Magnetic Gradient Concentrators / Magneto-Resistance Detectors for Molecular Detection

Abstract

Disclosed herein are devices for molecular detection and methods of using detection devices for molecular detection such as nucleic acid sequencing. In some embodiments, the detection device includes: one or more pole shoes; one or more sensors, each of the one or more sensors coupled to at least one of the one or more pole shoes; and a detection circuit coupled to the one or more sensors. The detection circuit is configured to detect a characteristic of each of the one or more sensors, the characteristic indicating the presence or absence of one or more magnetic nanoparticles (MNPs) coupled to at least one of the multiple molecules to be detected, and at least one of the one or more pole shoes is operable to attract the one or more MNPs to at least one of the one or more sensors.

Description

[0001] CROSS-REFERENCE TO RELATED APPLICATIONS

[0002] This application claims U.S. Provisional Application No. 62 / 938,984, filed on November 22, 2019, entitled “Magnetic Gradient Concentrator / Reluctance Detector for Molecule Detection” (Agent Docket No. WDA-4627P-US) and U.S. Non-Provisional Application No. 16 / 823,592, filed on March 19, 2020, entitled “MAGNETIC GRADIENT CONCENTRATOR / RELUCTANCE DETECTOR FOR MOLECULE DETECTION” (Agent Docket No. WDA-4627-US). Background Art

[0003] Sequencing by synthesis (SBS) is a nucleic acid sequencing for example for DNA sequencing. SBS involves the combination of primer hybridization template DNA, the incorporation of deoxynucleoside triphosphates (dNTPs) and the detection of the incorporated dNTPs. Conventional SBS for DNA sequencing relies on the detection of fluorescence. Specifically, the fluorescence-based techniques (e.g., in fluorescence-based nucleic acid sequencing techniques) for distinguishing different bases in a sample rely on, for example, the quality of the signal generated by the detection portion associated with a particular type of nucleotide. For example, conventional fluorescence sequencing techniques utilize identifiable different fluorescent moieties, each of which is attached to one of the four nucleotides A, T, C and G utilized in the sequencing reaction.

[0004] A conventional DNA sequencing method involves adapting single-stranded DNA (ssDNA) to a solid support attached to a sequencing device, and using a technique such as polymerase chain reaction (PCR) to amplify the amount of ssDNA to produce many DNA molecules with short leader sequences. PCR is a process in which a single DNA molecule can be amplified (copied) into thousands or even millions of copies of a molecule by order of magnitude. The process relies on circulating a PCR mixture containing a polymerase, dNTPs, a sample DNA template, and primers at different temperatures. In the first high temperature range, when the paired strands of the double-stranded sample DNA template are separated into two separate strands, denaturation occurs. In the second low temperature range, annealing of primers complementary to the sample DNA template region targeted for amplification occurs. In the third medium temperature range, extension of the primer complementary sequence occurs, during which the polymerase adheres to the primer and uses nucleotides to replicate each separated sample DNA template strand. The cycle is typically repeated several times (usually many times) to increase the amount of replicated DNA exponentially until there is the amount required for a specific experiment.

[0005] After amplification, an oligonucleotide complementary to the short leader sequence can be added so that a short stretch of double-stranded DNA (dsDNA) is present at the leader sequence. The double-stranded portion of the binding molecule is a primer for a suitable DNA polymerase (e.g., Taq polymerase), which can operate at high temperatures.

[0006] The sequencing process can then use one of several methods. For example, sequencing can use a mixture of four fluorescently labeled 3'-blocked NTPs (fluorescently labeled dideoxynucleotide terminators), where the fluorescent label is part of the 3'-blocking group. The fluorescent marker is used as a "reversible terminator" for the polymerization reaction. Each NTP in the NTP is labeled with a different marker (i.e., each of the A, G, C, and T nucleotides has a different marker), and the different markers can be distinguished by fluorescence spectroscopy or by other optical means.

[0007] In conventional sequencing methods, four kinds of fluorescently labeled nucleotide precursors are used for sequencing millions of DNA chain clusters in parallel. DNA polymerase catalyzes the incorporation of fluorescently labeled dNTPs into the DNA template strand during the continuous cycle of DNA synthesis. In each sequencing cycle, the bound double-stranded DNA molecule is exposed to a mixture of DNA polymerase and four kinds of fluorescently labeled 3'-blocking NTPs. Polymerase adds one of the four kinds of dNTPs to the growing oligonucleotide chain (no matter which dNTP is complementary to the next unpaired base in ssDNA). Then the unincorporated dNTPs and other impurities that remain unreacted or generated during the reaction are washed at a temperature that prevents free dNTPs from binding to ssDNA but not high enough to dehybridize dsDNA, and are separated near the DNA bound by the support.

[0008] Because only one of the four types of dNTPs will be added to the oligonucleotide, and the four fluorescent markers are distinguishable, the type of dNTP incorporated can be identified by laser excitation and imaging. Specifically, each of the four filters is used to determine whether to emit light of a specific wavelength (e.g., color). The fluorescent marker can then be cleaved to allow the next round of incorporation. Because each base type can be paired with one and only one other base type, the type of the just-paired base in the unknown sequence of ssDNA can be known based on the type of dNTP incorporated (which is known based on the wavelength of the emitted light). Therefore, the base is identified directly based on the fluorescence measurement results during each cycle.

[0009] One drawback of the above methods is that complex optical systems are required to filter out different wavelengths of light to detect the fluorescent labels of the incorporated dNTPs and distinguish between the different emission colors. Other methods have been developed to simplify the optical systems, but they are slower and require intermediate chemical steps within each sequencing cycle. As a result, these methods have been introduced into smaller, cheaper entry-level sequencing systems, but not into more advanced systems that require fast throughput.

[0010] Therefore, there is a need for improvements in DNA sequencing and, in general, in molecular detection. Summary of the invention

[0011] This Summary represents non-limiting embodiments of the present disclosure.

[0012] In some embodiments, the detection device includes: one or more pole shoes; one or more sensors, each of the one or more sensors is coupled to at least one pole shoe of the one or more pole shoes; and a detection circuit coupled to the one or more sensors. In some embodiments, the detection circuit is configured to detect a characteristic of each of the one or more sensors, wherein the characteristic indicates the presence or absence of one or more magnetic nanoparticles (MNPs) coupled to at least one molecule of the plurality of molecules to be detected. The characteristic detected by the detection circuit may include voltage, current, resistance, frequency, phase, noise, or temperature; a change in voltage, current, resistance, frequency, phase, noise, or temperature; or a change in a statistical property (e.g., mean, variance, standard deviation, etc.) of voltage, current, resistance, frequency, phase, noise, or temperature. In some embodiments, at least one pole shoe of the one or more pole shoes is operable to attract the one or more MNPs to at least one sensor of the one or more sensors. The one or more sensors may include one or more of a temperature sensor, a magnetoresistive (MR) sensor, a magnetic tunnel junction (MTJ), a spin torque oscillator (STO), or a spin valve.

[0013] In some embodiments, the detection device also has at least one reagent area, and the at least one reagent area is configured to accommodate a fluid containing multiple molecules to be detected. The at least one reagent area may include a fluid channel. In some embodiments with at least one reagent area, one or more surfaces in the reagent area provide one or more sites for combining multiple molecules to be detected, and the one or more sites are located between the one or more sensors. At least one magnetic shield may be arranged between at least two sites in the one or more sites.

[0014] In some embodiments, the detection device further comprises a barrier material (eg, an insulator or a metal) encapsulating the one or more sensors and used to provide a barrier between the one or more sensors and at least one molecule of the plurality of molecules to be detected.

[0015] In some embodiments, the one or more pole shoes include at least one line coupling at least one of the one or more sensors to a detection circuit. In some embodiments, at least one of the one or more pole shoes has a conical, triangular, or pyramidal shape. In some embodiments, at least one of the one or more pole shoes is configured to assist in generating a magnetic field gradient for attracting at least a portion of the one or more MNPs toward one or more of the one or more sensors.

[0016] The detection device may further include one or more solenoids or ferromagnetic components. In some such embodiments, at least one of the one or more sensors is disposed between its corresponding pole shoe in the one or more pole shoes and a corresponding solenoid or ferromagnetic component in the one or more solenoids or ferromagnetic components.

[0017] In some embodiments including one or more solenoids or ferromagnetic components, the detection device further includes one or more magnetic yokes, wherein at least one of the one or more solenoids or ferromagnetic components is disposed between its corresponding sensor and a corresponding magnetic yoke of the one or more magnetic yokes, thereby forming one or more magnetic circuits. In some such embodiments, at least one ferromagnetic component has a coercive force such that the ferromagnetic component can be selectively magnetized or selectively demagnetized by an external magnetic field. The remanence of each ferromagnetic component can be selected so that the ferromagnetic component can detect one or more MNPs.

[0018] In some embodiments, the detection device further comprises at least one magnetic component configured to generate a magnetic field through the one or more pole pieces.

[0019] In some embodiments, the one or more sensors include a plurality of sensors arranged in a cross-point array, the cross-point array including a first top line, a second top line, a first bottom line, and a second bottom line, and the first top line is coupled to the first bottom line at a first position, the first top line is coupled to the second bottom line at a second position, the second top line is coupled to the first bottom line at a third position, and the second top line is coupled to the second bottom line at a fourth position. In some such embodiments, the first top line and the second top line are substantially parallel to each other, the first bottom line and the second bottom line are substantially parallel to each other, and the first top line and the second top line are substantially perpendicular to the first bottom line and the second bottom line.

[0020] In some embodiments, the detection device is a sequencing device and the plurality of molecules to be detected include biomolecules (eg, nucleic acids).

[0021] In some embodiments, the detection circuit includes one or more selector devices, and at least one of the one or more selector devices is coupled to a corresponding sensor of the one or more sensors. In some embodiments where the detection circuit includes one or more selector devices, at least one of the one or more selector devices includes a transistor. In some embodiments where the detection circuit includes one or more selector devices, at least one of the one or more selector devices includes an in-stack selector.

[0022] In some embodiments, the one or more sensors include a plurality of sensors, wherein a first subset of the plurality of sensors is arranged in a first row, a second subset of the plurality of sensors is arranged in a second row substantially parallel to the first row, and at least one reagent area is disposed between the first row and the second row.

[0023] In some embodiments, the method of using a detection device including one or more pole shoes, one or more sensors, a reagent area, and a detection circuit includes labeling a nucleotide precursor with one or more MNPs, adding the labeled nucleotide precursor to the reagent area, detecting the characteristics of at least one of the one or more sensors, and for the sensor, determining whether the labeled nucleotide precursor has been detected based at least in part on the detected characteristics. In some embodiments, the method also includes binding the nucleic acid chain to be sequenced to the reagent area of ​​the detection device before adding the labeled nucleotide precursor to the reagent area. In some embodiments, the method also includes applying a magnetic field to the detection device, and using the detection circuit to detect the characteristics of at least one of the one or more sensors while applying the magnetic field. In some embodiments, after detecting the characteristics of at least one of the one or more sensors, disconnect the magnetic field, and while disconnecting the magnetic field, remove (e.g., cut) the MNP and wash the reagent area. BRIEF DESCRIPTION OF THE DRAWINGS

[0024] The objects, features and advantages of the present disclosure will become apparent from the following description of certain embodiments in conjunction with the accompanying drawings, in which:

[0025] Figure 1A , Figure 1B and Figure 1C An exemplary detection device according to some embodiments is shown.

[0026] Figure 1D is a block diagram illustrating an exemplary detection system for molecular detection according to some embodiments.

[0027] Figure 1E , Figure 1F , Figure 1G and Figure 1H Portions of an exemplary detection device are shown according to some embodiments.

[0028] Fig. 1I and Figure 1J An exemplary sensor selection method according to some embodiments is shown.

[0029] Figure 2A Shown are DNA template strands distributed over a two-dimensional area on or around an exemplary support structure after an amplification process, according to some embodiments.

[0030] Figure 2B An exemplary sensor with DNA strands, each with an MNP label attached to the last dNTP incorporated into the target DNA strand, is shown according to some embodiments.

[0031] Figure 3 An exemplary pole shoe for generating a magnetic field is shown in accordance with some embodiments.

[0032] Figure 4A A sensor coupled to and disposed between a solenoid and a conical pole piece is shown according to some embodiments.

[0033] Figure 4B A sensor coupled to and disposed between a solenoid and a rectangular pole piece is shown according to some embodiments.

[0034] Figure 4C A sensor coupled to and disposed between a solenoid and a pole piece is shown according to some embodiments.

[0035] Figure 4D An exemplary configuration is shown in accordance with some embodiments, where a sensor is assisted by multiple pole pieces, and where certain pole pieces assist multiple sensors.

[0036] Figure 5 An exemplary embodiment is shown in which an external magnetic component is used to generate a magnetic field according to some embodiments.

[0037] Figure 6 is a conceptual diagram of an exemplary embodiment of a detection device including a magnetic shield according to some embodiments.

[0038] Figure 7 An exemplary method of performing nucleic acid sequencing using a detection device according to some embodiments is shown. DETAILED DESCRIPTION

[0039] To simplify the description, the following disclosure will be illustrated and discussed using DNA, although the various embodiments are generally applicable to molecular detection.

[0040] Magnetic nanoparticles (MNPs) have been proposed for use in molecular detection such as for nucleic acid sequencing (eg, DNA sequencing) as an alternative to the use of fluorescent labels. See, for example, U.S. application Ser. No. 16 / 791,599, filed on February 14, 2020, entitled “SPINTORQUE OSCILLATOR (STO) SENSORS USED IN NUCLEIC ACID SEQUENCING ARRAYS AND DETECTION SCHEMES FOR NUCLEIC ACID SEQUENCING” (Attorney Docket No. WDA-4277-US), U.S. application Ser. No. 16 / 819,636, filed on March 16, 2020, entitled “DEVICES AND METHODS FOR FREQUENCY-AND PHASE-BASED DETECTION OF MAGNETICALLY-LABELED MOLECULES USING SPIN TORQUE OSCILLATOR (STO) SENSORS” (Attorney Docket No. WDA-4278-US), U.S. application Ser. No. 16 / 819,636, filed on March 16, 2020, entitled “DEVICES AND METHODS FOR FREQUENCY-AND PHASE-BASED DETECTION OF MAGNETICALLY-LABELED MOLECULES USING SPIN TORQUE OSCILLATOR (STO) SENSORS” (Attorney Docket No. WDA-4279-US), and U.S. application Ser. No. 16 / 727,064, filed on Nov. 26, 2019, entitled “THERMAL SENSOR ARRAY FOR MOLECULEDETECTION AND RELATED DETECTION SCHEMES” (Attorney Docket No. WDA-4279-US), Ser. No. 16 / 697,013, filed on Nov. 26, 2019, entitled “THERMAL SENSOR ARRAY FOR MOLECULEDETECTION AND RELATED DETECTION SCHEMES” (Attorney Docket No. WDA-4280-US), and Ser. No. 16 / 659,383, filed on Oct. 21, 2019, entitled “MAGNETORESISTIVE SENSOR ARRAY FOR MOLECULE DETECTION AND RELATED DETECTION SCHEMES” (Attorney Docket No. WDA-4281-US), all of which are hereby incorporated by reference in their entirety for all purposes.

[0041] In a method for DNA sequencing application using magnetic nanoparticles as markers, four nucleotide precursors (each with different MNP type labels) can be used for many (e.g., millions) DNA chain clusters in parallel sequencing. As with conventional methods, DNA polymerase catalyzes the incorporation of dNTPs into the DNA template strand during the continuous cycle of DNA synthesis. However, compared with conventional methods, dNTPs are magnetically labeled. In each sequencing cycle, the combined double-stranded DNA molecules are exposed to a mixture of 3'-blocking NTPs of DNA polymerase and four magnetically labeled. One of the four dNTPs is added to the growing oligonucleotide chain (no matter which dNTP is complementary to the next unpaired base in ssDNA) by polymerase. Then unincorporated dNTPs and other impurities that remain unreacted or generated during the reaction are separated near the DNA bound by the support by washing at a temperature that prevents free dNTPs from being combined with ssDNA but not high enough to dehybridize dsDNA. Because only one of the four types of dNTPs will be added to each oligonucleotide and the four magnetic labels are distinguishable, the type of dNTP incorporated can be identified using various types of sensors and detection circuits disclosed, for example, in U.S. Applications 16 / 791,759, 16 / 819,636, 16 / 727,064, 16 / 697,013, and 16 / 659,383.

[0042] In another method, all nucleotide precursors are labeled by the same type of MNPs, and only one of the four magnetically labeled nucleotide precursors is tested at a time. After adding each nucleotide precursor, the polymerase adds a dNTP to the oligonucleotide chain, where the next unpaired base is a base complementary to the added magnetically labeled dNTP. Because the type of nucleotide precursor added is known, the last completed base of each ssDNA chain incorporating the magnetically labeled dNTP can be determined based on the signal sensed by the sensor.

[0043] A number of sensor embodiments have been disclosed (see, e.g., U.S. Application Nos. 16 / 791,759, 16 / 819,636, 16 / 727,064, 16 / 697,013, and 16 / 659,383). These sensors can be, for example, sensors that sense the heat generated by the MNPs when exposed to an alternating magnetic field (e.g., disclosed in U.S. Application Nos. 16 / 697,013 (Attorney Docket No. WDA-4280-US) and 16 / 727,064 (Attorney Docket No. WDA-4279-US)). As another example, each sensor can be a magnetoresistive (MR) sensor (e.g., a magnetic tunnel junction (MTJ)) whose resistance changes depending on whether the MNPs are in its vicinity (e.g., disclosed in U.S. Application No. 16 / 659,383 (Attorney Docket No. WDA-4281-US)). As another example, the sensor may use a spin torque oscillator (STO), a spin valve, or a similar structure that generates a radio frequency (RF) signal in response to the presence of MNPs nearby (e.g., as disclosed in U.S. Application Nos. 16 / 791,759 (Agent Docket No. WDA-4277-US) and 16 / 819,636 (Agent Docket No. WDA-4278-US)). In such embodiments, the presence or absence of MNPs near the sensor may be determined by sensing, for example, the presence or absence of an RF signal generated by the STO, or the frequency (or frequency change), phase (or phase change), or noise of an RF signal generated by the STO. Other types of sensors (e.g., optical sensors) are possible and contemplated. The examples provided herein are not intended to be limiting.

[0044] Devices for MNP-based molecular detection have been disclosed in the patent applications cited above. Figure 1A , Figure 1B and Figure 1C An exemplary detection device 100 according to some embodiments is shown. The exemplary detection device 100 includes a plurality of sensors 105 arranged in an array 110, the array being disposed adjacent to a reagent area 115, the reagent area being disposed at Figures 1A to 1C The fluid channel is shown in FIG. Figure 1A This is a top view of the device. Figure 1B Is Figure 1A A cross-sectional view at a position indicated by a dotted line labeled “1B”, and Figure 1C Is Figure 1A Another cross-sectional view at the location indicated by the dashed line labeled "1C" in FIG. Sensor 105 can be any sensor capable of detecting the presence or absence of MNPs in reagent region 115, some examples of which are described above. It should be understood that although Figure 1A , Figure 1B and Figure 1C An exemplary device including a plurality of sensors 105 is shown, but an embodiment may have as few as one sensor 105 .

[0045] like Figure 1A As shown, the exemplary detection device 100 includes a sensor array 110, which includes a plurality of sensors 105, of which four sensors 105A, 105B, 105C, and 105D are shown. (For simplicity, this document refers to the sensor by the reference numeral 105. Individual sensors are represented by the reference numeral 105 followed by a letter.) It should be understood that the detection device 100 may include more or less than four sensors 105. Figure 1A The sensor array 110 shown in the exemplary embodiment is a linear array.

[0046] In some embodiments, each sensor in the plurality of sensors 105 is coupled to at least one wire 120 for reading a characteristic of one or more of the sensors 105. (For simplicity, this document refers to a wire by reference numeral 120. Individual wires are represented by reference numeral 120 followed by a letter.) The characteristic provides an indication of whether one or more MNPs are in the vicinity of the sensor 105. For example, as described above and in the applications incorporated by reference, the characteristic may be temperature or temperature changes, resistance or resistance changes, voltage or voltage changes, current or current changes, the presence or absence of an RF signal, a characteristic of an RF signal (e.g., phase, noise, frequency), a change in an aspect of an RF signal (e.g., its phase, noise, frequency), or any other characteristic that indicates whether one or more MNPs are in the vicinity of the sensor 105.

[0047] exist Figure 1A In the exemplary embodiment shown, each sensor 105 of the sensor array 110 is coupled to two wires 120. Specifically, sensor 105A is coupled to wires 120A and 120E, sensor 105B is coupled to wires 120B and 120E, sensor 105C is coupled to wires 120C and 120E, and sensor 105D is coupled to wires 120D and 120E. In the exemplary embodiment, wires 120A, 120B, 120C, and 120D are located below sensors 105A, 105B, 105C, and 105D, respectively, and wire 120E is located above sensor 105. Figure 1B Sensor 105D is shown in relation to lines 120D and 120E.

[0048] The detection device 100 also includes a reagent area 115 adjacent to the sensor array 110. As the name implies, the reagent area 115 is configured to contain a reagent (e.g., a fluid such as a liquid, a gas, a plasma) when the detection device 100 is in use. The reagent area 115 can have any suitable shape (regular or irregular) to contain a fluid, and it can include at least one movable member (e.g., a stopper, a baffle, etc.) to allow the reagent to enter and / or leave the reagent area 115. Figures 1A to 1C In the exemplary embodiment shown, the reagent area 115 is a fluid channel. The reagent area 115 may include or may be coupled to a pump or similar device that forces the fluid into and / or out of the reagent area 115 (e.g., through a membrane, an opening, etc.). It should be understood that although Figures 1A to 1C The detection device 100 including the reagent area 115 is shown, but the detection device 100 need not include the reagent area 115. For example, in some embodiments, the detection device 100 can be mounted on a needle and inserted into a subject (e.g., a human, an animal, etc.) to test the subject's in vivo blood. In such embodiments, the subject's blood vessel will be used as the reagent area 115.

[0049] like Figure 1B As shown, the reagent region 115 has a wall 117 adjacent to the sensor array 110. The wall 117 has properties and characteristics that protect the sensor 105 from any fluid in the reagent region 115, while still allowing the sensor 105 to detect MNPs near the sensor 105 within the reagent region 115. For example, the material of the wall 117 (and the material of the remaining portion of the possible reagent region 115) may be or may include an insulator or a metal (e.g., polypropylene, gold, glass, silicon, etc.). The thickness of the wall 117 may be selected so that the sensor 105 can detect the MNPs within the reagent region 115. The thickness of the wall 117 may be, for example, between about 2 nm and about 20 nm. In general, the reagent region 115 and the wall 117 may have any shape that allows the sensor 105 to detect the presence of MNPs near or attached to the wall 117 within the reagent region 115.

[0050] Figure 1C is along Figure 1A 1C. Because the cross section is taken at a point within the reagent region 115, the sensor 105 and line 120 will not be visible and are therefore shown using dashed lines to illustrate their locations within the detection device 100. Figure 1CAs shown, in some embodiments, the wall 117 has a support structure 114 (or multiple support structures 114) that is configured to anchor molecules to be sensed (e.g., molecules of nucleic acids or nucleic acid polymerases) to the wall 117 near the sensor 105. (For simplicity, this document refers to the support structure by the reference numeral 114. Individual support structures are represented by the reference numeral 114 followed by a letter.) Figure 1C Four separate support structures 114A, 114B, 114C, and 114D are shown, each corresponding to a respective sensor 105 (e.g., support structure 114A corresponds to sensor 105A, support structure 114B corresponds to sensor 105B, etc.). One support structure 114 (or multiple support structures 114) of wall 117 may include cavities or ridges to which molecules (e.g., nucleic acids, polymerases, etc.) may be attached or anchored. Although Figure 1C A separate support structure 114 is shown corresponding to each sensor 105, but the detection device 100 may have fewer or more support structures 114 than shown. For example, there may be more support structures 114 than sensors 105, such that each sensor 105 is proximate to multiple support structures 114. As another example, multiple sensors 105 may share a single support structure 114. As another example, multiple sensors 105 may share multiple support structures 114. In embodiments where the detection device 100 includes multiple support structures 114, those support structures 114 may be the same or similar to each other, or some or all of them may be different from each other.

[0051] In some embodiments, it may be desirable to detect MNPs coupled to a single corresponding support structure 114 for each sensor 105. For example, in some types of SBS, a long chain of DNA (or multiple long chains of DNA from a single donor organism) is cut into smaller random length fragments before sequencing. All of these smaller chains from the same donor are randomized subchains of the complete chain to be sequenced. For example, if the complete chain includes the sequence ATGGCTTAG, the smaller chain may include, for example, different subchains (e.g., ATGG and CTTAG), and if multiple longer chains are cut into subchains, the smaller chain may include subchains (e.g., TGGC and GCTTA) that partially or completely overlap with other subchains. All smaller randomized subchains can be sequenced simultaneously, possibly after amplification. In such applications, it should be understood that because the subchains do not represent the same subsequence, it may be desirable to detect the characteristics (or changes in characteristics) caused by the MNP near the sensor 105 independently and for each sensor 105, because the sequencing of the subchains will not be coordinated (or synchronized) between the subchains. For example, during a single sequencing cycle, the first daughter strand may incorporate cytosine, the second daughter strand may incorporate thymine, and the third daughter strand may incorporate adenine. In order to sequence multiple random fragments of a larger nucleic acid chain, it is desirable to determine in each sequencing cycle whether each dNTP type is incorporated and at which physical position each dNTP type is incorporated.

[0052] To simplify the explanation, Figure 1A , Figure 1B and Figure 1C An exemplary detection device 100 is shown with a single reagent area 115 and only four sensors 105A, 105B, 105C, 105D in the sensor array 110. It should be understood that the detection device 100 may have more sensors 105 in the sensor array 110, and it may have additional reagent areas 115 or a more complex single reagent area 115 (e.g., with different shapes or with interconnected channels). In general, any configuration of sensors 105 and reagent areas 115 that allows for detection of a property (or change in a property) caused by MNPs in the vicinity of that sensor 105 in the reagent area 115 for each sensor 105.

[0053] Furthermore, it should be understood that although Figures 1A to 1C A detection device 100 is shown having a sensor 105 arranged to detect molecules coupled to a wall 117 of a reagent region 115, but other configurations are possible. For example, in DNA sequencing applications, a sensor 105 may be provided at or near the center of, for example, a DNA strand cluster or ring.

[0054] Figure 1Dis a block diagram illustrating an exemplary detection system 300 for molecular detection according to some embodiments. Figure 1D As shown, system 300 includes detection device 100 (as shown, including detection circuit 130 coupled to sensor array 110 via line 120). Figure 1D As shown, the detection system 300 may also include one or more magnetic components 150 and / or a current driver 160 coupled to the magnetic component 150. The magnetic component 150 may include, for example, an electromagnet, a distributed coil, a solenoid, a permanent magnet, or a superconducting magnet, which can be used to generate a magnetic field, as described in further detail below. In some embodiments, the magnetic component 150 includes an electromagnet, which may be advantageous because the magnetic field can be disconnected. In other embodiments, the magnetic component 150 includes a permanent magnet.

[0055] As an example of a detection device 100 having a larger number of sensors 105 in the sensor array 110, Figure 1E , Figure 1F , Figure 1G and Figure 1H Several reagent areas 115 are shown, and according to some embodiments, one or more of these reagent areas may be separate reagent areas 115, or a collection of these reagent areas may be considered a single reagent area 115. Figure 1E , Figure 1F , Figure 1G and Figure 1H In the illustrated embodiment of the detection device 100, the plurality of sensors 105 of the sensor array 110 are arranged in a rectangular grid pattern forming an array of intersections. Each of the lines 120 identifies a row or column of the sensor array 110. It should be understood that the terms "row" and "column" generally refer to two dimensions of the rectangular grid of sensors 105, but the designation of which dimension constitutes a row and which constitutes a column is arbitrary. It should also be understood that Figure 1E , Figure 1F , Figure 1G and Figure 1H Only a portion of the detection device 100 is shown to avoid obscuring the components of the detection device 100 being discussed. It should be understood that various illustrated components (e.g., wire 120, sensor 105, reagent area 115, etc.) may not be visible in a physical instantiation of the detection device 100 (e.g., some or all may be covered by a protective material such as an insulator material).

[0056] Figure 1E1 is a perspective view of an exemplary detection device 100 according to some embodiments. Detection device 100 includes nine lines 120, labeled 120A, 120B, 120C, 120D, 120E, 120F, 120G, 120H and 120I. It also includes five reagent areas, labeled 115A, 115B, 115C, 115D and 115E. As described above, reagent areas 115A, 115B, 115C, 115D and 115E can be regarded as separate reagent areas 115 or single reagent areas 115. Detection device 100 also has a bottom surface 119.

[0057] Figure 1F Is from Figure 1E 1. A top view of an exemplary detection device 100 of FIG. 1. Lines 120G, 120H, and 120I that are not visible from the top view are shown using dashed lines to indicate their locations. Lines 120A-120F are shown in solid lines, but as described above, lines 120A-120F may also not be visible in the top view (e.g., they may be covered by a protective material such as an insulator material).

[0058] Figure 1G is along Figure 1E 1G. As shown, each of the lines 120A, 120B, 120C, 120D, 120E, and 120F contacts the top of one of the sensors 105 along the cross section (i.e., line 120A contacts sensor 105A, line 120B contacts sensor 105B, line 120C contacts sensor 105C, line 120D contacts sensor 105D, line 120E contacts sensor 105E, and line 120F contacts sensor 105F). Line 120H contacts the bottom of each of the sensors 105A, 105B, 105C, 105D, 105E, and 105F. It should be understood that although Figure 1E to Figure 1H Wire 120 is shown in contact with sensor 105, and wire 120 may generally be coupled to sensor 105 (ie, they may be directly connected, or there may be intervening components disposed between wire 120 and sensor 105).

[0059] like Figure 1E to Figure 1H As shown, each line 120 above the top of the sensor 105 (top line 120) is coupled to multiple lines 120 below the sensor 105 (bottom line 120). Figure 1G As shown, line 120E located above sensor 105E is coupled to line 120H located below sensor 105E. Line 120H is also located below sensors 105A, 105B, 105C, 105D, and 105F. Figure 1HAs shown, line 120E is also located above sensors 105G and 105H. Sensor 105G is also coupled to line 120G located below sensor 105G, and sensor 105H is also coupled to line 120I located below sensor 105I. Each of the sensors 105 can be selected by a unique pair of lines 120, one line being the top line 120 and the other line being the bottom line 120. Thus, when the sensors 105 are arranged in a cross-point configuration, such as Figure 1E to Figure 1H In the exemplary configuration shown, a first top line 120 (a line 120 located above the sensor array 110) is coupled to a first bottom line 120 (a line 120 located below the sensor array 110) at a first position (corresponding to a sensor 105), and the first top line 120 is coupled to a second bottom line 120 at a second position (corresponding to a different sensor 105). Similarly, the second top line 120 is coupled to the first bottom line 120 at a third position (corresponding to yet another sensor 105), and the second top line 120 is coupled to the second bottom line at a fourth position (corresponding to yet another sensor 105). The first top line and the second top line 120 (which may select a column or row of the sensor array 110) are substantially parallel to each other and substantially perpendicular to the first and second bottom lines 120. Similarly, the first and second bottom lines 120 are substantially parallel to each other and substantially perpendicular to the first and second top lines 120.

[0060] See also Figure 1G , sensors 105A and 105B are formed by reagent area 115A (at Figure 1G Not marked in Figure 1E 115B). Similarly, sensors 105B and 105C are separated by reagent area 115B, sensors 105C and 105D are separated by reagent area 115C, sensors 105D and 105E are separated by reagent area 115D, and sensors 105E and 105F are separated by reagent area 115E. As discussed further below, any one or both of the vertical walls of each reagent area 115 may be wall 117.

[0061] In some embodiments, each sensor 105 is assigned to a single reagent zone 115. For example, Figure 1E to Figure 1HIn the exemplary device shown, the sensor 105 coupled to line 120A may be configured to sense MNPs in reagent area 115A, the sensor 105 coupled to line 120B may be configured to sense MNPs in reagent area 115B, the sensor 105 coupled to line 120C may be configured to sense MNPs in reagent area 115C, the sensor 105 coupled to line 120D may be configured to sense MNPs in reagent area 115D, and the sensor 105 coupled to line 120E may be configured to sense MNPs in reagent area 115E.

[0062] exist Figure 1E to Figure 1H In the exemplary embodiment shown, there are more columns of sensors 105 than reagent areas 115 (i.e., in the exemplary embodiment shown, there are six columns corresponding to lines 120A-120F and only five reagent areas 115A-115E). In such an embodiment, each vertical wall of one reagent area 115 may be a wall 117. In other words, a single reagent area 115 may be sensed by twice as many sensors 105 as each of the other reagent areas 115. For example, in Figure 1E to Figure 1H In an exemplary embodiment of the present invention, any one of the reagent areas 115 may be sensed by two columns of sensors 105. For example, reagent area 115B may be sensed by sensors 105 coupled to both lines 120B and 120C. In this example, the sensor 105 coupled to line 120A would be assigned to sense the contents of reagent area 120A, the sensor 105 coupled to line 120D would be assigned to sense the contents of reagent area 120C, the sensor 105 coupled to line 120E would be assigned to sense the contents of reagent area 120D, and the sensor 105 coupled to line 120F would be assigned to sense the contents of reagent area 120E.

[0063] Figure 1H is along Figure 1E 1 is a cross-sectional view of the detection device 100 marked as "1H" in FIG. As shown, the line 120E contacts the top of each of the sensors 105G, 105E and 105H along the cross section. Each of the lines 120G, 120H and 120I contacts the bottom of one of the sensors 105 along the cross section (i.e., the line 120G contacts the sensor 105G, the line 120H contacts the sensor 105E, and the line 120I contacts the sensor 105H). As described above, Figure 1H The wires 120 shown need not be in direct contact with the sensor 105; instead, they may be connected through intervening components.

[0064] In some embodiments (see, e.g., Fig. 1I , Figure 1J), the detection device 100 includes one or more selector elements 111, each of which is coupled to a corresponding sensor in the one or more sensors 105, wherein each of the selector elements 111 exhibits a threshold behavior such that for a signal above a given value (i.e., V th ), the selector element 111 has a high conductivity, and below this voltage, the conductivity of the selector element 111 is substantially zero. The selector element 111 may include, for example, a transistor, a diode, etc. One of ordinary skill in the art will appreciate that different schemes for addressing (selecting) the sensors 105 (individually or in groups) may be used to ensure that only the voltage drop across the intended sensors 105 is above V th Thus, the selector element 111 may be used to reduce the likelihood of “sneak” currents that may propagate through adjacent elements and degrade the performance of the detection device 100 .

[0065] Fig. 1I An exemplary sensor 105 selection method according to some embodiments is shown. Fig. 1I In the exemplary embodiment shown, a corresponding selector element 111 (e.g., shown as a CMOS transistor) is coupled in series with the sensor 105. In this exemplary embodiment, three lines 120A, 120B, and 120C allow for sensing of characteristics of the sensor 105. Conceptually, line 120A may be considered a readout line, line 120C may be considered a control line, and line 120B may be considered either or both a readout line and a control line. For configurations such as Fig. 1I For more details on the exemplary configuration shown, see BN Engel, J. B. Butcher, RWDave, M. DeHerrera, M. Durlam, G. Grynkewich, J. Janesky, SVPietambaram, NDRizzo, JMSlaughter, K. Smith, JJSun, and S. Tehrani, “A 4-MbToggle MRAM Based on a Novel Bit and Switching Method,” IEEE Transactions on Magnetics, vol. 41, p. 132 (2005).

[0066] Figure 1J Another exemplary sensor 105 selection method according to some embodiments is shown. Figure 1JIn the exemplary embodiment shown, the selector element 111 (e.g., a diode or similar threshold element known in the art, such as a semiconductor diode, an operational transconductance amplifier (OTA), a vanadium oxide layer, a capacitive threshold logic gate, etc.) is deposited "in-stack" with the magnetic film of the sensor 105 and then placed in a cross-point architecture. Figure 1J The in-stack selector element 111 is shown below the sensor 105, but it should be understood that the order of the in-stack selector element 111 and the sensor 105 can be reversed. Corresponding selector devices (e.g., CMOS transistors) can be used to turn on each line 120A, 120B to address / access each sensor 105 in the detection device 100. The use of CMOS select transistors may be simple due to the ubiquity of foundries available for manufacturing front ends (i.e., nanofabrication for building CMOS transistors and underlying circuitry), but the type of current used for operation can use a cross-point design to ultimately achieve the desired density. Additional details of configurations suitable for selecting sensor 105 (e.g., in a cross-point array) can be found in C. Chappert, A. Fert, and F. N. Van Daul, “The emergence of spinelectronics in data storage,” Nature Materials, Vol. 6, p. 813 (2007) and J. Woo et al., “Selector-less RRAM with non-linearity of device for cross-point array applications,” Microelectronic Engineering, Vol. 109, pp. 360-363 (2013).

[0067] Using MNPs and a detection device 100 such as Figures 1A to 1H As a result of PCR amplification of the method of the exemplary detection device 100 shown in FIG. 1 , the resulting DNA template strand clusters may be spread over a two-dimensional area on or around the support structure 114 within the reagent area 115 (e.g., on the wall 117), as shown in FIG. Figure 2A As shown. Typically, after the PCR amplification process, the DNA template strands are spaced about 40 nm apart from each other. In addition, as the sequencing protocol proceeds, the DNA strands become longer. Therefore, as each nucleotide precursor labeled by the MNP is incorporated, the distance between the sensor 105 and the MNP marker of the last incorporated nucleotide precursor also increases. Figure 2BSensor 105 and four DNA strands are shown, each with an MNP label attached to the last dNTP incorporated into the target DNA strand. DNA strand 109A is attached at a lateral distance 206A on support structure 114 of wall 117 (or elsewhere within reagent region 115) from sensor 105. The MNP is distance 205A from sensor 105. Similarly, DNA strand 109B is attached at a lateral distance 206B on support structure 114 of wall 117 (or elsewhere within reagent region) from sensor 105, and its MNP is distance 205B from sensor 105.

[0068] Depending on the distance between the MNPs and the sensor 105, MNPs labeled with dNTPs incorporated into a DNA template strand attached to a support structure 114 near a particular sensor 105 may be too far away for the sensor 105 to reliably detect them. It is desirable to have the MNPs closer to the sensor 105 to improve the probability of detection and the signal-to-noise ratio (SNR) of the detection process.

[0069] Disclosed herein are devices and methods for reducing the distance between MNPs labeling the molecules being detected and the sensor 105 detecting those MNPs. Generally, the MNPs are moved closer to the sensor 105 by an applied magnetic field, which results in a gradient that attracts the MNPs toward the area near the sensor 105 with the largest gradient.

[0070] Figure 3 105 and the like. The pole shoe 210 is an example illustrating the operating principle of at least some of the disclosed embodiments and is not intended to limit them. A pole shoe 210, which acts as a field concentrator, is coupled to the sensor 105 and is disposed between the sensor 105 and the wall 117. The pole shoe 210 emits a magnetic field (shown as a curved dashed line) having a maximum gradient near the sensor 105. The gradient attracts the MNPs toward the sensor 105, thereby reducing the distance between the MNPs and the sensor 105. The pole shoe 210 may be connected to or may include, for example, the wire 120. The pole shoe 210 may be made of any suitable material, such as a magnetic material (e.g., a FeNi alloy, etc.). For example, the pole shoe 210 may include Permalloy (a nickel-iron magnetic alloy) or any other material having a high magnetic permeability and a low coercivity. Figure 3 The shape of the pole piece 210 shown is an exemplary illustration. The shape may be different, as further explained below.

[0071] Apart from Figure 3 Besides the exemplary pole pieces shown, the magnetic field can be generated in a variety of ways. Figure 4A An exemplary embodiment is shown in which the sensor 105 is coupled to and disposed between the solenoid 215 and the conical pole piece 210. The applied magnetic field attracts the MNPs toward the top of the pole piece 210, such as Figure 4A It should be understood that Figure 4A A cross section of a pole shoe 210 is shown, and the three-dimensional pole shoe 210 may have, for example, a pyramidal shape or any other shape that facilitates directing or concentrating the magnetic field. For example, the pole shoe 210 may include edges or points. It should also be understood that although Figure 4A A solenoid 215 is shown, but the solenoid 215 may alternatively be a ferromagnetic component, such as a ferromagnet, as explained in further detail below.

[0072] Figure 4B Another exemplary embodiment is shown in which the sensor 105 is coupled to and disposed between the solenoid 215 and the rectangular pole piece 210. The applied magnetic field attracts the MNPs toward the edge of the rectangular pole piece 210.

[0073] Figure 4C Yet another exemplary embodiment is shown in which the sensor 105 is coupled to and disposed between the solenoid 215 and the pole piece 210. Figure 4C In an exemplary embodiment, the solenoid 215 is coupled to the yoke 220, which can increase the sensitivity of the sensor 105. The pole shoe 210 is functionally similar to the write pole of a magnetic recording write head used in a hard disk drive, and the yoke 220 is functionally similar to the return path of the magnetic recording write head. A magnetic field similar to the write field of the magnetic recording write head attracts the MNPs toward the gap between the pole shoe 210 and the yoke 220, which has a magnetic field gradient. The MNPs change magnetic resistance as they move toward the gap. In this sense, the MNPs act similar to a switch in the magnetic circuit formed by the yoke 220, the pole shoe 210, the sensor 105, and the solenoid 215. For example, when the MNPs are near or in the gap, the MNPs operate in a manner similar to a closed switch.

[0074] In some embodiments, the magnetic field is selectively turned on and off depending on whether it is desired to draw the MNPs into the gap between the pole piece 210 and the magnetic yoke 220. For example, when the magnetic field is on, the MNPs are drawn into the gap between the pole piece 210 and the magnetic yoke 220, thereby pulling them closer to the sensor 105. When the magnetic field is off, the MNPs are not drawn into the gap and can be washed out (e.g., between sequencing cycles).

[0075] As mentioned above, Figure 4C An exemplary embodiment using a solenoid 215 is shown. Other embodiments replace the solenoid 215 with a magnet (e.g., a ferromagnet), which does not require wiring and may be cheaper and / or simpler to manufacture than the solenoid 215. In some embodiments, for example, the yoke 220 is made of a soft magnetic material and replaced by a ferromagnet made of a material that has some coercive field rather than a very hard magnetic material. Figure 4CSolenoid 215 is shown. An external magnetic field can be used to magnetize the ferromagnet to attract the MNPs into the gap between the pole piece 210 and the yoke 220. When the external magnetic field is turned off, the MNPs are no longer attracted into the gap. They can then be washed out (e.g., between sequencing cycles).

[0076] In some embodiments, multiple sensors 105 may share a particular pole shoe 210. In other words, a single pole shoe 210 may assist multiple sensors 105. Additionally or alternatively, a particular sensor 105 may be assisted by multiple pole shoes 210 (e.g., the sensor may sense MNP directed toward it via multiple pole shoes). In general, a sensor 105 may be assisted by one or more pole shoes 210, and a pole shoe 210 may assist one or more sensors 105. Figure 4D Some such exemplary configurations are shown in which a sensor 105 is aided by multiple pole shoes 210 and certain pole shoes 210 aid multiple sensors 105. Figure 4D As shown, sensor 105A is near two pole shoes 210A and 210B. As shown, pole shoe 210A can be spaced a distance from sensor 105A. Pole shoe 210A can, for example, be attached to or formed by or on the back side of reagent area 115. Sensor 105A can also be assisted by one or more other pole shoes 210 (e.g., pole shoe 210B). Figure 4D As shown, pole shoe 210B may be shared by sensors 105A and 105B (and possibly by an additional sensor 105. Similarly, sensor 105B may be assisted by two or more pole shoes, namely pole shoe 210B (shown as being shared by sensor 105A) and pole shoe 210C (which may be shared by another sensor 105 (not shown)).

[0077] It should be understood that 4A to 4D The exemplary embodiment shown is merely exemplary. It should be understood that other structures having various shapes and sizes may be used as pole piece 210. Also, alternatively or in addition, structures other than solenoid 215 and / or yoke 220 may be used. Figure 4D As shown and described above, some structures (eg, solenoid 215 , yoke 220 , pole piece 210 , etc.) may be shared by more than one sensor 105 .

[0078] In some embodiments, instead of coupling each sensor 105 to a solenoid 215, a yoke 220, or the like, an external magnetic component (e.g., Figure 1D The magnetic component 150 shown is used to generate a magnetic field. Figure 5Such an embodiment is shown. Pole piece 210 is shown as having a triangular shape (in cross section), but as mentioned above, the triangular shape is merely exemplary. Other shapes are possible (eg, rectangular cross section, etc.) and are specifically contemplated.

[0079] The magnetic field may be adjusted to accommodate the increased distance between the sensor 105 and the MNPs coupled or attached to the support structure 114 assigned to the sensor 105. For example, in a DNA sequencing application, the distance between the MNPs and the sensor 105 will increase as the sequencing process proceeds and the DNA strands grow longer. To compensate, the magnetic field may be adjusted (increased) in later sequencing cycles relative to earlier sequencing cycles to move the MNPs a greater distance, closer to the sensor 105, thereby mitigating the drop in SNR as the strands being sequenced grow longer.

[0080] In some embodiments, a magnetic shield is disposed between adjacent support structures 114 and / or sensors 105 . Figure 6 2 is a conceptual diagram of an exemplary embodiment of a detection device 100 according to some embodiments, the detection device including a magnetic shield 230 that shields adjacent support structures 114 (and sensors 105) from each other. In the illustrated embodiment, it is assumed that the sensors 105 and the support structures 114 are in a one-to-one relationship. The magnetic shield 230 helps to reduce the possibility that a DNA strand coupled or attached to a particular support structure 114 will be attracted toward an adjacent sensor 105. For example, the magnetic shield 230A reduces the possibility that an MNP attached to a nucleotide precursor incorporated into a DNA strand bound to the support structure 114A will be attracted toward a sensor 105, which is arranged to detect the presence of an MNP attached to a nucleotide precursor incorporated into a DNA strand bound to the support structure 114B. Similarly, the magnetic shield 230B reduces the possibility that an MNP attached to a nucleotide precursor incorporated into a DNA strand bound to the support structure 114A will be attracted toward a sensor 105, which is arranged to detect the presence of an MNP attached to a nucleotide precursor incorporated into a DNA strand bound to the support structure 114C. When magnetic shields 230 are disposed between support structures 114 , they may also limit the area over which DNA strands to be detected by a particular sensor 105 are amplified.

[0081] Figure 7 An exemplary method 500 for nucleic acid sequencing using the detection device 100 according to some embodiments is shown. At 502, the method 500 begins. At 504, the selected nucleotide precursors are magnetically labeled using MNPs. At 506, the nucleic acid strands can optionally be bound to the detection device 100 in the reagent area 115. At 508, the magnetically labeled nucleotide precursors are added to the reagent area 115. At 510, optionally, a magnetic field can be applied to the detection device (e.g., as described above in Figures 3 to 5 ). At 512, a characteristic of each of the one or more sensors is detected. As described above, the characteristic may be, for example, voltage, current, resistance, frequency, phase, noise, or temperature; a change in voltage, current, resistance, frequency, phase, noise, or temperature; or a change in a statistical property of voltage, current, resistance, frequency, phase, noise, or temperature (e.g., mean, variance, standard deviation, etc.). At 514, it is determined whether the MNP has been detected by the sensor 105. If not, at 526, the method 500 ends. If yes, at 516, it is determined that the tested magnetically labeled nucleotide precursor is detected. Optionally, at 518, the type of the detected nucleotide precursor may be recorded, or in a DNA sequencing application, the type of base complementary to the detected nucleotide precursor may be recorded. Optionally, at 520, the magnetic field applied at step 510 may be disconnected. Optionally, at 522, the MNP may be removed (e.g., cut from a nucleic acid strand bound to the detection device 100 in the reagent region 115). Optionally, at 524, the reagent area 115 may be washed to flush away the removed MNPs and other residues before performing the method 500 again to test another nucleotide precursor or to start a new detection cycle.

[0082] It should be understood that Figure 7 This is exemplary only. Method 500 may include steps not shown. For example, in a DNA sequencing application, a polymerase may be added to the reagent area prior to detecting the properties of sensor 105, and / or an additional washing step may be performed (e.g., after step 508 and before step 512). Also, as will be appreciated by one of ordinary skill in the art, some steps may be performed in a different order. For example, the order of steps 504 and 506 may be different. Figure 7 Therefore, Figure 7 This is merely one example of how the detection device 100 may be used and is not intended to be limiting.

[0083] It should also be understood that although Figure 7Although the explanation only relates to a single nucleotide precursor, if each type of nucleotide precursor is labeled by a different MNP type selected, the method 500 can be used to test more than one nucleotide precursor simultaneously, so that the characteristics detected by the sensor 105 allow the detection circuit 130 to distinguish between different MNP types. Methods that allow detection of multiple nucleotide precursors during a single sequencing cycle are disclosed in the applications incorporated by reference herein (e.g., U.S. Applications 16 / 791,759, 16 / 819,636, 16 / 727,064, 16 / 697,013, and 16 / 659,383). The disclosure herein may be used in conjunction with those method embodiments (e.g., method embodiments of U.S. Applications 16 / 791,759, 16 / 819,636, 16 / 727,064, 16 / 697,013, and 16 / 659,383 may be used with a detection device 100 comprising a pole piece 210 operable to attract MNPs toward a sensor 105 as disclosed herein). Similarly, it should be understood that Figure 7 The method 500 shown can be performed more than once during a sequencing cycle (e.g., once for each nucleotide precursor tested if the same MNP type is used to label all nucleotide precursors tested) and multiple times over the course of multiple sequencing cycles. For example, if the same MNP type labels each of four nucleotide precursors, the method 500 can be performed four times in the first sequencing cycle, then four more times in the second sequencing cycle, and so on. As another example, if each of the four nucleotide precursors is labeled by a different, distinguishable MNP type, the method 500 can be performed once during each sequencing cycle.

[0084] In the foregoing description and drawings, specific terminology has been set forth to provide a thorough understanding of the disclosed embodiments. In some instances, the terminology or drawings may suggest specific details that are not necessary to practice the invention.

[0085] In order to avoid unnecessarily obscuring the present disclosure, well-known components are shown in block diagram form and / or not discussed in detail or, in some cases, not discussed at all.

[0086] Unless otherwise expressly defined herein, all terms should be given their broadest possible interpretation, including the meaning implied by the specification and drawings and the meaning understood by those skilled in the art and / or as defined in dictionaries, monographs, etc. As expressly provided herein, some terms may not be subject to their ordinary or customary meaning.

[0087] As used in this specification and the appended claims, the singular forms "a", "an", and "the" do not exclude plural references unless otherwise indicated. Unless otherwise indicated, the word "or" should be interpreted as inclusive. Thus, the phrase "A or B" should be interpreted as all of the following meanings: "both A and B", "A but not B", and "B but not A". Any use of "and / or" herein does not mean that the word "or" alone is exclusive.

[0088] As used in this specification and the appended claims, phrases of the form "at least one of A, B, and C," "at least one of A, B, or C," "one or more of A, B, or C," and "one or more of A, B, and C" are interchangeable and each encompasses all of the following meanings: "only A," "only B," "only C," "A and B but not C," "A and C but not B," "B and C but not A," and "all of A, B, and C."

[0089] The term "coupled" is used herein to refer to both direct connection / attachment as well as connection / attachment through one or more intervening elements or structures. Thus, for example, with reference to Fig. 1I , lines 120B and 120C are coupled, and lines 120B and 120A are also coupled. Similarly, each of lines 120A, 120B, and 120C is coupled to sensor 105 (line 120A is directly coupled, and lines 120B and 120C are coupled through an intermediate element (e.g., selector element 111)).

[0090] To the extent that the terms "including," "having," and variations thereof are used in the detailed description or claims, such terms are intended to be inclusive in a manner similar to the term "comprising," ie, meaning "including, but not limited to."

[0091] The terms "exemplary" and "implementation" are used to indicate examples, not preferences or requirements.

[0092] As used herein, the terms "above," "below," "between," and "on" refer to the relative position of one feature with respect to other features. For example, a feature disposed "above" or "below" another feature may be directly in contact with the other feature, or may have intervening materials. Additionally, a feature disposed "between" two features may be directly in contact with both features, or may have one or more intervening features or materials. Conversely, a first feature "on" a second feature is in contact with the second feature. The drawings are not necessarily drawn to scale, and the sizes, shapes, and dimensions of the features may vary significantly from how they are depicted in the drawings.

[0093] It should be understood that while portions of the present invention are in the context of nucleic acid sequencing, particularly DNA sequencing, the disclosure herein is generally applicable to detecting molecules by using MNPs as tags or markers. It should be understood by those skilled in the art that the concepts discussed and many disclosed embodiments are applicable to other types of molecular detection (e.g., inorganic molecules).

[0094] Although specific embodiments have been disclosed, it will be apparent that various modifications and changes may be made thereto without departing from the broader spirit and scope of the present disclosure. For example, at least where practicable, features or aspects of any one of the embodiments may be applied in combination with any other embodiment of the embodiments, or in place of corresponding features or aspects thereof. Accordingly, the specification and drawings are to be regarded in an illustrative rather than a restrictive sense.

Claims

1. A detection device, comprising: one or more pole shoes; at least one magnetic component configured to generate a magnetic field through the one or more pole pieces; a plurality of sensors, each sensor of the plurality of sensors coupled to at least one pole piece of the one or more pole pieces; and a detection circuit coupled to the plurality of sensors, in: The detection circuit is configured to detect a characteristic of each of the plurality of sensors, the characteristic being indicative of the presence or absence of one or more magnetic nanoparticles coupled to at least one molecule of the plurality of molecules to be detected, and At least one of the one or more pole pieces is operable to attract the one or more magnetic nanoparticles toward at least one sensor of the plurality of sensors, And among them: a first subset of the plurality of sensors arranged in a first row; a second subset of the plurality of sensors is arranged in a second row, the second row being substantially parallel to the first row; and At least one reagent area is disposed between the first row and the second row. 2 . The detection device according to claim 1 , wherein the at least one reagent area is configured to contain a fluid containing the plurality of molecules to be detected.

3. The detection device of claim 2, wherein the at least one reagent area comprises a fluid channel.

4. The detection device according to claim 2, wherein one or more surfaces within the reagent area provide one or more sites for binding the plurality of molecules to be detected, and the one or more sites are located between the plurality of sensors. 5 . The detection device of claim 4 , wherein the one or more sites include a plurality of sites, and further comprising at least one magnetic shield disposed between at least two of the plurality of sites.

6. The detection device according to claim 1, further comprising: A barrier material encapsulates the plurality of sensors and is used to provide a barrier between the plurality of sensors and the at least one molecule of the plurality of molecules to be detected. The detection device according to claim 6 , wherein the barrier material comprises an insulator or a metal.

8. The detection device according to claim 1, wherein the characteristics include: Voltage, current, resistance, frequency, phase, noise or temperature.

9. The detection device according to claim 1, wherein the characteristics include: Changes in voltage, current, resistance, frequency, phase, noise, or temperature.

10. The detection device according to claim 1, wherein the characteristics include: Variations in the statistical properties of voltage, current, resistance, frequency, phase, noise, or temperature. 11 . The detection device according to claim 1 , wherein the plurality of sensors include a temperature sensor, a magnetoresistive sensor, a magnetic tunnel junction, a spin torque oscillator or a spin valve. 12 . The detection device of claim 1 , wherein at least one of the one or more pole shoes has a conical or triangular shape.

13. The detection device according to claim 1, wherein at least one of the one or more pole shoes is configured to assist in generating a magnetic field gradient for attracting at least a portion of the one or more magnetic nanoparticles toward at least one sensor of the plurality of sensors.

14. The detection device of claim 1, further comprising at least one magnetic component configured to generate a magnetic field through the one or more pole pieces.

15. The detection device of claim 1, wherein the plurality of sensors are arranged in a cross-point array, the cross-point array comprising a first top line, a second top line, a first bottom line, and a second bottom line, wherein: the first top line is coupled to the first bottom line at a first location, the first top line is coupled to the second bottom line at a second location, The second top line is coupled to the first bottom line at a third location, and The second top line is coupled to the second bottom line at a fourth location.

16. The detection device according to claim 15, wherein: The first top line and the second top line are substantially parallel to each other, The first bottom line and the second bottom line are substantially parallel to each other, and The first top line and the second top line are substantially perpendicular to the first bottom line and the second bottom line.

17. The detection device according to claim 1, wherein the detection device is a sequencing device, and wherein the plurality of molecules to be detected include biomolecules. The detection device according to claim 17 , wherein the biomolecule is a nucleic acid.

19. The detection device according to claim 1, wherein the detection circuit comprises: One or more selector devices, at least one of the one or more selector devices being coupled to a corresponding sensor of the plurality of sensors.

20. The detection device of claim 19, wherein at least one of the one or more selector devices comprises a transistor.

21. The detection device of claim 19, wherein at least one of the one or more selector devices comprises an in-stack selector.

22. A device for molecular detection, the device comprising: Pole shoes; a solenoid or ferromagnetic component configured to generate a magnetic field through the pole piece; a plurality of sensors, at least one sensor of the plurality of sensors being disposed between and coupled to the pole piece and the solenoid or ferromagnetic component, wherein the plurality of sensors are capable of sensing the presence or absence of a magnetic nanoparticle marker coupled to a molecule to be detected; and a detection circuit coupled to the plurality of sensors and configured to detect a characteristic of each of the plurality of sensors, wherein the characteristic indicates whether the magnetic nanoparticle marker has been detected, wherein a first subset of the plurality of sensors arranged in a first row; a second subset of the plurality of sensors is arranged in a second row, the second row being substantially parallel to the first row; and At least one reagent area is disposed between the first row and the second row.

23. The apparatus of claim 22, further comprising a yoke, wherein the solenoid or ferromagnetic component is disposed between the corresponding sensor and the yoke to form a magnetic circuit.

24. The apparatus of claim 23, wherein the solenoid or the ferromagnetic component is a ferromagnetic component having a coercive force that enables the ferromagnetic component to be selectively magnetized or selectively demagnetized by an external magnetic field.

25. The apparatus of claim 24, wherein the remanent magnetization of the ferromagnetic component is selected to enable the ferromagnetic component to detect the magnetic nanoparticle marker.

26. The apparatus of claim 22, wherein: The reagent area is configured to contain a fluid containing the molecule to be detected.

27. A method of using the apparatus according to claim 24, comprising: The external magnetic field is applied to selectively magnetize or selectively demagnetize the ferromagnetic component.

28. A method of using the apparatus of claim 23, comprising: The presence or absence of the magnetic nanoparticle marker is detected by detecting the change in magnetic resistance of the magnetic circuit.

29. A method for nucleic acid sequencing using a detection device, the detection device comprising a pole shoe, a magnetic component configured to generate a magnetic field through the pole shoe, a plurality of sensors coupled to the pole shoe, a reagent area, and a detection circuit coupled to the plurality of sensors, wherein: a first subset of the plurality of sensors is arranged in a first row, a second subset of the plurality of sensors is arranged in a second row, the second row is substantially parallel to the first row, and the reagent area is disposed between the first row and the second row, The method comprises: magnetically labeling the nucleotide precursors with one or more magnetic nanoparticles; adding the magnetically labeled nucleotide precursor to the reagent zone; After adding the magnetically labeled nucleotide precursor to the reagent zone, detecting a property of the sensor that indicates the presence or absence of at least one of the one or more magnetic nanoparticles; and Based at least in part on the detected characteristic, it is determined whether the magnetically labeled nucleotide precursor has been detected by the sensor.

30. The method of claim 29, further comprising: The nucleic acid strand to be sequenced is bound to the reagent area of ​​the detection device before the magnetically labeled nucleotide precursor is added to the reagent area.

31. The method of claim 29, further comprising: applying a magnetic field to the detection device; as well as Using the detection circuit, the characteristic of the sensor is detected while the magnetic field is applied.

32. The method of claim 31 further comprising: after detecting the characteristic of the sensor, disconnecting the magnetic field; as well as When the magnetic field is disconnected: removing at least some of the one or more magnetic nanoparticles, and The at least one reagent zone is washed.

33. The method of claim 29, further comprising: In response to determining that the magnetically labeled nucleotide precursor has been detected by the sensor, the kind of the magnetically labeled nucleotide precursor or the kind of a base complementary to the magnetically labeled nucleotide precursor is recorded.

Images