve actuator showing where it contacts a cartridge, with transparent cartridge for ease of viewing.

[0045] FIG. 30 is an illustration of a cartridge bottom with three rotary valves oriented for instrument loading and unloading, in accordance with some embodiments.

[0046] FIG. 31 is an illustration of an instrument back without a cover, showing power and communications connection at the bottom.

[0047] FIG. 32 is an exploded view of an instrument showing communications and controller modules, according to some embodiments.

[0048] FIGS. 33A-33B depict representations of illustrative microfluidic devices comprising a plurality of chambers fluidically connected in sequence, corresponding to a detection region of a cartridge in accordance with some embodiments. Each of the illustrated chambers comprises a well, an inlet channel, an outlet, and a capillary valve. The locations of wells, capillary valves, and outlets are labeled. FIGS. 33A and 33B present alternative arrangements of the capillary valves and outlets relative to the respective wells. In FIG. 33A, an outlet defines a volume of the respective chamber that is separate from but fluidically connected to the respective well. In FIG. 33B, an outlet corresponds to an opening of the respective well, which may optionally be sealed by an air-permeable membrane (not shown).

[0049] FIGS. 34A-34C depict different views of a microfluidic device in accordance with some embodiments. FIG. 34A shows a perspective view of a top surface of a detection region of the microfluidic device. FIG. 34B shows a perspective cross-sectional view of the top surface of the detection region. FIG. 34C shows a plan view of the top surface of the detection region. The illustrated microfluidic device comprises a plurality of chambers fluidically connected in sequence, in which each chamber of the plurality of chambers comprises a well, an inlet channel, an outlet, and a capillary valve. The arrangement of features in the device and fluid flow within the device is similar to those illustrated in FIG. 33A.

[0050] FIG. 35 depicts a perspective view of a bottom surface of the detection region of the microfluidic device shown in FIGS. 34A-34C. Optional features added to the bottom of thedevice around the outlets to help ultrasonically weld an air-permeable membrane to the device are shown.

[0051] FIG. 36 depicts a perspective view of a top surface of a microfluidic device in accordance with some embodiments. The illustrated device is similar to that illustrated in FIGS. 34A-34C, except a film is used instead of a molded lid.

[0052] FIG. 37 depicts a perspective cross-sectional view of a microfluidic device in accordance with some embodiments. The illustrated device is similar to that illustrated in FIGS. 34A-34C, except the membrane can be compounded with an adhesive backing to adhere to the device instead of using laser welding or ultrasonic welding or heat staking.

[0053] FIGS. 38A-38D depict an exemplary detection region of a microfluidic device in accordance with some embodiments. FIGS. 38A-38B show perspective and plan views of the top of the device, respectively. FIG. 38C-38D show perspective and plan views of the bottom of the device, respectively. The illustrated device includes a plurality of chambers fluidically connected in sequence, and connected to an upstream first inlet channel by way of a bubble purge channel (or a bubble trap) disposed therebetween. In operation, bubbles in the liquid of the first inlet channel enter the bubble purge channel and escape through a hydrophobic or oleophobic membrane covering the bottom surface of the bubble purge channel. The liquid itself is substantially prevented from passing through the membrane and instead continues to flow along the bubble purge channel towards its exit into a second inlet channel, reduced in or substantially free of bubbles. The second inlet channel feeds into the plurality of chambers. Also illustrated is the location of the hydrophobic and / or oleophobic membrane that covers at least a portion of a bottom surface of the device.

[0054] FIG. 39 depicts a surface comprising an immobilized programmable nuclease-guide nucleic acid complex and a plurality of reporters, where one reporter has been cleaved by an activated programmable nuclease, in accordance with embodiments.

[0055] FIGS. 40A-40E depict exemplary reporters immobilized on a substrate, in accordance with embodiments. Arrows indicate signal (e.g., fluorescence) change when the reporter is cleaved by a programmable nuclease.

[0056] FIG. 41 depicts an exemplary high-level workflow for using a multiplex detection system, in accordance with some embodiments. The illustrated process provides a multiplex method for detecting target nucleic acids from influenza virus A (IVA), influenza virus B (IVB), respiratory syncytial virus (RSV), SARS-CoV-2 (SC2), and RNase P (RP). The illustratedreaction containers correspond to reaction locations withing a cartridge described herein (e.g., lysis, mixing, and amplification / detection regions).

[0057] FIG. 42 depicts an exemplary sample collection workflow, in accordance with embodiments.DETAILED DESCRIPTION

[0058] In the following detailed description, reference is made to the accompanying figures, which form a part hereof. In the figures, similar symbols typically identify similar components, unless context dictates otherwise. The illustrative embodiments described in the detailed description, figures, and claims are not meant to be limiting. Other embodiments may be utilized, and other changes may be made, without departing from the scope of the subject matter presented herein. It will be readily understood that aspects of the present disclosure, as generally described herein, and illustrated in the figures, can be arranged, substituted, combined, separated, and designed in a wide variety of different configurations, all of which are explicitly contemplated herein.

[0059] Although certain embodiments and examples are disclosed below, inventive subject matter extends beyond the specifically disclosed embodiments to other alternative embodiments and / or uses, and to modifications and equivalents thereof. Thus, the scope of the claims appended hereto is not limited by any of the particular embodiments described below. For example, in any method or process disclosed herein, the acts or portions of the method or process may be performed in any suitable sequence and are not necessarily limited to any particular disclosed sequence. Various operations may be described as multiple discrete operations in turn, in a manner that may be helpful to understanding certain embodiments, however, the order of the description should not be construed to imply that these operations are order dependent.Additionally, structures, systems, and / or devices described herein may be embodied as integrated components or as separate components.

[0060] For the purposes of comparing various embodiments, certain aspects and advantages of these embodiments are described. Not necessarily all such aspects or advantages are achieved by any particular embodiment. Thus, for example, various embodiments may be carried out in a manner that achieves or optimizes one advantage or group of advantages taught herein without necessarily achieving other aspects or advantages as may also be taught or suggested herein.

[0061] The present disclosure is described in relation to systems, devices, or methods for in vitro diagnostics, and in particular for detection of an ailment such as a disease, cancer, or geneticdisorder. However, one of ordinary skill in the art will appreciate that this is not intended to be limiting and the devices and methods disclosed herein may be used in other nucleic acid testing including, but not limited to, detecting genetic information, such as for phenotyping, genotyping, determining ancestry, or the like.

[0062] The systems, devices, and compositions provided herein are described in relation to methods of in vitro diagnostics utilizing programmable nuclease-based detection assays. However, one of ordinary skill in the art will appreciate that this is not intended to be limiting and that the devices, systems, and compositions described herein may be used to perform other methods or assays including, but not limited to, other diagnostic assays such as (RT-)PCR-based molecular diagnostic assays, (RT-)HDA-based detection assays, (RT-)LAMP -based detection assays, probe-based detection assays, antibody-based detection assays, sequencing-based detection assays, antigen detection assays, or the like. It will also be understood by one of ordinary skill in the art that individual elements of the systems and devices described herein (such as the reagent capsules, jumpers, microwells, reporters, etc.) may be applicable to use in other fluidic systems or other assays and the description thereof is not intended to be limiting to any particular configuration or use.I. NUCLEIC ACID DETECTION SYSTEM

[0063] The present disclosure provides systems and methods for nucleic acid target detection. The systems and methods of the present disclosure can be implemented using devices that are configured for programmable nuclease-based detection. In some embodiments, the devices can be configured for single reaction detection. In some embodiments, the devices can be configured for multiplexed detection. The target can comprise a target sequence or target nucleic acid. As used herein, a target can be referred to interchangeably as a target nucleic acid. Further, a target can be referred to as a target amplicon or a target nucleic acid amplicon if such target undergoes amplification (e.g., through a thermocycling or isothermal process as described elsewhere herein). The target nucleic acid or amplicon thereof can be a portion of a nucleic acid of interest, e.g., a target nucleic acid from any plant, animal, virus, or microbe of interest. The devices provided herein can be used to perform rapid tests in a single integrated system.

[0064] In some embodiments, one or more programmable nucleases as disclosed herein can be activated to initiate trans cleavage activity of a reporter (also referred to herein as a reporter molecule). A programmable nuclease as disclosed herein can, in some cases, bind to a target sequence or target nucleic acid to initiate trans cleavage of a reporter and generation of a signal, directly or indirectly, therefrom. In some embodiments, cleavage of a reporter by aprogrammable nuclease may release a detection moiety which generates a detectable signal when cleaved from the reporter. In some embodiments, the signal may be an increase in a signal (e.g., an increase in fluorescence upon release of a quencher as described herein), a decrease in signal (e.g., a decrease in fluorescence upon release of a fluorophore as described herein), or any other change in signal (e.g., a color change) as will be understood by one of ordinary skill in the art. In some embodiments, the detection moiety may trigger a downstream signal amplification reaction (e.g., the detection moiety may comprise an enzyme which, upon release from the reporter, can contact its substrate and result in a detectable color change) which can increase the amount of detectable signal generated per reporter cleavage event.II. PROGRAMMABLE NUCLEASE-BASED ASSAYS AND REAGENTSA. ReagentsTarget Nucleic Acids

[0065] The present disclosure provides systems and methods for target nucleic acid detection. The systems and methods of the present disclosure can be implemented using devices that are configured for programmable nuclease-based detection. In some embodiments, the devices can be configured for single reaction detection. In some embodiments, the devices can be disposable devices. The devices disclosed herein can be particularly well-suited for carrying out highly efficient, rapid, and accurate reactions for detecting whether a target is present in a sample. The target can comprise a target sequence or target nucleic acid. As used herein, a target can be referred to interchangeably as a target nucleic acid. Further, a target can be referred to as a target amplicon or a target nucleic acid amplicon if such target undergoes amplification (e.g., through a thermocycling or isothermal process as described elsewhere herein). The target nucleic acid can be a portion of a nucleic acid of interest, e.g., a target nucleic acid from any plant, animal, virus, or microbe of interest. The devices provided herein can be used to perform rapid tests in a single integrated system.

[0066] The target nucleic acid can be a nucleic acid or a portion of a nucleic acid from a pathogen, virus, bacterium, fungi, protozoa, worm, or other agent(s) or organism(s) responsible for and / or related to a disease or condition in living organisms (e.g., humans, animals, plants, crops, and the like). The target nucleic acid can be a nucleic acid, or a portion thereof. The target nucleic acid can be a portion of a nucleic acid from a gene expressed in a cancer or genetic disorder in the sample. The target nucleic acid can be a portion of an RNA or DNA from anyorganism in the sample. The sample can be used for identifying a disease status or condition. For example, a sample is any sample described herein, and is obtained from a subject for use in identifying a disease status of a subject. Sometimes, a method comprises obtaining a serum sample from a subject and identifying a disease status or condition of the subject. Sometimes, a method comprises obtaining a nasal swab from a subject and identifying a disease status or condition of the subject. In certain embodiments, the sample comprises a target nucleic acid. In certain embodiments, the sample comprises a plurality of target nucleic acids.

[0067] In some instances, the target nucleic acid is a single stranded nucleic acid. Alternatively, or in combination, the target nucleic acid is a double stranded nucleic acid and is prepared into single stranded nucleic acids before or upon contacting the reagents. The target nucleic acid may be a RNA, DNA, synthetic nucleic acids, or nucleic acids found in biological or environmental samples. The target nucleic acids include but are not limited to mRNA, rRNA, tRNA, noncoding RNA, long non-coding RNA, and microRNA (miRNA). In some cases, the target nucleic acid is mRNA. In some cases, the target nucleic acid is from a virus, a parasite, or a bacterium described herein. In some cases, the target nucleic acid is transcribed from a gene as described herein.

[0068] A number of target nucleic acids are consistent with the methods and compositions disclosed herein. Some methods described herein can detect a target nucleic acid present in the sample in various concentrations or amounts as a target nucleic acid population. In some cases, the sample has at least two copies of the target nucleic acids. In some cases, the sample has at least 3, 5, 10, 20, 30, 40, 50, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 2000, 3000, 4000, 5000, 6000, 7000, 8000, 9000, or 10000 target nucleic acid copies. In some cases, the method detects target nucleic acid present at least at one copy per 101non-target nucleic acids, 102non-target nucleic acids, 103non-target nucleic acids, 104non-target nucleic acids, 105nontarget nucleic acids, 106non-target nucleic acids, 107non-target nucleic acids, 108non-target nucleic acids, 109non-target nucleic acids, or 1010non-target nucleic acids.

[0069] The systems and methods of the present disclosure can be used to detect one or more target sequences or nucleic acids in one or more samples. The one or more samples can comprise one or more target sequences or nucleic acids for detection of an ailment, such as a disease, cancer, or genetic disorder, or genetic information, such as for phenotyping, genotyping, or determining ancestry and are compatible with the reagents and support mediums as described herein. Generally, a sample can be taken from any place where a nucleic acid can be found. Samples can be taken from an individual / human, a non-human animal, or a crop, or anenvironmental sample can be obtained to test for presence of a disease, virus, pathogen, cancer, genetic disorder, or any mutation or pathogen of interest. A biological sample can be blood, serum, plasma, lung fluid, exhaled breath condensate, saliva, spit, urine, stool, feces, mucus, lymph fluid, peritoneal , cerebrospinal fluid, amniotic fluid, breast milk, gastric secretions, bodily discharges, secretions from ulcers, pus, nasal secretions, sputum, pharyngeal exudates, urethral secretions / mucus, vaginal secretions / mucus, anal secretion / mucus, semen, tears, an exudate, an effusion, tissue fluid, interstitial fluid (e.g., tumor interstitial fluid), cyst fluid, tissue, or, in some instances, any combination thereof. A sample can be an aspirate of a bodily fluid from an animal (e.g., human, animals, livestock, pet, etc.) or plant. A tissue sample can be from any tissue that can be infected or affected by a pathogen (e.g., a wart, lung tissue, skin tissue, and the like). A tissue sample (e.g., from animals, plants, or humans) can be dissociated or liquified prior to application to detection system of the present disclosure. A sample can be from a plant (e.g., a crop, a hydroponically grown crop or plant, and / or house plant). Plant samples can include extracellular fluid, from tissue (e.g., root, leaves, stem, trunk etc.). A sample can be taken from the environment immediately surrounding a plant, such as hydroponic fluid / water, or soil. A sample from an environment can be from soil, air, or water. In some instances, the environmental sample is taken as a swab from a surface of interest or taken directly from the surface of interest. In some instances, the raw sample is applied to the detection system. In some instances, the sample is diluted with a buffer or a fluid or concentrated prior to application to the detection system. In some cases, the sample is contained in no more than about 200 nanoliters (nL). In some cases, the sample is contained in about 200 nL. In some cases, the sample is contained in a volume that is greater than about 200 nL and less than about 20 microliters (pL). In some cases, the sample is contained in no more than 20 pl. In some cases, the sample is contained in no more than 1, 5, 10, 15, 20, 25, 30, 35 40, 45, 50, 55, 60, 65, 70, 75, 80, 90, 100, 200, 300, 400, 500 pl, or any of value from 1 pl to 500 pl. In some cases, the sample is contained in from 1 pL to 500 pL, from 10 pL to 500 pL, from 50 pL to 500 pL, from 100 pL to 500 pL, from 200 pL to 500 pL, from 300 pL to 500 pL, from 400 pL to 500 pL, from 1 pL to 200 pL, from 10 pL to 200 pL, from 50 pL to 200 pL, from 100 pL to 200 pL, from 1 pL to 100 pL, from 10 pL to 100 pL, from 50 pL to 100 pL, from 1 pL to 50 pL, from 10 pL to 50 pL, from 1 pL to 20 pL, from 10 pL to 20 pL, or from 1 pL to 10 pL. Sometimes, the sample is contained in more than 500 pl.

[0070] In some instances, the sample is taken from a single-cell eukaryotic organism; a plant or a plant cell; an algal cell; a fungal cell; an animal or an animal cell, tissue, or organ; a cell, tissue, or organ from an invertebrate animal; a cell, tissue, fluid, or organ from a vertebrate animal suchas fish, amphibian, reptile, bird, and mammal; a cell, tissue, fluid, or organ from a mammal such as a human, a non-human primate, an ungulate, a feline, a bovine, an ovine, and a caprine. In some instances, the sample is taken from nematodes, protozoans, helminths, or malarial parasites. In some cases, the sample may comprise nucleic acids from a cell lysate from a eukaryotic cell, a mammalian cell, a human cell, a prokaryotic cell, or a plant cell. In some cases, the sample may comprise nucleic acids expressed from a cell.

[0071] The sample used for disease testing can comprise at least one target sequence that can bind to a guide nucleic acid of the reagents described herein. In some cases, the target sequence is a portion of a nucleic acid. A nucleic acid can be from a genomic locus, a transcribed mRNA, or a reverse transcribed cDNA. A nucleic acid can be from 5 to 100, 5 to 90, 5 to 80, 5 to 70, 5 to 60, 5 to 50, 5 to 40, 5 to 30, 5 to 25, 5 to 20, 5 to 15, or 5 to 10 nucleotides in length. A nucleic acid can be from 10 to 90, from 20 to 80, from 30 to 70, or from 40 to 60 nucleotides in length. A nucleic acid sequence can be from 10 to 95, from 20 to 95, from 30 to 95, from 40 to 95, from 50 to 95, from 60 to 95, from 10 to 75, from 20 to 75, from 30 to 75, from 40 to 75, from 50 to 75, from 5 to 50, from 15 to 50, from 25 to 50, from 35 to 50, or from 45 to 50 nucleotides in length. A nucleic acid can be 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 50, 60, 70, 80, 90, or 100 nucleotides in length. The target nucleic acid can be reverse complementary to a guide nucleic acid. In some cases, at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24,25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 50, 60, 70, 80, 90, or 100 nucleotides of a guide nucleic acid can be reverse complementary to a target nucleic acid.

[0072] In some cases, the target sequence is a portion of a nucleic acid from a virus or a bacterium or other agents responsible for a disease in the sample. The target sequence, in some cases, is a portion of a nucleic acid from a sexually transmitted infection or a contagious disease, in the sample. The target sequence, in some cases, is a portion of a nucleic acid from an upper respiratory tract infection, a lower respiratory tract infection, or a contagious disease, in the sample. The target sequence, in some cases, is a portion of a nucleic acid from a hospital acquired infection or a contagious disease, in the sample. The target sequence, in some cases, is a portion of a nucleic acid from sepsis, in the sample. These diseases can include but are not limited to respiratory viruses (e.g., SARS-CoV-2 (i.e., a virus that causes COVID-19), SARS, MERS, influenza, Adenovirus, Coronavirus HKU1, Coronavirus NL63, Coronavirus 229E, Coronavirus OC43, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), Human Metapneumovirus (hMPV), Human Rhinovirus / Enterovirus, Influenza A, Influenza A / Hl, Influenza A / H3, Influenza A / Hl-2009, Influenza B, Influenza C, Parainfluenza Virus 1,Parainfluenza Virus 2, Parainfluenza Virus 3, Parainfluenza Virus 4, Respiratory Syncytial Virus) and respiratory bacteria (e.g. Bordetella parapertussis, Bordetella pertussis, Chlamydia pneumoniae, Mycoplasma pneumoniae). Other viruses include human immunodeficiency virus (HIV), human papillomavirus (HPV), chlamydia, gonorrhea, syphilis, trichomoniasis, sexually transmitted infection, malaria, Dengue fever, Ebola, chikungunya, and leishmaniasis. Pathogens include viruses, fungi, helminths, protozoa, malarial parasites, Plasmodium parasites, Toxoplasma parasites, and Schistosoma parasites. Helminths include roundworms, heartworms, and phytophagous nematodes, flukes, Acanthocephala, and tapeworms. Protozoan infections include infections from Giardia spp., Trichomonas spp., African trypanosomiasis, amoebic dysentery, babesiosis, balantidial dysentery, Chaga's disease, coccidiosis, malaria and toxoplasmosis. Examples of pathogens such as parasitic / protozoan pathogens include, but are not limited to: Plasmodium falciparum, P. vivax, Trypanosoma cruzi and Toxoplasma gondii. Fungal pathogens include, but are not limited to Cryptococcus neoformans, Histoplasma capsulatum, Coccidioides immitis, Blastomyces dermatitidis, Chlamydia trachomatis, Chlamydia pneumoniae, Chlamydia psittaci, and Candida albicans. Pathogenic viruses include but are not limited to: respiratory viruses (e.g., adenoviruses, parainfluenza viruses, severe acute respiratory syndrome (SARS), coronavirus, MERS), gastrointestinal viruses (e.g., noroviruses, rotaviruses, some adenoviruses, astroviruses), exanthematous viruses (e.g., the virus that causes measles, the virus that causes rubella, the virus that causes chickenpox / shingles, the virus that causes roseola, the virus that causes smallpox, the virus that causes fifth disease, chikungunya virus infection); hepatic viral diseases (e.g., hepatitis A, B, C, D, E); cutaneous viral diseases (e.g., warts (including genital, anal), herpes (including oral, genital, anal), molluscum contagiosum); hemmorhagic viral diseases (e.g. Ebola, Lassa fever, dengue fever, yellow fever, Marburg hemorrhagic fever, Crimean-Congo hemorrhagic fever); neurologic viruses (e.g., polio, viral meningitis, viral encephalitis, rabies), sexually transmitted viruses (e.g., HIV, HPV, and the like), immunodeficiency virus (e.g., HIV); influenza virus; dengue; West Nile virus; herpes virus; yellow fever virus; Hepatitis Virus C; Hepatitis Virus A; Hepatitis Virus B; papillomavirus; and the like. Pathogens include, e.g., HIV virus, Mycobacterium tuberculosis, Klebsiella pneumoniae, Acinetobacter baumannii, Bacillus anthracis, Bortadella pertussis, Burkholderia cepacia, Corynebacterium diphtheriae, Coxiella burnetii, Streptococcus agalactiae, methicillin-resistant Staphylococcus aureus, Legionella longbeachae, Legionella pneumophila, Leptospira interrogans, Moraxella catarrhalis, Streptococcus pyogenes, Escherichia coli, Neisseria gonorrhoeae, Neisseria meningitidis, Neisseria elongate, Neisseria gonorrhoeae, Parechovirus, Pneumococcus, Pneumocystis jirovecii, Cryptococcus neoformans,Histoplasma capsulatum, Haemophilus influenzae B, Treponema pallidum, Lyme disease spirochetes, Pseudomonas aeruginosa, Mycobacterium leprae, Brucella abortus, rabies virus, influenza virus, cytomegalovirus, herpes simplex virus I, herpes simplex virus II, human serum parvo-like virus, respiratory syncytial virus (RSV), M. genitalium, T. Vaginalis, varicella-zoster virus, hepatitis B virus, hepatitis C virus, measles virus, adenovirus, human T-cell leukemia viruses, Epstein-Barr virus, murine leukemia virus, mumps virus, vesicular stomatitis virus, Sindbis virus, lymphocytic choriomeningitis virus, wart virus, blue tongue virus, Sendai virus, feline leukemia virus, Reovirus, polio virus, simian virus 40, mouse mammary tumor virus, dengue virus, rubella virus, West Nile virus, Plasmodium falciparum, Plasmodium vivax, Toxoplasma gondii, Trypanosoma rangeli, Trypanosoma cruzi, Trypanosoma rhodesiense, Trypanosoma brucei, Schistosoma mansoni, Schistosoma japonicum, Babesia bovis, Eimeria tenella, Onchocerca volvulus, Leishmania tropica, Mycobacterium tuberculosis, Trichinella spiralis, Theileria parva, Taenia hydatigena, Taenia ovis, Taenia saginata, Echinococcus granulosus, Mesocestoides corti, Mycoplasma arthritidis, M. hyorhinis, M. orale, M. arginini, Acholeplasma laidlawii, M. salivarium, M. pneumoniae, Enterobacter cloacae, Kiebsiella aerogenes, Proteus vulgaris, Serratia macesens, Enterococcus faecalis, Enterococcus faecium, Streptococcus intermdius, Streptococcus pneumoniae, and Streptococcus pyogenes. Often the target nucleic acid may comprise a sequence from a virus or a bacterium or other agents responsible for a disease that can be found in the sample. In some cases, the target nucleic acid is a portion of a nucleic acid from a genomic locus, a transcribed mRNA, or a reverse transcribed cDNA from a gene locus in at least one of: human immunodeficiency virus (HIV), human papillomavirus (HPV), chlamydia, gonorrhea, syphilis, trichomoniasis, sexually transmitted infection, malaria, Dengue fever, Ebola, chikungunya, and leishmaniasis. Pathogens include viruses, fungi, helminths, protozoa, malarial parasites, Plasmodium parasites, Toxoplasma parasites, and Schistosoma parasites. Helminths include roundworms, heartworms, and phytophagous nematodes, flukes, Acanthocephala, and tapeworms. Protozoan infections include infections from Giardia spp., Trichomonas spp., African trypanosomiasis, amoebic dysentery, babesiosis, balantidial dysentery, Chaga's disease, coccidiosis, malaria and toxoplasmosis. Examples of pathogens such as parasitic / protozoan pathogens include, but are not limited to: Plasmodium falciparum, P. vivax, Trypanosoma cruzi and Toxoplasma gondii. Fungal pathogens include, but are not limited to Cryptococcus neoformans, Histoplasma capsulatum, Coccidioides immitis, Blastomyces dermatitidis, Chlamydia trachomatis, and Candida albicans. Pathogenic viruses include but are not limited to immunodeficiency virus (e.g., HIV); influenza virus; dengue; West Nile virus; herpes virus; yellow fever virus; Hepatitis Virus C; Hepatitis Virus A;Hepatitis Virus B; papillomavirus; and the like. Pathogens include, e.g., HIV virus, Mycobacterium tuberculosis, Streptococcus agalactiae, methicillin-resistant Staphylococcus aureus, Staphylococcus epidermidis, Legionella pneumophila, Streptococcus pyogenes, Streptococcus salivarius, Escherichia coli, Neisseria gonorrhoeae, Neisseria meningitidis, Pneumococcus, Cryptococcus neoformans, Histoplasma capsulatum, Hemophilus influenzae B, Treponema pallidum, Lyme disease spirochetes, Pseudomonas aeruginosa, Mycobacterium leprae, Brucella abortus, rabies virus, influenza virus, cytomegalovirus, herpes simplex virus I, herpes simplex virus II, human serum parvo-like virus, respiratory syncytial virus (RSV), M. genitalium, T. vaginalis, varicella-zoster virus, hepatitis B virus, hepatitis C virus, measles virus, adenovirus, human T-cell leukemia viruses, Epstein-Barr virus, murine leukemia virus, mumps virus, vesicular stomatitis virus, Sindbis virus, lymphocytic choriomeningitis virus, wart virus, blue tongue virus, Sendai virus, feline leukemia virus, Reovirus, polio virus, simian virus 40, mouse mammary tumor virus, dengue virus, rubella virus, West Nile virus, Plasmodium falciparum, Plasmodium vivax, Toxoplasma gondii, Trypanosoma rangeli, Trypanosoma cruzi, Trypanosoma rhodesiense, Trypanosoma brucei, Schistosoma mansoni, Schistosoma japonicum, Babesia bovis, Eimeria tenella, Onchocerca volvulus, Leishmania tropica, Mycobacterium tuberculosis, Trichinella spiralis, Theileria parva, Taenia hydatigena, Taenia ovis, Taenia saginata, Echinococcus granulosus, Mesocestoides corti, Mycoplasma arthritidis, M. hyorhinis, M. or ale, M. arginini, Acholeplasma laidlawii, M. salivarium and AL pneumoniae. In some cases, the target sequence is a portion of a nucleic acid from a genomic locus, a transcribed mRNA, or a reverse transcribed cDNA from a gene locus of bacterium or other agents responsible for a disease in the sample comprising a mutation that confers resistance to a treatment, such as a single nucleotide mutation that confers resistance to antibiotic treatment.

[0073] The sample used for cancer testing or cancer risk testing can comprise at least one target sequence or target nucleic acid segment that can bind to a guide nucleic acid of the reagents described herein. The target nucleic acid segment, in some cases, is a portion of a nucleic acid from a gene with a mutation associated with cancer, from a gene whose overexpression is associated with cancer, a tumor suppressor gene, an oncogene, a checkpoint inhibitor gene, a gene associated with cellular growth, a gene associated with cellular metabolism, or a gene associated with cell cycle. Sometimes, the target nucleic acid encodes for a cancer biomarker, such as a prostate cancer biomarker or non-small cell lung cancer. In some cases, the assay can be used to detect “hotspots” in target nucleic acids that can be predictive of cancer, such as lung cancer, cervical cancer, in some cases, the cancer can be a cancer that is caused by a virus. Some non-limiting examples of viruses that cause cancers in humans include Epstein-Barr virus (e.g.,Burkitt’s lymphoma, Hodgkin’s Disease, and nasopharyngeal carcinoma); papillomavirus (e.g., cervical carcinoma, anal carcinoma, oropharyngeal carcinoma, penile carcinoma); hepatitis B and C viruses (e.g., hepatocellular carcinoma); human adult T-cell leukemia virus type 1 (HTLV-1) (e.g., T-cell leukemia); and Merkel cell polyomavirus (e.g., Merkel cell carcinoma). One skilled in the art will recognize that viruses can cause or contribute to other types of cancers. In some cases, the target nucleic acid is a portion of a nucleic acid that is associated with a blood fever. In some cases, the target nucleic acid segment is a portion of a nucleic acid from a genomic locus, a transcribed mRNA, or a reverse transcribed cDNA from a locus of at least one of: ALK, APC, ATM, AXIN2, BAP1, BARD1, BLM, BMPR1A, BRCA1, BRCA2, BRIP1, CASR, CDC73, CDH1, CDK4, CDKN1B, CDKN1C, CDKN2A, CEBPA, CHEK2, CTNNA1, DICER1, DIS3L2, EGFR, EPCAM, FH, FLCN, GATA2, GPC3, GREM1, H0XB13, HRAS, KRAS, KIT, MAX, MEN1, MET, MITF, MLH1, MSH2, MSH3, MSH6, MUTYH, NBN, NF1, NF2, NTHL1, PALB2, PDGFRA, PH0X2B, PMS2, POLDI, POLE, POTI, PRKAR1A, PTCHI, PTEN, RAD50, RAD51C, RAD51D, RBI, RECQL4, RET, RUNX1, SDHA, SDHAF2, SDHB, SDHC, SDHD, SMAD4, SMARCA4, SMARCB1, SMARCE1, STK11, SUFU, TERC, TERT, TMEM127, TP53, TSC1, TSC2, VHL, WRN, and WT1.

[0074] The sample used for genetic disorder testing can comprise at least one target sequence or target nucleic acid segment that can bind to a guide nucleic acid of the reagents described herein. In some embodiments, the genetic disorder is hemophilia, sickle cell anemia, P-thalassemia, Duchene muscular dystrophy, severe combined immunodeficiency, or cystic fibrosis. The target nucleic acid segment, in some cases, is a portion of a nucleic acid from a gene with a mutation associated with a genetic disorder, from a gene whose overexpression is associated with a genetic disorder, from a gene associated with abnormal cellular growth resulting in a genetic disorder, or from a gene associated with abnormal cellular metabolism resulting in a genetic disorder. In some cases, the target nucleic acid segment is a portion of a nucleic acid from a genomic locus, a transcribed mRNA, or a reverse transcribed cDNA from a locus of at least one of: CFTR, FMRI, SMN1, ABCB11, ABCC8, ABCD1, ACAD9, AC ADM, ACADVL, ACAT1, ACOX1, ACSF3, ADA, ADAMTS2, ADGRG1, AGA, AGL, AGPS, AGXT, AIRE, ALDH3A2, ALDOB, ALG6, ALMS1, ALPL, AMT, AQP2, ARG1, ARSA, ARSB, ASL, ASNS, ASP A, ASS1, ATM, ATP6V1B1, ATP7A, ATP7B, ATRX, BBS1, BBS10, BBS12, BBS2, BCKDHA, BCKDHB, BCS1L, BLM, BSND, CAPN3, CBS, CDH23, CEP290, CERKL, CHM, CHRNE, CIITA, CLN3, CLN5, CLN6, CLN8, CLRN1, CNGB3, COL27A1, COL4A3, COL4A4, COL4A5, COL7A1, CPS1, CPT1A, CPT2, CRB1, CTNS, CTSK, CYBA, CYBB, CYP11B1, CYP11B2, CYP17A1, CYP19A1, CYP27A1, DBT, DCLRE1C, DHCR7, DHDDS, DLD, DMD,DNAH5, DNAI1, DNAI2, DYSF, EDA, EIF2B5, EMD, ERCC6, ERCC8, ESC02, ETFA, ETFDH, ETHE1, EVC, EVC2, EYS, F9, FAH, FAM161A, FANCA, FANCC, FANCG, FH, FKRP, FKTN, G6PC, GAA, GALC, GALK1, GALT, GAMT, GBA, GBE1, GCDH, GFM1, GJB1, GJB2, GLA, GLB1, GLDC, GLE1, GNE, GNPTAB, GNPTG, GNS, GRHPR, HADHA, HAX1, HBA1„ HBA2, HBB, HEXA, HEXB, HGSNAT, HLCS, HMGCL, H0GA1, HPS1, HPS3, HSD17B4, HSD3B2, HYAL1, HYLS1, IDS, IDUA, IKBKAP, IL2RG, IVD, KCNJ11, LAMA2, LAMA3, LAMB3, LAMC2, LCA5, LDLR, LDLRAP1, LHX3, LIFR, LIPA, LOXHD1, LPL, LRPPRC, MAN2B1, MCOLN1, MED17, MESP2, MFSD8, MKS1, MLC1, MMAA, MMAB, MMACHC, MMADHC, MPI, MPL, MPV17, MTHFR, MTM1, MTRR, MTTP, MUT, MY07A, NAGLU, NAGS, NBN, NDRG1, NDUFAF5, NDUFS6, NEB, NPC1, NPC2, NPHS1, NPHS2, NR2E3, NTRK1, OAT, OP A3, OTC, PAH, PC, PCCA, PCCB, PCDH15, PDHA1, PDHB, PEX1, PEX10, PEX12, PEX2, PEX6, PEX7, PFKM, PHGDH, PKHD1, PMM2, POMGNT1, PPT1, PROP1, PRPS1, PSAP, PTS, PUS1, PYGM, RAB23, RAG2, RAPSN, RARS2, RDH12, RMRP, RPE65, RPGRIP1L, RSI, RTEL1, SACS, SAMHD1, SEPSECS, SGCA, SGCB, SGCG, SGSH, SLC12A3, SLC12A6, SLC17A5, SLC22A5, SLC25A13, SLC25A15, SLC26A2, SLC26A4, SLC35A3, SLC37A4, SLC39A4, SLC4A11, SLC6A8, SLC7A7, SMARCAL1, SMPD1, STAR, SUMF1, TAT, TCIRG1, TECPR2, TFR2, TGM1, TH, TMEM216, TPP1, TRMU, TSFM, TTP A, TYMP, USH1C, USH2A, VPS13A, VPS13B, VPS45, VRK1, VSX2, WNT10A, XPA, XPC, and ZFYVE26.

[0075] The sample used for phenotyping testing can comprise at least one target nucleic acid segment that can bind to a guide nucleic acid of the reagents described herein. The target nucleic acid segment, in some cases, is a portion of a nucleic acid from a gene associated with a phenotypic trait.

[0076] The sample used for genotyping testing can comprise at least one target nucleic acid segment that can bind to a guide nucleic acid of the reagents described herein. The target nucleic acid segment, in some cases, is a portion of a nucleic acid from a gene associated with a genotype.

[0077] The sample used for ancestral testing can comprise at least one target nucleic acid segment that can bind to a guide nucleic acid of the reagents described herein. The target nucleic acid segment, in some cases, is a portion of a nucleic acid from a gene associated with a geographic region of origin or ethnic group.

[0078] The sample can be used for identifying a disease status. For example, a sample is any sample described herein, and is obtained from a subject for use in identifying a disease status ofa subject. The disease can be a cancer or genetic disorder. Sometimes, a method may comprise obtaining a serum sample from a subject; and identifying a disease status of the subject. Often, the disease status is prostate disease status. In any of the embodiments described herein, the device can be configured for asymptomatic, pre-symptomatic, and / or symptomatic diagnostic applications, irrespective of immunity. In any of the embodiments described herein, the device can be configured to perform one or more serological assays on a sample (e.g., a sample comprising blood).

[0079] In some embodiments, the sample can be used to identify a mutation in a target nucleic acid of a plant or of a bacteria, virus, or microbe associated with a plant or soil. The devices and methods of the present disclosure can be used to identify a mutation of a target nucleic acid that affects the expression of a gene. A mutation that affects the expression of gene can be a mutation of a target nucleic acid within the gene, a mutation of a target nucleic acid comprising RNA associated with the expression of a gene, or a target nucleic acid comprising a mutation of a nucleic acid associated with regulation of expression of a gene, such as an RNA or a promoter, enhancer, or repressor of the gene. Often, the mutation is a single nucleotide mutation.

[0080] In some instances, the target nucleic acid is a single stranded nucleic acid. Alternatively, or in combination, the target nucleic acid is a double stranded nucleic acid and is prepared into single stranded nucleic acids before or upon contacting the reagents. The target nucleic acid can be a RNA, DNA, synthetic nucleic acids, or nucleic acids found in biological or environmental samples. The target nucleic acids include but are not limited to mRNA, rRNA, tRNA, noncoding RNA, long non-coding RNA, and microRNA (miRNA). In some cases, the target nucleic acid is mRNA. In some cases, the target nucleic acid is from a virus, a parasite, or a bacterium described herein. In some cases, the target nucleic acid is transcribed from a gene as described herein.

[0081] A number of target nucleic acids are consistent with the systems and methods disclosed herein. Some methods described herein can detect a target nucleic acid present in the sample in various concentrations or amounts as a target nucleic acid population. In some cases, the sample has at least 2 target nucleic acids. In some cases, the sample has at least 3, 5, 10, 20, 30, 40, 50, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 2000, 3000, 4000, 5000, 6000, 7000, 8000, 9000, or 10000 target nucleic acids. In some cases, the sample has from 1 to 10,000, from 100 to 8000, from 400 to 6000, from 500 to 5000, from 1000 to 4000, or from 2000 to 3000 target nucleic acids. In some cases, the sample has from 100 to 9500, from 100 to 9000, from 100 to 8500, from 100 to 8000, from 100 to 7500, from 100 to 7000, from 100 to 6500, from 100 to6000, from 100 to 5500, from 100 to 5000, from 250 to 9500, from 250 to 9000, from 250 to8500, from 250 to 8000, from 250 to 7500, from 250 to 7000, from 250 to 6500, from 250 to6000, from 250 to 5500, from 250 to 5000, from 2500 to 9500, from 2500 to 9000, from 2500 to8500, from 2500 to 8000, from 2500 to 7500, from 2500 to 7000, from 2500 to 6500, from 2500 to 6000, from 2500 to 5500, or from 2500 to 5000 target nucleic acids. In some cases, the method detects target nucleic acid present at least at one copy per 101non-target nucleic acids,102non-target nucleic acids, 103non-target nucleic acids, 104non-target nucleic acids, 105nontarget nucleic acids, 106non-target nucleic acids, 107non-target nucleic acids, 108non-target nucleic acids, 109non-target nucleic acids, or 1010non-target nucleic acids.

[0082] A number of target nucleic acid populations are consistent with the systems and methods disclosed herein. Some methods described herein can be implemented to detect two or more target nucleic acid populations present in the sample in various concentrations or amounts. In some cases, the sample has at least 2 different target nucleic acid populations. In some cases, the sample has at least 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, or 50 target nucleic acid populations. In some cases, the sample has from 3 to 50, from 5 to 40, or from 10 to 25 target nucleic acid populations. In some cases, the sample has from 2 to 50, from 5 to 50, from 10 to 50, from 2 to 25, from 3 to 25, from 4 to 25, from 5 to 25, from 10 to 25, from 2 to 20, from 3 to 20, from 4 to 20, from 5 to 20, from 10 to 20, from 2 to 10, from 3 to 10, from 4 to 10, from 5 to 10, from 6 to 10, from 7 to 10, from 8 to 10, or from 9 to 10 target nucleic acid populations. In some cases, the methods of the present disclosure can be implemented to detect target nucleic acid populations that are present at least at one copy per 101non-target nucleic acids, 102non-target nucleic acids,103non-target nucleic acids, 104non-target nucleic acids, 105non-target nucleic acids, 106non- target nucleic acids, 107non-target nucleic acids, 108non-target nucleic acids, 109non-target nucleic acids, or 1010non-target nucleic acids. The target nucleic acid populations can be present at different concentrations or amounts in the sample.

[0083] In some embodiments, the target nucleic acid is indicative of a respiratory disorder or respiratory pathogen. In some embodiments, the respiratory disorder or respiratory pathogen selected from the group consisting of SARS-CoV-2 and corresponding variants, 29E, NL63, OC43, HKU1, MERS-CoV, (MERS), SARS-CoV (SARS), Flu A, Flu B, RSV, Rhinovirus, Strep A, and TB. In some embodiments, the device is configured to differentiate between a viral infection and a bacterial infection. In some embodiments, the target nucleic acid is indicative of a sexually transmitted infection (STI) or infection related to a woman’s health. In some embodiments, the STI or infection related to a woman’s health is selected from the group consisting of CT, NG, MG, TV, HPV, Candida, B. Vaginosis Syphilis, and UTI. In someembodiments, the target nucleic acid comprises a single nucleotide polymorphism (SNP). In some embodiments, the SNP is indicative of NASH disorder or Alpha-1 disorder. In some embodiments, the target nucleic acid is a blood borne pathogen selected from the group consisted of HIV, HBV, HCV, and Zika. In some embodiments, the target nucleic acid is indicative of H. Pylori, C. Difficile, Norovirus, HSV, and Meningitis.Programmable Nucleases

[0084] Disclosed herein are programmable nucleases and uses thereof, e.g., detection and editing of target nucleic acids. In some cases, a programmable nuclease is capable of being activated when complexed with the guide nucleic acid and the target nucleic acid segment. A programmable nuclease can be capable of being activated when complexed with a guide nucleic acid and the target sequence. The programmable nuclease can be activated upon binding of the guide nucleic acid to its target nucleic acid and can non-specifically degrade a non-target nucleic acid in its environment. The programmable nuclease has trans cleavage activity once activated. A programmable nuclease can be a Cas protein (also referred to, interchangeably, as a Cas nuclease or Cas effector protein). A guide nucleic acid (e.g., crRNA) and Cas protein can form a CRISPR enzyme (also referred to herein as a programmable nuclease complex or probe).

[0085] In some embodiments, one or more programmable nucleases as disclosed herein can be activated to initiate trans cleavage activity of a reporter (also referred to herein as a reporter molecule). A programmable nuclease as disclosed herein can, in some cases, bind to a target sequence or target nucleic acid to initiate trans cleavage of a reporter. The programmable nuclease can be referred to as an RNA-activated programmable RNA nuclease. In some instances, the programmable nuclease as disclosed herein can bind to a target DNA to initiate trans cleavage of an RNA reporter. Such a programmable nuclease can be referred to herein as a DNA-activated programmable RNA nuclease. In some cases, a programmable nuclease as described herein can be activated by a target RNA or a target DNA. For example, a programmable nuclease, e.g., a Cas enzyme, can be activated by a target RNA nucleic acid or a target DNA nucleic acid to cleave RNA reporters. In some embodiments, the programmable nuclease can bind to a target ssDNA which initiates trans cleavage of RNA reporters. In some instances, a programmable nuclease as disclosed herein can bind to a target DNA to initiate trans cleavage of a DNA reporter, and this programmable nuclease can be referred to as a DNA- activated programmable DNA nuclease.

[0086] The nucleic acids described and referred to herein can comprise a plurality of base pairs. A base pair can be a biological unit comprising two nucleobases bound to each other byhydrogen bonds. Nucleobases can comprise adenine, guanine, cytosine, thymine, and / or uracil. In some cases, the nucleic acids described and referred to herein can comprise different base pairs. In some cases, the nucleic acids described and referred to herein can comprise one or more modified base pairs. The one or more modified base pairs can be produced when one or more base pairs undergo a chemical modification leading to new bases. The one or more modified base pairs can be, for example, Hypoxanthine, Inosine, Xanthine, Xanthosine, 7-Methylguanine, 7-Methylguanosine, 5,6-Dihydrouracil, Dihydrouridine, 5-Methylcytosine, 5-Methylcytidine, 5- hydroxymethylcytosine (5hmC), 5 -formylcytosine (5fC), or 5-carboxylcytosine (5caC).

[0087] The programmable nuclease can become activated after binding of a guide nucleic acid that is complexed with the programmable nuclease with a target nucleic acid, and the activated programmable nuclease can cleave the target nucleic acid, which can result in a trans cleavage activity. Trans cleavage activity can be non-specific cleavage of nearby single-stranded nucleic acids by the activated programmable nuclease, such as trans cleavage of reporter nucleic acids comprising a detection moiety. Once the reporter is cleaved by the activated programmable nuclease, the detection moiety can be released or separated from the reporter and can directly or indirectly generate a detectable signal. The reporter and / or the detection moiety can be immobilized, dried, or otherwise deposited on a support medium. Often the detection moiety is at least one of a fluorophore, a dye, a polypeptide, or a nucleic acid. Sometimes the detection moiety binds to a capture molecule on the support medium to be immobilized. The detectable signal can be visualized on the support medium to assess the presence or concentration of one or more target nucleic acids associated with an ailment, such as a disease, cancer, or genetic disorder.

[0088] The systems and methods of the present disclosure can be implemented using a device that is compatible with any type of programmable nuclease that is human-engineered or naturally occurring. The programmable nuclease can comprise a nuclease that is capable of being activated when complexed with a guide nucleic acid and a target nucleic acid segment or a portion thereof. A programmable nuclease can become activated when complexed with a guide nucleic acid and a target sequence of a target gene of interest. The programmable nuclease can be activated upon binding of a guide nucleic acid to a target nucleic acid and can exhibit or enable trans cleavage activity once activated. In any instances or embodiments where a CRISPR- based programmable nuclease is described or used, it is recognized herein that any other type of programmable nuclease can be used in addition to or in substitution of such CRISPR-based programmable nuclease.

[0089] The systems and methods of the present disclosure can be implemented using a device that is compatible with a plurality of programmable nucleases. The device can comprise a plurality of programmable nuclease probes (also referred to herein as programmable nuclease complexes) comprising the plurality of programmable nucleases and one or more corresponding guide nucleic acids. The plurality of programmable nuclease probes can be the same. Alternatively, the plurality of programmable nuclease probes can be different. For example, the plurality of programmable nuclease probes can comprise different programmable nucleases and / or different guide nucleic acids associated with the programmable nucleases.

[0090] As used herein, a programmable nuclease generally refers to any enzyme that can cleave nucleic acid. The programmable nuclease can be any enzyme that can be or has been designed, modified, or engineered by human contribution so that the enzyme targets or cleaves the nucleic acid in a sequence-specific manner. Programmable nucleases can include, for example, zinc- finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and / or RNA- guided nucleases such as the bacterial clustered regularly interspaced short palindromic repeat (CRISPR)-Cas (CRISPR-associated) nucleases or Cpfl. Programmable nucleases can also include, for example, PfAgo and / or NgAgo.

[0091] ZFNs can cut genetic material in a sequence- specific matter and can be designed, or programmed, to target specific viral targets. A ZFN is composed of two domains: a DNA- binding zinc-finger protein linked to the Fokl nuclease domain. The DNA-binding zinc-finger protein is fused with the non-specific Fokl cleave domain to create ZFNs. The protein will typically dimerize for activity. Two ZFN monomers form an active nuclease; each monomer binds to adjacent half- sites on the target. The sequence specificity of ZFNs is determined by ZFPs. Each zinc-finger recognizes a 3 -bp DNA sequence, and 3-6 zinc-fingers are used to generate a single ZFN subunit that binds to DNA sequences of 9-18 bp. The DNA-binding specificities of zinc-fingers is altered by mutagenesis. New ZFPs are programmed by modular assembly of pre-characterized zinc fingers.

[0092] Transcription activator-like effector nucleases (TALENs) can cut genetic material in a sequence-specific matter and can be designed, or programmed, to target specific viral targets. TALENs contain the Fokl nuclease domain at their carboxyl termini and a class of DNA binding domains known as transcription activator- like effectors (TALEs). TALENs are composed of tandem arrays of 33-35 amino acid repeats, each of which recognizes a single base-pair in the major groove of target viral DNA. The nucleotide specificity of a domain comes from the two amino acids at positions 12 and 13 where Asn-Asn, Asn-Ile, His- Asp and Asn-Gly recognizeguanine, adenine, cytosine and thymine, respectively. That pattern allows one to program TALENs to target various nucleic acids.

[0093] The programmable nuclease can comprise any type of engineered enzyme. Alternatively, the programmable nuclease can comprise CRISPR enzymes derived from naturally occurring bacteria or phage. A programmable nuclease can be a Cas effector protein (also referred to, interchangeably, as a Cas nuclease). A guide nucleic acid (e.g., a crRNA) and Cas effector protein can form a CRISPR enzyme. The programmable nuclease can be a CRISPR-Cas (clustered regularly interspaced short palindromic repeats - CRISPR associated) nucleoprotein complex with trans cleavage activity, which can be activated by binding of a guide nucleic acid with a target nucleic acid. The programmable nuclease can comprise one or more amino acid modifications. The programmable nuclease can be a nuclease derived from a CRISPR-Cas system. The programmable nuclease can be a nuclease derived from recombineering. In some embodiments, the programmable nuclease further comprises a Cas enzyme. In some embodiments, the Cas enzyme is selected from the group consisting of Casl2, Casl3, Casl4, Casl4a, Casl4al, and CasPhi.

[0094] In some cases, the programmable nuclease is Casl3. Sometimes the Casl3 is Casl3a, Casl3b, Casl3c, Casl3d, Casl3e, or Casl3f. In some cases, the programmable nuclease is Mad7 or Mad2. In some cases, the programmable nuclease is Casl2. Sometimes the Casl2 is Casl2a, Cas 12b, Cas 12c, Cas 12d, Casl2e, Casl2f, Cas 12g, Casl2h, Casl2i, Casl2j, or Cas 12k. In some cases, the programmable nuclease is Csml, Cas9, C2c4, C2c8, C2c5, C2cl0, C2c9, or CasZ. Sometimes, the Csml is also called smCmsl, miCmsl, obCmsl, or suCmsl. Sometimes Casl3a is also called C2c2. Sometimes CasZ is also called Casl4a, Casl4b, Casl4c, Casl4d, Casl4e, Casl4f, Casl4g, or Casl4h. Sometimes, the programmable nuclease is a type V CRISPR-Cas system. In some cases, the programmable nuclease is a type VI CRISPR-Cas system. Sometimes the programmable nuclease is a type III CRISPR-Cas system. In some cases, the programmable nuclease is from at least one of Leptotrichia shahii (Lsh), Listeria seeligeri (Lse), Leptotrichia buccalis (Lbu), Leptotrichia wadeu (Lwa), Rhodobacter capsulatus (Rea), Herbinix hemicellulosilytica (Hhe), Paludibacter propionicigenes (Ppr), Lachnospiraceae bacterium (Lba), [Eubacterium] rectale (Ere), Listeria newyorkensis (Lny), Clostridium aminophilum (Cam), Prevotella sp. (Psm), Capnocytophaga canimorsus (Cea Lachnospiraceae bacterium (Lba), Bergeyella zoohelcum (Bzo), Prevotella intermedia (Pin), Prevotella buccae (Pbu), Alistipes sp. (Asp), Riemerella anatipestifer (Ran), Prevotella aurantiaca (Pau), Prevotella saccharolytica (Psa), Prevotella intermedia (Pin2), Capnocytophaga canimorsus (Cea), Porphyromonas gulae (Pgu), Prevotella sp. (Psp), Porphyromonas gingivalis (Pig), Prevotellaintermedia (Pin3), Enterococcus italicus (Ei), Lactobacillus salivarius (Ls), or Thermus thermophilus (Tt). Sometimes the Casl3 is at least one of LbuCasl3a, LwaCasl3a, LbaCasl3a, HheCasl3a, PprCasl3a, EreCasl3a, CamCasl3a, or LshCasl3a.

[0095] Disclosed herein are programmable nucleases and uses thereof, e.g., detection and editing of target nucleic acids. In some instances, programmable nucleases comprise a Type V CRISPR / Cas protein. In some instances, Type V CRISPR / Cas proteins comprise nucleic acid cleavage activity. In some instances, Type V CRISPR / Cas proteins cleave or nick singlestranded nucleic acids, double, stranded nucleic acids, or a combination thereof. In some cases, Type V CRISPR / Cas proteins cleave single-stranded nucleic acids. In some cases, Type V CRISPR / Cas proteins cleave double-stranded nucleic acids. In some cases, Type V CRISPR / Cas proteins nick double-stranded nucleic acids. Typically, guide nucleic acids of Type V CRISPR / Cas proteins hybridize to ssDNA or dsDNA. However, the trans cleavage activity of Type V CRISPR / Cas protein is typically directed towards ssDNA. In some cases, the Type V CRISPR / Cas protein comprises a catalytically inactive nuclease domain. A catalytically inactive domain of a Type V CRISPR / Cas protein may comprise at least 1, at least 2, at least 3, at least 4, or at least 5 mutations relative to a wild-type nuclease domain of the Type V CRISPR / Cas protein. Said mutations may be present within a cleaving or active site of the nuclease.

[0096] In some instances, the Type V Cas protein is a Cas protein. A Cas protein can function as an endonuclease that catalyzes cleavage at a specific sequence in a target nucleic acid. A programmable Cas nuclease may have a single active site in a RuvC domain that is capable of catalyzing pre-crRNA processing and nicking or cleaving of nucleic acids. This compact catalytic site may render the programmable Cas nuclease especially advantageous for genome engineering and new functionalities for genome manipulation.

[0097] In some instances, the programmable nuclease is a Type VI Cas protein. In some embodiments, the Type VI Cas protein is a programmable Cas 13 nuclease. The general architecture of a Cas 13 protein includes an N-terminal domain and two HEPN (higher eukaryotes and prokaryotes nucleotide-binding) domains separated by two helical domains. The HEPN domains each comprise aR-X4-H motif. Shared features across Casl3 proteins include that upon binding of the crRNA of the guide nucleic acid to a target nucleic acid, the protein undergoes a conformational change to bring together the HEPN domains and form a catalytically active RNase. Thus, two activatable HEPN domains are characteristic of a programmable Cas 13 nuclease of the present disclosure. However, programmable Casl3 nucleases also consistent with the present disclosure include Casl3 nucleases comprising mutations in the HEPN domain thatenhance the Cast 3 proteins cleavage efficiency or mutations that catalytically inactivate the HEPN domains. Programmable Casl3 nucleases consistent with the present disclosure also Cast 3 nucleases comprising catalytic components. In some instances, the Cas effector is a Cas 13 effector. In some instances, the Cas 13 effector is a Cas 13 a, a Cas 13b, a Cas 13c, a Cas 13d, or a Cas 13e effector protein.

[0098] In some embodiments, the programmable nuclease comprises a Casl2 protein, wherein the Cas 12 enzyme binds and cleaves double stranded DNA and single stranded DNA. In some embodiments, programmable nuclease comprises a Casl3 protein, wherein the Casl3 enzyme binds and cleaves single stranded RNA. In some embodiments, programmable nuclease comprises a Casl4 protein, wherein the Casl4 enzyme binds and cleaves both double stranded DNA and single stranded DNA.

[0099] Table 1 provides illustrative amino acid sequences of programmable nucleases having trans-cleavage activity. The programmable nuclease may comprise an amino acid sequence that is at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to any one of SEQ ID Nos: 1-61 or 81-92. The programmable nuclease may consist of an amino acid sequence that is at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to any one or SEQ ID Nos: 1-61 or 81-92. The programmable nuclease may comprise at least about 50, at least about 100, at least about 150, at least about 200, at least about 250, at least about 300, at least about 350, at least about 400, at least about 450, at least about 500 consecutive amino acids of any one of SEQ ID Nos: 1-61 or 81-92.

[0100] Table 1 : Amino Acid Sequences of Exemplary Programmable Nucleases

[0101] Other Exemplary protein sequences are described in the following applications:PCT / US2021 / 033271; PCT / US2021 / 035031, and PCT / US2022 / 028865, all of which are hereinincorporated by reference in their entirety.

[0102] In some cases, the effector proteins comprise a RuvC domain (e.g., a partial RuvC domain). In some instances, the RuvC domain may be defined by a single, contiguous sequence, or a set of partial RuvC domains that are not contiguous with respect to the primary amino acid sequence of the protein. An effector protein of the present disclosure may include multiple partial RuvC domains, which may combine to generate a RuvC domain with substrate binding or catalytic activity. For example, an effector protein may include three partial RuvC domains (RuvC-I, RuvC-II, and RuvC-III, also referred to herein as subdomains) that are not contiguous with respect to the primary amino acid sequence of the effector protein, but form a RuvC domain once the protein is produced and folds. In some cases, effector proteins comprise a recognition domain with a binding affinity for a guide nucleic acid or for a guide nucleic acid-target nucleic acid heteroduplex. In some instances, the effector protein does not comprise a zinc finger domain. In some instances, the effector protein does not comprise an HNH domain.

[0103] Effector proteins disclosed herein may function as an endonuclease that catalyzes cleavage at a specific position (e.g., at a specific nucleotide within a nucleic acid sequence) in a target nucleic acid. The target nucleic acid may be single stranded RNA (ssRNA), double stranded DNA (dsDNA) or single-stranded DNA (ssDNA). In some instances, the target nucleic acid is single-stranded DNA. In some instances, the target nucleic acid is single-stranded RNA. The effector proteins may provide cis cleavage activity, trans cleavage activity, nickase activity, or a combination thereof. Cis cleavage activity is cleavage of a target nucleic acid that is hybridized to a guide nucleic acid (e.g., a dual gRNA or a sgRNA), wherein cleavage occurs within or directly adjacent to the region of the target nucleic acid that is hybridized to guide nucleic acid. Trans cleavage activity (also referred to as transcollateral cleavage) is cleavage of ssDNA or ssRNA that is near, but not hybridized to the guide nucleic acid. Trans cleavage activity is triggered by the hybridization of guide nucleic acid to the target nucleic acid. Nickase activity is a selective cleavage of one strand of a dsDNA.

[0104] Effector proteins of the present disclosure, dimers thereof, and multimeric complexes thereof may cleave or nick a target nucleic acid within or near a protospacer adjacent motif (PAM) sequence of the target nucleic acid. In some instances, cleavage occurs within 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 nucleosides of a 5’ or 3’ terminus of a PAM sequence. A target nucleic acid may comprise a PAM sequence adjacent to a sequence that is complementary to a guide nucleic acid spacer region.

[0105] In some instances, the Type V CRISPR / Cas protein has been modified (also referred to asan engineered protein). For example, a Type V CRISPR / Cas protein disclosed herein or a variant thereof may comprise a nuclear localization signal (NLS). Type V CRISPR / Cas proteins may be codon optimized for expression in a specific cell, for example, a bacterial cell, a plant cell, a eukaryotic cell, an animal cell, a mammalian cell, or a human cell. In some embodiments, the Type V CRISPR / Cas protein is codon optimized for a human cell.

[0106] Several programmable nucleases are consistent with the methods and devices of the present disclosure. For example, Cas proteins are programmable nucleases used in the methods and systems disclosed herein. Cas proteins can include any of the known Classes and Types of CRISPR / Cas enzymes. Programmable nucleases disclosed herein include Class 1 Cas proteins, such as the Type I, Type IV, or Type III Cas proteins. Programmable nucleases disclosed herein also include the Class 2 Cas proteins, such as the Type II, Type V, and Type VI Cas proteins. Programmable nucleases included in the devices disclosed herein and methods of use thereof include a Type V or Type VI Cas proteins.

[0107] In some instances, the programmable nuclease is a Type V Cas protein. In general, a Type V Cas effector protein comprises a RuvC domain, but lacks an HNH domain. In most instances, the RuvC domain of the Type V Cas effector protein comprises three patrial RuvC domains (RuvC-I, RuvC-II, and RuvC-III, also referred to herein as subdomains). In some instances, the three RuvC subdomains are located within the C-terminal half of the Type V Cas effector protein. In some instances, none of the RuvC subdomains are located at the N terminus of the protein. In some instances, the RuvC subdomains are contiguous. In some instances, the RuvC subdomains are not contiguous with respect to the primary amino acid sequence of the Type V Cas protein, but form a ruvC domain once the protein is produced and folds. In some instances, there are zero to about 50 amino acids between the first and second RuvC subdomains. In some instances, there are zero to about 50 amino acids between the second and third RuvC subdomains. In some instances, the Cas effector is a Casl4 effector. In some instances, the Casl4 effector is a Casl4a, Casl4al, Casl4b, Casl4c, Casl4d, Casl4e, Casl4f, Casl4g, Casl4h, or Casl4u effector. In some instances, the Cas effector is a CasPhi effector. In some instances, the Cas effector is a Casl2 effector. In some instances, the Casl2 effector is a Casl2a, Casl2b, Casl2c, Casl2d, Casl2e, or Casl2j effector.

[0108] In some instances, the Type V CRISPR / Cas protein comprises a Casl4 protein. Casl4 proteins may comprise a bilobed structure with distinct amino-terminal and carboxy-terminal domains. The amino- and carboxy-terminal domains may be connected by a flexible linker. The flexible linker may affect the relative conformations of the amino- and carboxyl-terminaldomains. The flexible linker may be short, for example less than 10 amino acids, less than 8 amino acids, less than 6 amino acids, less than 5 amino acids, or less than 4 amino acids in length. The flexible linker may be sufficiently long to enable different conformations of the amino- and carboxy -terminal domains among two Cast 4 proteins of a Cast 4 dimer complex (e.g., the relative orientations of the amino- and carboxy-terminal domains differ between two Casl4 proteins of a Casl4 homodimer complex). The linker domain may comprise a mutation which affects the relative conformations of the amino- and carboxyl-terminal domains. The linker may comprise a mutation which affects Casl4 dimerization. For example, a linker mutation may enhance the stability of a Cast 4 dimer.

[0109] In some instances, the amino-terminal domain of a Casl4 protein comprises a wedge domain, a recognition domain, a zinc finger domain, or any combination thereof. The wedge domain may comprise a multi-strand P-barrel structure. A multi-strand P-barrel structure may comprise an oligonucleotide / oligosaccharide-binding fold that is structurally comparable to those of some Cast 2 proteins. The recognition domain and the zinc finger domain may each (individually or collectively) be inserted between P-barrel strands of the wedge domain. The recognition domain may comprise a 4-a-helix structure, structurally comparable but shorter than those found in some Casl2 proteins. The recognition domain may comprise a binding affinity for a guide nucleic acid or for a guide nucleic acid-target nucleic acid heteroduplex. In some cases, a REC lobe may comprise a binding affinity for a PAM sequence in the target nucleic acid. The amino-terminal may comprise a wedge domain, a recognition domain, and a zinc finger domain. The carboxy-terminal may comprise a RuvC domain, a zinc finger domain, or any combination thereof. The carboxy-terminal may comprise one RuvC and one zinc finger domain.

[0110] Casl4 proteins may comprise a RuvC domain or a partial RuvC domain. The RuvC domain may be defined by a single, contiguous sequence, or a set of partial RuvC domains that are not contiguous with respect to the primary amino acid sequence of the Cast 4 protein. In some instances, a partial RuvC domain does not have any substrate binding activity or catalytic activity on its own. A Casl4 protein of the present disclosure may include multiple partial RuvC domains, which may combine to generate a RuvC domain with substrate binding or catalytic activity. For example, a Casl4 may include 3 partial RuvC domains (RuvC-I, RuvC-II, and RuvC-III, also referred to herein as subdomains) that are not contiguous with respect to the primary amino acid sequence of the Casl4 protein, but form a RuvC domain once the protein is produced and folds. A Casl4 protein may comprise a linker loop connecting a carboxy terminal domain of the Cast 4 protein with the amino terminal domain of the Cas 14 protein, and wherein the carboxy terminal domain comprises one or more RuvC domains and the amino terminaldomain comprises a recognition domain.[oni] Casl4 proteins may comprise a zinc finger domain. In some instances, a carboxy terminal domain of a Casl4 protein comprises a zinc finger domain. In some instances, an amino terminal domain of a Casl4 protein comprises a zinc finger domain. In some instances, the amino terminal domain comprises a wedge domain (e.g., a multi-P-barrel wedge structure), a zinc finger domain, or any combination thereof. In some cases, the carboxy terminal domain comprises the RuvC domains and a zinc finger domain, and the amino terminal domain comprises a recognition domain, a wedge domain, and a zinc finger domain.

[0112] Cast 4 proteins may be relatively small compared to many other Cas proteins, making them suitable for nucleic acid detection or gene editing. For instance, a Cas 14 protein may be less likely to adsorb to a surface or another biological species due to its small size. The smaller nature of these proteins also allows for them to be more easily packaged as a reagent in a system or assay, and delivered with higher efficiency as compared to other larger Cas proteins. In some cases, a Casl4 protein is 400 to 800 amino acid residues long, 400 to 600 amino acid residues long, 440 to 580 amino acid residues long, 460 to 560 amino acid residues long, 460 to 540 amino acid residues long, 460 to 500 amino acid residues long, 400 to 500 amino acid residues long, or 500 to 600 amino acid residues long. In some cases, a Casl4 protein is less than about 550 amino acid residues long. In some cases, a Casl4 protein is less than about 500 amino acid residues long.

[0113] In some instances, a Cas 14 protein may function as an endonuclease that catalyzes cleavage at a specific position within a target nucleic acid. In some instances, a Casl4 protein is capable of catalyzing non-sequence-specific cleavage of a single stranded nucleic acid. In some cases, a Casl4 protein is activated to perform trans cleavage activity after binding of a guide nucleic acid with a target nucleic acid. This trans cleavage activity is also referred to as “collateral” or “transcollateral” cleavage. Trans cleavage activity may be non-specific cleavage of nearby single-stranded nucleic acid by the activated programmable nuclease, such as trans cleavage of reporters with a detection moiety.

[0114] In some embodiments, the Type V CRISPR / Cas enzyme is a programmable Casl2 nuclease. Type V CRISPR / Cas enzymes (e.g., Casl2 or Casl4) lack an HNH domain. A Casl2 nuclease of the present disclosure cleaves a nucleic acid via a single catalytic RuvC domain. The RuvC domain is within a nuclease, or “NUC” lobe of the protein, and the Casl2 nucleases further comprise a recognition, or “REC” lobe. The REC and NUC lobes are connected by a bridge helix and the Cas 12 proteins additionally include two domains for PAM recognitiontermed the PAM interacting (PI) domain and the wedge (WED) domain. In some instances, a programmable Cast 2 nuclease can be a Cast 2a protein, a Cast 2b protein, Cast 2c protein, Cast 2d protein, or a Casl2e protein.

[0115] In some embodiments, the programmable nuclease can be Cast 3. Sometimes the Cast 3 can be Cast 3 a, Cast 3b, Cast 3 c, Cast 3d, or Casl3e. In some cases, the programmable nuclease can be Mad7 or Mad2. In some cases, the programmable nuclease can be Casl2. Sometimes the Casl2 can be Casl2a, Casl2b, Casl2c, Casl2d, or Casl2e. In some cases, the Casl2 can be Casl2M08, which is a specific protein variant within the Casl2 protein family / classification). In some cases, the programmable nuclease can be Csml, Cas9, C2c4, C2c8, C2c5, C2cl0, C2c9, or CasZ. Sometimes, the Csml can also be also called smCmsl, miCmsl, obCmsl, or suCmsl. Sometimes Casl3a can also be also called C2c2. Sometimes CasZ can also be called Casl4a, Cast 4b, Cast 4c, Casl4d, Casl4e, Casl4f, Cast 4g, or Casl4h. Sometimes, the programmable nuclease can be a type V CRISPR-Cas system. In some cases, the programmable nuclease can be a type VI CRISPR-Cas system. Sometimes the programmable nuclease can be a type III CRISPR-Cas system. Sometimes the programmable nuclease can be an engineered nuclease that is not from a naturally occurring CRISPR-Cas system. In some cases, the programmable nuclease can be from at least one of Leptotrichia shahii (Lsh), Listeria seeligeri (Lse), Leptotrichia buccalis (Lbu), Leptotrichia wadeu (Lwa), Rhodobacter capsulatus (Rea), Herbinix hemicellulosilytica (Hhe), Paludibacter propionicigenes (Ppr), Lachnospiraceae bacterium (Lba), [Eubacterium] rectale (Ere), Listeria newyorkensis (Lny), Clostridium aminophilum (Cam), Prevotella sp. (Psm), Capnocytophaga canimorsus (Cea, Lachnospiraceae bacterium (Lba), Bergeyella zoohelcum (Bzo), Prevotella intermedia (Pin), Prevotella buccae (Pbu), Alistipes sp. (Asp), Riemerella anatipestifer (Ran), Prevotella aurantiaca (Pau), Prevotella saccharolytica (Psa), Prevotella intermedia (Pin2), Capnocytophaga canimorsus (Cea), Porphyromonas gulae (Pgu), Prevotella sp. (Psp), Porphyromonas gingivalis (Pig), Prevotella intermedia (Pin3), Enterococcus italicus (Ei), Lactobacillus salivarius (Ls), or Thermus thermophilus (Tt). Sometimes the Casl3 is at least one of LbuCasl3a, LwaCasl3a, LbaCasl3a, HheCasl3a, PprCasl3a, EreCasl3a, CamCasl3a, or LshCasl3a. The trans cleavage activity of the CRISPR enzyme can be activated when the crRNA is complexed with the target nucleic acid. The trans cleavage activity of the CRISPR enzyme can be activated when the guide nucleic acid comprising a tracrRNA and crRNA are complexed with the target nucleic acid. The target nucleic acid can be RNA or DNA.

[0116] In some embodiments, a programmable nuclease as disclosed herein is an RNA-activated programmable RNA nuclease. In some embodiments, a programmable nuclease as disclosedherein is a DNA-activated programmable RNA nuclease. In some embodiments, a programmable nuclease is capable of being activated by a target RNA to initiate trans cleavage of an RNA reporter and is capable of being activated by a target DNA to initiate trans cleavage of an RNA reporter, such as a Type VI CRISPR / Cas enzyme (e.g., a Casl3 nuclease). For example, Casl3a of the present disclosure can be activated by a target RNA to initiate trans cleavage activity of the Cast 3a for the cleavage of an RNA reporter and can be activated by a target DNA to initiate trans cleavage activity of the Cast 3a for trans cleavage of an RNA reporter. An RNA reporter can be an RNA-based reporter. In some embodiments, the Cast 3a recognizes and detects ssDNA to initiate transcleavage of RNA reporters. Multiple Casl3a isolates can recognize, be activated by, and detect target DNA, including ssDNA, upon hybridization of a guide nucleic acid with the target DNA. For example, Lbu-Casl3a and Lwa-Casl3a can both be activated to transcollaterally cleave RNA reporters by target DNA. Thus, Type VI CRISPR / Cas enzyme (e.g., a Casl3 nuclease, such as Casl3a) can be DNA-activated programmable RNA nucleases, and therefore can be used to detect a target DNA using the methods as described herein. DNA- activated programmable RNA nuclease detection of ssDNA can be robust at multiple pH values. For example, target ssDNA detection by Casl3 can exhibit consistent cleavage across a wide range of pH conditions, such as from a pH of 6.8 to a pH of 8.2. In contrast, target RNA detection by Casl3 can exhibit high cleavage activity of pH values from 7.9 to 8.2. In some embodiments, a DNA-activated programmable RNA nuclease that also is capable of being an RNA-activated programmable RNA nuclease, can have DNA targeting preferences that are distinct from its RNA targeting preferences. For example, the optimal ssDNA targets for Cast 3a have different properties than optimal RNA targets for Cast 3 a. As one example, gRNA performance on ssDNA can not necessarily correlate with the performance of the same gRNAs on RNA. As another example, gRNAs can perform at a high level regardless of target nucleotide identity at a 3’ position on a target RNA sequence. In some embodiments, gRNAs can perform at a high level in the absence of a G at a 3’ position on a target ssDNA sequence. Furthermore, target DNA detected by Casl3 disclosed herein can be directly taken from organisms or can be indirectly generated by nucleic acid amplification methods, such as PCR and LAMP or any amplification method described herein. Key steps for the sensitive detection of a target DNA, such as a target ssDNA, by a DNA-activated programmable RNA nuclease, such as Cast 3 a, can include: (1) production or isolation of DNA to concentrations above about 0.1 nM per reaction for in vitro diagnostics, (2) selection of a target sequence with the appropriate sequence features to enable DNA detection as these features are distinct from those required for RNA detection, and (3) buffer composition that enhances DNA detection.

[0117] The detection of a target DNA by a DNA-activated programmable RNA nuclease can be connected to a variety of readouts including fluorescence, lateral flow, electrochemistry, or any other readouts described herein. Multiplexing of programmable DNA nuclease, such as a Type V CRISPR-Cas protein, with a DNA-activated programmable RNA nuclease, such as a Type VI protein, with a DNA reporter and an RNA reporter, can enable multiplexed detection of target ssDNAs or a combination of a target dsDNA and a target ssDNA, respectively. Multiplexing of different RNA-activated programmable RNA nucleases that have distinct RNA reporter cleavage preferences can enable additional multiplexing. Methods for the generation of ssDNA for DNA- activated programmable RNA nuclease-based diagnostics can include (1) asymmetric PCR, (2) asymmetric isothermal amplification, such as RPA, LAMP, SDA, etc. (3) NEAR for the production of short ssDNA molecules, and (4) conversion of RNA targets into ssDNA by a reverse transcriptase followed by RNase H digestion. Thus, DNA-activated programmable RNA nuclease detection of target DNA is compatible with the various systems, kits, compositions, reagents, and methods disclosed herein. For example, target ssDNA detection by Casl3a can be employed in a detection device as disclosed herein.

[0118] Other Exemplary protein sequences are described in the following applications: PCT / US2021 / 033271; PCT / US2021 / 035031, and PCT / US2022 / 028865, all of which are herein incorporated by reference in their entirety.

[0119] In some embodiments a programmable nuclease is referred to as an effector protein. In some instances, an effector protein disclosed herein is an engineered protein. The engineered protein is not identical to a naturally-occurring protein. The engineered protein may provide enhanced nuclease or nickase activity as compared to a naturally occurring nuclease or nickase. By way of non-limiting example, some engineered proteins exhibit optimal activity at lower salinity and viscosity than the protoplasm of their bacterial cell of origin. Also by way of nonlimiting example, bacteria often comprise protoplasmic salt concentrations greater than 250 mM and room temperature intracellular viscosities above 2 centipoise, whereas engineered proteins exhibit optimal activity (e.g., cis-cleavage activity) at salt concentrations below 150 mM and viscosities below 1.5 centipoise. The present disclosure leverages these dependencies by providing engineered proteins in solutions optimized for their activity and stability.

[0120] Compositions and systems described herein may comprise an engineered protein in a solution comprising a room temperature viscosity of less than about 15 centipoise, less than about 12 centipoise, less than about 10 centipoise, less than about 8 centipoise, less than about 6 centipoise, less than about 5 centipoise, less than about 4 centipoise, less than about 3 centipoise,less than about 2 centipoise, or less than about 1.5 centipoise. Compositions and systems may comprise an engineered protein in a solution comprising an ionic strength of less than about 500 mM, less than about 400 mM, less than about 300 mM, less than about 250 mM, less than about 200 mM, less than about 150 mM, less than about 100 mM, less than about 80 mM, less than about 60 mM, or less than about 50 mM. Compositions and systems may comprise an engineered protein and an assay excipient, which may stabilize a reagent or product, prevent aggregation or precipitation, or enhance or stabilize a detectable signal (e.g., a fluorescent signal). Examples of assay excipients include, but are not limited to, saccharides and saccharide derivatives (e.g., sodium carboxymethyl cellulose and cellulose acetate), detergents, glycols, polyols, esters, buffering agents, alginic acid, and organic solvents (e.g., DMSO).

[0121] An engineered protein may comprise a modified form of a wildtype counterpart protein. The modified form of the wildtype counterpart may comprise an amino acid change (e.g., deletion, insertion, or substitution) that reduces the nucleic acid-cleaving activity of the programmable nuclease. For example, a nuclease domain (e.g., RuvC domain) of a Type V CRISPR / Cas protein may be deleted or mutated so that it is no longer functional or comprises reduced nuclease activity. The modified form of the programmable nuclease may have less than 90 %, less than 80 %, less than 70%, less than 60%, less than 50%, less than 40%, less than 30%, less than 20%, less than 10%, less than 5%, or less than 1% of the nucleic acid-cleaving activity of the wild-type counterpart. Engineered proteins may have no substantial nucleic acid-cleaving activity. Engineered proteins may be enzymatically inactive or “dead,” that is it may bind to a nucleic acid but not cleave it. An enzymatically inactive protein may comprise an enzymatically inactive domain (e.g., inactive nuclease domain). Enzymatically inactive may refer to an activity less than 1%, less than 2%, less than 3%, less than 4%, less than 5%, less than 6%, less than 7%, less than 8%, less than 9%, or less than 10% activity compared to the wild-type counterpart. A dead protein may associate with an engineered guide nucleic acid to activate or repress transcription of a target nucleic acid sequence. In some embodiments, the enzymatically inactive protein is fused with a protein comprising recombinase activity.

[0122] In some instances, a programmable nuclease is a fusion protein, wherein the fusion protein comprises a protein comprising the amino acid sequence of any one of SEQ ID NOs: 1- 61 or 81-92. In some instances, the fusion protein comprises a programmable nuclease and a fusion partner protein.

[0123] A fusion partner protein is also simply referred to herein as a fusion partner. In some cases, the fusion partner promotes the formation of a multimeric complex of the programmablenuclease. In some cases, the fusion partner is an additional programmable nuclease. In some cases, the multimeric complex comprising the programmable nuclease and the additional programmable nuclease binds a guide nucleic acid. The programmable nucleases of the multimeric complex may bind the guide nucleic acid in an asymmetric fashion. In some cases, one programmable nuclease of the multimeric complex interacts more strongly with the guide nucleic acid than the additional programmable nuclease of the multimeric complex. In some cases, a programmable nuclease interacts more strongly with a target nucleic acid when it is complexed with the guide nucleic acid relative to when the programmable nuclease or the multimeric complex is not complexed with the guide nucleic acid.

[0124] In some cases, the fusion partner has enzymatic activity in the presence of its enzyme substrate. For example, the fusion partner may comprise an enzyme such as horse radish peroxidase (HRP) which can catalyze a detectable color change reaction in the presence of its substrate (e.g., TMB).

[0125] In some instances, fusion partners include, but are not limited to, a protein that directly and / or indirectly provides for increased or decreased transcription and / or translation of a target nucleic acid (e.g., a transcription activator or a fragment thereof, a protein or fragment thereof that recruits a transcription activator, a small molecule / drug-responsive transcription and / or translation regulator, a translation-regulating protein, etc.). In some instances, fusion partners that increase or decrease transcription include a transcription activator domain or a transcription repressor domain, respectively.

[0126] In some cases, a terminus of the programmable nuclease is linked to a terminus of the fusion partner through an amide bond. In some cases, a programmable nuclease is coupled to a fusion partner via a linker protein. In some cases, a programmable nuclease is coupled to a fusion partner via a linker protein. The linker protein may have any of a variety of amino acid sequences. A linker protein may comprise a region of rigidity (e.g., beta sheet, alpha helix), a region of flexibility, or any combination thereof. In some instances, the linker comprises small amino acids, such as glycine and alanine, that impart high degrees of flexibility. The ordinarily skilled artisan will recognize that design of a peptide conjugated to any desired element may include linkers that are all or partially flexible, such that the linker may include a flexible linker as well as one or more portions that confer less flexible structure. Suitable linkers include proteins of 4 linked amino acids to 40 linked amino acids in length, or between 4 linked amino acids and 25 linked amino acids in length. These linkers may be produced by using synthetic, linker-encoding oligonucleotides to couple the proteins, or may be encoded by a nucleic acidsequence encoding a fusion protein (e.g., an programmable nuclease coupled to a fusion partner). Examples of linker proteins include glycine polymers (G)n (SEQ ID NO: 70), glycine-serine polymers (including, for example, (GS)n (SEQ ID NO: 71), GSGGSn (SEQ ID NO: 72), GGSGGSn (SEQ ID NO: 73), and GGGSn (SEQ ID NO: 74), where n is an integer of at least one), glycine-alanine polymers, and alanine-serine polymers. Exemplary linkers may comprise amino acid sequences including, but not limited to, GGSG (SEQ ID NO: 75), GGSGG (SEQ ID NO: 76), GSGSG (SEQ ID NO: 77), GSGGG (SEQ ID NO: 78), GGGSG (SEQ ID NO: 79), and GSSSG (SEQ ID NO: 80).

[0127] Disclosed herein are non-naturally occurring compositions and systems comprising at least one of an engineered Cas protein and an engineered guide nucleic acid, which may simply be referred to herein as a Cas protein and a guide nucleic acid, respectively. In general, an engineered Cas protein and an engineered guide nucleic acid refer to a Cas protein and a guide nucleic acid, respectively, that are not found in nature. In some instances, systems and compositions comprise at least one non-naturally occurring component. For example, compositions and systems may comprise a guide nucleic acid, wherein the sequence of the guide nucleic acid is different or modified from that of a naturally-occurring guide nucleic acid. In some instances, compositions and systems comprise at least two components that do not naturally occur together. For example, compositions and systems may comprise a guide nucleic acid comprising a repeat region and a spacer region which do not naturally occur together. Also, by way of example, compositions and systems may comprise a guide nucleic acid and a Cas protein that do not naturally occur together. Conversely, and for clarity, a Cas protein or guide nucleic acid that is “natural,” “naturally-occurring,” or “found in nature” includes Cas proteins and guide nucleic acids from cells or organisms that have not been genetically modified by a human or machine.

[0128] In some instances, the guide nucleic acid may comprise a non-natural nucleobase sequence. In some instances, the non-natural sequence is a nucleobase sequence that is not found in nature. The non-natural sequence may comprise a portion of a naturally occurring sequence, wherein the portion of the naturally occurring sequence is not present in nature absent the remainder of the naturally-occurring sequence. In some instances, the guide nucleic acid may comprise two naturally occurring sequences arranged in an order or proximity that is not observed in nature. In some instances, compositions and systems comprise a ribonucleotide complex comprising a programmable nuclease and a guide nucleic acid that do not occur together in nature. Engineered guide nucleic acids may comprise a first sequence and a second sequence that do not occur naturally together. For example, an engineered guide nucleic acidmay comprise a sequence of a naturally occurring repeat region and a spacer region that is complementary to a naturally occurring eukaryotic sequence. The engineered guide nucleic acid may comprise a sequence of a repeat region that occurs naturally in an organism and a spacer region that does not occur naturally in that organism. An engineered guide nucleic acid may comprise a first sequence that occurs in a first organism and a second sequence that occurs in a second organism, wherein the first organism and the second organism are different. The guide nucleic acid may comprise a third sequence disposed at a 3’ or 5’ end of the guide nucleic acid, or between the first and second sequences of the guide nucleic acid. For example, an engineered guide nucleic acid may comprise a naturally occurring crRNA and tracrRNA coupled by a linker sequence.

[0129] In some instances, compositions and systems described herein comprise an engineered Cas protein that is similar to a naturally occurring Cas protein. The engineered Cas protein may lack a portion of the naturally occurring Cas protein. The Cas protein may comprise a mutation relative to the naturally-occurring Cas protein, wherein the mutation is not found in nature. The Cas protein may also comprise at least one additional amino acid relative to the naturally- occurring Cas protein. For example, the Cas protein may comprise an addition of a nuclear localization signal relative to the natural occurring Cas protein. In certain embodiments, the nucleotide sequence encoding the Cas protein is codon optimized (e.g., for expression in a eukaryotic cell) relative to the naturally occurring sequence.

[0130] Described herein are various embodiments of thermostable programmable nucleases. In some embodiments, a programmable nuclease is referred to as a programmable nuclease. A programmable nuclease may be thermostable. In some instances, known programmable nucleases (e.g., Casl2 nucleases) are relatively thermo-sensitive and only exhibit activity (e.g., cis and / or trans cleavage) sufficient to produce a detectable signal in a diagnostic assay at temperatures less than 40° C, and optimally at about 37° C. A thermostable protein may have enzymatic activity, stability, or folding comparable to those at 37 °C. In some instances, the trans cleavage activity (e.g., the maximum trans cleavage rate as measured by fluorescent signal generation) of a programmable nuclease in a trans cleavage assay at 40 °C may be at least 50% of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 40 °C may be at least 55% of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 40 °C may be at least 60 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 40 °C may be at least 65% of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 40 °C may be atleast 70 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 40 °C may be at least 75% of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 40 °C may be at least 80% of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 40 °C may be at least 85% of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 40 °C may be at least 90% of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 40 °C may be at least 95% of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 40°C may be at least 100% of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 40 °C may be at least 1-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 40 °C may be at least 2-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 40 °C may be at least 3-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 40 °C may be at least 4-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 40 °C may be at least 5-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 40 °C may be at least 6-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 40 °C may be at least 7-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 40 °C may be at least 8-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 40 °C may be at least 9-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 40 °C may be at least 10-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 40 °C may be at least 11 -fold, at least 12-fold, at least 13 -fold, at least 14- fold, at least 15-fold, at least 20-fold, at least 25-fold, at least 30-fold, at least 35-fold, at least 40-fold, at least 45-fold, at least 50-fold or more of that at 37 °C.

[0131] In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 45 °C may be at least 50 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 45 °C may be at least 55 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 45 °C may be at least 60 % of that at 37 °C. In some instances, thetrans cleavage activity of a programmable nuclease in a trans cleavage assay at 45 °C may be at least 65 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 45 °C may be at least 70 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 45 °C may be at least 75 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 45 °C may be at least 80 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 45 °C may be at least 85 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 45 °C may be at least 90 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 45 °C may be at least 95 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 45 °C may be at least 100 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 45 °C may be at least 1-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 45 °C may be at least 2-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 45 °C may be at least 3-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 45 °C may be at least 4-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 45 °C may be at least 5-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 45 °C may be at least 6-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 45 °C may be at least 7-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 45 °C may be at least 8-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 45°C may be at least 9-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 45 °C may be at least 10-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 45°C may be at least 11-fold, at least 12-fold, at least 13-fold, at least 14-fold, at least 15-fold, at least 20-fold, at least 25-fold, at least 30-fold, at least 35-fold, at least 40-fold, at least 45-fold, at least 50-fold or more of that at 37 °C.

[0132] In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 50 °C may be at least 50 % of that at 37 °C. In some instances, the transcleavage activity of a programmable nuclease in a trans cleavage assay at 50 °C may be at least 55 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 50 °C may be at least 60 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 50 °C may be at least 65 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 50 °C may be at least 70 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 50 °C may be at least 75 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 50 °C may be at least 80 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 50 °C may be at least 85 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 50 °C may be at least 90 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 50 °C may be at least 95 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 50 °C may be at least 100 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 50 °C may be at least 1-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 50 °C may be at least 2-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 50 °C may be at least 3-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 50 °C may be at least 4-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 50 °C may be at least 5-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 50 °C may be at least 6-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 50 °C may be at least 7-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 50 °C may be at least 8-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 50 °C may be at least 9-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 50 °C may be at least 10-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 50 °C may be at least 11-fold, at least 12-fold, at least 13-fold, at least 14-fold, at least 15-fold, at least 20-fold, at least 25-fold, at least 30-fold, at least 35-fold, at least 40-fold, at least 45-fold, atleast 50-fold or more of that at 37 °C.

[0133] In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 55 °C may be at least 50 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 55 °C may be at least 55 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 55 °C may be at least 60 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 55 °C may be at least 65 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 55 °C may be at least 70 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 55 °C may be at least 75 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 55 °C may be at least 80 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 55 °C may be at least 85 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 55 °C may be at least 90 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 55 °C may be at least 95 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 55 °C may be at least 100 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 55 °C may be at least 1-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 55 °C may be at least 2-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 55 °C may be at least 3-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 55 °C may be at least 4-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 55 °C may be at least 5-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 55 °C may be at least 6-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 55 °C may be at least 7-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 55 °C may be at least 8-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 55 °C may be at least 9-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 55 °C may be at least 10-fold of that at 37 °C. In someinstances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 55 °C may be at least 11-fold, at least 12-fold, at least 13-fold, at least 14-fold, at least 15-fold, at least 20-fold, at least 25-fold, at least 30-fold, at least 35-fold, at least 40-fold, at least 45-fold, at least 50-fold or more of that at 37 °C.

[0134] In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 60 °C may be at least 50 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 60 °C may be at least 55 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 60 °C may be at least 60 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 60 °C may be at least 65 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 60 °C may be at least 70 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 60 °C may be at least 75 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 60 °C may be at least 80 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 60 °C may be at least 85 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 60 °C may be at least 90 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 60 °C may be at least 95 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 60 °C may be at least 100 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 60 °C may be at least 1-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 60 °C may be at least 2-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 60 °C may be at least 3-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 60 °C may be at least 4-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 60 °C may be at least 5-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 60 °C may be at least 6-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 60 °C may be at least 7-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 60 °C may be at least 8-fold of that at 37 °C. In some instances, thetrans cleavage activity of a programmable nuclease in a trans cleavage assay at 60 °C may be at least 9-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 60 °C may be at least 10-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 60 °C may be at least 11-fold, at least 12-fold, at least 13-fold, at least 14-fold, at least 15-fold, at least 20-fold, at least 25-fold, at least 30-fold, at least 35-fold, at least 40-fold, at least 45-fold, at least 50-fold or more of that at 37 °C.

[0135] In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 65 °C may be at least 50 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 65 °C may be at least 55 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 65 °C may be at least 60 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 65 °C may be at least 65 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 65 °C may be at least 70 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 65 °C may be at least 75 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 65 °C may be at least 80 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 65 °C may be at least 85 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 65 °C may be at least 90 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 65 °C may be at least 95 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 65 °C may be at least 100 % of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 65 °C may be at least 1-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 65 °C may be at least 2-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 65 °C may be at least 3-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 65 °C may be at least 4-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 65 °C may be at least 5-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 65 °C may be at least 6-fold of that at 37 °C. In some instances, the transcleavage activity of a programmable nuclease in a trans cleavage assay at 65 °C may be at least 7-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 65 °C may be at least 8-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 65 °C may be at least 9-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 65 °C may be at least 10-fold of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 65 °C may be at least 11-fold, at least 12-fold, at least 13-fold, at least 14-fold, at least 15-fold, at least 20-fold, at least 25-fold, at least 30-fold, at least 35-fold, at least 40-fold, at least 45-fold, at least 50-fold or more of that at 37 °C. In some instances, the trans cleavage activity of a programmable nuclease in a trans cleavage assay at 70 °C, 75 °C. 80 °C, or more may be at least 50, at least 60 %, at least 65 %, at least 70 %, at least 75 %, at least 80 %, at least 85 %, at least 95 %, at least 100 %, at least 1-fold, at least 2-fold , at least 3-fold , at least 4-fold , at least 5-fold , at least 6-fold , at least 7-fold , at least 8-fold , at least 9-fold , at least 10-fold , at least 11 -fold, at least 12-fold, at least 13-fold, at least 14-fold, at least 15-fold, at least 20-fold, at least 25-fold, at least 30-fold, at least 35-fold, at least 40-fold, at least 45-fold, at least 50-fold or more of that at 37 °C.

[0136] In some instances, the trans cleavage activity may be measured against a negative control in a trans cleavage assay. In some instances, the trans cleavage activity of a programmable nuclease against a nucleic acid in a trans cleavage assay at 37 °C may be at least 50 %, at least 55 %, at least 60 %, at least 65 %, at least 70 %, at least 75 %, at least 80 %, at least 85 %, at least 90 %, at least 95 %, at least 100 %, at least 1-fold, at least 2-fold, at least 3 -fold, at least 4- fold, at least 5-fold, at least 6-fold, at least 7-fold, at least 8-fold, at least 9-fold, or at least 10- fold of that against a negative control nucleic acid. In some instances, the trans cleavage activity of a programmable nuclease against a nucleic acid in a trans cleavage assay at 37 °C may be at least 11-fold, at least 12-fold, at least 13-fold, at least 14-fold, at least 15-fold, at least 20-fold, at least 25-fold, at least 30-fold, at least 35-fold, at least 40-fold, at least 45-fold, at least 50-fold or more of that against a negative control nucleic acid. In some instances, the trans cleavage activity of a programmable nuclease against a nucleic acid in a trans cleavage assay at 40 °C may be at least 50 %, at least 55 %, at least 60 %, at least 65 %, at least 70 %, at least 75 %, at least 80 %, at least 85 %, at least 90 %, at least 95 %, at least 100 %, at least 1-fold, at least 2-fold, at least 3- fold, at least 4-fold, at least 5-fold, at least 6-fold, at least 7-fold, at least 8-fold, at least 9-fold, or at least 10-fold of that against a negative control nucleic acid. In some instances, the trans cleavage activity of a programmable nuclease against a nucleic acid in a trans cleavage assay at40 °C may be at least 11-fold, at least 12-fold, at least 13-fold, at least 14-fold, at least 15-fold, at least 20-fold, at least 25-fold, at least 30-fold, at least 35-fold, at least 40-fold, at least 45-fold, at least 50-fold or more of that against a negative control nucleic acid. In some instances, the trans cleavage activity of a programmable nuclease against a nucleic acid in a trans cleavage assay at 45 °C may be at least 50 %, at least 55 %, at least 60 %, at least 65 %, at least 70 %, at least 75 %, at least 80 %, at least 85 %, at least 90 %, at least 95 %, at least 100 %, at least 1-fold, at least 2-fold, at least 3-fold, at least 4-fold, at least 5-fold, at least 6-fold, at least 7-fold, at least 8-fold, at least 9-fold, or at least 10-fold of that against a negative control nucleic acid. In some instances, the trans cleavage activity of a programmable nuclease against a nucleic acid in a trans cleavage assay at 45 °C may be at least 11 -fold, at least 12-fold, at least 13 -fold, at least 14-fold, at least 15-fold, at least 20-fold, at least 25-fold, at least 30-fold, at least 35-fold, at least 40-fold, at least 45-fold, at least 50-fold or more of that against a negative control nucleic acid. In some instances, the trans cleavage activity of a programmable nuclease against a nucleic acid in a trans cleavage assay at 50 °C may be at least 50 %, at least 55 %, at least 60 %, at least 65 %, at least 70 %, at least 75 %, at least 80 %, at least 85 %, at least 90 %, at least 95 %, at least 100 %, at least 1-fold, at least 2-fold, at least 3-fold, at least 4-fold, at least 5-fold, at least 6-fold, at least 7- fold, at least 8-fold, at least 9-fold, or at least 10-fold of that against a negative control nucleic acid. In some instances, the trans cleavage activity of a programmable nuclease against a nucleic acid in a trans cleavage assay at 50 °C may be at least 11-fold, at least 12-fold, at least 13-fold, at least 14-fold, at least 15-fold, at least 20-fold, at least 25-fold, at least 30-fold, at least 35-fold, at least 40-fold, at least 45-fold, at least 50-fold or more of that against a negative control nucleic acid. In some instances, the trans cleavage activity of a programmable nuclease against a nucleic acid in a trans cleavage assay at 55 °C may be at least 50 %, at least 55 %, at least 60 %, at least 65 %, at least 70 %, at least 75 %, at least 80 %, at least 85 %, at least 90 %, at least 95 %, at least 100 %, at least 1-fold, at least 2-fold, at least 3-fold, at least 4-fold, at least 5-fold, at least 6-fold, at least 7-fold, at least 8-fold, at least 9-fold, or at least 10-fold of that against a negative control nucleic acid. In some instances, the trans cleavage activity of a programmable nuclease against a nucleic acid in a trans cleavage assay at 55 °C may be at least 11 -fold, at least 12-fold, at least 13-fold, at least 14-fold, at least 15-fold, at least 20-fold, at least 25-fold, at least 30-fold, at least 35-fold, at least 40-fold, at least 45-fold, at least 50-fold or more of that against a negative control nucleic acid. In some instances, the trans cleavage activity of a programmable nuclease against a nucleic acid in a trans cleavage assay at 60 °C may be at least 50 %, at least 55 %, at least 60 %, at least 65 %, at least 70 %, at least 75 %, at least 80 %, at least 85 %, at least 90 %, at least 95 %, at least 100 %, at least 1-fold, at least 2-fold, at least 3 -fold, at least 4-fold, at least 5-fold, at least 6-fold, at least 7-fold, at least 8-fold, at least 9-fold, or at least 10- fold of that against a negative control nucleic acid. In some instances, the trans cleavage activity of a programmable nuclease against a nucleic acid in a trans cleavage assay at 60 °C may be at least 11-fold, at least 12-fold, at least 13-fold, at least 14-fold, at least 15-fold, at least 20-fold, at least 25-fold, at least 30-fold, at least 35-fold, at least 40-fold, at least 45-fold, at least 50-fold or more of that against a negative control nucleic acid. In some instances, the trans cleavage activity of a programmable nuclease against a nucleic acid in a trans cleavage assay at 65 °C may be at least 50 %, at least 55 %, at least 60 %, at least 65 %, at least 70 %, at least 75 %, at least 80 %, at least 85 %, at least 90 %, at least 95 %, at least 100 %, at least 1-fold, at least 2-fold, at least 3- fold, at least 4-fold, at least 5-fold, at least 6-fold, at least 7-fold, at least 8-fold, at least 9-fold, or at least 10-fold of that against a negative control nucleic acid. In some instances, the trans cleavage activity of a programmable nuclease against a nucleic acid in a trans cleavage assay at 65 °C may be at least 11-fold, at least 12-fold, at least 13-fold, at least 14-fold, at least 15-fold, at least 20-fold, at least 25-fold, at least 30-fold, at least 35-fold, at least 40-fold, at least 45-fold, at least 50-fold or more of that against a negative control nucleic acid. In some instances, the trans cleavage activity of a programmable nuclease against a nucleic acid in a trans cleavage assay at 70 °C, 75 °C, 80 °C, or more may be at least 50 %, at least 55 %, at least 60 %, at least 65 %, at least 70 %, at least 75 %, at least 80 %, at least 85 %, at least 90 %, at least 95 %, at least 100 %, at least 1-fold, at least 2-fold, at least 3-fold, at least 4-fold, at least 5-fold, at least 6-fold, at least 7-fold, at least 8-fold, at least 9-fold, or at least 10-fold of that against a negative control nucleic acid. In some instances, the trans cleavage activity of a programmable nuclease against a nucleic acid in a trans cleavage assay at 70 °C, 75 °C, 80 °C, or more may be at least 11-fold, at least 12- fold, at least 13-fold, at least 14-fold, at least 15-fold, at least 20-fold, at least 25-fold, at least 30-fold, at least 35-fold, at least 40-fold, at least 45-fold, at least 50-fold or more of that against a negative control nucleic acid.

[0137] The reporters described herein can be RNA reporters. The RNA reporters can comprise at least one ribonucleic acid and a detectable moiety. In some embodiments, a programmable nuclease probe or a CRISPR probe comprising a programmable nuclease can recognize and detect ssDNA and, further, can specifically trans-cleave RNA reporters. The detection of the target nucleic acid in the sample can indicate the presence of the disease (or disease-causing agent) in the sample and can provide information for taking action to reduce the transmission of the disease to individuals in the disease-affected environment or near the disease-carrying individual.

[0138] Cleavage of a reporter (i.e., a protein-nucleic acid or detector nucleic acid) can produce a-n-signal. The signal can indicate a presence of the target nucleic acid in the sample, and an absence of the signal can indicate an absence of the target nucleic acid in the sample. In some cases, cleavage of the reporter can produce a calorimetric signal, a potentiometric signal, an amperometric signal, an optical signal, or a piezo-electric signal. Various devices and / or sensors can be used to detect these different types of signals, which indicate whether a target nucleic acid is present in the sample. The sensors and detectors usable to detect such signals can include, for example, optical sensors (e.g., imaging devices for detecting fluorescence or optical signals with various wavelengths and frequencies), electric potential sensors, surface plasmon resonance (SPR) sensors, interferometric sensors, or any other type of sensor or detector suitable for detecting calorimetric signals, potentiometric signals, amperometric signals, optical signals, or piezo-electric signals.

[0139] In an aspect, the present disclosure provides a method for target detection. The method can comprise sample collection. The method can further comprise sample preparation. The method can further comprise detection of one or more target molecules in the collected and prepared sample. In some embodiments, sample preparation can include nucleic acid amplification and the target molecules can include target amplicons.

[0140] In another aspect, the present disclosure provides a detection device for target detection. The detection device can be configured for multiplexed target detection. The detection device can be used to collect one or more samples, prepare or process the one or more samples for detection, and optionally divide the one or more samples into a plurality of droplets, aliquots, volumes, or subsamples for amplification of one or more target sequences or target nucleic acids. The target sequences may comprise, for example, a biological sequence. The biological sequence can comprise a nucleic acid sequence (e.g., a DNA sequence or an RNA sequence). In some embodiments, the target sequences are associated with an organism of interest, a disease of interest, a disease state of interest, a phenotype of interest, a genotype of interest, or a gene of interest.

[0141] The detection device can be configured to amplify target nucleic acids contained within the plurality of aliquots or subsamples. The detection device can be configured to amplify the target sequences or target nucleic acids contained within the plurality volumes by individually processing each of the plurality of volumes (e.g., by using a thermocycling process or any other suitable amplification process as described in greater detail below). In some cases, the plurality of volumes can undergo separate thermocycling processes. In some cases, the thermocycling processes can occur simultaneously. In other cases, the thermocycling processes can occur atdifferent times for each droplet or volume. In some embodiments, amplification is an isothermal amplification process.

[0142] The detection device can be configured to provide the sample aliquots, volumes, or subsamples to a detection region of the device, or otherwise partition a sample into separate volumes within a plurality of partitions within the detection region (e.g., a plurality of chambers or wells). In some embodiments, plurality of partitions are fluidically connected, such as by channels and / or valves (e.g., capillary valves). The detection region may comprise a plurality of programmable nuclease probes. The detection chamber can be configured to direct the aliquots, volumes, or subsamples along one or more fluid flow paths such that the aliquots, volumes, or subsamples are in contact with the one or more programmable nuclease probes.

[0143] The instrument and / or detection device can comprise one or more sensors or detectors. The one or more sensors or detectors of the instrument and / or detection device can be configured to detect one or more signals that are generated after one or more programmable nucleases of the one or more programmable nuclease probes become activated due to a binding of a guide nucleic acid of the programmable nuclease probes with a target nucleic acid present in the sample or amplicon thereof. As described elsewhere herein, the activated programmable nuclease can bind or cleave the target nucleic acid, which can result in a trans cleavage activity. Trans cleavage activity can be a non-specific cleavage of nearby single-stranded nucleic acids by the activated programmable nuclease, such as trans cleavage of reporter nucleic acids with a detection moiety. Once the reporter nucleic acids are cleaved by the activated programmable nucleases, the detection moiety can be released or separated from the reporter, thereby generating one or more detectable signals. The one or more sensors or detectors of the instrument or detection device can be configured to register and / or process the one or more detectable signals to confirm a presence and / or an absence of a particular target (e.g., a target nucleic acid) in a sample.

[0144] The one or more programmable nuclease probes of the detection device can be configured for multiplexed detection. In some cases, each programmable nuclease probe can be configured to detect a particular target. In other cases, each programmable nuclease probe can be configured to detect a plurality of targets. In some cases, a first programmable nuclease probe can be configured to detect a first target or a first set of targets, and a second programmable nuclease probe can be configured to detect a second target or a second set of targets. In other cases, a first programmable nuclease probe can be configured to detect a first set of targets, and a second programmable nuclease probe can be configured to detect a second set of targets. The programmable nuclease probes of the present disclosure can be used to detect a plurality ofdifferent target sequences or target nucleic acids. In any of the embodiments described herein, the sample provided to the detection device can comprise a plurality of target sequences or target nucleic acids. In any of the embodiments described herein, the sample provided to the detection device can comprise multiple classes of target sequences or target nucleic acids. Each class of target sequences or class of target nucleic acids can comprise a plurality of target sequences or target nucleic acids associated with a particular organism, disease state, phenotype, or genotype present within the sample. In some cases, each programmable nuclease probe can be used to detect a particular class of target sequences, or a particular class of target nucleic acids associated with a particular organism, disease state, phenotype, or genotype present within the sample. In some cases, two or more programmable nuclease probes can be used to detect different classes of target sequences or different classes of target nucleic acids. In such cases, the two or more programmable nuclease probes can comprise different sets or classes of guide nucleic acids complexed to the programmable nucleases of the probes.Guide nucleic acids

[0145] Guide nucleic acids are compatible for use in the devices described herein and may be used in conjunction with compositions disclosed herein (e.g., programmable nucleases, reagents for in vitro transcription, reagents for amplification, reagents for reverse transcription, and reporters, or any combination thereof) to carry out highly efficient, rapid, and accurate reactions for detecting whether a target nucleic acid is present in a sample (e.g., DETECTR reactions). The guide nucleic acid binds to the single stranded or double stranded target nucleic acid comprising a portion of a nucleic acid from a virus or a bacterium or other agents responsible for a disease as described herein. The guide nucleic acid can bind to the single stranded or double stranded target nucleic acid comprising a portion of a nucleic acid from a bacterium or other agents responsible for a disease as described herein and further comprising a mutation, such as a single nucleotide polymorphism (SNP), which can confer resistance to a treatment, such as antibiotic treatment. The guide nucleic acid binds to the single stranded or double stranded target nucleic acid comprising a portion of a nucleic acid from a cancer gene or gene associated with a genetic disorder as described herein. The guide nucleic acid is complementary to the target nucleic acid or a portion thereof. Often the guide nucleic acid binds specifically to the target nucleic acid. The target nucleic acid may be a RNA, DNA, or synthetic nucleic acids. A guide nucleic acid can comprise a sequence that is reverse complementary to the sequence of a target nucleic acid. A guide nucleic acid can be a crRNA. Sometimes, a guide nucleic acid may comprise a crRNA and tracrRNA. The guide nucleic acid can bind specifically to the target nucleic acid. In some cases,the guide nucleic acid is not naturally occurring. In some cases, the guide nucleic acid is not naturally occurring and made by artificial combination of otherwise separate segments of sequence. Often, the artificial combination is performed by chemical synthesis, by genetic engineering techniques, or by the artificial manipulation of isolated segments of nucleic acids. The target nucleic acid can be designed and made to provide desired functions. In some cases, the targeting region of a guide nucleic acid is 20 nucleotides in length. The targeting region of the guide nucleic acid may have a length of at least 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides in length. In some instances, the targeting region ofthe guide nucleic acid is 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides in length. In some cases, the targeting region of a guide nucleic acid has a length from exactly or about 12 nucleotides (nt) to about 80 nt, from about 12 nt to about 50 nt, from about 12 nt to about 45 nt, from about 12 nt to about 40 nt, from about 12 nt to about 35 nt, from about 12 nt to about 30 nt, from about 12 nt to about 25 nt, from about 12 nt to about 20 nt, from about 12 nt to about 19 nt, from about 19 nt to about 20 nt, from about 19 nt to about 25 nt, from about 19 nt to about 30 nt, from about 19 nt to about 35 nt, from about 19 nt to about 40 nt, from about 19 nt to about 45 nt, from about 19 nt to about 50 nt, from about 19 nt to about 60 nt, from about 20 nt to about 25 nt, from about 20 nt to about 30 nt, from about 20 nt to about 35 nt, from about 20 nt to about 40 nt, from about 20 nt to about 45 nt, from about 20 nt to about 50 nt, or from about 20 nt to about 60 nt. In some cases, the targeting region of a guide nucleic acid has a length of from about 10 nt to about 60 nt, from about 20 nt to about 50 nt, or from about 30 nt to about 40 nt. In some cases, the targeting region of a guide nucleic acid has a length of from 15 nt to 55 nt, from 25 nt to 55 nt, from 35 nt to 55 nt, from 45 nt to 55 nt, from 15 nt to 45 nt, from 25 nt to 45 nt, from 35 nt to 45 nt, from 15 nt to 35 nt, from 25 nt to 35 nt, or from 15 nt to 25 nt. It is understood that the sequence of a polynucleotide need not be 100% complementary to that of its target nucleic acid to be specifically hybridizable or hybridizable or bind specifically. The guide nucleic acid can have a sequence comprising at least one uracil in a region from nucleic acid residue 5 to 20 that is reverse complementary to a modification variable region in the target nucleic acid. The guide nucleic acid, in some cases, has a sequence comprising at least one uracil in a region from nucleic acid residue 5 to 9, 10 to 14, or 15 to 20 that is reverse complementary to a modification variable region in the target nucleic acid. The guide nucleic acid can have a sequence comprising at least one uracil in a region from nucleic acid residue 5 to 20 that is reverse complementary to a methylation variable region in the target nucleic acid. The guide nucleic acid, in some cases, has a sequence comprising at least one uracil in a region from nucleic acid residue 5 to 9, 10 to 14, or 15 to 20 that is reverse complementary to a methylationvariable region in the target nucleic acid.

[0146] The guide nucleic acid can be selected from a group of guide nucleic acids that have been tiled against the nucleic acid of a strain of an infection or genomic locus of interest. The guide nucleic acid can be selected from a group of guide nucleic acids that have been tiled against the nucleic acid of a strain of HPV 16 or HPV 18, for example. Often, guide nucleic acids that are tiled against the nucleic acid of a strain of an infection or genomic locus of interest can be pooled for use in a method described herein. Often, these guide nucleic acids are pooled for detecting a target nucleic acid in a single assay. The pooling of guide nucleic acids that are tiled against a single target nucleic acid can enhance the detection of the target nucleic using the methods described herein. The pooling of guide nucleic acids that are tiled against a single target nucleic acid can ensure broad coverage of the target nucleic acid within a single reaction using the methods described herein. The tiling, for example, is sequential along the target nucleic acid. Sometimes, the tiling is overlapping along the target nucleic acid. In some instances, the tiling may comprise gaps between the tiled guide nucleic acids along the target nucleic acid. In some instances, the tiling of the guide nucleic acids is non-sequential. Often, a method for detecting a target nucleic acid may comprise contacting a target nucleic acid to a pool of guide nucleic acids and a programmable nuclease, wherein a guide nucleic acid of the pool of guide nucleic acids has a sequence selected from a group of tiled guide nucleic acid that is reverse complementary to a sequence of a target nucleic acid; and assaying for a signal produce by cleavage of at least some reporters of a population of reporters. Pooling of guide nucleic acids can ensure broad spectrum identification, or broad coverage, of a target species within a single reaction. This can be particularly helpful in diseases or indications, like sepsis, that may be caused by multiple organisms.Reporters

[0147] Reporters, which can be referred to interchangeably reporter molecules, or detector nucleic acids, described herein are compatible for use in the devices described herein and may be used in conjunction with compositions disclosed herein (e.g., programmable nucleases, guide nucleic acids, reagents for in vitro transcription, reagents for amplification, reagents for reverse transcription, reporters, or any combination thereof) to carry out highly efficient, rapid, and accurate reactions for detecting whether a target nucleic acid is present in a sample (e.g., DETECTR reactions). Described herein is a reporter comprising a single stranded nucleic acid and a detection moiety, wherein the reporter is capable of being cleaved by the activated programmable nuclease, thereby generating a first detectable signal. As used herein, a detectornucleic acid is used interchangeably with reporter or reporter molecule. In some cases, the reporter comprises a single-stranded nucleic acid. In some cases, the reporter comprises a double-stranded nucleic acid. In some cases, the reporter can comprise a single-stranded nucleic acid coupled to a double-stranded nucleic acid. In some cases, the reporter comprises a singlestranded nucleic acid comprising deoxyribonucleotides. In some cases, the reporter comprises a double-stranded nucleic acid comprising deoxyribonucleotides. In some cases, the reporter comprises a single-stranded nucleic acid comprising ribonucleotides. The reporter can comprise a single-stranded nucleic acid comprising at least one deoxyribonucleotide and at least one ribonucleotide. In some cases, the reporter comprises a single-stranded nucleic acid comprising at least one ribonucleotide residue at an internal position that functions as a cleavage site. In some cases, the reporter may comprise at least 2, 3, 4, 5, 6, 7, 8, 9, or 10 ribonucleotide residues at an internal position. In some cases, the reporter may comprise from 2 to 10, from 3 to 9, from 4 to 8, or from 5 to 7 ribonucleotide residues at an internal position. In some cases, the reporter may comprise from 3 to 10, from 4 to 10, from 5 to 10, from 6 to 10, from 7 to 10, from 8 to 10, from 9 to 10, from 2 to 8, from 3 to 8, from 5 to 8, from 6 to 8, from 7 to 8, from 2 to 5, from 3 to 5, or from 4 to 5 ribonucleotide residues at an internal position. Sometimes the ribonucleotide residues are continuous. Alternatively, the ribonucleotide residues are interspersed in between non-ribonucleotide residues. In some cases, the reporter has only ribonucleotide residues. In some cases, the reporter has only deoxyribonucleotide residues. In some cases, the reporter may comprise nucleotides resistant to cleavage by the programmable nuclease described herein. In some cases, the reporter may comprise synthetic nucleotides. In some cases, the reporter may comprise at least one ribonucleotide residue and at least one non-ribonucleotide residue. In some cases, the reporter is 5-20, 5-15, 5-10, 7-20, 7-15, or 7-10 nucleotides in length. In some cases, the reporter is from 3 to 20, from 4 to 20, from 5 to 20, from 6 to 20, from 7 to 20, from 8 to 20, from 9 to 20, from 10 to 20, from 15 to 20, from 3 to 15, from 4 to 15, from 5 to 15, from 6 to 15, from 7 to 15, from 8 to 15, from 9 to 15, from 10 to 15, from 3 to 10, from 4 to 10, from 5 to 10, from 6 to 10, from 7 to 10, from 8 to 10, from 9 to 10, from 3 to 8, from 4 to 8, from 5 to 8, from 6 to 8, or from 7 to 8 nucleotides in length. In some cases, the reporter may comprise at least one uracil ribonucleotide. In some cases, the reporter may comprise at least two uracil ribonucleotides. Sometimes the reporter has only uracil ribonucleotides. In some cases, the reporter may comprise at least one adenine ribonucleotide. In some cases, the reporter may comprise at least two adenine ribonucleotide. In some cases, the reporter has only adenine ribonucleotides. In some cases, the reporter may comprise at least one cytosine ribonucleotide. In some cases, the reporter may comprise at least two cytosine ribonucleotide. In some cases, thereporter may comprise at least one guanine ribonucleotide. In some cases, the reporter may comprise at least two guanine ribonucleotide. A reporter can comprise only unmodified ribonucleotides, only unmodified deoxyribonucleotides, or a combination thereof. In some cases, the reporter is from 5 to 12 nucleotides in length. In some cases, the reporter is at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides in length. In some cases, the reporter is 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides in length. For cleavage by a programmable nuclease comprising Casl3, a reporter can be 5, 8, or 10 nucleotides in length. For cleavage by a programmable nuclease comprising Casl2, a reporter can be 10 nucleotides in length.

[0148] In some embodiments, the reporter may comprise a nucleic acid and a detection moiety. In some embodiments, a reporter is connected to a surface by a linkage. In some embodiments, a reporter may comprise at least one of a nucleic acid, a chemical functionality, a detection moiety, a quenching moiety, or a combination thereof. In some embodiments, a reporter is configured for the detection moiety to remain immobilized to the surface and the quenching moiety to be released into solution upon cleavage of the reporter. In some embodiments, a reporter is configured for the quenching moiety to remain immobilized to the surface and for the detection moiety to be released into solution, upon cleavage of the reporter. Often the detection moiety is at least one of a label, a polypeptide, a dendrimer, or a nucleic acid or a combination thereof. In some embodiments, the reporter contains a label. In some embodiments, label may be FITC, DIG, TAMRA, Cy5, AF594, or Cy3. In some embodiments, the label may comprise a dye, a nanoparticle configured to produce a signal, or the like. In some embodiments, the dye may be a fluorescent dye. In some embodiments, the at least one chemical functionality may comprise biotin. In some embodiments, the at least one chemical functionality may be configured to be captured by a capture probe. In some embodiments, the at least one chemical functionality may comprise biotin and the capture probe may comprise anti-biotin, streptavidin, avidin or other molecule configured to bind with biotin. In some embodiments, the dye is the chemical functionality. In some embodiments, a capture probe may comprise a molecule that is complementary to the chemical functionality of the reporter. In some embodiments, the capture antibodies are anti-FITC, anti-DIG, anti-TAMRA, anti-Cy5, anti-AF594, or any other appropriate capture antibody capable of binding the detection moiety or conjugate. In some embodiments, the detection moiety can be the chemical functionality.

[0149] In some embodiments, the reporter may comprise a quenching moiety. In some embodiments, a quenching moiety is any entity that decreases the fluorescence intensity of agiven substance. Exemplary embodiments of reporters, labels, quenchers, chemical functionalities, detection moieties, dendrimers, quenching moieties and other reporter elements are described in: PCT / US2021 / 033271; PCT / US2021 / 035031, and PCT / US2022 / 028865, all of which are herein incorporated by reference in their entirety.

[0150] In some cases, the reporter comprises a detection moiety and a quenching moiety. In some instances, the reporter comprises a cleavage site, wherein the detection moiety is located at a first site on the reporter and the quenching moiety is located at a second site on the reporter, wherein the first site and the second site are separated by the cleavage site. Sometimes the quenching moiety is a fluorescence quenching moiety. In some cases, the quenching moiety is 5' to the cleavage site and the detection moiety is 3' to the cleavage site. In some cases, the detection moiety is 5' to the cleavage site and the quenching moiety is 3' to the cleavage site. Sometimes the quenching moiety is at the 5' terminus of the nucleic acid of a reporter. Sometimes the detection moiety is at the 3' terminus of the nucleic acid of a reporter. In some cases, the detection moiety is at the 5' terminus of the nucleic acid of a reporter. In some cases, the quenching moiety is at the 3' terminus of the nucleic acid of a reporter.

[0151] Suitable fluorescent proteins include, but are not limited to, green fluorescent protein (GFP) or variants thereof, blue fluorescent variant of GFP (BFP), cyan fluorescent variant of GFP (CFP), yellow fluorescent variant of GFP (YFP), enhanced GFP (EGFP), enhanced CFP (ECFP), enhanced YFP (EYFP), GFPS65T, Emerald, Topaz (TYFP), Venus, Citrine, mCitrine, GFPuv, destabilised EGFP (dEGFP), destabilised ECFP (dECFP), destabilised EYFP (dEYFP), mCFPm, Cerulean, T-Sapphire, CyPet, YPet, mKO, HcRed, t-HcRed, DsRed, DsRed2, DsRed- monomer, J-Red, dimer2, t-dimer2(12), mRFPl, pocilloporin, Renilla GFP, Monster GFP, paGFP, Kaede protein and kindling protein, Phycobiliproteins and Phycobiliprotein conjugates including B-Phycoerythrin, R-Phycoerythrin and Allophycocyanin. Suitable enzymes include, but are not limited to, horseradish peroxidase (HRP), alkaline phosphatase (AP), betagalactosidase (GAL), glucose-6-phosphate dehydrogenase, beta-N-acetylglucosaminidase, CE<- glucuronidase, invertase, Xanthine Oxidase, firefly luciferase, and glucose oxidase (GO).

[0152] In some instances, the detection moiety comprises an invertase. The substrate of the invertase may be sucrose. A DNS reagent may be included in the system to produce a colorimetric change when the invertase converts sucrose to glucose. In some cases, the reporter nucleic acid and invertase are conjugated using a heterobifunctional linker via sulfo-SMCC chemistry.

[0153] Suitable fluorophores may provide a detectable fluorescence signal in the same range as6-Fluorescein (Integrated DNA Technologies), IRDye 700 (Integrated DNA Technologies), TYE 665 (Integrated DNA Technologies), Alex Fluor 594 (Integrated DNA Technologies), or ATTO TM 633 (NHS Ester) (Integrated DNA Technologies). Non-limiting examples of fluorophores are fluorescein amidite, 6-Fluorescein, IRDye 700, TYE 665, Alex Fluor 594, or ATTO TM 633 (NHS Ester). The fluorophore may be an infrared fluorophore. The fluorophore may emit fluorescence in the range of 500 nm and 720 nm. In some cases, the fluorophore emits fluorescence at a wavelength of 700 nm or higher. In other cases, the fluorophore emits fluorescence at about 665 nm. In some cases, the fluorophore emits fluorescence in the range of 500 nm to 520 nm, 500 nm to 540 nm, 500 nm to 590 nm, 590 nm to 600 nm, 600 nm to 610 nm,610 nm to 620 nm, 620 nm to 630 nm, 630 nm to 640 nm, 640 nm to 650 nm, 650 nm to 660 nm,660 nm to 670 nm, 670 nm to 680 nm, 690 nm to 690 nm, 690 nm to 700 nm, 700 nm to 710 nm,710 nm to 720 nm, or 720 nm to 730 nm. In some cases, the fluorophore emits fluorescence in the range 450 nm to 750 nm, 500 nm to 650 nm, or 550 to 650 nm.

[0154] Systems may comprise a quenching moiety. A quenching moiety may be chosen based on its ability to quench the detection moiety. A quenching moiety may be a non-fluorescent fluorescence quencher. A quenching moiety may quench a detection moiety that emits fluorescence in the range of 500 nm and 720 nm. A quenching moiety may quench a detection moiety that emits fluorescence in the range of 500 nm and 720 nm. In some cases, the quenching moiety quenches a detection moiety that emits fluorescence at a wavelength of 700 nm or higher. In other cases, the quenching moiety quenches a detection moiety that emits fluorescence at about 660 nm or about 670 nm. In some cases, the quenching moiety quenches a detection moiety that emits fluorescence in the range of 500 to 520, 500 to 540, 500 to 590, 590 to 600, 600 to 610, 610 to 620, 620 to 630, 630 to 640, 640 to 650, 650 to 660, 660 to 670, 670 to 680, 690 to 690, 690 to 700, 700 to 710, 710 to 720, or 720 to 730 nm. In some cases, the quenching moiety quenches a detection moiety that emits fluorescence in the range 450 nm to 750 nm, 500 nm to 650 nm, or 550 to 650 nm. A quenching moiety may quench fluorescein amidite, 6- Fluorescein, IRDye 700, TYE 665, Alex Fluor 594, or ATTO TM 633 (NHS Ester). A quenching moiety may be Iowa Black RQ, Iowa Black FQ or IRDye QC-1 Quencher. A quenching moiety may quench fluorescein amidite, 6-Fluorescein (Integrated DNA Technologies), IRDye 700 (Integrated DNA Technologies), TYE 665 (Integrated DNA Technologies), Alex Fluor 594 (Integrated DNA Technologies), or ATTO TM 633 (NHS Ester) (Integrated DNA Technologies). A quenching moiety may be Iowa Black RQ (Integrated DNA Technologies), Iowa Black FQ (Integrated DNA Technologies) or IRDye QC-1 Quencher (LiCor). Any of the quenching moieties described herein may be from any commerciallyavailable source, may be an alternative with a similar function, a generic, or a non-trade name of the quenching moieties listed.

[0155] The generation of the detectable signal from the release of the detection moiety indicates that cleavage by the programmable nucleases has occurred and that the sample contains the target nucleic acid. In some cases, the detection moiety comprises a fluorescent dye. Sometimes the detection moiety comprises a fluorescence resonance energy transfer (FRET) pair. In some cases, the detection moiety comprises an infrared (IR) dye. In some cases, the detection moiety comprises an ultraviolet (UV) dye. Alternatively, or in combination, the detection moiety comprises a protein. Sometimes the detection moiety comprises a biotin. Sometimes the detection moiety comprises at least one of avidin or streptavidin. In some instances, the detection moiety comprises a polysaccharide, a polymer, or a nanoparticle. In some instances, the detection moiety comprises a gold nanoparticle or a latex nanoparticle.

[0156] A detection moiety may be any moiety capable of generating a calorimetric, potentiometric, amperometric, optical (e.g., fluorescent, colorimetric, etc.), or piezo-electric signal. A nucleic acid of a reporter, sometimes, is protein-nucleic acid that is capable of generating a calorimetric, potentiometric, amperometric, optical (e.g., fluorescent, colorimetric, etc.), or piezo-electric signal upon cleavage of the nucleic acid. Often a calorimetric signal is heat produced after cleavage of the nucleic acids of a reporter. Sometimes, a calorimetric signal is heat absorbed after cleavage of the nucleic acids of a reporter. A potentiometric signal, for example, is electrical potential produced after cleavage of the nucleic acids of a reporter. An amperometric signal may be movement of electrons produced after the cleavage of nucleic acid of a reporter. Often, the signal is an optical signal, such as a colorimetric signal or a fluorescence signal. An optical signal is, for example, a light output produced after the cleavage of the nucleic acids of a reporter. Sometimes, an optical signal is a change in light absorbance between before and after the cleavage of nucleic acids of a reporter. Often, a piezo-electric signal is a change in mass between before and after the cleavage of the nucleic acid of a reporter. Other methods of detection can also be used, such as optical imaging, surface plasmon resonance (SPR), and / or interferometric sensing.

[0157] The detectable signal may be a colorimetric signal or a signal visible by eye. In some instances, the detectable signal may be fluorescent, electrical, chemical, electrochemical, or magnetic. In some cases, a detectable signal (e.g., a first detectable signal) may be generated by binding of the detection moiety to the capture molecule in the detection region, where the detectable signal indicates that the sample contained the target nucleic acid. Sometimes systemsare capable of detecting more than one type of target nucleic acid, wherein the system comprises more than one type of guide nucleic acid and more than one type of reporter nucleic acid. In some cases, the detectable signal may be generated directly by the cleavage event. Alternatively, or in combination, the detectable signal may be generated indirectly by the cleavage event. Sometimes the detectable signal is not a fluorescent signal. In some instances, the detectable signal may be a colorimetric or color-based signal. In some cases, the detected target nucleic acid may be identified based on its spatial location on the detection region of the support medium. In some cases, a second detectable signal may be generated in a spatially distinct location than a first detectable signal when two or more detectable signals are generated.

[0158] In some cases, the one or more detectable signals generated after cleavage can produce an index of refraction change or one or more electrochemical changes. In some cases, real-time detection of the Cas reaction can be achieved using fluorescence, electrochemical detection, and / or electrochemiluminescence.

[0159] In some cases, the detectable signals can be detected and analyzed in various ways. For example, the detectable signals can be detected using an imaging device. The imaging device can a digital camera, such a digital camera on a mobile device. The mobile device can have a software program or a mobile application that can capture fluorescence, ultraviolet (UV), infrared (IR), or visible wavelength signals. Any suitable detection or measurement device can be used to detect and / or analyze the colorimetric, fluorescence, amperometric, potentiometric, or electrochemical signals described herein. In some embodiments, the colorimetric, fluorescence, amperometric, potentiometric, or another electrochemical sign can be detected using a measurement device connected to a detection chamber of the device (e.g., a fluorescence measurement device, a spectrophotometer, and / or an oscilloscope).

[0160] Often, the reporter is an enzyme-nucleic acid. The enzyme may be sterically hindered when present as in the enzyme-nucleic acid, but then functional upon cleavage from the nucleic acid by the programmable nuclease. Often, the enzyme is an enzyme that produces a reaction with an enzyme substrate. An enzyme can be invertase. Often, the substrate of invertase is sucrose and DNS reagent.

[0161] Sometimes the reporter is a substrate-nucleic acid. Often the substrate is a substrate that produces a reaction with an enzyme. Release of the substrate upon cleavage by the programmable nuclease may free the substrate to react with the enzyme.

[0162] A reporter may be attached to a solid support. The solid support, for example, is a surface. A surface can be an electrode. Sometimes the solid support is a bead. Often the bead is amagnetic bead. Upon cleavage, the detection moiety is liberated from the solid support and interacts with other mixtures. For example, the detection moiety is an enzyme, and upon cleavage of the nucleic acid of the enzyme-nucleic acid, the enzyme flows through a chamber into a mixture comprising the substrate. When the enzyme meets the enzyme substrate, a reaction occurs, such as a colorimetric reaction, which is then detected. As another example, the detection moiety is an enzyme substrate, and upon cleavage of the nucleic acid of the enzyme substrate-nucleic acid, the enzyme flows through a chamber into a mixture comprising the enzyme. When the enzyme substrate meets the enzyme, a reaction occurs, such as a calorimetric reaction, which is then detected.

[0163] In some embodiments, the reporter comprises a nucleic acid conjugated to an affinity molecule which is in turn conjugated to the fluorophore (e.g., nucleic acid - affinity molecule - fluorophore) or the nucleic acid conjugated to the fluorophore which is in turn conjugated to the affinity molecule (e.g., nucleic acid - fluorophore - affinity molecule). In some embodiments, a linker conjugates the nucleic acid to the affinity molecule. In some embodiments, a linker conjugates the affinity molecule to the fluorophore. In some embodiments, a linker conjugates the nucleic acid to the fluorophore. A linker can be any suitable linker known in the art. In some embodiments, the nucleic acid of the reporter can be directly conjugated to the affinity molecule and the affinity molecule can be directly conjugated to the fluorophore or the nucleic acid can be directly conjugated to the fluorophore and the fluorophore can be directly conjugated to the affinity molecule. In this context, “directly conjugated” indicates that no intervening molecules, polypeptides, proteins, or other moieties are present between the two moieties directly conjugated to each other. For example, if a reporter comprises a nucleic acid directly conjugated to an affinity molecule and an affinity molecule directly conjugated to a fluorophore - no intervening moiety is present between the nucleic acid and the affinity molecule and no intervening moiety is present between the affinity molecule and the fluorophore. The affinity molecule can be biotin, avidin, streptavidin, or any similar molecule.

[0164] In some cases, the reporter comprises a substrate-nucleic acid. The substrate may be sequestered from its cognate enzyme when present as in the substrate-nucleic acid, but then is released from the nucleic acid upon cleavage, wherein the released substrate can contact the cognate enzyme to produce a detectable signal. Often, the substrate is sucrose and the cognate enzyme is invertase, and a DNS reagent can be used to monitor invertase activity.

[0165] A reporter may be a hybrid nucleic acid reporter. A hybrid nucleic acid reporter comprises a nucleic acid with at least one deoxyribonucleotide and at least one ribonucleotide. Insome embodiments, the nucleic acid of the hybrid nucleic acid reporter can be of any length and can have any mixture of DNAs and RNAs. For example, in some cases, longer stretches of DNA can be interrupted by a few ribonucleotides. Alternatively, longer stretches of RNA can be interrupted by a few deoxyribonucleotides. Alternatively, every other base in the nucleic acid may alternate between ribonucleotides and deoxyribonucleotides. A major advantage of the hybrid nucleic acid reporter is increased stability as compared to a pure RNA nucleic acid reporter. For example, a hybrid nucleic acid reporter can be more stable in solution, lyophilized, or vitrified as compared to a pure DNA or pure RNA reporter.

[0166] The reporter can be lyophilized or vitrified. The reporter can be suspended in solution or immobilized on a surface. For example, the reporter can be immobilized, dried, or otherwise deposited on the surface of a chamber in a device as disclosed herein. In some cases, the reporter is immobilized on beads, such as magnetic beads, in a chamber of a device as disclosed herein where they can be held in position by a magnet placed below the chamber.

[0167] In some cases, the reporter is a single-stranded nucleic acid comprising deoxyribonucleotides. In some cases, the reporter nucleic acid is a single-stranded nucleic acid sequence comprising ribonucleotides. The nucleic acid of a reporter may be a single-stranded nucleic acid sequence comprising at least one ribonucleotide. In some cases, the nucleic acid of a reporter is a single-stranded nucleic acid comprising at least one ribonucleotide residue at an internal position that functions as a cleavage site. In some cases, the nucleic acid of a reporter comprises at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, or at least 10 ribonucleotide residues at an internal position. In some cases, the nucleic acid of a reporter comprises from 2 to 10, from 3 to 9, from 4 to 8, or from 5 to 7 ribonucleotide residues at an internal position. In some cases, the reporter may comprise from 3 to 10, from 4 to 10, from 5 to 10, from 6 to 10, from 7 to 10, from 8 to 10, from 9 to 10, from 2 to 8, from 3 to 8, from 5 to 8, from 6 to 8, from 7 to 8, from 2 to 5, from 3 to 5, or from 4 to 5 ribonucleotide residues at an internal position. Sometimes the ribonucleotide residues are continuous. Alternatively, the ribonucleotide residues are interspersed in between non-ribonucleotide residues. In some cases, the nucleic acid of a reporter has only ribonucleotide residues. In some cases, the nucleic acid of a reporter has only deoxyribonucleotide residues. In some cases, the nucleic acid comprises nucleotides resistant to cleavage by the programmable nuclease described herein. In some cases, the nucleic acid of a reporter comprises synthetic nucleotides. In some cases, the nucleic acid of a reporter comprises at least one ribonucleotide residue and at least one non-ribonucleotide residue.

[0168] In some cases, the nucleic acid of a reporter comprises at least one uracil ribonucleotide. In some cases, the nucleic acid of a reporter comprises at least two uracil ribonucleotides. Sometimes the nucleic acid of a reporter has only uracil ribonucleotides. In some cases, the nucleic acid of a reporter comprises at least one adenine ribonucleotide. In some cases, the nucleic acid of a reporter comprises at least two adenine ribonucleotide. In some cases, the nucleic acid of a reporter has only adenine ribonucleotides. In some cases, the nucleic acid of a reporter comprises at least one cytosine ribonucleotide. In some cases, the nucleic acid of a reporter comprises at least two cytosine ribonucleotide. In some cases, the nucleic acid of a reporter comprises at least one guanine ribonucleotide. In some cases, the nucleic acid of a reporter comprises at least two guanine ribonucleotide. In some instances, a nucleic acid of a reporter comprises a single unmodified ribonucleotide. In some instances, a nucleic acid of a reporter comprises only unmodified ribonucleotides. In some instances, a nucleic acid of a reporter comprises only unmodified deoxyribonucleotides.

[0169] In some cases, the nucleic acid of a reporter is 5 to 20, 5 to 15, 5 to 10, 7 to 20, 7 to 15, or 7 to 10 nucleotides in length. In some cases, the nucleic acid of a reporter is 3 to 20, 4 to 20, 5 to 20, 6 to 20, 7 to 20, 8 to 20, 9 to 20, 10 to 20, 13 to 20, 15 to 20, 3 to 15, 4 to 15, 5 to 15, 6 to 15, 7 to 15, 8 to 15, 9 to 15, 10 to 15, 3 to 10, 4 to 10, 5 to 10, 6 to 10, 7 to 10, 8 to 10, 9 to 10, 3 to 8, 4 to 8, 5 to 8, 6 to 8, or 7 to 8, nucleotides in length. In some cases, the nucleic acid of a reporter is 5 to 12 nucleotides in length. In some cases, the reporter nucleic acid is at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, at least 28, at least 29, or at least 30 nucleotides in length. In some cases, the reporter nucleic acid is 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides in length. For cleavage by a programmable nuclease comprising Casl3, a reporter can be 5, 8, or 10 nucleotides in length. For cleavage by a programmable nuclease comprising Casl2, a reporter can be 10 nucleotides in length.

[0170] In some cases, systems comprise a plurality of reporters. The plurality of reporters may comprise a plurality of signals. In some cases, systems comprise at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 20, at least 30, at least 40, or at least 50 reporters. In some cases, there are 2 to 50, 3 to 40, 4 to 30, 5 to 20, or 6 to 10 different reporters.

[0171] In some instances, systems comprise a Type V CRISPR / Cas protein and a reporternucleic acid configured to undergo transcollateral cleavage by the Type V CRISPR / Cas protein. Transcollateral cleavage of the reporter may generate a signal from the reporter or alter a signal from the reporter. In some cases, the signal is an optical signal, such as a fluorescence signal or absorbance band. Transcollateral cleavage of the reporter may alter the wavelength, intensity, or polarization of the optical signal. For example, the reporter may comprise a fluorophore and a quencher, such that transcollateral cleavage of the reporter separates the fluorophore and the quencher thereby increasing a fluorescence signal from the fluorophore. Herein, detection of reporter cleavage to determine the presence of a target nucleic acid sequence may be referred to as 'DETECTR'. In some embodiments described herein is a method of assaying for a target nucleic acid in a sample comprising contacting the target nucleic acid with a programmable nuclease, a non-naturally occurring guide nucleic acid that hybridizes to a segment of the target nucleic acid, and a reporter nucleic acid, and assaying for a change in a signal, wherein the change in the signal is produced by cleavage of the reporter nucleic acid.

[0172] In the presence of a large amount of non-target nucleic acids, an activity of a programmable nuclease (e.g., a Type V CRISPR / Cas protein as disclosed herein) may be inhibited. If total nucleic acids are present in large amounts, they may outcompete reporters for the programmable nucleases. In some instances, systems comprise an excess of reporter(s), such that when the system is operated and a solution of the system comprising the reporter is combined with a sample comprising a target nucleic acid, the concentration of the reporter in the combined solution-sample is greater than the concentration of the target nucleic acid. In some instances, the sample comprises amplified target nucleic acid. In some instances, the sample comprises an unamplified target nucleic acid. In some instances, the concentration of the reporter is greater than the concentration of target nucleic acids and non-target nucleic acids. The nontarget nucleic acids may be from the original sample, either lysed or unlysed. The non-target nucleic acids may comprise byproducts of amplification. In some instances, systems comprise a reporter wherein the concentration of the reporter in a solution 1.5 fold, at least 2 fold, at least 3 fold, at least 4 fold, at least 5 fold, at least 6 fold, at least 7 fold, at least 8 fold, at least 9 fold, at least 10 fold, at least 11 fold, at least 12 fold, at least 13 fold, at least 14 fold, at least 15 fold, at least 16 fold, at least 17 fold, at least 18 fold, at least 19 fold, at least 20 fold, at least 30 fold, at least 40 fold, at least 50 fold, at least 60 fold, at least 70 fold, at least 80 fold, at least 90 fold, at least 100 fold excess of total nucleic acids. 1.5 fold to 100 fold, 2 fold to 10 fold, 10 fold to 20 fold, 20 fold to 30 fold, 30 fold to 40 fold, 40 fold to 50 fold, 50 fold to 60 fold, 60 fold to 70 fold, 70 fold to 80 fold, 80 fold to 90 fold, 90 fold to 100 fold, 1.5 fold to 10 fold, 1.5 fold to 20 fold, 10 fold to 40 fold, 20 fold to 60 fold, or 10 fold to 80 fold excess of total nucleic acids.Immobilized Reporter Systems

[0173] Disclosed herein are immobilized reporter systems, compositions, and methods of use thereof, e.g., for detection of a target nucleic acid or a plurality of target nucleic acids.

[0174] In some instances, systems comprise a Type V CRISPR / Cas protein and a reporter configured to undergo transcollateral cleavage by the Type V CRISPR / Cas protein. In some instances, systems comprise a Type VI CRISPR / Cas protein and a reporter configured to undergo transcollateral cleavage by the Type VI CRISPR / Cas protein. Transcollateral cleavage of the reporter may generate a signal from the reporter, alter a signal from the reporter, or trigger a downstream reaction capable of generating or changing a signal in response to cleavage of the reporter and release of a detection moiety therefrom. In some cases, the signal is an optical signal, such as a fluorescence signal or absorbance signal. Transcollateral cleavage of the reporter may alter the wavelength, intensity, and / or polarization of the optical signal. For example, the reporter may comprise a fluorophore and a quencher, such that transcollateral cleavage of the reporter separates the fluorophore and the quencher thereby increasing a fluorescence signal from the fluorophore. In some embodiments described herein is a method of assaying for a target nucleic acid in a sample comprising contacting the target nucleic acid with a programmable nuclease, a non-naturally occurring guide nucleic acid that hybridizes to a segment of the target nucleic acid, and a reporter, and assaying for a change in a signal, wherein the change in the signal is produced by cleavage of the reporter.

[0175] Reporter systems disclosed herein may comprise one or more reporters. Described herein are compositions and methods of use thereof comprising one or more reporter molecules. In some examples, the one or more reporter molecules comprise one or more different reporter molecules. In an example, the one or more reporter molecules comprise a first reporter molecule, a second reporter molecule, a third reporter molecule, and / or more reporter molecules or a plurality of each reporter molecule wherein each reporter molecule can be present in multiple copies (e.g., at a predefined concentration) in the composition. In some examples, the compositions and methods comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45,46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71,72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97,98, 99, 100, 150, 200, 250, 300, 350, 400, 450, 500, 1000, 2000, 3000, 4000, 5000, 10000, 100000 or more reporter molecules or sequences.

[0176] By way of non-limiting and illustrative example, a reporter may comprise a single stranded nucleic acid and a detection moiety (e.g., a labeled single stranded RNA reporter), wherein the nucleic acid is capable of being cleaved by a programmable nuclease (e.g., a Type V or Type VI CRISPR / Cas protein as disclosed herein) or a multimeric complex thereof, releasing the detection moiety, and, generating a detectable signal. In some instances, the reporter additionally comprises a double stranded nucleic acid. As used herein, “reporter” is used interchangeably with “reporter molecule”. The programmable nucleases disclosed herein, activated upon hybridization of a guide RNA to a target nucleic acid, may cleave the reporter. Cleaving the “reporter” may be referred to herein as cleaving the “reporter nucleic acid,” the “reporter molecule,” or the “nucleic acid of the reporter.” Reporters may comprise RNA. Reporters may comprise DNA. Reporters may be double-stranded. Reporters may be singlestranded.

[0177] In some instances, a reporter may be immobilized on a substrate. In some cases, a reporter may be immobilized to a surface of the substrate. In some cases, the reporter may be immobilized to a detection location of a substrate. In some instances, the reporter may be immobilized on the substrate. The reporter can be attached to a solid support. The solid support, for example, is a surface. A surface can be an electrode. Sometimes the solid support is a bead. In some cases, the bead is a magnetic bead. The surface can also be an array or a slide.

[0178] The reporter comprising a nucleic acid, in some cases, may be immobilized at the 5 ’end of the nucleic acid. In some cases, the reporter may be immobilized at the 3’ end of the nucleic acid. In some cases, the reporter may be immobilized at the 5’ and 3’ end of the nucleic acid.

[0179] In some instances, a reporter may be immobilized to a substrate via covalent bonding. In some cases, the reporter may comprise a thiol or an amine group for immobilization.

[0180] In some embodiments, the one or more detection reagents can be immobilized in discrete detection locations using NHS-amine chemistry as described herein. For example, a primary amine-modified guide nucleic acid and a primary amine-modified reporter may be conjugated to an NHS-coated surface of the detection region. In some cases, the amine may form an amide bond with the substrate. For example, the substrate may comprise graphene oxide. NHS-amine,in some cases, may have a structure of

[0181] In some cases, the immobilization moiety of a reporter may comprise a thiol group. The thiol group may form an Au-S bond with the substrate. The substrate may comprise gold. In some embodiments, the one or more detection reagents may be immobilized using maleimide- thiol chemistry as described herein. For example, a thiol-modified guide nucleic acid and a thiol- modified reporter may be conjugated to a maleimide-coated surface of the detection region. Thiol group, in some cases, may have a structure of S-H, wherein S is sulfur.

[0182] In some cases, a reporter may be immobilized to a substrate via non-covalent bonding. In some embodiments, the one or more detection reagents may be immobilized using avidin / streptavidin-biotin chemistry as described herein. For example, a biotinylated reporter and a biotinylated guide nucleic acid may be immobilized to a streptavidin-coated surface of the detection region.

[0183] In some instances, the immobilization of the reporter on a substrate may comprise an immobilization moiety. In some cases, the reporter may comprise an amino group moiety, a peptide moiety, a polypeptide moiety, or a protein moiety. The amino group moiety, peptide moiety, polypeptide moiety, or protein moiety may be the immobilization moiety. The immobilization moiety may comprise an amino modifier. The immobilization moiety may be 5’ or 3’ of the nucleic acid of the reporter.

[0184] In some instances, a reporter may be immobilized by surface adsorption. In some cases, the reporter may be immobilized on the surface via electrostatic interaction between the reporter and the surface. For example, a reporter may comprise a negative charge and a surface may comprise a positive charge. In some cases, the surface of a substrate may be coated with a material. The coated material may comprise polyamine, poly-L-lysine, polypyrrole, polyaniline, polyethyleneimine, or a combination thereof.

[0185] In some instances, the immobilization moiety may also be used to immobilize a guide nucleic acid. In some cases, the immobilization moiety can be located at an end of a guide nucleic acid. In some cases, the immobilization moiety can be located at the 5’ end of a guide nucleic acid. In some cases, the immobilization moiety can be located at the 3’ end of a guide nucleic acid. In some cases, the immobilization moiety can be located at the 5’ and 3’ end of a guide nucleic acid.Reporter design

[0186] In some instances, a reporter may comprise a nucleic acid. In some cases, the nucleic acid may have a polynucleotide sequence. In some cases, the polynucleotide sequence may compriseabout 10 nucleotides. In some cases, the polynucleotide sequence may comprise about 11 nucleotides. In some cases, the polynucleotide sequence may comprise about 12 nucleotides. In some cases, the polynucleotide sequence may comprise about 13 nucleotides. In some cases, the polynucleotide sequence may comprise about 14 nucleotides. In some cases, the polynucleotide sequence may comprise about 15 nucleotides. In some cases, the polynucleotide sequence may comprise about 16 nucleotides. In some cases, the polynucleotide sequence may comprise about 17 nucleotides. In some cases, the polynucleotide sequence may comprise about 18 nucleotides. In some cases, the polynucleotide sequence may comprise about 19 nucleotides. In some cases, the polynucleotide sequence may comprise about 20 nucleotides. In some cases, the polynucleotide sequence may comprise about 21 nucleotides. In some cases, the polynucleotide sequence may comprise about 22 nucleotides. In some cases, the polynucleotide sequence may comprise about 23 nucleotides. In some cases, the polynucleotide sequence may comprise about 24 nucleotides. In some cases, the polynucleotide sequence may comprise about 25 nucleotides. In some cases, the polynucleotide sequence may comprise about 26 nucleotides. In some cases, the polynucleotide sequence may comprise about 27 nucleotides. In some cases, the polynucleotide sequence may comprise about 28 nucleotides. In some cases, the polynucleotide sequence may comprise about 29 nucleotides. In some cases, the polynucleotide sequence may comprise about 30 nucleotides. In some cases, the polynucleotide sequence may comprise about 31 nucleotides. In some cases, the polynucleotide sequence may comprise about 32 nucleotides. In some cases, the polynucleotide sequence may comprise about 33 nucleotides. In some cases, the polynucleotide sequence may comprise about 34 nucleotides. In some cases, the polynucleotide sequence may comprise about 35 nucleotides. In some cases, the polynucleotide sequence may comprise about 36 nucleotides. In some cases, the polynucleotide sequence may comprise about 37 nucleotides. In some cases, the polynucleotide sequence may comprise about 38 nucleotides. In some cases, the polynucleotide sequence may comprise about 39 nucleotides. In some cases, the polynucleotide sequence may comprise about 40 nucleotides. In some cases, the polynucleotide sequence may comprise about 41 nucleotides. In some cases, the polynucleotide sequence may comprise about 42 nucleotides. In some cases, the polynucleotide sequence may comprise about 43 nucleotides. In some cases, the polynucleotide sequence may comprise about 44 nucleotides. In some cases, the polynucleotide sequence may comprise about 45 nucleotides. In some cases, the polynucleotide sequence may comprise about 46 nucleotides. In some cases, the polynucleotide sequence may comprise about 47 nucleotides. In some cases, the polynucleotide sequence may comprise about 48 nucleotides. In some cases, the polynucleotide sequence may comprise about 49 nucleotides. In some cases, the polynucleotidesequence may comprise about 50 nucleotides. In some cases, the polynucleotide sequence may comprise about 51 nucleotides. In some cases, the polynucleotide sequence may comprise about 52 nucleotides. In some cases, the polynucleotide sequence may comprise about 53 nucleotides. In some cases, the polynucleotide sequence may comprise about 54 nucleotides. In some cases, the polynucleotide sequence may comprise about 55 nucleotides. In some cases, the polynucleotide sequence may comprise about 56 nucleotides. In some cases, the polynucleotide sequence may comprise about 57 nucleotides. In some cases, the polynucleotide sequence may comprise about 58 nucleotides. In some cases, the polynucleotide sequence may comprise about 59 nucleotides. In some cases, the polynucleotide sequence may comprise about 60 nucleotides. In some cases, the polynucleotide sequence may comprise about 61 nucleotides. In some cases, the polynucleotide sequence may comprise about 62 nucleotides. In some cases, the polynucleotide sequence may comprise about 63 nucleotides. In some cases, the polynucleotide sequence may comprise about 64 nucleotides. In some cases, the polynucleotide sequence may comprise about 65 nucleotides. In some cases, the polynucleotide sequence may comprise about 66 nucleotides. In some cases, the polynucleotide sequence may comprise about 67 nucleotides. In some cases, the polynucleotide sequence may comprise about 68 nucleotides. In some cases, the polynucleotide sequence may comprise about 69 nucleotides. In some cases, the polynucleotide sequence may comprise about 70 nucleotides. In some cases, the polynucleotide sequence may comprise about 71 nucleotides. In some cases, the polynucleotide sequence may comprise about 72 nucleotides. In some cases, the polynucleotide sequence may comprise about 73 nucleotides. In some cases, the polynucleotide sequence may comprise about 74 nucleotides. In some cases, the polynucleotide sequence may comprise about 75 nucleotides. In some cases, the polynucleotide sequence may comprise about 76 nucleotides. In some cases, the polynucleotide sequence may comprise about 77 nucleotides. In some cases, the polynucleotide sequence may comprise about 78 nucleotides. In some cases, the polynucleotide sequence may comprise about 79 nucleotides. In some cases, the polynucleotide sequence may comprise about 80 nucleotides. In some cases, the polynucleotide sequence may comprise about 81 nucleotides. In some cases, the polynucleotide sequence may comprise about 82 nucleotides. In some cases, the polynucleotide sequence may comprise about 83 nucleotides. In some cases, the polynucleotide sequence may comprise about 84 nucleotides. In some cases, the polynucleotide sequence may comprise about 85 nucleotides. In some cases, the polynucleotide sequence may comprise about 86 nucleotides. In some cases, the polynucleotide sequence may comprise about 87 nucleotides. In some cases, the polynucleotide sequence may comprise about 88 nucleotides. In some cases, the polynucleotide sequence may comprise about 89 nucleotides. In some cases,the polynucleotide sequence may comprise about 90 nucleotides. In some cases, the polynucleotide sequence may comprise about 91 nucleotides. In some cases, the polynucleotide sequence may comprise about 92 nucleotides. In some cases, the polynucleotide sequence may comprise about 93 nucleotides. In some cases, the polynucleotide sequence may comprise about 94 nucleotides. In some cases, the polynucleotide sequence may comprise about 95 nucleotides. In some cases, the polynucleotide sequence may comprise about 96 nucleotides. In some cases, the polynucleotide sequence may comprise about 97 nucleotides. In some cases, the polynucleotide sequence may comprise about 98 nucleotides. In some cases, the polynucleotide sequence may comprise about 99 nucleotides. In some cases, the polynucleotide sequence may comprise about 100 nucleotides. In some cases, the polynucleotide sequence may comprise at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 350, 400, 450, 500 or more nucleotides. In some cases, the polynucleotide sequence may comprise at most about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 350, 400, 450, or 500 nucleotides. For cleavage by a programmable nuclease comprising Casl3, a reporter can comprise any numbers of nucleotides described thereof. In some cases, a reporter can be 5, 8, or 10 nucleotides in length. For cleavage by a programmable nuclease comprising Casl2, a reporter can comprise any numbers of nucleotides described thereof. In some cases, a reporter can be about 10 nucleotides in length.

[0187] Reporters may comprise RNA. Reporters may comprise DNA. Reporters may also comprise both DNA and RNA. Reporters may be double-stranded. Reporters may be singlestranded. A reporter may comprise a single-stranded region. A reporter may comprise a doublestranded region. In some cases, reporters may comprise both single-stranded and doubles- stranded regions. In some instances, cleavage of the reporter produces, changes, or reduces a signal and thereby indicate the presence of the target nucleic acid in the sample. The systems and devices disclosed herein can be used to detect these signals, which can indicate whether a target nucleic acid is present in the sample.

[0188] The reporter can comprise a single-stranded nucleic acid sequence comprising at least one deoxyribonucleotide and at least one ribonucleotide. The reporter can comprise a doublestranded nucleic acid sequence comprising at least one deoxyribonucleotide and at least one ribonucleotide. The reporter can comprise a single-stranded nucleic acid sequence and a doublestranded nucleic acid region, each comprising at least one deoxyribonucleotide and at least oneribonucleotide.

[0189] In some instances, the single-stranded region of a reporter may comprise at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 350, 400, 450, 500 or more nucleotides. In some cases, the singlestranded region of the reporter may comprise at most about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 350, 400, 450, or 500 nucleotides. In some cases, the single-stranded region may comprise about 5 to about 15 nucleotides. In some cases, the single-stranded region may comprise about 5 to about 20 nucleotides. In some cases, the single-stranded region may comprise about 5 to about 25 nucleotides. In some cases, the single-stranded region may comprise about 5 to about 50 nucleotides. In some cases, the single-stranded region may comprise about 5 to about 100 nucleotides. In some cases, the single-stranded region may comprise about 5 to about 200 nucleotides. In some cases, the single-stranded region may comprise about 5 to about 500 nucleotides. In some cases, the single-stranded region may comprise about 4 to about 15 nucleotides. In some cases, the single-stranded region may comprise about 3 to about 15 nucleotides. In some cases, the single-stranded region may comprise about 2 to about 15 nucleotides. In some cases, the single-stranded region may comprise about 1 to about 15 nucleotides. In some cases, the single-stranded region may comprise about 1 nucleotides. In some cases, the single-stranded region may comprise about 2 nucleotides. In some cases, the single-stranded region may comprise about 3 nucleotides. In some cases, the single-stranded region may comprise about 4 nucleotides. In some cases, the single-stranded region may comprise about 5 nucleotides. In some cases, the single-stranded region may comprise about 6 nucleotides. In some cases, the single-stranded region may comprise about 7 nucleotides. In some cases, the single-stranded region may comprise about 8 nucleotides. In some cases, the single-stranded region may comprise about 9 nucleotides. In some cases, the single-stranded region may comprise about 10 nucleotides. In some cases, the single-stranded region may comprise about 11 nucleotides. In some cases, the single-stranded region may comprise about 12 nucleotides. In some cases, the single-stranded region may comprise about 13 nucleotides. In some cases, the single-stranded region may comprise about 14 nucleotides. In some cases, the single-stranded region may comprise about 15 nucleotides. In some cases, the single-stranded region may comprise about 20 nucleotides. In some cases, the single-stranded region may comprise about 30 nucleotides. In some cases, the single-stranded region may comprise about 40nucleotides. In some cases, the single-stranded region may comprise about 50 nucleotides. In some cases, the single-stranded region may comprise about 100 nucleotides. In some cases, the single-stranded region may comprise about 150 nucleotides. In some cases, the single-stranded region may comprise about 200 nucleotides. In some cases, the single-stranded region may comprise about 500 nucleotides.

[0190] In some instances, the double-stranded region of a reporter may comprise at least about 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45,46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 80,90, 100, 150, 200, 250, 300, 350, 400, 450, 500 or more nucleotide pairs. In some instances, the double-stranded region of a reporter may comprise at most about 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53,54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 80, 90, 100, 150, 200, 250, 300,350, 400, 450, 500 or more nucleotide pairs.

[0191] In some cases, the double-stranded region may comprise a length of about 10 nucleotides. In some cases, the double-stranded region may comprise a length of about 15 nucleotides. In some cases, the double-stranded region may comprise a length of about 20 nucleotides. In some cases, the double-stranded region may comprise a length of about 25 nucleotides. In some cases, the double-stranded region may comprise a length of about 30 nucleotides. In some cases, the double-stranded region may comprise a length of about 35 nucleotides. In some cases, the double-stranded region may comprise a length of about 40 nucleotides. In some cases, the double-stranded region may comprise a length of about 45 nucleotides. In some cases, the double-stranded region may comprise a length of about 50 nucleotides. In some cases, the double-stranded region may comprise a length of about 55 nucleotides. In some cases, the double-stranded region may comprise a length of about 60 nucleotides. In some cases, the double-stranded region may comprise a length of about 65 nucleotides. In some cases, the double-stranded region may comprise a length of about 70 nucleotides. In some cases, the double-stranded region may comprise a length of about 75 nucleotides. In some cases, the double-stranded region may comprise a length of about 80 nucleotides. In some cases, the double-stranded region may comprise a length of about 85 nucleotides. In some cases, the double-stranded region may comprise a length of about 90 nucleotides. In some cases, the double-stranded region may comprise a length of about 95 nucleotides. In some cases, the double-stranded region may comprise a length of about 100 nucleotides. In some cases, the double-stranded region may comprise a length of about 150 nucleotides. In some cases, the double-stranded region may comprise a length of about 200 nucleotides. In some cases, thedouble-stranded region may comprise a length of about 300 nucleotides. In some cases, the double-stranded region may comprise a length of about 400 nucleotides. In some cases, the double-stranded region may comprise a length of about 500 nucleotides.

[0192] In some instances, the double-stranded region of a reporter may comprise at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 60, 70, 80, 90,100, 150, 200, 250, 300, 350, 400, 450, 500 or more nucleotide pairs. In some cases, the doublestranded region of the reporter may comprise at most about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39,40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 350, 400, 450, or 500 nucleotide pairs. In some cases, the double-stranded region may comprise a length of about 45 to about 55 nucleotides. In some cases, the double-stranded region may comprise a length of about 40 to about 55 nucleotides. In some cases, the double-stranded region may comprise a length of about 35 to about 55 nucleotides. In some cases, the double-stranded region may comprise a length of about 30 to about 55 nucleotides. In some cases, the double-stranded region may comprise a length of about 25 to about 55 nucleotides. In some cases, the doublestranded region may comprise a length of about 20 to about 55 nucleotides. In some cases, the double-stranded region may comprise a length of about 15 to about 55 nucleotides. In some cases, the double-stranded region may comprise a length of about 10 to about 55 nucleotides. In some cases, the double-stranded region may comprise a length of about 45 to about 60 nucleotides. In some cases, the double-stranded region may comprise a length of about 45 to about 70 nucleotides. In some cases, the double-stranded region may comprise a length of about 45 to about 80 nucleotides. In some cases, the double-stranded region may comprise a length of about 45 to about 90 nucleotides. In some cases, the double-stranded region may comprise a length of about 45 to about 100 nucleotides. In some cases, the double-stranded region may comprise a length of about 45 to about 200 nucleotides. In some cases, the double-stranded region may comprise a length of about 45 to about 500 nucleotides. In some cases, the doublestranded region may comprise a length of about 5 to about 15 nucleotides. In some cases, the double-stranded region may comprise a length of about 5 to about 20 nucleotides. In some cases, the double-stranded region may comprise a length of about 5 to about 25 nucleotides. In some cases, the double-stranded region may comprise a length of about 5 to about 50 nucleotides. In some cases, the double-stranded region may comprise a length of about 5 to about 100 nucleotides. In some cases, the double-stranded region may comprise a length of about 5 to about 200 nucleotides. In some cases, the double-stranded region may comprise a length of about 5 toabout 500 nucleotides. In some cases, the double-stranded region may comprise a length of about 4 to about 15 nucleotides. In some cases, the double-stranded region may comprise a length of about 3 to about 15 nucleotides. In some cases, the double-stranded region may comprise a length of about 2 to about 15 nucleotides. In some cases, the double-stranded region may comprise a length of about 1 to about 15 nucleotides.

[0193] In some cases, the single-stranded region may comprise about 1 nucleotide, and the double-stranded region may comprise about 35 nucleotides. In some cases, the single-stranded region may comprise about 1 nucleotide, and the double-stranded region may comprise about 40 nucleotides. In some cases, the single-stranded region may comprise about 1 nucleotide, and the double-stranded region may comprise about 45 nucleotides. In some cases, the single-stranded region may comprise about 1 nucleotide, and the double-stranded region may comprise about 50 nucleotides. In some cases, the single-stranded region may comprise about 1 nucleotide, and the double-stranded region may comprise about 55 nucleotides. In some cases, the single-stranded region may comprise about 1 nucleotide, and the double-stranded region may comprise about 60 nucleotides. In some cases, the single-stranded region may comprise about 1 nucleotide, and the double-stranded region may comprise about 65 nucleotides. In some cases, the single-stranded region may comprise about 1 nucleotide, and the double-stranded region may comprise about 35 nucleotides. In some cases, the single-stranded region may comprise about 1 nucleotide, and the double-stranded region may comprise about 40 nucleotides. In some cases, the single-stranded region may comprise about 5 nucleotides, and the double-stranded region may comprise about 45 nucleotides. In some cases, the single-stranded region may comprise about 5 nucleotides, and the double-stranded region may comprise about 50 nucleotides. In some cases, the singlestranded region may comprise about 5 nucleotides, and the double-stranded region may comprise about 55 nucleotides. In some cases, the single-stranded region may comprise about 5 nucleotides, and the double-stranded region may comprise about 60 nucleotides. In some cases, the single-stranded region may comprise about 5 nucleotides, and the double-stranded region may comprise about 65 nucleotides. In some cases, the single-stranded region may comprise about 9 nucleotides, and the double-stranded region may comprise about 35 nucleotides. In some cases, the single-stranded region may comprise about 9 nucleotides, and the double-stranded region may comprise about 40 nucleotides. In some cases, the single-stranded region may comprise about 9 nucleotides, and the double-stranded region may comprise about 45 nucleotides. In some cases, the single-stranded region may comprise about 9 nucleotides, and the double-stranded region may comprise about 50 nucleotides. In some cases, the single-stranded region may comprise about 9 nucleotides, and the double-stranded region may comprise about55 nucleotides. In some cases, the single-stranded region may comprise about 9 nucleotides, and the double-stranded region may comprise about 60 nucleotides. In some cases, the singlestranded region may comprise about 9 nucleotides, and the double-stranded region may comprise about 65 nucleotides. In some cases, the single-stranded region may comprise about 15 nucleotides, and the double-stranded region may comprise about 35 nucleotides. In some cases, the single-stranded region may comprise about 15 nucleotides, and the double-stranded region may comprise about 40 nucleotides. In some cases, the single-stranded region may comprise about 15 nucleotides, and the double-stranded region may comprise about 45 nucleotides. In some cases, the single-stranded region may comprise about 15 nucleotides, and the doublestranded region may comprise about 50 nucleotides. In some cases, the single-stranded region may comprise about 15 nucleotides, and the double-stranded region may comprise about 55 nucleotides. In some cases, the single-stranded region may comprise about 15 nucleotides, and the double-stranded region may comprise about 60 nucleotides. In some cases, the singlestranded region may comprise about 15 nucleotides, and the double-stranded region may comprise about 65 nucleotides. In some cases, the single-stranded region may comprise about 20 nucleotides, and the double-stranded region may comprise about 35 nucleotides. In some cases, the single-stranded region may comprise about 20 nucleotides, and the double-stranded region may comprise about 40 nucleotides. In some cases, the single-stranded region may comprise about 20 nucleotides, and the double-stranded region may comprise about 45 nucleotides. In some cases, the single-stranded region may comprise about 20 nucleotides, and the doublestranded region may comprise about 50 nucleotides. In some cases, the single-stranded region may comprise about 20 nucleotides, and the double-stranded region may comprise about 55 nucleotides. In some cases, the single-stranded region may comprise about 20 nucleotides, and the double-stranded region may comprise about 60 nucleotides. In some cases, the singlestranded region may comprise about 20 nucleotides, and the double-stranded region may comprise about 65 nucleotides.

[0194] In some cases, the reporter comprises a nucleic acid comprising at least one ribonucleotide residue at an internal position that functions as a cleavage site. In some cases, the reporter comprises at least 2, 3, 4, 5, 6, 7, 8, 9, or 10 ribonucleotide residues at an internal position. In some cases, the reporter comprises from 2 to 10, from 3 to 9, from 4 to 8, or from 5 to 7 ribonucleotide residues at an internal position. Sometimes the ribonucleotide residues are continuous. Alternatively, the ribonucleotide residues are interspersed in between nonribonucleotide residues. In some cases, the reporter has only ribonucleotide residues. In some cases, the reporter compirses a nucleic acid comprising at least one deoxyribonucleotide residueat an internal position that functions as a cleavage site. In some cases, the reporter comprises at least 2, 3, 4, 5, 6, 7, 8, 9, or 10 deoxyribonucleotide residues at an internal position. In some cases, the reporter comprises from 2 to 10, from 3 to 9, from 4 to 8, or from 5 to 7 deoxyribonucleotide residues at an internal position. Sometimes the deoxyribonucleotide residues are continuous. Alternatively, the deoxyribonucleotide residues may be interspersed in between non-deoxyribonucleotide residues. In some cases, the reporter has only deoxyribonucleotide residues.

[0195] In some cases, the reporter has only deoxyribonucleotide residues. In some cases, the reporter comprises nucleotides resistant to cleavage by the programmable nuclease described herein. In some cases, the reporter comprises synthetic nucleotides. In some cases, the reporter comprises at least one ribonucleotide residue and at least one non-ribonucleotide residue. In some cases, the reporter comprises at least one uracil ribonucleotide. In some cases, the reporter comprises at least two uracil ribonucleotides. Sometimes the reporter has only uracil ribonucleotides. In some cases, the reporter comprises at least one adenine ribonucleotide. In some cases, the reporter comprises at least two adenine ribonucleotides. In some cases, the reporter has only adenine ribonucleotides. In some cases, the reporter comprises at least one cytosine ribonucleotide. In some cases, the reporter comprises at least two cytosine ribonucleotides. In some cases, the reporter comprises at least one guanine ribonucleotide. In some cases, the reporter comprises at least two guanine ribonucleotides. A reporter can comprise only unmodified ribonucleotides, only unmodified deoxyribonucleotides, or a combination thereof. A reporter can comprise a combination of modified and unmodified ribonucleotides and / or deoxyribonucleotides.

[0196] In some examples, a reporter molecule comprises a single stranded nucleic acid comprising a detection moiety, wherein the nucleic acid of the reporter molecule is capable of being cleaved by the activated programmable nuclease, thereby generating a first detectable signal. In some cases, the reporter molecule comprises a single-stranded nucleic acid sequence comprising ribonucleotides. In some cases, the reporter molecule comprises a single-stranded nucleic acid sequence comprising deoxyribonucleotides. In some cases, the reporter molecule comprises a single-stranded nucleic acid sequence comprising deoxyribonucleotides and ribonucleotides. As described herein, nucleic acid sequences can be detected using a programmable RNA nuclease, a programmable DNA nuclease, or a combination thereof, as disclosed herein. The programmable nuclease can be activated and cleave the reporter molecule upon binding of a guide nucleic acid to a target nucleic acid. Additionally, different compositions of reporter molecules can allow for multiplexing using different programmablenucleases (e.g., a programmable RNA nuclease and a programmable DNA nuclease). In some instances, the reporter may comprise any design detailed in Table 2 below or described herein.Table 2. Exemplary Reporter Designs / 36-FAM / : 3' 6-Fluorescein (Integrated DNA Technologies) / 3IABkFQ / : 3' Iowa Black FQ (Integrated DNA Technologies)A6-FAMK / : internal 6-Fluorescein (Azide) with dT base (Integrated DNA Technologies) / 5AmMC6 / : 5’ amino modifier with 6 carbons (Integrated DNA Technologies) / 5AmMC12 / : 5’ amino modifier with 12 carbons (Integrated DNA Technologies) *This Table refers to the fluorophore, quencher moiety, and immobilization moiety as their tradenames and their source is identified. However, alternatives, generics, or non-tradename moieties with similar function from other sources can also be used.

[0197] In some instances, the reporter may comprise a nucleic acid sequence at least about 50 %, 55 %, 60 %, 65 %, 70 %, 75 %, 80 %, 85 %, 90 %, 95 %, 96 %, 97 %, 98 %, 99 %, or 100 % identical to any one of the sequences described in Table 2. The reporter may comprise a nucleic acid sequence at least about 50 % identical to any one of SEQ IDs NO: 62-67. The reporter may comprise a nucleic acid sequence at least about 55 % identical to any one of SEQ IDs NO: 62- 67. The reporter may comprise a nucleic acid sequence at least about 60 % identical to any one of SEQ IDs NO: 62-67. The reporter may comprise a nucleic acid sequence at least about 65 % identical to any one of SEQ IDs NO: 62-67. The reporter may comprise a nucleic acid sequence at least about 70 % identical to any one of SEQ IDs NO: 62-67. The reporter may comprise a nucleic acid sequence at least about 75 % identical to any one of SEQ IDs NO: 62-67. The reporter may comprise a nucleic acid sequence at least about 80 % identical to any one of SEQ IDs NO: 62-67. The reporter may comprise a nucleic acid sequence at least about 85 % identical to any one of SEQ IDs NO: 62-67. The reporter may comprise a nucleic acid sequence at leastabout 90 % identical to any one of SEQ IDs NO: 62-67. The reporter may comprise a nucleic acid sequence at least about 95 % identical to any one of SEQ IDs NO: 62-67. The reporter may comprise a nucleic acid sequence at least about 96 % identical to any one of SEQ IDs NO: 62- 67. The reporter may comprise a nucleic acid sequence at least about 97 % identical to any one of SEQ IDs NO: 62-67. The reporter may comprise a nucleic acid sequence at least about 98 % identical to any one of SEQ IDs NO: 62-67. The reporter may comprise a nucleic acid sequence at least about 99 % identical to any one of SEQ IDs NO: 62-67. The reporter may comprise a nucleic acid sequence of any one of SEQ IDs NO: 62-67.

[0198] In some instances, the reporter may comprise at least two nucleic acid sequences at least about 50 %, 55 %, 60 %, 65 %, 70 %, 75 %, 80 %, 85 %, 90 %, 95 %, 96 %, 97 %, 98 %, 99 %, or 100 % identical to any two of SEQ IDs NO: 62-67. The reporter may comprise at least two nucleic acid sequences at least about 50 % identical to any two of SEQ IDs NO: 62-67. The reporter may comprise at least two nucleic acid sequences at least about 55 % identical to any two of SEQ IDs NO: 62-67. The reporter may comprise at least two nucleic acid sequences at least about 60 % identical to any two of SEQ IDs NO: 62-67. The reporter may comprise at least two nucleic acid sequences at least about 65 % identical to any two of SEQ IDs NO: 62-67. The reporter may comprise at least two nucleic acid sequences at least about 70 % identical to any two of SEQ IDs NO: 62-67. The reporter may comprise at least two nucleic acid sequences at least about 75 % identical to any two of SEQ IDs NO: 62-67. The reporter may comprise at least two nucleic acid sequences at least about 80 % identical to any two of SEQ IDs NO: 62-67. The reporter may comprise at least two nucleic acid sequences at least about 85 % identical to any two of SEQ IDs NO: 62-67. The reporter may comprise at least two nucleic acid sequences at least about 90 % identical to any two of SEQ IDs NO: 62-67. The reporter may comprise at least two nucleic acid sequences at least about 95 % identical to any two of SEQ IDs NO: 62-67. The reporter may comprise at least two nucleic acid sequences at least about 96 % identical to any two of SEQ IDs NO: 62-67. The reporter may comprise at least two nucleic acid sequences at least about 97 % identical to any two of SEQ IDs NO: 62-67. The reporter may comprise at least two nucleic acid sequences at least about 98 % identical to any two of SEQ IDs NO: 62-67. The reporter may comprise at least two nucleic acid sequences at least about 99 % identical to any two of SEQ IDs NO: 62-67. The reporter may comprise at least two nucleic acid sequences of any two of SEQ IDs NO: 62-67.

[0199] In some instances, the reporter may comprise at least two nucleic acid sequences at least about 50 %, 55 %, 60 %, 65 %, 70 %, 75 %, 80 %, 85 %, 90 %, 95 %, 96 %, 97 %, 98 %, 99 %, or 100 % identical to SEQ ID NOs: 62, 63, 68, and 69. The reporter may comprise at least twonucleic acid sequences at least about 50 % identical to SEQ ID NOs: 62, 63, 68, and 69. The reporter may comprise at least two nucleic acid sequences at least about 55 % identical to SEQ ID NOs: 62, 63, 68, and 69. The reporter may comprise at least two nucleic acid sequences at least about 60 % identical to SEQ ID NOs: 62, 63, 68, and 69. The reporter may comprise at least two nucleic acid sequences at least about 65 % identical to SEQ ID NOs: 62, 63, 68, and 69. The reporter may comprise at least two nucleic acid sequences at least about 70 % identical to SEQ ID NOs: 62, 63, 68, and 69. The reporter may comprise at least two nucleic acid sequences at least about 75 % identical to SEQ ID NOs: 62, 63, 68, and 69. The reporter may comprise at least two nucleic acid sequences at least about 80 % identical to SEQ ID NOs: 62, 63, 68, and 69. The reporter may comprise at least two nucleic acid sequences at least about 85 % identical to SEQ ID NOs: 62, 63, 68, and 69. The reporter may comprise at least two nucleic acid sequences at least about 90 % identical to SEQ ID NOs: 62, 63, 68, and 69. The reporter may comprise at least two nucleic acid sequences at least about 95 % identical to SEQ ID NOs: 62, 63, 68, and 69. The reporter may comprise at least two nucleic acid sequences at least about 96 % identical to SEQ ID NOs: 62, 63, 68, and 69. The reporter may comprise at least two nucleic acid sequences at least about 97 % identical to SEQ ID NOs: 62, 63, 68, and 69. The reporter may comprise at least two nucleic acid sequences at least about 98 % identical to SEQ ID NOs: 62, 63, 68, and 69. The reporter may comprise at least two nucleic acid sequences at least about 99 % identical to SEQ ID NOs: 62, 63, 68, and 69. The reporter may comprise at least two nucleic acid sequences of SEQ ID NOs: 62, 63, 68, and 69.

[0200] In some embodiments, the reporter molecule comprises a detection moiety capable of generating a detectable signal. A signal can be a calorimetric, potentiometric, amperometric, optical (e.g., fluorescent, colorimetric, etc.), or piezo-electric. Suitable detectable labels and / or moieties that may provide a signal include, but are not limited to, an enzyme, a radioisotope, a member of a specific binding pair, a fluorophore, a fluorescent protein, a quantum dot, and the like.

[0201] In some instances, a detection moiety can be located at an end of a reporter. In some cases, a detection moiety can be located at an end of a nucleic acid of a reporter. Cleavage of the nucleic acid can release the detection moiety, thereby decreasing the signal a reporter. In some cases, a detection moiety can be located at the 3’ end of a nucleic acid of a reporter. For example, a fluorophore can be located at the 3’ end of a reporter, as shown in FIGs. 40A, 40C, or 40E. In other cases, the fluorophore can be at the 5’ end of a reporter. Optionally, a quenching moiety is on the other side of the cleavage site. Sometimes the quenching moiety is a fluorescence quenching moiety. For example, from 5’ to 3’, the reporter may comprise animmobilization moiety, a first nucleic acid, a fluorophore, a second nucleic acid, and a quencher moiety, as shown in FIGs. 40B or 40D. The quencher moiety may quench the signal of the fluorophore. Cleavage of the second nucleic acid may release the quencher moiety, thereby increasing the signal of the reporter.

[0202] In some cases, the quenching moiety is 5’ to the cleavage site and the fluorophore is 3’ to the cleavage site. In some cases, the fluorophore is 5’ to the cleavage site and the quenching moiety is 3’ to the cleavage site. Sometimes the quenching moiety is at the 5’ terminus of the reporter molecule. Sometimes the fluorophore is at the 3’ terminus of the reporter molecule. In some cases, the fluorophore is at the 5’ terminus of the reporter molecule. In some cases, the quenching moiety is at the 3’ terminus of the reporter molecule.Multiplex Reporter Systems

[0203] In some instances, systems and methods may be used for multiple detection of target nucleic acids. In some cases, a substrate and / or detection region may comprise multiple reporters, multiple guide nucleic acids, or a combination thereof that are immobilized, dried, or otherwise deposited thereto. Localizing the guide nucleic acids and reporter may localize the detectable signal for each target nucleic acid to the detection spot, thus enabling the spatial multiplexing. For example, in some embodiments, the detection region may comprise an array of detection spots at discrete locations. Each detection spot of the array may comprise an immobilized reporter and a different immobilized guide nucleic acid which is complementary to a different target nucleic acid of a plurality of target nucleic acids. In some embodiments, at each detection spot of the array, upon addition of a programmable nuclease, the immobilized reporter is cleaved by a complex comprising the programmable nuclease and the different immobilized guide nucleic acid to generate a different signal of a plurality of signals. Each different signal may therefore be indicative of the presence or absence of a different target nucleic acid. The target nucleic acids may be freely available within the fluid volume of the detection region. In some embodiments, the array may comprise a number of spots within a range of about 1 to about 200, within a range of about 3 to about 200, or within a range of about 10 to about 200. In some embodiments, the array may comprise at about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42,43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68,69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94,95, 96, 97, 98, 99, 100, 150, 200, 250, 300, 350, 400, 450, 500, 1000, 2000, 3000, 4000, 5000,10000, 100000 or more spots. In some embodiments, multiple guide nucleic acids for a singletarget nucleic acid may be combined within a single detection spot in order to increase a rate of reaction.

[0204] In some instances, a substrate may comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41,42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67,68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93,94, 95, 96, 97, 98, 99, 100, 150, 200, 250, 300, 350, 400, 450, 500, 1000, 2000, 3000, 4000,5000, 10000, 100000 same or different reporters and / or guide nucleic acids immobilized thereto. In some cases, a detection region may comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42,43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68,69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94,95, 96, 97, 98, 99, 100, 150, 200, 250, 300, 350, 400, 450, 500, 1000, 2000, 3000, 4000, 5000, 10000, 100000 same or different reporters and / or guide nucleic acids immobilized thereto. In some cases, each detection location may comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more reporters and / or guide nucleic acids immobilized thereto.Buffers

[0205] The reagents described herein can also include buffers, which are compatible with the devices, systems, fluidic devices, kits, and methods disclosed herein. The buffers described herein are compatible for use in the devices described herein and may be used in conjunction with compositions disclosed herein (e.g., programmable nucleases, guide nucleic acids, reagents for in vitro transcription, reagents for amplification, reagents for reverse transcription, reporters, or any combination thereof) to carry out highly efficient, rapid, and accurate reactions for detecting whether the target nucleic acid is in the sample (e.g., DETECTR reactions). These buffers are compatible with the other reagents, samples, and support mediums as described herein for detection of an ailment, such as a disease, cancer, or genetic disorder, or genetic information, such as for phenotyping, genotyping, or determining ancestry. The methods described herein can also include the use of buffers, which are compatible with the methods disclosed herein. For example, a buffer may comprise HEPES, MES, TCEP, EGTA, Tween 20, KC1, MgCl2, glycerol, TIPP, or any combination thereof. In some instances, a buffer may comprise Tris-HCl pH 8.8, VLB, EGTA, CH3COOH, TCEP, IsoAmp, (NH4)2SO4, KC1, MgSO4, Tween20, KO Ac, MgOAc, BSA, or any combination thereof. In some instances the buffer may comprise from 0 to 100, 0 to 75, 0 to 50, 0 to 25, 0 to 20, 0 to 10, 0 to 5, 5 to 10,5 to15, 5 to 20, 5 to 25, to 30, 5 to 40, 5 to 50, 5 to 75, 5 to 100, 10 to 20, 10 to 30, 10 to 40, 10 to 50, 15 to 20, 15 to 25, 15 to 30, 15 to 4, 15 to 50, 20 to 25, 20 to 30, 20 to 40, or 20 to 50 mM HEPES pH 6.8. The buffer can comprise to 0 to 500, 0 to 400, 0 to 300, 0 to 250, 0 to 200, 0 to 150, 0 to 100, 0 to 75, 0 to 50, 0 to 25, 0 to 20, 0 to 10, 0 to 5, 5 to 10, 5 to 15, 5 to 20, 5 to 25, to 30, 5 to 40, 5 to 50, 5 to 75, 5 to 100, 5 to 150, 5 to 200, 5 to 250, 5 to 300, 5 to 400, 5 to 500, 25 to 50, 25 to 75, 25 to 100, 50 to 100, 50 150, 50 to 200, 50 to 250, 50 to 300, 100 to 200, 100 to 250, 100 to 300, or 150 to 250 mM KC1. In other instances the buffer may comprise 0 to 100, 0 to 75, 0 to 50, 0 to 25, 0 to 20, 0 to 10, 0 to 5, 5 to 10, 5 to 15, 5 to 20, 5 to 25, to 30, 5 to 40, 5 to 50, 5 to 75, 5 to 100, 10 to 20, 10 to 30, 10 to 40, 10 to 50, 15 to 20, 15 to 25, 15 to 30, 15 to 4, 15 to 50, 20 to 25, 20 to 30, 20 to 40, or 20 to 50 mM MgCl2. The buffer can comprise 0 to 25, 0 to 20, 0 to 10, 0 to 5, 5 to 10, 5 to 15, 5 to 20, 5 to 25, 5 to 30% glycerol. The buffer can comprise from 0% to 30%, from 5% to 30%, from 10% to 30%, from 15% to 30%, from 20% to 30%, from 25% to 30%, from 0% to 25%, from 2% to 25%, from 5% to 25%, from 10% to 25%, from 15% to 25%, from 20% to 25%, from 0% to 20%, from 5% to 20%, from 10% to 20%, from 15% to 20%, from 0% to 15%, from 5% to 15%, from 10% to 15%, from 0% to 10%, from 5% to 10%, or from 0% to 5% glycerol. The buffer can comprise to 0 to 500, 0 to 400, 0 to 300, 0 to 250, 0 to 200, 0 to 150, 0 to 100, 0 to 75, 0 to 50, 0 to 25, 0 to 20, 0 to 10, 0 to 5, 5 to 10, 5 to 15, 5 to 20, 5 to 25, to 30, 5 to 40, 5 to 50, 5 to 75, 5 to 100, 5 to 150, 5 to 200, 5 to 250, 5 to 300, 5 to 400, 5 to 500, 25 to 50, 25 to 75, 25 to 100, 50 to 100, 50 150, 50 to 200, 50 to 250, 50 to 300, 100 to 200, 100 to 250, 100 to 300, or 150 to 250 mM Tris-HCl pH 8.8. The buffer can comprise to 0 to 500, 0 to 400, 0 to 300, 0 to 250, 0 to 200, 0 to 150, 0 to 100, 0 to 75, 0 to 50, 0 to 25, 0 to 20, 0 to 10, 0 to 5, 5 to 10, 5 to 15, 5 to 20, 5 to 25, to 30, 5 to 40, 5 to 50, 5 to 75, 5 to 100, 5 to 150, 5 to 200, 5 to 250, 5 to 300, 5 to 400, 5 to 500, 25 to 50, 25 to 75, 25 to 100, 50 to 100, 50 150, 50 to 200, 50 to 250, 50 to 300, 100 to 200, 100 to 250, 100 to 300, or 150 to 250 mM KO Ac. The buffer can comprise to 0 to 500, 0 to 400, 0 to 300, 0 to 250, 0 to 200, 0 to 150, 0 to 100, 0 to 75, 0 to 50, 0 to 25, 0 to 20, 0 to 10, 0 to 5, 5 to 10, 5 to 15, 5 to 20, 5 to 25, to 30, 5 to 40, 5 to 50, 5 to 75, 5 to 100, 5 to 150, 5 to 200, 5 to 250, 5 to 300, 5 to 400, 5 to 500, 25 to 50, 25 to 75, 25 to 100, 50 to 100, 50 150, 50 to 200, 50 to 250, 50 to 300, 100 to 200, 100 to 250, 100 to 300, or 150 to 250 mM MgOAc. In some instances the buffer may comprise from 0 to 100, 0 to 75, 0 to 50, 0 to 25, 0 to 20, 0 to 10, 0 to 5, 5 to 10,5 to 15, 5 to 20, 5 to 25, to 30, 5 to 40, 5 to 50, 5 to 75, 5 to 100, 10 to 20, 10 to 30, 10 to 40, 10 to 50, 15 to 20, 15 to 25, 15 to 30, 15 to 4, 15 to 50, 20 to 25, 20 to 30, 20 to 40, or 20 to 50 mM EGTA. The buffer can comprise from 0% to 30%, from 5% to 30%, from 10% to 30%, from 15% to 30%, from 20% to 30%, from 25% to 30%, from 0% to 25%, from 2% to 25%, from 5% to 25%, from 10% to 25%,from 15% to 25%, from 20% to 25%, from 0% to 20%, from 5% to 20%, from 10% to 20%, from 15% to 20%, from 0% to 15%, from 5% to 15%, from 10% to 15%, from 0% to 10%, from 5% to 10%, or from 0% to 5% Tween 20.B. Programmable nuclease-based assay

[0206] Described herein are various embodiments of a programmable nuclease-based assay. In some embodiments, a programmable nuclease-based assay is referred to as a DETECTR assay. In some embodiments, one or more programmable nucleases as disclosed herein can be activated to initiate trans cleavage activity of a reporter (also referred to herein as a reporter molecule). A programmable nuclease as disclosed herein can, in some cases, bind to a target sequence or target nucleic acid to initiate trans cleavage of a reporter. Herein, detection (directly or indirectly) of reporter cleavage by a programmable nuclease to determine the presence of a target nucleic acid sequence may be referred to as 'DETECTR'. The programmable nuclease can, in some cases, be referred to as an RNA-activated programmable RNA nuclease. In some instances, the programmable nuclease as disclosed herein can bind to a target DNA to initiate trans cleavage of an RNA reporter. Such a programmable nuclease can be referred to herein as a DNA-activated programmable RNA nuclease. In some cases, a programmable nuclease as described herein can be activated by a target RNA or a target DNA. For example, a programmable nuclease, e.g., a Cas enzyme, can be activated by a target RNA nucleic acid or a target DNA nucleic acid to cleave RNA reporters. In some embodiments, the Cas enzyme can bind to a target ssDNA which initiates trans cleavage of RNA reporters. In some instances, a programmable nuclease as disclosed herein can bind to a target DNA to initiate trans cleavage of a DNA reporter, and this programmable nuclease can be referred to as a DNA-activated programmable DNA nuclease.

[0207] The programmable nuclease can become activated after binding of a guide nucleic acid that is complexed with the programmable nuclease with a target nucleic acid, and the activated programmable nuclease can cleave the target nucleic acid, which can result in a trans cleavage activity. Trans cleavage activity can be non-specific cleavage of nearby single-stranded nucleic acids by the activated programmable nuclease, such as trans cleavage of detector nucleic acids with a detection moiety. Once the target nucleic acid is cleaved by the activated programmable nuclease, the detection moiety can be released or separated from the reporter and can directly or indirectly generate a detectable signal. The reporter and / or the detection moiety can be immobilized, dried, or otherwise deposited on a support medium. Often the detection moiety is at least one of a fluorophore, a dye, a polypeptide, or a nucleic acid. Sometimes the detectionmoiety binds to a capture molecule on the support medium to be immobilized. The detectable signal can be visualized on the support medium to assess the presence or concentration of one or more target nucleic acids associated with an ailment, such as a disease, cancer, or genetic disorder.

[0208] The devices, systems, fluidic devices, kits, and methods for detecting the presence of a target nucleic acid in a sample described herein may comprise a generation of a signal indicative of the presence or absence of the target nucleic acid in the sample. The generation of a signal indicative of the presence or absence of the target nucleic acid in the sample as described herein is compatible with the methods and devices described herein and may result from the use of compositions disclosed herein (e.g. programmable nucleases, guide nucleic acids, reagents for in vitro transcription, reagents for amplification, reagents for reverse transcription, reporters, or any combination thereof) to carry out highly efficient, rapid, and accurate reactions for detecting whether a target nucleic acid is present in a sample (e.g., DETECTR reactions). As disclosed herein, in some embodiments, detecting the presence or absence of a target nucleic acid of interest involves measuring a signal emitted from a detection moiety present in a reporter, after cleavage of the reporter by an activated programmable nuclease. Alternatively, or in combination, in some embodiments, detecting the presence or absence of a target nucleic acid of interest involves measuring a signal emitted from a conjugate bound to a detection moiety present in a reporter, after cleavage of the reporter by an activated programmable nuclease. The conjugate may comprise a nanoparticle, a gold nanoparticle, a latex nanoparticle, a quantum dot, a chemiluminescent nanoparticle, a carbon nanoparticle, a selenium nanoparticle, a fluorescent nanoparticle, a liposome, or a dendrimer. The surface of the conjugate may be coated by a conjugate binding molecule that binds to the detection moiety or another affinity molecule of the cleaved detector molecule as described herein. Thus, the detecting steps disclosed herein may involve indirectly (e.g., via a reporter) measuring the presence of a target nucleic acid, quantifying how much of the target nucleic acid is present, and / or measuring a signal indicating that the target nucleic acid is absent in a sample. In some embodiments, a signal is generated upon cleavage of the reporter by the programmable nuclease. In other embodiments, the signal changes upon cleavage of the reporter by the programmable nuclease. In other embodiments, a signal may be present in the absence of reporter cleavage and disappear or reduce upon cleavage of the target nucleic acid by the programmable nuclease. For example, a signal may be produced in a microfluidic device or lateral flow device after contacting a sample with a composition comprising a programmable nuclease.

[0209] In some embodiments, the workflow method may comprise: (1) sample collection fromthe patient and delivery to the device, (2) optional lysis, (3) optional amplification of the target nucleic acids, and (4) detection / readout. In some embodiments, amplification and detection are carried out in one reaction volume and is referred to as a one-pot reaction. In some embodiments, sample amplification is carried in a first reaction volume and detection is carried in a second reaction volume. Such embodiments, wherein sample amplification is carried in a first reaction volume and detection is carried in a second reaction volume are referred to as two-pot reactions. In some embodiments, carrying out multiple reactions in multiple reaction volumes is referred to as a multi-pot reaction. Exemplary embodiments for one-pot, two-pot, and multi-pot reactions can be found in: PCT / US2021 / 033271, PCT / US2021 / 035031, PCT / US2021 / 063405, PCT / US2021 / 063844, PCT / US2022 / 034596, PCT / US2022 / 081842, and PCT / US2022 / 034110, all of which are herein incorporated by reference in their entireties.

[0210] In some embodiments, the running of a programmable nuclease-based assay is referred to as a detection step. In some embodiments, the detection step may be preceded or coincide with nucleic acid amplification In some embodiments, nucleic acid amplification may comprise PCR. In some embodiments, nucleic acid amplification may comprise Loop-Mediated Isothermal Amplification (LAMP).

[0211] Described herein are various methods of nucleic acid amplification and detection in a single reaction volume. Any of the devices described herein may be configured to perform amplification and detection in a same well, chamber, channel, or volume in the device. In certain instances, methods include simultaneous amplification and detection in the same volume. In certain instances, methods include sequential amplification and detection in the same volume. In certain instances, methods include simultaneous amplification and detection in the same volume. In some embodiments, nucleic acid amplification may comprise LAMP amplification or a variation thereof. In some embodiments, nucleic acid amplification may comprise PCR amplification or a variation thereof.

[0212] In some embodiments, the limit of detection for a programmable nuclease-based assay is 1 copy of a target nucleic acid per reaction. In some embodiments, the limit of detection for a programmable nuclease-based assay is 10 copies of a target nucleic acid per reaction. In some embodiments, the limit of detection for a programmable nuclease-based assay is from 1 to 10 copies of a target nucleic acid per reaction. In some embodiments, the limit of detection for a programmable nuclease-based assay is from 10 to 20 copies of a target nucleic acid per reaction. In some embodiments, the limit of detection for a programmable nuclease-based assay is from 20 to 30 copies of a target nucleic acid per reaction. In some embodiments, the limit of detection fora programmable nuclease-based assay is from 30 to 40 copies of a target nucleic acid per reaction. In some embodiments, the limit of detection for a programmable nuclease-based assay is from 40 to 50 copies of a target nucleic acid per reaction. In some embodiments, the limit of detection for a programmable nuclease-based assay is from 50 to 100 copies of a target nucleic acid per reaction. In some embodiments, the limit of detection for a programmable nuclease- based assay is from 100 to 1000 copies of a target nucleic acid per reaction. In some embodiments, the limit of detection for a programmable nuclease-based assay is greater than 1000 copies of a target nucleic acid per reaction.Reagent Immobilization Strategies

[0213] Programmable nuclease-based diagnostic reactions are generally performed in solution where the programmable nuclease-guide nucleic acid complexes can freely bind target molecules and reporters. However, reactions where all components are in solution can limit the designs of nucleic acid diagnostic assays, especially in microfluidic devices. A system where various components of the programmable nuclease-based diagnostic reaction are immobilized on a surface may enable designs where multiple readouts can be accomplished within a single reaction chamber and / or in a single cartridge.

[0214] One or more components or reagents of a programmable nuclease-based detection reaction may be suspended in solution or immobilized on a surface. Programmable nucleases, guide nucleic acids, and / or reporters may be suspended in solution or immobilized on a surface. For example, the reporter, programmable nuclease, and / or guide nucleic acid can be immobilized on the surface of a chamber in a device as disclosed herein. In some cases, the reporter, programmable nuclease, and / or guide nucleic acid can be immobilized on beads, such as magnetic beads, in a chamber of a device as disclosed herein where they are held in position by a magnet placed below the chamber. An immobilized programmable nuclease can be capable of being activated and cleaving a free-floating or immobilized reporter. An immobilized guide nucleic acid can be capable of binding a target nucleic acid and activating a programmable nuclease complexed thereto. An immobilized reporter can be capable of being cleaved by the activated programmable nuclease, thereby generating a detectable signal.

[0215] Described herein are various methods to immobilize programmable nuclease-based diagnostic reaction components to the surface of a reaction chamber or other surface (e.g., a surface of a bead). Any of the devices described herein may comprise one or more immobilized detection reagent components (e.g., programmable nuclease, guide nucleic acid, and / or reporter). In certain instances, methods include immobilization of programmable nucleases (e.g., Casproteins or Cas enzymes), reporters, and / or guide nucleic acids (e.g., gRNAs). In some embodiments, various programmable nuclease-based diagnostic reaction components are modified with biotin. In some embodiments, these biotinylated programmable nuclease-based diagnostic reaction components are tested for immobilization on surfaces coated with streptavidin. In some embodiments, the biotin-streptavidin interaction is used as a model system for other immobilization chemistries. In some embodiments, NHS-Amine chemistry is used for immobilization of programmable nuclease-based reaction components. In some embodiments, amino modifications are used for immobilization of programmable nuclease-based reaction components. In some embodiments, maleimide-thiol chemistry is used for immobilization of programmable nuclease-based reaction components. In some embodiments, epoxy-amine chemistry is used for immobilization of programmable nuclease-based reaction components. In some embodiments, hydrogels are used for immobilization of programmable nuclease-based reaction components.

[0216] In some embodiments, chemical modifications of amino acid residues in the Cas protein enable attachment to a surface. In some embodiments, guide nucleic acids are immobilized by adding various chemical modifications at the 5’ or 3’ end of the guide nucleic acids that are compatible with a selected surface chemistry. In some embodiments, fluorescence-quenching (FQ), or other reporter detection moiety chemistries, are attached to surfaces using similar chemical modifications as gRNAs. In some embodiments, these attached reporters are cleaved by a programmable nuclease, which leads to either activated molecules (e.g., detection moieties) that remain attached to the surface or activated molecules that are released into solution.

[0217] For some embodiments, described herein the programmable nuclease complex may be immobilized by a guide nucleic acid and cleave surrounding fluorophore-quencher reporters that are also immobilized to a surface. Here, the quencher may be released into solution, leaving a localized fluorescent signal. In other embodiments, the fluorophore may be released into solution, thereby generating a fluorescent signal in solution.

[0218] In some embodiments, the programmable nuclease, guide nucleic acid, reporter, or a combination thereof can be immobilized to a device surface (e.g., by a linkage). In some embodiments, the linkage comprises a covalent bond, a non-covalent bond, an electrostatic bond, an interaction (e.g., a covalent or noncovalent bond) between members of a binding pair (e.g., streptavidin and biotin), an amide bond, or any combination thereof. In embodiments where more than one element is immobilized to the surface (e.g., reporters and guide nucleic acid, programmable nuclease and reporters, or all three), the linkage may be the same or different foreach species. For example, the guide nucleic acid may be immobilized to the surface by a singlestranded linker polynucleotide, and the reporters may be immobilized by the interaction between a first member of a binding pair on the reporters and a second member of a binding pair on the surface. In general, the term “binding pair” refers to a first and a second moiety that have a specific binding affinity for each other. In some embodiments, a binding pair has a dissociation constant Kd of less than or equal to about: 10'8mol / L, 10'9mol / L, IO'10mol / L, 10'11mol / L, 10'12mol / L, 10'13mol / L, 10'14mol / L, 10'15mol / L, or ranges including two of these values as endpoints. Non limiting examples of binding pairs include an antibody or an antigen-binding portion thereof and an antigen (e.g., fluorescein, digoxin, digoxigenin); a biotin (bio) moiety and an avidin (or streptavidin) moiety; a dinitrophenol (DNP) and an anti-DNP antibody; a hapten and an anti hapten; folate and a folate binding protein; vitamin B 12 and an intrinsic factor; a carbohydrate and a lectin or carbohydrate receptor; a polysaccharide and a polysaccharide binding moiety; a lectin and a receptor; a ligand and a receptor; a drug and a drug receptor; complementary chemical reactive groups (e.g., sulfhydryl / maleimide, thiol / maleimide, sulfhydryl / haloacetyl derivative, amine / epoxy, amine / isotriocyanate, amine / succinimidyl ester, and amine / sulfonyl halides); an antibody (e.g., IgG) and protein A or protein G; a toxin and a toxin receptor; and an enzyme substrate and an enzyme. In some embodiments, the binding pair comprises biotin and either of avidin or streptavidin.

[0219] In some embodiments, the linkage utilizes non-specific absorption. In some embodiments, the programmable nuclease is immobilized to the device surface by the linkage, wherein the linkage is between the programmable nuclease and the surface. In some embodiments, the reporter is immobilized to the device surface by the linkage, wherein the linkage is between the reporter and the surface. In some embodiments, the guide nucleic acid is immobilized to the surface by the linkage, wherein the linkage is between the 5’ end of the guide nucleic acid and the surface. In some embodiments, the guide nucleic acid is immobilized to the surface by the linkage, wherein the linkage is between the 3’ end of the guide nucleic acid and the surface. In some embodiments, the programmable nuclease, guide nucleic acid, and / or the reporter are immobilized to or within a polymer matrix. The polymer matrix may comprise a hydrogel. Co-polymerization of the programmable nuclease, guide nucleic acid, or the reporter into the polymer matrix may result in a higher density of reporter / unit volume or reporter / unit area than other immobilization methods utilizing surface immobilization (e.g., onto beads, after matrix polymerization, etc.). Co-polymerization of the programmable nuclease, guide nucleic acid, or the reporter into the polymer matrix may result in less undesired release of the reporter (e.g., during an assay, a measurement, or on the shelf), and thus may cause less backgroundsignal, than other immobilization strategies (e.g., conjugation to a pre-formed hydrogel, bead, etc.). In at least some instances this may be due to better incorporation of reporters into the polymer matrix as a co-polymer and fewer “free” reporter molecules retained on the hydrogel via non-covalent interactions or non-specific binding interactions.

[0220] In some embodiments, a plurality of oligomers and a plurality of polymerizable oligomers may comprise an irregular or non-uniform mixture. The irregularity of the mixture of polymerizable oligomers and unfunctionalized oligomers may allow pores to form within the hydrogel (i.e., the unfunctionalized oligomers may act as a porogen). For example, the irregular mixture of oligomers may result in phase separation during polymerization that allows for the generation of pores of sufficient size for free-floating programmable nucleases to diffuse into the hydrogel and access immobilized internal reporter molecules. The relative percentages and / or molecular weights of the oligomers may be varied to vary the pore size of the hydrogel. For example, pore size may be tailored to increase the diffusion coefficient of the programmable nucleases.

[0221] In some embodiments, the functional groups attached to the reporters and / or guide nucleic acids may be selected to preferentially incorporate the reporters and / or guide nucleic acids into the polymer matrix via covalent binding at the functional group versus other locations along the nucleic acid backbone of the reporter and / or guide nucleic acid. In some embodiments, the functional groups attached to the reporters and / or guide nucleic acids may be selected to favorably transfer free radicals from the functionalized ends of polymerizable oligomers to the functional group on the end of the reporter and / or guide nucleic acid (e.g., 5’ end), thereby forming a covalent bond and immobilizing the reporter and / or guide nucleic acid rather than destroying other parts of the reporter and / or guide nucleic acid molecules, respectively. In some embodiments, the functional group may comprise a single stranded nucleic acid, a double stranded nucleic acid, an acrydite group, a 5’ thiol modifier, a 3’ thiol modifier, an amine group, a I-Linker™ group, methacryl group, or any combination thereof. One of ordinary skill in the art will recognize that a variety of functional groups may be used depending on the desired properties of the immobilized components.Programmable nuclease-based assay multiplexing

[0222] Methods consistent with the present disclosure include a multiplexing method of assaying for a plurality of target nucleic acids in a sample. A multiplexing method may comprise a) contacting the sample to a programmable nuclease complex comprising a guide nucleic acid comprising a segment that is reverse complementary to a segment of the target nucleic acid and aprogrammable nuclease that exhibits sequence independent cleavage upon forming a complex comprising the segment of the guide nucleic acid binding to the segment of the target nucleic acid; and b) assaying for a signal indicating cleavage of at least some reporters (e.g., protein- nucleic acids) of a population of reporter molecules (e.g., protein-nucleic acids), wherein the signal indicates a presence of the target nucleic acid in the sample and wherein absence of the signal indicates an absence of the target nucleic acid in the sample.

[0223] Multiplexing can comprise spatial multiplexing wherein multiple different target nucleic acids are detected at the same time, but the reactions are spatially separated. In some cases, the multiple target nucleic acids are detected using the same programmable nuclease, but different guide nucleic acids. The multiple target nucleic acids sometimes are detected using different programmable nucleases. In the case wherein multiple target nucleic acids are detected using different programmable nucleases, the method may involve using a first programmable nuclease, which upon activation (e.g., after binding of a first guide nucleic acid to a first target), cleaves a nucleic acid of a first reporter and using a second programmable nuclease, which upon activation (e.g., after binding of a second guide nucleic acid to a second target) cleaves a nucleic acid of a second reporter. Spatially separated reactions may, for example, occur within an array comprising a plurality of different detection locations each comprising one or more immobilized detection reaction component(s) thereon. In some embodiments, spatially separated reactions may occur in different wells of a detection region, e.g., within different microwells, each microwell containing different detection reaction components configured to detect different target nucleic acids.

[0224] Sometimes, multiplexing can be single reaction multiplexing, wherein multiple different target acids are detected in a single reaction volume. Often, at least two different programmable nucleases are used in single reaction multiplexing. For example, multiplexing can be enabled by immobilization of multiple categories of detector nucleic acids within a fluidic system, to enable detection of multiple target nucleic acids within a single fluidic system. Multiplexing allows for detection of multiple target nucleic acids in one kit or system. In some cases, the multiple target nucleic acids comprise different target nucleic acids from a virus, a bacterium, or a pathogen responsible for one disease. In some cases, the multiple target nucleic acids comprise different target nucleic acids associated with a cancer or genetic disorder. Multiplexing for one disease, cancer, or genetic disorder increases at least one of sensitivity, specificity, or accuracy of the assay to detect the presence of the disease in the sample. In some cases, the multiple target nucleic acids comprise target nucleic acids directed to different viruses, bacteria, or pathogens responsible for more than one disease. In some cases, multiplexing allows for discriminationbetween multiple target nucleic acids, such as target nucleic acids that comprise different genotypes of the same bacteria or pathogen responsible for a disease, for example, for a wildtype genotype of a bacteria or pathogen and for genotype of a bacteria or pathogen comprising a mutation, such as a single nucleotide polymorphism (SNP) that can confer resistance to a treatment, such as antibiotic treatment. Multiplexing, thus, allows for multiplexed detection of multiple genomic alleles. For example, multiplexing may comprise method of assaying comprising a single assay for a microorganism species using a first programmable nuclease and an antibiotic resistance pattern in a microorganism using a second programmable nuclease. Sometimes, multiplexing allows for discrimination between multiple target nucleic acids of different pathogen strains, for example, HP VI 6 and HP VI 8. In some instances, multiplexing allows for discrimination between multiple target nucleic acids of different variants of a pathogen, for example, alpha and delta SARS-CoV-2 variants. In some cases, the multiple target nucleic acids comprise target nucleic acids directed to different cancers or genetic disorders. Often, multiplexing allows for discrimination between multiple target nucleic acids, such as target nucleic acids that comprise different genotypes, for example, for a wild-type genotype and for SNP genotype. Multiplexing for multiple diseases, cancers, or genetic disorders provides the capability to test a panel of diseases from a single sample. For example, multiplexing for multiple diseases can be valuable in a broad panel testing of a new patient or in epidemiological surveys. Often multiplexing is used for identifying bacterial pathogens in sepsis or other diseases associated with multiple pathogens.

[0225] Furthermore, signals from multiplexing can be quantified. For example, a method of quantification for a disease panel may comprise assaying for a plurality of unique target nucleic acids in a plurality of aliquots from a sample, assaying for a control nucleic acid control in a second aliquot of the sample, and quantifying a plurality of signals of the plurality of unique target nucleic acids by measuring signals produced by cleavage of detector nucleic acids compared to the signal produced in the second aliquot. In this context, a unique target nucleic acid refers to the sequence of a nucleic acid that has an at least one nucleotide difference from the sequences of the other nucleic acids in the plurality. Multiple copies of each target nucleic acid can be present. For example, a unique target nucleic population can comprise multiple copies of the unique target nucleic acid. Often the plurality of unique target nucleic acids is from a plurality of bacterial pathogens in the sample.

[0226] In some instances, the multiplexed devices, systems, fluidic devices, kits, and methods detect at least 2 different target nucleic acids in a single reaction. In some instances, the multiplexed devices, systems, fluidic devices, kits, and methods detect at least 3 different targetnucleic acids in a single reaction. In some instances, the multiplexed devices, systems, fluidic devices, kits, and methods detect at least 4 different target nucleic acids in a single reaction. In some instances, the multiplexed devices, systems, fluidic devices, kits, and methods detect at least 5 different target nucleic acids in a single reaction. In some cases, the multiplexed devices, systems, fluidic devices, kits, and methods detect at least 6, 7, 8, 9, or 10 different target nucleic acids in a single reaction. In some instances, the multiplexed kits detect at least 2 different target nucleic acids in a single kit. In some instances, the multiplexed kits detect at least 3 different target nucleic acids in a single kit. In some instances, the multiplexed kits detect at least 4 different target nucleic acids in a single kit. In some instances, the multiplexed kits detect at least 5 different target nucleic acids in a single kit. In some instances, the multiplexed kits detect at least 6, 7, 8, 9, or 10 different target nucleic acids in a single kit. In some instances, the multiplexed kits detect from 2 to 10, from 3 to 10, from 4 to 10, from 5 to 10, from 6 to 10, from 7 to 10, from 8 to 10, from 9 to 10, from 2 to 9, from 3 to 9, from 4 to 9, from 5 to 9, from 6 to 9, from 7 to 9, from 8 to 9, from 2 to 8, from 3 to 8, from 4 to 8, from 5 to 8, from 6 to 8, from 7 to 8, from 2 to 7, from 3 to 7, from 4 to 7, from 5 to 7, from 6 to 7, from 2 to 6, from 3 to 6, from 4 to 6, from 5 to 6, from 2 to 5, from 3 to 5, from 4 to 5, from 2 to 4, from 3 to 4, or from 2 to 3 different target nucleic acids in a single kit. Multiplexing can be carried out in a single-pot or “one-pot” reaction, where reverse transcription, amplification, in vitro transcription, or any combination thereof, and detection are carried out in a single volume. Multiplexing can be carried out in a “two-pot reaction”, where reverse transcription, amplification, in vitro transcription, or any combination thereof, are carried out in a first volume and detection is carried out in a second volume.

[0227] In some cases, multiplexing can comprise detecting multiple targets with a single probe. Alternatively, multiplexing can comprise detecting multiple targets with multiple probes. The multiple probes can be configured to detect a presence of a particular sequence, target nucleic acid, or a plurality of different target sequences or nucleic acids.Sample preparation and lyophilization strategies

[0228] Described herein are various methods of sample preparation and reagent storage. Any of the devices described herein may comprise one or more sample preparation reagents. Any of the devices described herein may comprise sample preparation reagents as dried reagents. Dried reagents may comprise solids and / or semi-solids. In certain instances, dried reagents may comprise lyophilized reagents. Any of the devices described herein may comprise one or more lyophilized reagents (e.g., amplification reagents, programmable nucleases, buffers, excipients,etc.). In certain instances, methods include sample lysis, concentration, and / or filtration. In certain instances, methods include reconstitution of one or more lyophilized reagents. In some embodiments, lyophilized reagents may be in the form of lyophilized beads, spheres, and / or particulates. In some embodiments, the lyophilized bead, sphere, and / or particulate may comprise either single or multiple compounds. In some embodiments, the lyophilized bead, sphere, and / or particulate may be adjusted to various moisture levels or hygroscopy. In some embodiments, the lyophilized bead, sphere, and / or particulate may comprise assay internal standards. In some embodiments, the lyophilized bead, sphere, and / or particulate may have diameters between about 0.5 millimeters to about 5 millimeters in diameter.

[0229] Described herein are various embodiments of a programmable nuclease-based detection (e.g., DETECTR) reaction involving optimization of sample preparation and lyophilization. Such embodiments allow for adapting the buffer for binding a substrate to perform a concentration step. In some embodiments, experiments may be performed to evaluate the lysis (sample is evaluated directly in the assay) and binding (the sample is eluted from magnetic beads) characteristics of buffers with different components. In such embodiments, the input sample is the same concentration as the eluted sample.

[0230] In some embodiments, crude lysis buffer is used in a one-pot assay with Casl4a.l (SEQ ID NO: 3).

[0231] In some embodiments, the enzyme having SEQ ID NO: 17 is used with the programmable nuclease-based detection assay.

[0232] In some embodiments, a control study involving sample preparation optimization of the LANCR (multiplexed isothermal amplification) assay. In such embodiments, crude lysis involves: 25 pL sample + 25 pL lysis buffer and incubation at 25C for 1 minute. In some embodiments, the LANCR reaction is run as follows: 5 pL sample in a 25 pL reaction volume (standard conditions). In some embodiments the DETECTR reaction is run as follows: 2 pL LANCR product in 20 pL reaction volume (standard conditions). Sample: 250 copies / rxn SeraCare SARS-CoV-2 reference RNA.

[0233] In some embodiments, Trehalose, Raffinose, PVP 40, sorbitol, Mannitol, Mannose, or a combination thereof are used for lyophilization. In some embodiments, Trehalose may be used to control the rate of the reaction.

[0234] Described herein are various methods and devices for carrying out programmable nuclease-based assays. In some embodiments, programmable nuclease-based assays utilize aCasl2 protein, a Cast 3 protein, a Cast 4 protein, or a CasPhi protein. In some embodiments, amplification (e.g., RT-LAMP) and programmable nuclease-based detection (e.g., DETECTR) master mixes of reagents are lyophilized in the same combined master mix. In some embodiments, amplification and programmable nuclease-based detection master mixes of reagents and target may be lyophilized in the same combined master mix. In some embodiments, one-pot refers to the combination of both amplification (e.g., RT-LAMP) and detection (e.g., DETECTR) reaction reagents in one volume. In some embodiments, an excipient is used to confirm reagent stability throughout the lyophilization process, comprising freezing and drying steps. In some embodiments, excipients are sugars.

[0235] In some embodiments, a master mix of assay reagents may be reconstituted after lyophilization. In some embodiments, a master mix of DETECTR assay reagents may be reconstituted after lyophilization. In some embodiments, a master mix of DETECTR assay reagents, including a Cast 2 protein for example, may be reconstituted after lyophilization. In some embodiments, a master mix of amplification and programmable nuclease-based detection (e.g., DETECTR) assay reagents, including a Casl2 for example, may be reconstituted after lyophilization. In some embodiments, a master mix of amplification (e.g., RT-LAMP) and programmable nuclease-based detection (e.g., DETECTR) assay reagents, including a Casl2 protein, may be reconstituted after lyophilization.

[0236] In some embodiments, the master mix of reagents and target for one assay is lyophilized. In some embodiments, the master mixes from more than one assay may be pooled and lyophilized.

[0237] In some embodiments, lyophilized master mixes of reagents from more than one assay may be prepared in volumes of less than 1 mL. In some embodiments, lyophilized master mixes of reagents from more than one assay may be prepared in volumes of less than 250 pL. In some embodiments, lyophilized master mixes of reagents from more than one assay may be prepared in volumes of less than 25 pL. In some embodiments, lyophilized master mixes of reagents from more than one assay may be prepared in volumes of less than 10 pL.

[0238] In some embodiments, an excipient is used to stabilize the sample throughout the lyophilization process that may comprise freezing and drying steps.

[0239] In some embodiments, a viral, bacterial, and / or high temperature inactivator may be used.

[0240] In some embodiments, programmable nuclease-based assays may comprise one or more controls. In some embodiments, the assay controls may comprise non-specific binding controls.In some embodiments, RNase may be used as a control against the programmable nuclease for cleavage activity. In some embodiments, DNase may be used as a control against the programmable nuclease for cleavage activity. In some embodiments, an assay control may comprise a no-target-control (NTC), wherein a particular control sample does not contain at least one target. In some embodiments, a control sample may comprise target nucleic acids added to the control sample at known concentrations.

[0241] Described herein are exemplary methods for programmable nuclease-based detection. The method can comprise collecting a sample. The sample can comprise any type of sample as described herein. The method can comprise preparing the sample. Sample preparation can comprise one or more sample preparation steps. The one or more sample preparation steps can be performed in any suitable order. The one or more sample preparation steps can comprise physical filtration of non-target materials using a macro filter. The one or more sample preparation steps can comprise nucleic acid purification. The one or more sample preparation steps can comprise nucleic acid concentration. The one or more sample preparation steps can comprise lysis. The one or more sample preparation steps can comprise heat inactivation. The one or more sample preparation steps can comprise chemical inactivation. The one or more sample preparation steps can comprise neutralization. The one or more sample preparation steps can comprise adding one or more enzymes or reagents to prepare the sample for target detection.

[0242] The method can comprise generating one or more droplets, aliquots, volumes, or subsamples from the sample. The one or more droplets, aliquots, volumes, or subsamples can correspond to a volumetric portion of the sample. The sample can be divided into 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, or more droplets, aliquots, volumes, or subsamples. In some embodiments, the sample is not divided into subsamples.

[0243] The method can comprise amplifying one or more targets within the sample. The method can comprise amplifying one or more targets within each droplet, aliquot, volumes, or subsample. Amplification of the one or more targets within each droplet or volume can be performed in parallel and / or simultaneously for each droplet or volume. Dividing the sample into a plurality of droplets or volumes can enhance a speed and / or an efficiency of the amplification process (e.g., a thermocycling process) since the droplets comprise a smaller volume of material than the bulk sample introduced. Amplifying the one or more targets within each individual droplet or volume can also permit effective amplification of various target nucleic acids that cannot be amplified as efficiently in a bulk sample containing the various target nucleic acids ifthe bulk sample were to undergo a singular amplification process. In some embodiments, amplification is performed on the bulk sample without first dividing the sample into subsamples.

[0244] The method can further comprise using a CRISPR-based or programmable nuclease- based detection module to detect one or more targets (e.g., target sequences or target nucleic acids) in the sample. In some cases, the sample can be divided into a plurality of droplets, aliquots, volumes, or subsamples to facilitate sample preparation and to enhance the detection capabilities of the devices of the present disclosure.

[0245] In some embodiments, the sample can be provided manually to the detection device of the present disclosure. For example, a swab sample can be dipped into a solution and the sample / solution can be pipetted into the device. In other embodiments, the sample can be provided via an automated syringe. The automated syringe can be configured to control a flow rate at which the sample is provided to the detection device. The automated syringe can be configured to control a volume of the sample that is provided to the detection device over a predetermined period.

[0246] In some embodiments, the sample can be provided directly to the detection device of the present disclosure. For example, a swab sample can be inserted into a sample receiver and / or a sample chamber on the detection device.

[0247] The sample can be prepared before one or more targets are detected within the sample. The sample preparation steps described herein can process a crude sample to generate a pure or purer sample. Sample preparation can comprise one or more physical or chemical processes, including, for example, nucleic acid purification, lysis, binding, washing, and / or elution. In certain instances, sample preparation can comprise the following steps, in any order, including sample collection, nucleic acid purification, heat inactivation, neutralization, and / or base / acid lysis.

[0248] In some embodiments, nucleic acid purification can be performed on the sample. Purification can comprise disrupting a biological matrix of a cell to release nucleic acids, denaturing structural proteins associated with the nucleic acids (nucleoproteins), inactivating nucleases that can degrade the isolated product (e.g., RNase and / or DNase), and / or removing contaminants (e.g., proteins, carbohydrates, lipids, biological or environmental elements, unwanted nucleic acids, and / or other cellular debris). In some embodiments, nucleic acid purification may involve liquid-liquid extraction, solid-liquid extraction, and / or solid-phase extraction techniques. In at least some instances, solid-phase extraction may be preferred for smaller sample volumes and / or improved cartridge-based performance (e.g., by reducing solventvolumes and / or simpler workflow automation). Solid-phase nucleic acid purification may utilize a silica-based method such as the Boom method. In some embodiments, silica particles (e.g., silica beads or silica magnetic beads), glass fiber filters, silica-coated membranes / meshes / filters, etc. may be used to capture nucleic acids from the sample prior to elution therefrom.Alternatively, or in combination, solid-phase nucleic acid purification may utilize charge switching for nucleic acid concentration. In some embodiments, particles (e.g., beads or magnetic beads) or surfaces (e.g., membranes, meshes, filters, etc.) may be coated with an ionizable coating such as chitosan. In some embodiments, the sample may be agitated (e.g., mixed, shaken, flown, sonicated, etc.) during purification and / or elution.

[0249] In some embodiments, lysis of a collected sample can be performed. Lysis can be performed using a protease (e.g., a Proteinase K or PK enzyme, and / or a savinase). In some cases, a solution of reagents can be used to lyse the cells in the sample and release the nucleic acids so that they are accessible to the programmable nuclease. Active ingredients of the solution can be chaotropic agents, detergents, salts, and can be of high osmolality, ionic strength, and pH. Chaotropic agents or chaotropes are substances that disrupt the three-dimensional structure in macromolecules such as proteins, DNA, or RNA. One example protocol may comprise a 4 M guanidinium isothiocyanate, 25 mM sodium citrate.2H2O, 0.5% (w / v) sodium lauryl sarcosinate, and 0.1 M P-mercaptoethanol), but numerous commercial buffers for different cellular targets can also be used. Alkaline buffers (i.e., buffers with a pH above 7) can also be used, and may be particularly effective for cells with hard shells, such as may be present in environmental samples. In some embodiments, the alkaline buffer has a pH of about or more than about 8, 8.5, 9, 9.5, 10, or higher. In some embodiments, acidic buffers (i.e., buffers with a pH below 7) are used for lysis. In some embodiments, the alkaline buffer has a pH of about 10. Any suitable base may be used for the alkaline buffer, including organic or inorganic bases. In some embodiments, the base is sodium hydroxide. In some embodiments, the acidic buffer has a pH of about or less than about 6, 5.5, 5, 4.5, 4, or lower. In some embodiments, the acidic buffer has a pH of about 5. Any suitable acid may be used for the acidic buffer, including organic or inorganic acids. In some embodiments, the acid is acetic acid. Detergents such as sodium dodecyl sulfate (SDS) and cetyl trimethylammonium bromide (CTAB) can also be implemented to chemical lysis buffers. Cell lysis can also be performed by physical, mechanical, thermal, or enzymatic means, in addition to or instead of chemically-induced cell lysis mentioned previously. In some cases, depending on the type of sample, nanoscale barbs, nanowires, acoustic generators (e.g., ultrasonic horns), integrated lasers, integrated heaters, and / or microcapillary probes can be used to perform lysis. In some embodiments, the sample may be agitated (e.g., mixed, shaken, flown,sonicated, etc.) during lysis. In some embodiments, lysis comprises exposure to both an acidic and an elevated temperature (e.g., 65 °C to 95 °C, 70 °C to 90 °C, or 75 °C to 85 °C).

[0250] In certain instances, inactivation can be performed on the sample to inactivate or neutralize conditions employed in a lysis step. In some embodiments, a processed / lysed sample can undergo heat inactivation to inactivate, in the lysed sample, the proteins used during lysing (e.g., a PK enzyme or a lysing reagent). In some embodiments, the sample may be agitated (e.g., mixed, shaken, flown, sonicated, bubbled, etc.) during heat-inactivation or neutralization. In some cases, a heating element integrated into the detection device or disposed within the instrument can be used for heat-inactivation. The heating element can be powered by a battery or another source of thermal or electric energy that is integrated with the detection device or instrument. In some embodiments, the heating element for heat-inactivation is the same as the heating element for lysis, amplification, and / or detection. In some embodiments, where a protease is used in the lysis step, inactivation may comprise introducing a protease inhibitor. In some embodiments, where an alkaline buffer is used for the lysis step, inactivation may comprise a neutralization step that lowers the pH of the solution, such as to a pH of about 7, 7.5, 8, or 8.5. In some embodiments, where an alkaline buffer is used for the lysis step, inactivation may comprise a neutralization step that lowers the pH of the solution, such as to a pH of about 8.8. In some embodiments, where an acidic buffer is used for the lysis step, inactivation may comprise a neutralization step that raises the pH of the solution, such as to a pH of about 7, 7.5, 8, or 8.5. In some embodiments, where an alkaline buffer is used for the lysis step, inactivation may comprise a neutralization step that raises the pH of the solution, such as to a pH of about 8.8.Neutralization may utilize any suitable base (e.g., potassium hydroxide or Tris) or acid (e.g., potassium acetate), depending on the pH of the lysis buffer, which may be provided in any suitable form (e.g., pellet or concentrated solution). A filtering step to remove debris may be included between lysis and inactivation, after inactivation, or both.

[0251] In some cases, a target nucleic acid within the sample can undergo amplification before binding to a guide nucleic acid, for example a crRNA of a CRISPR enzyme. The target nucleic acid within a purified sample can be amplified to generate a target amplicon. In some instances, amplification can be accomplished using loop mediated amplification (LAMP), isothermal recombinase polymerase amplification (RPA), and / or polymerase chain reaction (PCR). In some instances, digital droplet amplification can used. Such nucleic acid amplification of the sample can improve at least one of a sensitivity, specificity, or accuracy of the detection of the target nucleic acid. The reagents for nucleic acid amplification can comprise a recombinase, an oligonucleotide primer, a single-stranded DNA binding (SSB) protein, and a polymerase. Thenucleic acid amplification can be transcription mediated amplification (TMA). Nucleic acid amplification can be helicase dependent amplification (HD A) or circular helicase dependent amplification (cHDA). In additional cases, nucleic acid amplification is strand displacement amplification (SDA). The nucleic acid amplification can be recombinase polymerase amplification (RPA). The nucleic acid amplification can be at least one of loop mediated amplification (LAMP) or the exponential amplification reaction (EXPAR). Nucleic acid amplification is, in some cases, by rolling circle amplification (RCA), ligase chain reaction (LCR), simple method amplifying RNA targets (SMART), single primer isothermal amplification (SPIA), multiple displacement amplification (MDA), nucleic acid sequence-based amplification (NASBA), hinge-initiated primer-dependent amplification of nucleic acids (HIP), nicking enzyme amplification reaction (NEAR), or improved multiple displacement amplification (IMDA). The nucleic acid amplification can be performed for no greater than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 40, 50, or 60 minutes.Sometimes, the nucleic acid amplification is performed for from 1 to 60, from 5 to 55, from 10 to 50, from 15 to 45, from 20 to 40, or from 25 to 35 minutes. Sometimes, the nucleic acid amplification is performed for from 5 to 60, from 10 to 60, from 15 to 60, from 30 to 60, from 45 to 60, from 1 to 45, from 5 to 45, from 10 to 45, from 30 to 45, from 1 to 30, from 5 to 30, from 10 to 30, from 15 to 30, from 1 to 15, from 5 to 15, or from 10 to 15 minutes.

[0252] In some embodiments, amplification can comprise thermocycling of the sample. Thermocycling can be carried out for one or more droplets or volumes of the sample in parallel and / or independently in separate locations. In some embodiments, this can be accomplished by methods such as (1) by holding droplets or volumes stationary in locations where a heating element is in close proximity to the droplet or volume on one of the droplet or volume sides and a heat sink element is in close proximity to the other side of the droplet or volume, or (2) flowing the droplet of volume through zones in a fluid channel where heat flows across it from a heating source to a heat sink. In some cases, one or more resistive heating elements can be used to perform thermocycling. In some cases, thermocycling may comprise one or more reactions at different temperatures. In some cases, the reactions can include an annealing reaction, a denaturation reaction, and / or an extension reaction.

[0253] In some cases, an annealing temperature of the thermocycling reaction may be performed at a temperature around 45°C to 75°C. In some embodiments, the annealing temperature may be at a temperature of about 45 °C, about 47 °C, about 48 °C, about 49 °C, about 50 °C, about 52 °C, about 54 °C, about 56 °C, about 58 °C, about 60 °C, about 62 °C, about 64 °C, about 66 °C, about 68 °C, about 70 °C, about 72 °C, about 74 °C, or about 76 °C.

[0254] In some cases, a denaturation temperature of the thermocycling reaction may be performed at a temperature around 90°C to about 110°C. In some embodiments, the denaturation temperature may be at a temperature of about 90°C, about 91 °C, about 92°C, about 93 °C, about 94°C, about 95°C, about 96°C, about 97°C, about 98°C, about 99°C, about 100°C, about 101°C, about 102°C, about 103°C, about 104°C, about 105°C, about 106°C, about 107°C, about 108°C, about 109°C, or about 110°C.

[0255] In some cases, an extension temperature of the thermocycling reaction may be performed at a temperature from around 55°C to about 85°C. In some embodiments, the extension temperature may be at a temperature of about 55°C, about 57°C, about 59°C, about 60°C, about 61°C, about 62°C, about 63°C, about 64°C, about 65°C, about 66°C, about 68°C, about 70°C, about 71°C, about 72°C, about 73°C, about 75°C, about 76°C, about 78°C, about 80°C, about 81°C, about 82°C, about 83°C, about 84°C, or about 85°C.

[0256] In some embodiments, amplification can comprise isothermal amplification of the sample. Isothermal amplification ca be carried out for one or more droplets or volumes of the sample in parallel and / or independently in separate locations. In some embodiments, this can be accomplished by holding droplets or volumes stationary in locations where a heating element is in close proximity to the droplet or volume on one of the droplet or volume sides so as to maintain a constant temperature within the droplet or volume. In some cases, one or more resistive heating elements can be used to perform isothermal amplification. Sometimes, the nucleic acid amplification reaction is performed at a temperature of around 20-65°C. The nucleic acid amplification reaction can be performed at a temperature no greater than 20°C, 25°C, 30°C, 35°C, 37°C, 40°C, 45°C, 50°C, 55°C, 60°C, or 65°C. The nucleic acid amplification reaction can be performed at a temperature of at least 20°C, 25°C, 30°C, 35°C, 37°C, 40°C, 45°C, 50°C, 55°C, 60°C, or 65°C. In some cases, the nucleic acid amplification reaction is performed at a temperature of from 20°C to 45°C, from 25°C to 40°C, from 30°C to 40°C, or from 35°C to 40°C. In some cases, the nucleic acid amplification reaction is performed at a temperature of from 45°C to 65°C, from 50°C to 65°C, from 55°C to 65°C, or from 60°C to 65°C. In some cases, the nucleic acid amplification reaction can be performed at a temperature that ranges from about 20 °C to 45 °C, from 25 °C to 45 °C, from 30 °C to 45 °C, from 35 °C to 45 °C, from 40 °C to 45 °C, from 20 °C to 37 °C, from 25 °C to 37 °C, from 30 °C to 37 °C, from 35 °C to 37 °C, from 20 °C to 30 °C, from 25 °C to 30 °C, from 20 °C to 25 °C, or from about 22 °C to 25 °C. In some cases, the nucleic acid amplification reaction can be performed at a temperature that ranges from about 40 °C to 65 °C, from 45 °C to 65 °C, from 50 °C to 65 °C, from 55 °C to 65 °C, from 60 °C to 65 °C, from 40 °C to 60 °C, from 45 °C to 60 °C, from 50 °C to 60 °C, from 55 °C to 60 °C,from 40 °C to 55 °C, from 45 °C to 55 °C, from 50 °C to 55 °C, from 40 °C to 50 °C, or from about 45 °C to 50 °C.

[0257] Additionally, target nucleic acid can optionally be amplified before binding to the guide nucleic acid (e.g., crRNA) of the programmable nuclease complex (e.g., CRISPR enzyme). This amplification can, for example, be PCR amplification or isothermal amplification. This nucleic acid amplification of the sample can improve at least one of sensitivity, specificity, or accuracy of the detection the target RNA. The reagents for nucleic acid amplification can comprise a recombinase, a oligonucleotide primer, a single-stranded DNA binding (SSB) protein, and a polymerase. The nucleic acid amplification can be transcription mediated amplification (TMA). Nucleic acid amplification can be helicase dependent amplification (HD A) or circular helicase dependent amplification (cHDA). In additional cases, nucleic acid amplification is strand displacement amplification (SDA). The nucleic acid amplification can be recombinase polymerase amplification (RPA). The nucleic acid amplification can be at least one of loop mediated amplification (LAMP) or the exponential amplification reaction (EXPAR). Nucleic acid amplification is, in some cases, by rolling circle amplification (RCA), ligase chain reaction (LCR), simple method amplifying RNA targets (SMART), single primer isothermal amplification (SPIA), multiple displacement amplification (MDA), nucleic acid sequence-based amplification (NASBA), hinge-initiated primer-dependent amplification of nucleic acids (HIP), nicking enzyme amplification reaction (NEAR), or improved multiple displacement amplification (IMDA). The nucleic acid amplification can be performed for no greater than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 40, 50, or 60 minutes. Sometimes, the nucleic acid amplification reaction is performed at a temperature of around 20- 45°C. Sometimes, the nucleic acid amplification reaction is performed at a temperature of around 45-65 °C. The nucleic acid amplification reaction can be performed at a temperature no greater than 20°C, 25°C, 30°C, 35°C, 37°C, 40°C, 45°C, 50°C, 55°C, 60°C, or 65°C. The nucleic acid amplification reaction can be performed at a temperature of at least 20°C, 25°C, 30°C, 35°C, 37°C, 40°C, 45°C, 50°C, 55°C, 60°C, or 65°C.

[0258] In some embodiments, a target nucleic acid within the sample can undergo reverse transcription before binding to a guide nucleic acid, for example a crRNA of a CRISPR enzyme. The target nucleic acid within a purified sample can be reverse transcribed. In some instances, reverse transcription can be accomplished using a reverse transcriptase. Reverse transcription can be combined with any of the amplification techniques described herein. In some cases, a reverse transcription step may be performed at a temperature of around 45°C to about 75°C. In some embodiments, the reverse transcription may be at a temperature of about 45°C, about 47°C,about 48°C, about 49°C, about 50°C, about 52°C, about 54°C, about 55°C, about 57°C, about 59°C, about 60°C, about 61°C, about 63°C, about 65°C, about 66°C, about 68°C, about 70°C, about 72°C, about 73°C, or about 75°C.III. INSTRUMENTC. System Integration and User Interface

[0259] Described herein are various systems and devices for performing one or more nucleic acid-based assays. In some embodiments, the nucleic acid-based assay may be a programmable nuclease-based assay. Systems may comprise any of the instruments and / or cartridges described herein. In some embodiments, the instrument and the cartridge may be configured to mate with one another to enable mechanical manipulation, activation, control, and / or communication between electronic circuits (e.g., in the cartridge and the instrument), thermal interfaces, ultrasonic interfaces, pneumatic interfaces, and / or optical interfaces. In some embodiments, the instrument may comprise a receptacle (e.g., an open slot or dock) configured (e.g., sized and shaped) to receive the cartridge. In some embodiments, the cartridge may be self-aligning with and / or locked within the instrument after insertion into its receptacle. In some embodiments, there are mechanical features provided within the instrument or on the cartridge to facilitate correct relative alignment of the instrument and cartridge. In some embodiments, the selfalignment process may optionally connect one or more pressure ports of the cartridge and / or instrument. Alternatively, or in combination, the self-alignment process may engage one or more heat sources (e.g., thermal cycling heaters) of the instrument onto the cartridge.

[0260] In some embodiments, the instrument comprises one or more actuators configured to interface with the cartridge. In some embodiments, the cartridge remains stationary within the instrument after insertion therein and one or more of the actuators can move in X, Y, and / or Z directions to interact with different elements of the cartridge as described herein, which may enable more than one element on the cartridge to be actuated by a single actuator. In some embodiments, both the cartridge and the actuators remain stationary in the XY plane and the number of actuators provided on the instrument corresponds to the number of elements to be actuated on the cartridge as described herein. In some embodiments, the instrument is configured to move the cartridge in X, Y, and / or Z therewithin, which may enable more than one element on the cartridge to be actuated by a single actuator. Actuators may include, but are not limited to: heaters / chillers, bi-directional liquid and / or gas pumps, fluid valves, optical sensing modules of camera / illumination / lenses, barcode scanners, rare earth magnets, etc., as described herein.

[0261] In some aspects, the present disclosure provides a system for detecting target nucleicacids, the system including an instrument configured to interface with a cartridge. In some embodiments, (a) the instrument comprises: (i) one or more pumps; (ii) at least one valve actuator; (iii) a light source configured to illuminate a detection region of the cartridge; and (iv) an optical sensor configured to detect one or more signals from the detection region; (b) the cartridge comprises: (i) a sample interface configured to receive a sample comprising one or more nucleic acids; (ii) one or more reagent capsules; (iii) a sample preparation region; (iv) a detection region; (iv) and a plurality of pump interfaces fluidically connected to the sample interface, the one or more reagent capsules, the sample preparation region, and / or the detection region via a plurality of valves; (c) the one or more pumps is configured to apply positive and / or negative pressure through the plurality of pump interfaces; (d) the at least one valve actuator is configured to actuate the plurality of valves; (e) one or more pumps and at least one valve actuator are operable to move fluid between the sample interface, the one or more reagent capsules, the sample preparation region, and the detection region; and (f) the detection region comprises a plurality of chambers that are fluidically connected to one another.

[0262] In some embodiments, the instrument is no larger than 6” by 5” by 3.75”, though dimensions can be outside this range as desired (see FIGS. 1A-1B for exemplary dimensions). To keep the instrument small, part of the cartridge may be partially disposed outside of the instrument during testing. If necessary, an external accessory may be used to delineate loading and unloading areas for the cartridge.

[0263] In some embodiments, the sample collection workflow is for the specimen to be collected with the patient and transported to an instrument within the facility but potentially in a separate room. Other collection workflows may include the instrument being co-located with a patient. In some embodiments, the cartridge may be loaded into the instrument before a specimen is collected allowing for reagent incubations to begin. In some embodiments, a workflow may preclude reagent incubation while the specimen is being collected from the patient. In some embodiments, specimen container labeling of the patient / specimen information for transfer into the patient record is performed via the instrument. Sample collection in the same location as the instrument could permit the patient / specimen information to be entered directly into the instrument and the specimen inserted into the cartridge already in the instrument, thereby reducing or eliminating the information transfer step. FIG. 42 depicts an exemplary sample collection workflow in which the sample is collected and provided to the cartridge prior to loading the cartridge into the instrument.

[0264] FIGS. 1A-1C shows an exemplary embodiment of an instrument along with twoexemplary cartridge designs that might be used with the instrument. All dimensions are in inches. The two-pump, 4.2-inch-long cartridge in FIG. 1A is capable of a reagent nucleic acid extraction with no washing steps. This extraction may be feasible for specimen matrixes such as from nasal swab collected specimens or vaginal swab collected specimens. For more complex sample matrixes, or for those matrixes that contain inhibiting substances that could interfere with polymerase reactions (e.g., saliva, urine, whole blood, plasma, serum, wound pus or stool), the 3- pump, 6-inch cartridge in FIG. IB may incorporate multiple reagents for washing the inhibitors from the extracted nucleic acids and eluting the nucleic acids in a liquid reagent for the molecular detection reaction. The instrument is designed to accept either cartridge, and other cartridges may be designed to fit the instrument which can carry out any variation of the methods described herein as desired, as will be understood by one of ordinary skill in the art.

[0265] In some embodiments, a cartridge (e.g., a two-pump, and / or 4.2-inch cartridge) is used for tests for up...

Claims

CLAIMS1. A system for detecting target nucleic acids, the system comprising an instrument configured to interface with a cartridge; wherein:(a) the instrument comprises: (i) one or more pumps; (ii) at least one valve actuator; (iii) a light source configured to illuminate a detection region of the cartridge; and (iv) an optical sensor configured to detect one or more signals from the detection region;(b) the cartridge comprises: (i) a sample interface configured to receive a sample comprising one or more nucleic acids; (ii) one or more reagent capsules; (iii) a sample preparation region; (iv) a detection region; (iv) and a plurality of pump interfaces fluidically connected to the sample interface, the one or more reagent capsules, the sample preparation region, and the detection region via a plurality of valves;(c) the one or more pumps is configured to apply positive and / or negative pressure through the plurality of pump interfaces;(d) the at least one valve actuator is configured to actuate the plurality of valves;(e) one or more pumps and at least one valve actuator are operable to move fluid between the sample interface, the one or more reagent capsules, the sample preparation region, and the detection region; and(f) the detection region comprises a plurality of chambers that are fluidically connected to one another.

2. The system of claim 1, wherein each chamber of the plurality of chambers further comprises detection reagents comprising a guide nucleic acid and a reporter, and further wherein:(a) each guide nucleic acid (i) comprises a targeting sequence that hybridizes with a target nucleic acid of a plurality of different target nucleic acids or an amplicon thereof, and (ii) is effective to form a complex with a programmable nuclease that is activated upon binding the corresponding target nucleic acid or amplicon thereof;(b) the guide nucleic acid of a first chamber in the plurality of chambers comprises a different targeting sequence from the guide nucleic acid of a second chamber in the plurality of chambers; and(c) each reporter (i) comprises a cleavable nucleic acid and a detection moiety, and (ii) is configured to be cleaved to form a detectable cleavage product in response to activation of the complex in the respective chamber.

3. The system of claim 1, wherein (a) the one or more reagent capsules comprises dried reagents; (b) the cartridge comprises one or more fluid reservoirs; and (c) a pump of the one or more pumps is configured to move fluid from the fluid reservoir to the one or more reagent capsules.

4. The system of claim 1, wherein (a) the instrument comprises one or more heaters; and (b) at least one of the one or more heaters is configured to interface with the detection region and heat contents thereof.

5. The system of claim 1, wherein (a) the sample preparation region comprises a lysis region for the lysis one or more components of the sample; and optionally (b) at least one of the one or more reagent capsules comprises lysis reagents.

6. The system of claim 4, wherein at least one of the one or more heaters, is configured to interface with the sample preparation region and heat the contents thereof.

7. The system of claim 3, wherein (a) the cartridge further comprises a nucleic acid capture region; (b) the one or more pumps comprises an actuator operable to move a sample preparation fluid through the nucleic acid capture region to capture the one or more nucleic acids; and (c) the one or more pumps comprises an actuator operable to move an elution fluid from one of the one or more fluid reservoirs through the nucleic acid capture region to release the captured nucleic acids.

8. The system of claim 1, wherein at least one of the one or more reagent capsules or the plurality of chambers comprises a programmable nuclease.

9. The system of claim 8, wherein (a) the programmable nuclease comprises a Cas protein; and optionally (b) the Cas protein comprises Casl2, Casl3, Casl4, CasPhi, a thermostable Cas, or any combination thereof.

10. The system of claim 2, wherein (a) the detection reagents further comprise amplification reagents; and optionally (b) the amplification reagents in each chamber of the plurality of chambers comprises one or more primers for amplifying the target nucleic acid bound by the respective targeting sequence.

11. The system of claim 2, wherein (a) the detection reagents are in a lyophilized form, and / or (b) the guide nucleic acid and / or the reporter in each chamber are immobilized to a surface of the respective chamber.

12. The system of claim 1, further comprising a gear that translates the cartridge between two or more positions in the instrument.

13. The system of claim 12, wherein the two or more positions comprise positions in which(a) one of the one or more pumps aligns with one or more of the plurality of pump interfaces; (b) one of the at least one valve actuator aligns with one or more of the plurality of valves; (c) the optical sensor aligns with the detection region; or (d) any combination thereof.

14. The system of claim 4, wherein the two or more positions comprise a position in which at least one of the one or more heaters aligns with the sample preparation region or the detection region.

15. The system of claim 1, further comprising a user interface for receiving instructions from a user.

16. The system of claim 1, further comprising a non-transitory computer-readable medium with instructions stored thereon, that when executed by one or more processors, (a) activates the one or more pumps and the at least one valve actuator to move fluid between the sample interface, the one or more reagent capsules, the sample preparation region, and the detection region; (b) activates the light source; (c) stores detection results from the optical sensor; and (d) reports results to a user.

17. A method for detecting one or more of a plurality of different target nucleic acids in a system of any one of claims 1-16, the method comprising:(a) flowing a liquid comprising one or more of the different target nucleic acids or amplicons thereof into the plurality of chambers;(b) in one or more of the plurality of chambers, forming the activated complex and cleaving the reporters; and(c) detecting the detectable cleavage products in one or more of the plurality of chambers, wherein the location of a chamber comprising a detectable cleavage product identifies the target nucleic acid or amplicon thereof present in the chamber.

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