Surface stabilization of biosensors

Abstract

The present invention provides a sensor device (e.g., chemFET, ion-sensitive FET, ion-stimulating proton), which includes a substrate, a semiconductor device disposed on the substrate, the semiconductor device having a surface electrode structure and a sugar coating formed above the surface electrode structure. The sugar coating can be removed before use, such as in nucleic acid sequencing. The semiconductor device may include a well and a bead optionally bound to a nucleic acid disposed in the well.

Description

[0001] This application is a divisional application of an invention patent application with an international filing date of March 4, 2016, application number 201680013987.8 and name “Surface Stabilization of Biosensor”. Technical Field

[0002] Generally speaking, the present invention relates to surface stabilized biosensors and methods of stabilizing such biosensors. Background Art

[0003] There is a growing interest in electronic sensors for detecting chemical and biological agents, analytes or reaction byproducts. In addition, there is a push to develop sensors with greater sensitivity that can detect smaller and smaller changes in concentration or solution pH. There is also a trend to reduce reaction volumes, especially when detecting reaction byproducts.

[0004] In one exemplary system, pH-based sequencing of biomolecules such as nucleic acids or proteins utilizes small changes in pH in reaction volumes on the order of nanoliters or less. For example, a target nucleic acid can be placed in a volume less than a nanoliter and nucleotide incorporation along the target nucleic acid can be detected based on the small changes in pH resulting from nucleotide incorporation.

[0005] The reliability of such sensitive sensors can be affected by both the stability of the sensor device and the consistency of the sensor calibration. Such stability and consistent calibration may be affected by packaging, storage and transportation. Summary of the invention

[0006] In an exemplary embodiment, a sensor device includes a substrate, a semiconductor device disposed on the substrate, and a flow cell cover. The semiconductor device has a surface electrode structure. A hole structure may define a hole that exposes the surface electrode structure, and beads may be deposited in the hole. A flow cell is defined between the substrate and the flow cell cover. In one example, a sugar solution may be applied through the flow cell and through the semiconductor device to form a sugar coating on the surface electrode structure of the semiconductor device. The sensor device may be dried and packaged, leaving the sugar coating on the surface electrode structure during transportation and storage. When in use, a washing solution may be applied through the flow cell to remove the sugar coating and expose the surface electrode structure to a fluid transmitted through the flow cell. BRIEF DESCRIPTION OF THE DRAWINGS

[0007] The present invention may be better understood, and its numerous features and advantages made apparent to those skilled in the art by referencing the accompanying drawings.

[0008] Figure 1 , Figure 2A , Figure 2B and Figure 2C Included are illustrations of portions of an exemplary sensor device.

[0009] Figure 3 , Figure 4 , Figure 5 and Figure 6 Included are illustrations of exemplary sensor devices.

[0010] Figure 7 and Figure 8 Illustrations of exemplary methods for processing and using sensor devices are included.

[0011] Fig. 9 , Fig.10 , Fig.11 , Fig.12 and Fig.13 Illustration of an exemplary preparation manifold including a processing system.

[0012] Fig.14 Illustrations of exemplary processing systems are included.

[0013] Fig.15 Included are diagrams of exemplary sensing systems.

[0014] The use of the same reference symbols in different drawings indicates similar or identical items. DETAILED DESCRIPTION

[0015] In an exemplary embodiment, the sensor device includes a substrate, a semiconductor device disposed on the substrate, and a flow cell cover. The semiconductor device has a surface electrode structure. The semiconductor device may further include a pore structure defining a hole on the surface electrode structure. Optionally, beads may be disposed in the hole, and the beads may bind to nucleic acids. The flow cell is defined between the substrate and the flow cell cover. In one example, a sugar solution may be applied through the flow cell and through the semiconductor device to form a sugar coating on the surface electrode structure of the semiconductor device and optionally on the beads. The sensor device may be dried and packaged, leaving the sugar coating on the surface electrode structure during transportation and storage. When in use, a washing solution may be applied through the flow cell to remove the sugar coating and expose the surface electrode structure to a fluid transmitted through the flow cell.

[0016] In a specific embodiment, the sequencing system uses a sensor device that includes a flow cell that exposes a sensor array. The sequencing system includes a communication circuit that is electronically connected to the sensor array, and includes a container and a fluid control member that are fluidically connected to the flow cell. In one example, Figure 1An enlarged and cross-sectional view of a flow cell 100 is illustrated and a portion of a flow chamber 106 is illustrated. A reactant stream 108 flows across the surface of the microwell array 102, wherein the reactant stream 108 flows through the open ends of the microwells of the microwell array 102. The microwell array 102 and the sensor array 105 together may form an integrated unit that forms the lower wall (or floor) of the flow cell 100. A reference electrode 104 may be fluidly coupled to the flow chamber 106. Additionally, a flow cell cover or lid 130 encapsulates the flow chamber 106 to contain the reactant stream 108 within a defined area.

[0017] Figure 2A Description Figure 1 110 of the microwell 201 and the sensor 214 are shown in an enlarged view. The volume, shape, aspect ratio (e.g., bottom width to hole depth ratio) and other dimensional features of the microwell can be selected based on the nature of the reaction occurring, as well as the reactants, byproducts or labeling techniques (if any) employed. The sensor 214 can be a chemical field effect transistor (chemFET), more specifically an ion sensitive FET (ISFET), in which a floating gate 218 has a sensor plate 220 separated from the interior of the microwell, optionally by a passivation layer 216 or other metal, metal nitride or metal oxide layer or combination thereof. The sensor plate 220, the optional passivation layer 216 or other layers together form an electrode structure. The sensor 214 can respond to (and generate an output signal related to) the amount of charge 224 present on the passivation layer 216 opposite the sensor plate 220. Changes in the charge 224 can cause changes in the current between the source 221 and the drain 222 of the chemFET. In turn, the chemFET can be used directly to provide a current-based output signal or indirectly with additional circuitry to provide a voltage-based output signal.Reactants, wash solutions, and other reagents can move into and out of the microwells by diffusion mechanisms 240.

[0018] In one embodiment, the reaction carried out in the micropore 201 may be an analytical reaction for identifying or determining the characteristics or properties of the relevant analyte. Such reactions may directly or indirectly produce byproducts that affect the amount of charge near the sensor plate 220. If such byproducts are produced in small quantities or decay rapidly or react with other components, multiple copies of the same analyte may be analyzed in the micropore 201 at the same time to increase the output signal generated. In one embodiment, multiple copies of the analyte may be connected to a solid support 212 before or after being deposited in the micropore 201. The solid support 212 may be micron particles, nanoparticles, beads, solid or porous objects, etc. comprising a gel. For simplicity and ease of explanation, the solid support 212 is also referred to as a bead or particle in this article. For nucleic acid analytes, multiple connection copies may be made by rolling circle amplification (RCA), exponential RCA or similar techniques to produce amplicons without using a solid support.

[0019] The signal quality of the chemFET may be affected by the surface quality of the microwell 201 and the electrode structure. To protect or stabilize the surface, a sugar coating may be applied to the surface. Figure 2B As described in , after assembly and prior to use, a sugar coating 226 may be formed over the sensor structure 214. The sugar coating 226 may be conformal, such as Figure 2B Alternatively, the carbohydrate coating may fill microwells 201 and optionally portions of flow channel 106.

[0020] In another example, the beads can be disposed in a well. Figure 2C As illustrated in , the sugar coating 226 can be formed over the beads 212 and over the sensor structure 214. The sugar coating can be conformal or fill the microwells 201, and can optionally occupy a portion of the flow channel 106.

[0021] Prior to use, a wash solution may be applied via the flow cell 106 to remove the carbohydrate coating 226, providing the microwells 201 therein, for example, a solid support 212 may be provided and measurements of ion concentration or pH may be performed, or when the solid support is present prior to washing, the solid support may be exposed for measurement.

[0022] Flow cells can be assembled with microwell arrays and sensor arrays in a variety of ways. Figure 3-6 In one embodiment described in , a flow cell is made by connecting a fluidic interface element to a housing containing a sensor chip. Typically, the integrated microporous sensor array (i.e., sensor chip) is mounted in a housing or package that protects the chip and provides electrical contacts for communication with other devices. The fluidic interface element is designed to provide a chamber or flow chamber for reactants to pass through when it is sealingly connected to such a package. In one aspect, such connection is achieved by gluing the parts together. Figure 3 400 of a flow cell. In the illustrated embodiment, the complete flow cell is assembled by connecting the assembly 400 to a package (e.g., Figure 5 and 6 The ridge 401 protrudes from the surface 413 and when Figure 5 The chip 430 illustrated in FIG. 4A and FIG. 4B , when mated, forms the wall 410 of the elliptical flow chamber 408. The assembly 400 may be glued to the chip housing 430 to form a fluid tight seal. Figure 4A top view (or surface) 416 of assembly or element 400 is illustrated showing inlet and outlet collars 418 and 420 that permit a flow cell to be sealedly connected to a fluidic system. Inlet and outlet sleeves connected to elastomeric ring elements may be inserted into collars 418 and 420 such that the elastomeric material forms a seal along the floor and walls of collars 418 and 420. Other methods of connecting a flow cell to a fluidic system may be used, including other types of pressure fittings, clamp-type fittings, screw-on fittings, etc. Assembly 400 may be adapted to accommodate chips of different sizes with simple design changes, as illustrated by channels 422 and 424. In other words, for Figure 5 4, channels having openings at the center of the inlet collar 418 and the outlet collar 420 may be directed to the inlet and outlet ports on the array 430 via such channels toward the center of the assembly or element 400. Similarly, for the smaller array 434 illustrated in FIG. Figure 6 436, similar channels 442 and 444 can be directed away from the center of assembly 400 and to the inlet and outlet of array 436. Such a design advantageously provides a single basic flow cell design that can be used with multiple sensor array sizes. Protruding tabs 412 and beveled edges 414 can be used to ensure that the chip is properly oriented for placement in a complementary socket or fixture to achieve fluid and electrical connections with the rest of the device.

[0023] The chip or chip assembly may be treated to protect the sensors or beads disposed on the chip during transportation. Figure 7 , method 700 includes applying a flow cell cover on a semiconductor substrate to define a flow cell of a sensor device, as illustrated at 702. An access port through the flow cell cover may provide fluid access to a flow cell sensor device of the sensor device. The sensor device may include an electrode or gate structure exposed to a fluid applied through the flow cell cover and flowing through the flow cell.

[0024] As illustrated at 704, a cleaning solution may be applied through the flow tank. The cleaning solution may be an alkaline solution, such as a solution including NaOH, an acid solution, or a combination thereof. In one example, the acid solution is a non-aqueous solution including an anionic surfactant, such as a sulfonic acid surfactant, for example, dodecylbenzenesulfonic acid (DBSA). Specifically, the semiconductor substrate may be cleaned using a sequence of flowing a non-aqueous acid solution, water or alcohol, and an alkaline solution.

[0025] Optionally, beads may be deposited on a sensor device, such as in a well formed above a semiconductor substrate, as illustrated at 706. Optionally, beads may be bound to biomolecules, such as nucleic acids.

[0026] In one example, the beads can be formed from a polymer network, such as a non-nucleic acid polymer network. Exemplary non-nucleic polymer networks agarose; polyethylene glycol; polybutylene oxide; diethyl acrylamide; polyethylene oxide; polyacrylamide; polypropylene oxide; N,N-polydimethyl acrylamide; poly(N-isopropyl acrylamide); polyvinyl pyrrolidone; poly-N-hydroxy acrylamide; the like; or any combination thereof. In a particular example, the polymer network includes polyethylene glycol. In another example, the polymer network includes polyacrylamide. Specifically, the polymer network can form a hydrogel. For example, the beads can have 0.1% to 10% polymer by weight, such as 0.5% to 8% polymer or 0.8% to 5% polymer when in aqueous solution.

[0027] In another example, the bead can be associated with a biomolecule. In a specific example, the biomolecule can be covalently bonded to the polymer network of the bead directly or via a linker. The biomolecule can be a nucleic acid, such as DNA or RNA. Specifically, the nucleic acid can be an oligonucleotide, such as a capture probe or primer. In another example, the nucleic acid can be a polynucleotide to be sequenced.

[0028] In one example, the sugar solution can be applied via the flow cell, as illustrated at 708. In one example, the sugar solution is an aqueous solution including sugars. Optionally, the sugar solution can also include a surfactant. In another example, the sugar solution can include an alcohol.

[0029] The sugar may include monosaccharides, disaccharides, polysaccharides, derivatives thereof, or combinations thereof. In one example, the monosaccharide includes glucose, fructose, galactose, or a combination thereof. In another example, the disaccharide includes sucrose, trehalose, maltose, or lactose, or a combination thereof. In a specific example, the disaccharide includes sucrose. In another example, the disaccharide includes trehalose. In another example, the sugar may include hyaluronic acid. The sugar may be included in the sugar solution in a range of 5 wt % to 30 wt %, such as a range of 5 wt % to 20 wt %, a range of 10 wt % to 20 wt %, or a range of 10 wt % to 15 wt %.

[0030] The carbohydrate solution may further include a surfactant. The surfactant may be an ionic surfactant, an amphoteric or zwitterionic surfactant, a nonionic surfactant, or a combination thereof. The ionic surfactant may be an anionic surfactant. Exemplary anionic surfactants include sulfate surfactants, sulfonate surfactants, phosphate surfactants, carboxylate surfactants, or any combination thereof. Exemplary sulfate surfactants include: alkyl sulfates, such as ammonium lauryl sulfate, sodium lauryl sulfate (sodium dodecyl sulfate (SDS)), or a combination thereof; alkyl ether sulfates, such as sodium lauryl ether sulfate, sodium myristyl alcohol ether sulfate, or any combination thereof; or any combination thereof. Exemplary sulfonate surfactants include: alkyl sulfonates, such as sodium dodecyl sulfonate; octyl succinate, such as sodium octyl sulfosuccinate; alkylbenzene sulfonates (e.g., dodecylbenzene sulfonic acid or its salt); or any combination thereof. Exemplary phosphate surfactants include alkyl aryl ether phosphates, alkyl ether phosphates, or any combination thereof. Exemplary carboxylic acid surfactants include: alkyl carboxylates, such as fatty acid salts or sodium stearate; sodium lauryl sarcosinate; cholates, such as sodium deoxycholate; or any combination thereof.

[0031] In another example, the ionic surfactant may be a cationic surfactant. Exemplary cationic surfactants include primary, secondary or tertiary amines, quaternary ammonium surfactants, or any combination thereof. Exemplary quaternary ammonium surfactants include: alkyl trimethylammonium salts, such as cetyl trimethylammonium bromide (CTAB) or cetyl trimethylammonium chloride (CTAC); cetyl pyridinium chloride (CPC); polyethoxylated tallow amine (POEA); benzalkonium chloride (BAC); benzethonium chloride (BZT); 5-bromo-5-nitro-1,3-dioxane; dimethyldioctadecyl ammonium chloride; dioctadecyl dimethyl ammonium bromide (DODAB); or any combination thereof.

[0032] Exemplary amphoteric or zwitterionic surfactants include primary, secondary or tertiary amines or quaternary ammonium cations with sulfonate, carboxylate or phosphate anions. Exemplary sulfonate amphoteric surfactants include: (3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate); sulfobetaines, such as cocamidopropyl hydroxysulfobetaine; or any combination thereof. Exemplary carboxylic acid amphoteric surfactants include amino acids, imino acids, betaines (such as cocamidopropyl betaine) or any combination thereof. Exemplary phosphate amphoteric surfactants include lecithin. In another example, the amphoteric or zwitterionic surfactant may be an alkylaminoalkyl sulfonate, such as alkyldimethylammoniopropane sulfonate, wherein the alkyl group has between 5 and 20 carbons, such as between 8 and 18 carbons, between 8 and 14 carbons, or between 10 and 14 carbons. In a specific example, the surfactant includes n-dodecyl-N,N-dimethyl-3-ammonio-1-propanesulfonate.

[0033] In another example, the surfactant may be a nonionic surfactant, such as a polyethylene glycol surfactant, an alkyl pyrrolidine surfactant, an alkyl imidazolidinone surfactant, an alkyl morpholine surfactant, an alkyl imidazole surfactant, an alkyl imidazoline surfactant or a combination thereof. In a specific example, the polyethylene glycol surfactant includes a polyethylene glycol ether, such as an alkylphenol polyethoxylate. In another example, the nonionic surfactant may be an alkyl polysaccharide. In another example, the nonionic surfactant includes a nonionic fluorine surfactant, such as an ethoxylated fluorocarbon. In another example, the surfactant solution may include octyl pyrrolidine.

[0034] Specifically, the surfactant solution may include a combination of such surfactants. For example, the surfactant solution may include a combination of a zwitterionic surfactant and an anionic surfactant. In a specific example, the surfactant solution may include a zwitterionic surfactant, such as an alkylaminoalkyl sulfonate; and an anionic surfactant, such as a sulfate surfactant, for example SDS.

[0035] In one example, the surfactant solution may include one or more surfactants in a total concentration in the range of 0.001 wt % to 20 wt %. For example, the surfactant may be included in a total amount in the range of 0.01 wt % to 10.0 wt %, such as 0.01 wt % to 5.0 wt %, 0.05 wt % to 1.0 wt %, or 0.05 wt % to 0.5 wt %.

[0036] In another example, the surfactant solution may include an alcohol, such as methanol, ethanol, isopropanol, isobutanol, or a combination thereof. In one example, the alcohol may be included in an amount ranging from 5.0 wt % to 70.0 wt %, such as from 10 wt % to 50 wt %.

[0037] As illustrated at 710, the sugar solution can be removed from the flow cell, leaving a sugar coating on the semiconductor substrate. The sugar coating can be conformal. In another example, the sugar coating can fill a hole defined on the semiconductor substrate. Specifically, the sugar coating is disposed on an electrode structure of a sensor device on the semiconductor substrate.

[0038] As illustrated at 712, the sensor device may be packaged. For example, the sensor device may be dried and then inserted into a sealed package for shipping. In one example, the package has static dissipative features. In another example, the package may be water or moisture resistant. In another example, a desiccant may be added to the package. Thus, the sugar coating remains in contact with the sensor device for transport and storage of the sensor device.

[0039] When used, the sugar coating can be removed during the preparation of the sensor device. Figure 8As illustrated in , method 800 includes flowing a wash solution through a flow cell of a sensor device, as illustrated at 802. In one example, the wash solution may be water or an aqueous solution. In another example, the wash solution may include a surfactant. In another example, the wash solution may include an alcohol. Exemplary alcohols include ethanol, methanol, isopropanol, isobutanol, or a combination thereof. In one example, the alcohol may be included in an amount ranging from 5 wt % to 70 wt %, such as a range of 10 % to 50 %. In another example, pure alcohol may be used.

[0040] A wash solution flowing through the flow cell removes the sugar coating and exposes the sensor electrode structure and optionally the beads of the sensor device. After removal of the sugar coating, the sensor can be used.

[0041] For example, a biomolecular target, such as a nucleic acid or a protein, may be applied to a sensor device, as illustrated at 804. In a specific example, the nucleic acid or protein may be applied to a sensor electrode of a sensor device. In one example, the biomolecular target is attached to a bead and deposited in a hole of the sensor device. In another example, the hole of the sensor device may include beads before washing, and the biomolecular target may be captured by such beads. In a specific example, the nucleic acid target may be captured by beads with complementary oligonucleotides and optionally amplified to provide multiple copies of the nucleic acid target on the beads. Specifically, multiple copies of the nucleic acid may be applied to the sensor device and may be sequenced by synthesis via detection of pH changes in response to nucleotide incorporation.

[0042] As illustrated at 806, the sensor device may be applied to a detector system. For example, the sensor device may be fluidically connected to a set of reactants and may be electrically connected to a measurement and control system. A series of reactants may be applied to a flow cell of the sensor device, and a sensor device of the sensor device may be used to perform measurements. In a specific example, as illustrated at 808, such a detector system may be used to sequence a biomolecule target. For example, nucleic acids may be sequenced using synthetic sequencing and using a sensor device to detect pH changes.

[0043] Fig. 9 , Fig.10 , Fig.11 , Fig.12 and Fig.13 Included is an illustration of exemplary processing equipment for processing sensor devices in preparation for packaging and storage. Fig. 9 , the processing device 900 includes a deck 902 configured to hold a tray 904. The tray 904 includes a slot 906 to receive a sensor device 908. As illustrated, the sensor device 908 is applied to have an electronic interface facing upward and a fluidic interface with a flow tank facing downward. Alternatively, the sensor device 908 can be applied to have an electronic interface facing downward and a fluidic interface with a flow tank facing downward.

[0044] Using handle 910, deck 902 can be guided along rails 912 under fixture 914. When placed under fixture 914, deck 902 is aligned with the sensor device, and more specifically, fluidly accesses the flow channel of the sensor device having fluidics manifold 1022 and orifice 1124, as shown in FIG. Fig.10 and Fig.11 As described in .

[0045] The clamp 914 is supported by a support 918. The handle 916 can push the clamp 914 downward, pushing the deck 902 downward to engage the fluid manifold 1022. The engagement structure 1020 may include one or more resilient structures 1226 (at Fig.12 ) to engage the sensor device and push it against the fluid port 1124.

[0046] When the handle 916 is lowered, the structure 1020 engages the platform 902 and drives the deck 902 and tray 904 of the sensor device 908 downward. The platform 902 is driven along the shaft 1228 until the fluid port of the sensor device 908 engages the fluid port 1124 of the fluid manifold 1022. When the handle 916 is driven upward, the platform 902 is driven upward along the shaft 1228, disengaging the sensor device 908 from the fluid port 1124. The deck 902 and sensor device 908 can be pulled out from under the clamp 914 using the handle 910.

[0047] In certain examples, manifold 900 forms part of an apparatus to fluidically engage a fluid port of a sensor apparatus and apply one or more reagent solutions, including a sugar solution, through a flow channel of the sensor apparatus. Fig.14 1404, processing system 1400 includes a reactant container 1402 connected to a fluid manifold 1404. Fluid manifold 1404 is fluidly connected to sub-manifold 1406, which can be applied to fluid via the flow slot of sensor device 1408 via the use of processing equipment 900. In a particular example, fluid can be driven or extracted from reactant container 1402 by pressurizing the container or by using a pump that extracts fluid from container 1402. Manifold 1404 can selectively cause reactants to flow to sub-manifold 1406 from reactant container 1402. Fluid can then flow through manifold 1404 and sub-manifold 1406 via the flow slot of sensor device 1408, based on the control of downstream valve 1410. When one of valve 1410 is open, fluid can flow through the flow slot of sensor device 1408 and enter waste container 1412.

[0048] In one example, each of the valves 1410 can be open, allowing continuous flow through the system. Alternatively, the sensor devices can be individually processed by selectively flowing reactants through the manifold 1404 and the sub-manifold 1406 and selectively through one or more of the sensor devices 1408 based on the position of the downstream valve 1410 of the sensor device 1408.

[0049] For example, the system may include a washing solution, an acid or alkaline cleaning treatment solution, and a sugar solution as described above. For example, a washing solution may be applied to one or more sensor devices 1408. The sensor device may include beads in a well or may be free of beads. The sensor device may be treated with an acid or alkaline treatment solution. In one example, pretreatment of the sensor device may affect the concentration of surface hydroxyls, affecting the signal associated with the pH measurement. The surface may be stabilized by applying a sugar solution through a flow cell (sensor device) and leaving a sugar coating on the sensor electrodes of the sensor device and optionally on the beads. The sensor device 1408 may be removed from the treatment device, dried and packaged, ready for shipping and storage.

[0050] As described above, the surface stabilized biosensor can be washed and used to detect biomolecular targets or related byproducts. Specifically, the biosensor, eg, sensor device, can be washed as described above and applied to a detection system, such as a sequencing system.

[0051] In one example, beads or particles that can be biomolecules or connected biomolecules can be applied to a biosensor for determining the characteristics of biomolecules. Beads can be applied after washing the sugar coating or before being treated with a sugar solution. Specifically, the biosensor can be used to sequence the nucleic acid or protein target sequence to be bound to the amplified beads or particles. For example, sequencing can include label-free DNA sequencing, and specifically, pH-based DNA sequencing. Beads or particles including DNA templates and having primers and polymerases that can be operatively bound are loaded into a reaction chamber (such as a micropore of a sensor device), followed by a cycle of repeated deoxynucleoside triphosphate (dNTP) addition and washing. Alternatively, beads can exist before washing, and target nucleic acids can be applied to beads. Such templates are typically connected as clonal populations of beads or particles, and such clonal populations are loaded into a reaction chamber. In each addition step of the cycle, when the next base in the template is the complementary sequence of the added dNTP, the polymerase extends the primer by incorporating the added dNTP. When one complementary base is present, there is one incorporation, when two complementary bases are present, there are two incorporations, when three complementary bases are present, there are three incorporations, etc. With each such incorporation, a hydrogen ion is released, and collectively, a population of templates releases hydrogen ions, causing a very slight change in the local pH of the reaction chamber that is detected by the electronic sensor.

[0052] Fig.15 The diagram illustrates an apparatus for performing pH-based nucleic acid sequencing. Each electronic sensor of the sensor apparatus generates an output signal that depends on the value of a reference voltage. Fig.15 In the embodiment, a housing 600 containing a fluid circuit 602 is connected to a reagent storage tank 614 through an inlet, and a channel 632 is connected to a waste storage tank 620 and a flow tank 634 by connecting a fluidic node 630 to an inlet 638 of a flow tank 634. The reagents from the storage tank 614 can be driven to the fluid circuit 602 by a variety of methods, including pressure, a pump (such as a syringe pump), gravity supply, etc., and are selected by controlling a valve 650. A control system 618 includes a controller for the valve 650, which generates a signal to open and close via an electrical connection 616. The control system 618 also includes controllers for other components of the system, such as a wash solution valve 624 connected thereto by a control line 622 and a reference electrode 628. The control system 618 may also include control and data acquisition functions for the flow tank 634. In one mode of operation, fluid circuit 602 delivers a series of selected reactants (1, 2, 3, 4, or 5) to flow cell 634 under programmed control of control system 618 so as to flow among the selected reactants, pre-coat and wash fluid circuit 602, and wash flow cell 634. Fluid entering flow cell 634 exits via outlet 640 and is deposited in waste container 636. Throughout such operation, the reactions or measurements occurring in flow cell 634 have a stable reference voltage because reference electrode 628 has a continuous (i.e., uninterrupted) electrolyte path to flow cell 634, but is only in physical contact with the wash solution.

[0053] Examples

[0054] Example 1

[0055] pH-based sequencing devices (Ion Torrent) were treated with different solutions including sugars or polymers. TM Proton I).

[0056] The device was prepared by flowing a series of wash solutions through the flow cell of the device. A solution including 5 wt% dodecylbenzenesulfonic acid (DBSA) in undecane was flowed through the flow cell for 1 minute. Isopropanol was flowed through the flow cell to remove DBSA from the undecane. Water was applied through the flow cell, followed by a 10 mM NaOH solution for 2:45 minutes. Water was applied through the flow cell, followed by isopropanol (IPA) and then nitrogen.

[0057] After drying under nitrogen, an aqueous solution including 10 wt% or 20 wt% of the selected sugar or polymer was applied through the flow cell. The control was untreated. The sugars were selected from sucrose, galactose and trehalose. The polymer was selected from polyethylene glycol polymers (PEG 200 or PEG 1000), polypropylene glycol, ethylene oxide / propylene oxide block copolymers (Pluronic P65) and polyols (Pluronic F127). After applying the solution, the flow cell was flushed with nitrogen. The coating uniformity of the device surface was observed. The device was further tested for initial bead loading uniformity and bead loading uniformity after aging (heating at 70°C for 7 days). In ion torrent TM Ion Chef TM On the chip device, an ion torrent is used. TM Kit for bead loading.

[0058] Those devices treated with sucrose, galactose, and trehalose showed desired uniformity and both initial and aged bead loading, providing control improvements. Polyol polymers showed similar improvements over the control. Ethylene oxide / propylene oxide copolymer solutions provided similar to slightly better bead loading over the control. PEG and propylene glycol polymers provided less desired bead loading than the control.

[0059] Example 2

[0060] A pH-based sequencing device (Ion Torrent Proton I) was treated with sugar solutions incorporating different surfactants.

[0061] The device was prepared by flowing a series of wash solutions through the flow cell of the device. A solution including 5 wt% dodecylbenzenesulfonic acid (DBSA) in undecane was flowed through the flow cell for 1 minute. Isopropanol was flowed through the flow cell to remove DBSA from the undecane. Water was applied through the flow cell, followed by a 10 mM NaOH solution for 2:45 minutes. Water was applied through the flow cell, followed by isopropanol (IPA) and then nitrogen.

[0062] After drying under nitrogen, an aqueous sugar solution including 10 wt% or 20 wt% sucrose and between 0.05 wt% and 0.2 wt% of a selected surfactant was applied via the flow cell. The surfactant was selected from 0.05 wt% nonionic fluorosurfactant (Thetawet 8150), 0.02 wt% nonionic surfactant (Triton X-100), 0.1 wt% alkyl polysaccharide surfactant (Multitrope), 0.2 wt% dioctyl sodium sulfosuccinate, or 0.2% zwitterionic surfactant (Anzergent 3-12). After applying the sugar solution, the flow cell was flushed with nitrogen. The coating uniformity of the device surface was observed.

[0063] The sugar solution including 10 wt% sucrose provided a more uniform coating and less image tailing than the sugar solution including 20 wt% sucrose. Each of the surfactants had a similar effect on uniformity. However, the Triton X-100 surfactant produced sucrose beads on the lid of the flow cell.

[0064] Example 3

[0065] To evaluate the ion torrent TM Stability of pre-loaded cartridges on a 541 chip, the chip (device) was pre-loaded with polyacrylamide beads, coated with sucrose solution, and vacuum sealed in a foil pouch with desiccant.

[0066] A set of 16 sets including Ion Torrent 541 chips (device) and associated polyacrylamide beads were loaded by spinning the solution with beads on the device for 2 minutes, foam scraping and rinsing and vacuum aspiration. The beads bind to oligonucleotides, which are used to capture the target polynucleotide and are extended to produce complementary copies of the target polynucleotide.

[0067] Half of the device was coated with a sucrose solution including 1431 g H2O, 358 g sucrose, and 3.5 g Anzergent 3- 12. Each of the devices was placed in a tray and vacuum sealed in a foil pouch for storage.

[0068] Devices were tested at 1, 3 and 10 days of storage. Devices were washed to remove the sucrose coating and amplified to generate beads bound to the polynucleotides to be sequenced.

[0069] Day 1 devices (whether coated with sucrose or not) demonstrated similar sequencing performance characterized by similar loading percentage, key signal, and q20 average performance. However, Day 3 devices (stored without sucrose coating) demonstrated significantly reduced sequencing performance, while Day 3 devices (stored with sucrose coating) maintained sequencing performance. Day 10 devices (stored with sucrose coating) also maintained sequencing performance.

[0070] In a first aspect, a sensor apparatus includes a substrate, a semiconductor device disposed on the substrate, the semiconductor device having a surface electrode structure, and a sugar coating formed over the surface electrode structure.

[0071] In one example of the first aspect, the sensor apparatus further includes a pore structure defined on the semiconductor device and defining a pore exposing the surface electrode structure, and a saccharide coating at least partially within the pore.

[0072] In additional examples of the first aspect and the above examples, the device further includes beads disposed in the wells, a sugar coating formed over the beads. In one example, the beads bind to the nucleic acid. In another example, the beads are hydrogel beads. In another example, the beads comprise a polymer selected from the group consisting of: agarose; polyethylene glycol; polyoxybutylene; diethylacrylamide; polyethylene oxide; polyacrylamide; polypropylene oxide; N,N-polydimethylacrylamide; poly(N-isopropylacrylamide); polyvinyl pyrrolidone; poly-N-hydroxyacrylamide; and any combination thereof. In a specific example, the polymer is polyacrylamide.

[0073] In another example of the first aspect and the above examples, the sensor device further includes a flow cell cover disposed on the substrate and defining the flow cell between the substrate and the flow cell cover. The surface electrode structure is accessible via the flow cell.

[0074] In another example of the first aspect and the above examples, the semiconductor device includes a field effect transistor having a gate electrode structure. The surface electrode structure forms at least a portion of the gate electrode structure.

[0075] In an additional example of the first aspect and the above examples, the surface electrode structure includes a conductive structure and a sensor layer disposed on the conductive structure. For example, the sensor layer includes a ceramic layer.

[0076] In another example of the first aspect and the above examples, the surface electrode structure includes a floating gate structure.

[0077] In another example of the first aspect and the above examples, the sugar coating includes a monosaccharide, a disaccharide, a polysaccharide, a derivative thereof, or a combination thereof. For example, the monosaccharide may include glucose, fructose, galactose, or a combination thereof. In another example, the disaccharide includes sucrose, trehalose, maltose, or lactose. For example, the disaccharide includes sucrose. In another example, the disaccharide includes trehalose. In another example, the sugar includes hyaluronic acid.

[0078] In a second aspect, a sensor apparatus includes a semiconductor substrate, a semiconductor device formed on the semiconductor substrate, and a pore structure formed above the semiconductor device and defining a pore, wherein the semiconductor device includes a field effect transistor having a gate structure responsive to conditions within the pore, and a sugar coating disposed within the pore and above the gate structure.

[0079] In one example of the second aspect, the sensor device further includes: a flow channel cover, which is disposed on the semiconductor substrate and the hole structure and defines the flow channel between the substrate and the flow channel cover, and the hole is exposed to the flow channel.

[0080] In another example of the second aspect and the above examples, the device further comprises beads disposed in the wells, a carbohydrate coating disposed on the beads. In one example, the beads bind to the nucleic acid. In another example, the beads are hydrogel beads. In another example, the beads comprise a polymer selected from the group consisting of: agarose; polyethylene glycol; polyoxybutylene; diethylacrylamide; polyethylene oxide; polyacrylamide; polypropylene oxide; N,N-polydimethylacrylamide; poly(N-isopropylacrylamide); polyvinyl pyrrolidone; poly-N-hydroxyacrylamide; and any combination thereof. In a specific example, the polymer is polyacrylamide.

[0081] In another example of the second aspect and the above examples, the gate structure includes a conductive structure and a sensor layer disposed on the conductive structure. For example, the sensor layer includes a ceramic layer.

[0082] In another example of the second aspect and the above examples, the gate structure includes a floating gate structure.

[0083] In additional examples of the second aspect and the above examples, the sugar coating includes a monosaccharide, a disaccharide, a polysaccharide, a derivative thereof, or a combination thereof. For example, the monosaccharide includes glucose, fructose, galactose, or a combination thereof. In another example, the disaccharide includes sucrose, trehalose, maltose, or lactose. For example, the disaccharide includes sucrose. In another example, the disaccharide includes trehalose. In another example, the sugar includes hyaluronic acid.

[0084] In a third aspect, a sequencing method includes flowing a wash solution through a sensor device. The sensor device includes a substrate, a semiconductor device disposed on the substrate, the semiconductor device having a surface electrode structure, and a carbohydrate coating formed above the surface electrode structure. The wash solution removes the carbohydrate coating. The method further includes applying a nucleic acid target to the sensor device, applying the sensor device to a sequencing system, and sequencing the nucleic acid target using the sequencing system.

[0085] In one example of the third aspect, the sugar coating comprises a monosaccharide, a disaccharide, a polysaccharide, a derivative thereof, or a combination thereof. For example, the monosaccharide comprises glucose, fructose, galactose, or a combination thereof. In another example, the disaccharide comprises sucrose, trehalose, maltose, or lactose. In one example, the disaccharide comprises sucrose. In another example, the disaccharide comprises trehalose. In another example, the sugar comprises hyaluronic acid.

[0086] In an additional example of the third aspect and the above examples, the device further includes a pore structure defining a hole on the surface electrode structure, and the device further includes a bead disposed in the hole. Applying the nucleic acid target to the sensor device includes contacting the nucleic acid target with the bead. In one example, the bead includes an oligonucleotide complementary to a portion of the nucleic acid target, and the method further includes amplifying the nucleic acid target to form a copy of the nucleic acid target on the bead. For example, the bead is a hydrogel bead. In one example, the bead includes a polymer selected from the group consisting of: agarose; polyethylene glycol; polybutylene oxide; diethyl acrylamide; polyethylene oxide; polyacrylamide; polypropylene oxide; N,N-polydimethylacrylamide; poly(N-isopropylacrylamide); polyvinyl pyrrolidone; poly-N-hydroxyacrylamide; and any combination thereof. In a specific example, the polymer is polyacrylamide.

[0087] In a fourth aspect, a method for preparing a sensor device includes applying a cleaning solution through a flow cell cover on a semiconductor substrate defining a flow cell, wherein the semiconductor substrate includes a plurality of field effect transistors, each of which includes a gate structure exposed to the flow cell; applying a sugar solution through the flow cell, wherein the solution includes sugar; and removing the sugar solution from the flow cell, wherein a sugar layer remains on the gate structure.

[0088] In an example of the fourth aspect, applying the wash solution includes flowing an alkaline solution through a flow cell prior to applying the solution comprising the sugar.

[0089] In an additional example of the fourth aspect and the above examples, the pore structure defines a hole on the gate structure, and the method further includes applying beads to the hole before applying the sugar solution. In one example, the beads are bound to the nucleic acid. In another example, the beads are hydrogel beads. In another example, the beads include a polymer selected from the group consisting of: agarose; polyethylene glycol; polybutylene oxide; diethyl acrylamide; polyethylene oxide; polyacrylamide; polypropylene oxide; N,N-polydimethylacrylamide; poly(N-isopropylacrylamide); polyvinyl pyrrolidone; poly-N-hydroxyacrylamide; and any combination thereof. For example, the polymer is polyacrylamide.

[0090] In another example of the fourth aspect and the above examples, applying the wash solution includes flowing a non-aqueous surfactant solution through a flow channel before applying the solution including the sugar. For example, the non-aqueous surfactant solution includes a non-aqueous solvent containing a sulfonic acid surfactant.

[0091] In another example of the fourth aspect and the above examples, the sugar includes a monosaccharide, a disaccharide, a polysaccharide, a derivative thereof, or a combination thereof. For example, the monosaccharide includes glucose, fructose, galactose, or a combination thereof. In another example, the disaccharide includes sucrose, trehalose, maltose, or lactose. For example, the disaccharide includes sucrose. In another example, the disaccharide includes trehalose. In another example, the sugar includes hyaluronic acid.

[0092] In additional examples of the fourth aspect and the above examples, the carbohydrate solution includes carbohydrate in a range of 5 wt % to 30 wt %.

[0093] In another example of the fourth aspect and the above examples, the carbohydrate solution includes a surfactant in the range of 0.01 wt% to 10.0 wt%. For example, the surfactant may include a zwitterionic surfactant. In another example, the surfactant includes a nonionic surfactant.

[0094] In a fifth aspect, a method for preparing a sensor device includes applying a flow cell cover on a semiconductor substrate to define a flow cell, the semiconductor substrate including a plurality of field effect transistors, each of which includes a gate structure exposed to the flow cell and a pore structure defining a hole; applying beads into the pores; applying a solution through the flow cell, the solution including a sugar; and removing the solution from the flow cell, with a sugar layer remaining on the gate structure.

[0095] In an example of the fifth aspect, the method further comprises flowing the alkaline solution through the flow cell before applying the solution comprising the sugar.

[0096] In another example of the fifth aspect and the above examples, the pore structure defines a hole on the gate structure, and the method further includes applying beads to the hole before applying the sugar solution. For example, the beads are bound to the nucleic acid. In one example, the beads are hydrogel beads. In another example, the beads include a polymer selected from the group consisting of: agarose; polyethylene glycol; polybutylene oxide; diethyl acrylamide; polyethylene oxide; polyacrylamide; polypropylene oxide; N,N-polydimethylacrylamide; poly(N-isopropylacrylamide); polyvinyl pyrrolidone; poly-N-hydroxyacrylamide; and any combination thereof. In a specific example, the polymer is polyacrylamide.

[0097] In another example of the fifth aspect and the above examples, the method further comprises flowing a non-aqueous surfactant solution through the flow channel before applying the solution comprising the sugar. For example, the non-aqueous surfactant solution comprises a non-aqueous solvent comprising a sulfonic acid surfactant.

[0098] In another example of the fifth aspect and the above examples, the sugar coating includes a monosaccharide, a disaccharide, a polysaccharide, a derivative thereof, or a combination thereof. For example, the monosaccharide includes glucose, fructose, galactose, or a combination thereof. In one example, the disaccharide includes sucrose, trehalose, maltose, or lactose. For example, the disaccharide includes sucrose. In another example, the disaccharide includes trehalose. In another example, the sugar includes hyaluronic acid.

[0099] In additional examples of the fifth aspect and the above examples, the carbohydrate solution includes carbohydrate in a range of 5 wt % to 30 wt %.

[0100] In another example of the fifth aspect and the above examples, the carbohydrate solution includes a surfactant in the range of 0.01 wt% to 10.0 wt%. For example, the surfactant includes a zwitterionic surfactant. In another example, the surfactant includes a nonionic surfactant.

[0101] In a sixth aspect, a processing system includes a plurality of reactant containers, a manifold in fluid communication with the plurality of reactant containers, and a processing device including a slidable deck for receiving a sensor device, a clamp having an elastic device guide, and an access manifold in fluid communication with the manifold and including an orifice connected to the flow channel fluid of the sensor device, wherein when the slidable deck is positioned under the clamp, the clamp is movable to push the slidable deck downward to engage the access manifold.

[0102] In one example of the sixth aspect, the slidable deck receives the sensor device with a flow slot opening facing downwardly of the sensor device, and the elastic device guides and engages a side of the sensor device opposite to the flow slot opening.

[0103] Such methods and devices formed using such methods provide technical advantages involving improved measurement quality.It has been found that signal quality may degrade variably, depending on factors related to shipping and storage.

[0104] Reduced variability in signal quality provides more uniform signal measurements, allowing for more accurate sequence detection.

[0105] Specifically, pH-based sensor devices, such as those used in pH-based sequencing, are sensitive to factors related to shipping and storage. It is believed that surface groups, such as surface hydroxyl groups, affect signal quality, and the concentration of such surface groups may be affected by factors related to packaging, shipping, and storage, such as temperature and humidity. The proposed system and method provide less variability in signal quality.

[0106] It should be noted that not all activities described in the general description or examples above are required, a portion of a specific activity may not be required, and one or more other activities in addition to the activities described may be performed. Furthermore, the order in which the activities are listed is not necessarily the order in which the activities are performed.

[0107] In the foregoing description, the concepts have been described with reference to specific embodiments. However, it is understood by those skilled in the art that various modifications and changes may be made without departing from the scope of the invention as set forth in the following claims. Therefore, the description and drawings should be viewed in an illustrative rather than a restrictive sense, and all such modifications are intended to be included within the scope of the invention.

[0108] As used herein, the terms "comprises / comprising", "includes / including", "has / having" or any other variation thereof are intended to cover a non-exclusive inclusion. For example, a process, method, article, or apparatus that comprises a list of features is not necessarily limited to only those features, but may include other features not expressly listed or other features inherent to the process, method, article, or apparatus. In addition, unless expressly stated to the contrary, "or" refers to an inclusive or, not an exclusive or. For example, a condition A or B is satisfied by any of the following: A is true (or exists) and B is false (or does not exist), A is false (or does not exist) and B is true (or exists), and both A and B are true (or exist).

[0109] Likewise, the use of "a" or "an" is used to describe elements and components described herein. This is done only for convenience and to give a general sense of the scope of the invention. Unless it is obvious that it is intended otherwise, this specification should be read as including one or at least one, and the singular also includes the plural, or vice versa.

[0110] Benefits, other advantages, and solutions to problems are described above with respect to specific embodiments. However, these benefits, advantages, solutions to problems, and any features that may make any benefit, advantage, or solution occur or become more significant should not be construed as important, necessary, or essential features of any or all claims.

[0111] After reading this specification, the skilled artisan will appreciate that, for clarity, certain features described herein in the context of separate embodiments may also be provided in combination in a single embodiment. Conversely, for brevity, various features described in the context of a single embodiment may also be provided individually or in any sub-combination. In addition, reference to values ​​stated in ranges includes every value within that range.

[0112] The present invention also includes:

[0113] 1. A sequencing method, comprising:

[0114] flowing a wash solution through a sensor device comprising:

[0115] substrate;

[0116] A semiconductor device disposed on the substrate, the semiconductor device having a surface electrode structure;

[0117] a pore structure defining pores on the surface electrode structure, beads disposed in the pores; and

[0118] a sugar coating formed over the surface electrode structure and the beads;

[0119] The washing solution removes the sugar coating;

[0120] applying a nucleic acid target to the sensor device;

[0121] applying the sensor device to a sequencing system; and

[0122] The nucleic acid target is sequenced using the sequencing system.

[0123] 2. The method according to item 1, wherein the sugar coating comprises monosaccharides, disaccharides, polysaccharides, derivatives thereof or combinations thereof.

[0124] 3. The method according to claim 2, wherein the monosaccharide comprises glucose, fructose, galactose or a combination thereof.

[0125] 4. The method according to claim 2, wherein the disaccharide comprises sucrose, trehalose, maltose or lactose.

[0126] 5. A method according to claim 4, wherein the disaccharide comprises sucrose.

[0127] 6. The method of claim 4, wherein the disaccharide comprises trehalose.

[0128] 7. The method of claim 2, wherein the carbohydrate comprises hyaluronic acid.

[0129] 8. The method according to any one of items 1 to 7, wherein applying a nucleic acid target to the sensor device comprises contacting the nucleic acid target with the beads.

[0130] 9. A method according to claim 8, wherein the bead comprises an oligonucleotide complementary to a portion of the nucleic acid target, and the method further comprises amplifying the nucleic acid target to form a copy of the nucleic acid target on the bead.

[0131] 10. The method of claim 8, wherein the beads are hydrogel beads.

[0132] 11. A method according to claim 8, wherein the beads comprise a polymer selected from the group consisting of: agarose; polyethylene glycol; polyoxybutylene; diethylacrylamide; polyethylene oxide; polyacrylamide; polypropylene oxide; N,N-polydimethylacrylamide; poly(N-isopropylacrylamide); polyvinylpyrrolidone; poly-N-hydroxyacrylamide; and any combination thereof.

[0133] 12. The method according to item 11, wherein the polymer is polyacrylamide.

[0134] 13. A method of preparing a sensor device, the method comprising:

[0135] applying a cleaning solution through a flow cell cover on a semiconductor substrate defining a flow cell, the semiconductor substrate comprising a plurality of field effect transistors, each of which comprises a gate structure exposed to the flow cell, an aperture structure defining an aperture on the gate structure, and a bead disposed in the aperture;

[0136] applying a sugar solution through the flow cell, the solution comprising sugar; and

[0137] The sugar solution is removed from the flow cell, and a layer of the sugar remains on the gate structure and the beads.

[0138] 14. The method of item 13, further comprising applying beads to the wells prior to applying the sugar solution.

[0139] 15. A method according to item 14, wherein the beads are bound to nucleic acids.

[0140] 16. A method according to item 14, wherein the beads are hydrogel beads.

[0141] 17. A method according to claim 14, wherein the beads comprise a polymer selected from the group consisting of: agarose; polyethylene glycol; polyoxybutylene; diethylacrylamide; polyethylene oxide; polyacrylamide; polypropylene oxide; N,N-polydimethylacrylamide; poly(N-isopropylacrylamide); polyvinylpyrrolidone; poly-N-hydroxyacrylamide; and any combination thereof.

[0142] 18. The method of item 17, wherein the polymer is polyacrylamide.

[0143] 19. The method of any one of items 13 to 18, wherein applying the cleaning solution comprises flowing an alkaline solution through the flow cell prior to applying the carbohydrate solution.

[0144] 20. The method of any one of items 13 to 19, wherein applying the cleaning solution comprises flowing a non-aqueous surfactant solution through the flow channel prior to applying the carbohydrate solution.

[0145] 21. A method according to claim 20, wherein the non-aqueous surfactant solution comprises a non-aqueous solvent containing a sulfonic acid surfactant.

[0146] 22. The method according to any one of items 13 to 21, wherein the carbohydrate comprises a monosaccharide, a disaccharide, a polysaccharide, a derivative thereof, or a combination thereof.

[0147] 23. The method of claim 22, wherein the monosaccharide comprises glucose, fructose, galactose or a combination thereof.

[0148] 24. The method of claim 22, wherein the disaccharide comprises sucrose, trehalose, maltose or lactose.

[0149] 25. A method according to claim 24, wherein the disaccharide comprises sucrose.

[0150] 26. A method according to claim 24, wherein the disaccharide comprises trehalose.

[0151] 27. The method of claim 22, wherein the carbohydrate comprises hyaluronic acid.

[0152] 28. A method according to any one of items 13 to 27, wherein the carbohydrate solution comprises the carbohydrate in the range of 5 wt% to 30 wt%.

[0153] 29. A method according to any one of items 13 to 28, wherein the carbohydrate solution comprises a surfactant in the range of 0.01 wt% to 10.0 wt%.

[0154] 30. A method according to claim 29, wherein the surfactant is a zwitterionic surfactant.

[0155] 31. A method according to claim 29, wherein the surfactant is a non-ionic surfactant.

[0156] 32. A sensor device comprising:

[0157] substrate;

[0158] A semiconductor device disposed on the substrate, the semiconductor device having a surface electrode structure;

[0159] a hole structure defined on the semiconductor device and defining a hole exposing the surface electrode structure;

[0160] a bead disposed in the well; and

[0161] A sugar coating is formed over the surface electrode structure and the beads.

[0162] 33. A sensor device according to item 32, wherein the beads are bound to nucleic acids.

[0163] 34. A sensor device according to item 32 or item 33, wherein the beads are hydrogel beads.

[0164] 35. A sensor device according to any one of items 32 to 34, wherein the beads comprise a polymer selected from the group consisting of: agarose; polyethylene glycol; polyoxybutylene; diethylacrylamide; polyethylene oxide; polyacrylamide; polypropylene oxide; N,N-polydimethylacrylamide; poly(N-isopropylacrylamide); polyvinylpyrrolidone; poly-N-hydroxyacrylamide; and any combination thereof.

[0165] 36. A sensor device according to item 35, wherein the polymer is polyacrylamide.

[0166] 37. A sensor device according to any one of items 32 to 36, further comprising: a flow channel cover, which is disposed on the substrate and defines the flow channel between the substrate and the flow channel cover; and the surface electrode structure accessible through the flow channel.

[0167] 38. A sensor device according to any one of items 32 to 37, wherein the semiconductor device comprises a field effect transistor having a gate electrode structure, the surface electrode structure forming at least a part of the gate electrode structure.

[0168] 39. A sensor device according to any one of items 32 to 38, wherein the surface electrode structure comprises a conductive structure and a sensor layer disposed on the conductive structure.

[0169] 40. A sensor device according to item 39, wherein the sensor layer comprises a ceramic layer.

[0170] 41. A sensor device according to any one of items 32 to 40, wherein the surface electrode structure comprises a floating gate structure.

[0171] 42. The sensor device of any one of items 32 to 41, wherein the carbohydrate coating comprises monosaccharides, disaccharides, polysaccharides, derivatives thereof, or combinations thereof.

[0172] 43. A sensor device according to claim 42, wherein the monosaccharide comprises glucose, fructose, galactose or a combination thereof.

[0173] 44. A sensor device according to item 42, wherein the disaccharide comprises sucrose, trehalose, maltose or lactose.

[0174] 45. A sensor device according to claim 44, wherein the disaccharide comprises sucrose.

[0175] 46. ​​A sensor device according to claim 44, wherein the disaccharide comprises trehalose.

[0176] 47. A sensor device according to claim 42, wherein the sugar comprises hyaluronic acid.

[0177] 48. A sensor device comprising:

[0178] Semiconductor substrate;

[0179] a semiconductor device formed on the semiconductor substrate;

[0180] a pore structure formed above the semiconductor device and defining a pore, wherein the semiconductor device includes a field effect transistor having a gate structure responsive to a condition within the pore;

[0181] a bead disposed in the well; and

[0182] A sugar coating is disposed within the pores and over the gate structure and the beads.

[0183] 49. The sensor device according to item 48 further comprises: a flow channel cover, which is disposed on the semiconductor substrate and the hole structure and defines a flow channel between the substrate and the flow channel cover, and the hole is exposed to the flow channel.

[0184] 50. A sensor device according to item 48 or item 49, wherein the beads are bound to nucleic acids.

[0185] 51. A sensor device according to any one of items 48 to 50, wherein the beads are hydrogel beads.

[0186] 52. A sensor device according to any one of items 48 to 51, wherein the beads comprise a polymer selected from the group consisting of: agarose; polyethylene glycol; polyoxybutylene; diethylacrylamide; polyethylene oxide; polyacrylamide; polypropylene oxide; N,N-polydimethylacrylamide; poly(N-isopropylacrylamide); polyvinylpyrrolidone; poly-N-hydroxyacrylamide; and any combination thereof.

[0187] 53. A sensor device according to item 52, wherein the polymer is polyacrylamide.

[0188] 54. A sensor device according to any one of items 48 to 53, wherein the gate structure comprises a conductive structure and a sensor layer disposed on the conductive structure.

[0189] 55. A sensor device according to item 54, wherein the sensor layer comprises a ceramic layer.

[0190] 56. A sensor device according to any one of items 48 to 55, wherein the gate structure comprises a floating gate structure.

[0191] 57. The sensor device of any one of items 48 to 56, wherein the sugar coating comprises monosaccharides, disaccharides, polysaccharides, derivatives thereof, or combinations thereof.

[0192] 58. A sensor device according to claim 57, wherein the monosaccharide comprises glucose, fructose, galactose or a combination thereof.

[0193] 59. A sensor device according to item 57, wherein the disaccharide comprises sucrose, trehalose, maltose or lactose.

[0194] 60. A sensor device according to claim 59, wherein the disaccharide comprises sucrose.

[0195] 61. A sensor device according to claim 59, wherein the disaccharide comprises trehalose.

[0196] 62. A sensor device according to claim 57, wherein the sugar comprises hyaluronic acid.

[0197] 63. A method of preparing a sensor device, the method comprising:

[0198] Applying a flow channel cover on a semiconductor substrate to define a flow channel, the semiconductor substrate comprising a plurality of field effect transistors, each of which comprises a gate structure exposed to the flow channel, and a hole structure defining a hole on the gate structure;

[0199] depositing beads in the wells;

[0200] applying a sugar solution through the flow cell, the sugar solution comprising sugar; and

[0201] The sugar solution is removed from the flow cell, and a layer of sugar remains on the gate structure.

[0202] 64. A method according to claim 63, wherein the beads are bound to nucleic acids.

[0203] 65. A method according to claim 63 or claim 64, wherein the beads are hydrogel beads.

[0204] 66. A method according to any one of items 63 to 65, wherein the beads comprise a polymer selected from the group consisting of: agarose; polyethylene glycol; polyoxybutylene; diethylacrylamide; polyethylene oxide; polyacrylamide; polypropylene oxide; N,N-polydimethylacrylamide; poly(N-isopropylacrylamide); polyvinylpyrrolidone; poly-N-hydroxyacrylamide; and any combination thereof.

[0205] 67. A method according to item 66, wherein the polymer is polyacrylamide.

[0206] 68. The method of any one of items 63 to 67, further comprising flowing a base solution through the flow cell prior to applying the sugar solution.

[0207] 69. The method of any one of items 63 to 68, further comprising flowing a non-aqueous surfactant solution through the flow cell prior to applying the carbohydrate solution.

[0208] 70. A method according to claim 69, wherein the non-aqueous surfactant solution comprises a non-aqueous solvent containing a sulfonic acid surfactant.

[0209] 71. The method of any one of items 63 to 70, wherein the carbohydrate comprises a monosaccharide, a disaccharide, a polysaccharide, a derivative thereof, or a combination thereof.

[0210] 72. A method according to item 71, wherein the monosaccharide comprises glucose, fructose, galactose or a combination thereof.

[0211] 73. A method according to claim 71, wherein the disaccharide comprises sucrose, trehalose, maltose or lactose.

[0212] 74. A method according to claim 73, wherein the disaccharide comprises sucrose.

[0213] 75. A method according to claim 73, wherein the disaccharide comprises trehalose.

[0214] 76. A method according to claim 71, wherein the carbohydrate comprises hyaluronic acid.

[0215] 77. A method according to any one of items 63 to 76, wherein the carbohydrate solution comprises the carbohydrate in the range of 5 wt% to 30 wt%.

[0216] 78. A method according to any one of items 63 to 77, wherein the carbohydrate solution comprises a surfactant in the range of 0.01 wt% to 10.0 wt%.

[0217] 79. A method according to claim 78, wherein the surfactant comprises a zwitterionic surfactant.

[0218] 80. A method according to claim 78, wherein the surfactant comprises a non-ionic surfactant.

[0219] 81. A processing system comprising:

[0220] a plurality of reactant containers;

[0221] a manifold in fluid communication with the plurality of reactant containers; and

[0222] A processing device comprising a slidable deck for receiving a sensor device; a clamp having an elastic device guide; and an access manifold that is fluidly connected to the manifold and includes an orifice that is fluidly connected to a flow channel of the sensor device, and when the slidable deck is positioned under the clamp, the clamp is movable to push the slidable deck downward to engage the access manifold.

[0223] 82. A processing system according to item 81, wherein the slidable deck receives the sensor device with a flow slot opening facing downwardly of the sensor device, and the elastic device guide engages a side of the sensor device opposite to the flow slot opening.

Claims

1. A method for preparing a sensor device, the method comprising: applying a cleaning solution through the flow cell; The flow cell is defined between a substrate and a flow cell cover; A semiconductor device is disposed on a substrate, wherein applying a cleaning solution through the flow tank includes applying the cleaning solution onto the semiconductor device; applying a sugar solution through the flow cell and across the semiconductor device, the solution comprising sugar; and The sugar solution is removed from the flow cell, and the sugar coating remains on the surface electrode structure of the semiconductor device. wherein the sugar solution comprises a sugar in the range of 5 wt % to 30 wt % and a surfactant in the range of 0.01 wt % to 10.0 wt %, the sugar comprising a monosaccharide, a disaccharide or a combination thereof, and the surfactant comprising a nonionic fluorosurfactant, an alkyl polysaccharide surfactant, an alkyl sulfonate surfactant or a zwitterionic surfactant, The semiconductor device includes a field effect transistor having a gate electrode structure, and the surface electrode structure forms at least a part of the gate electrode structure.

2. The method of claim 1, wherein applying the cleaning solution comprises flowing an alkaline solution through the flow cell before flowing the carbohydrate solution.

3. The method of claim 2, wherein flowing the alkaline solution through the flow cell comprises flowing a sodium hydroxide solution through the flow cell.

4. The method of claim 1, wherein applying the cleaning solution comprises flowing a non-aqueous surfactant solution through a flow cell prior to applying the carbohydrate solution.

5. The method of claim 4, wherein the non-aqueous surfactant solution comprises a sulfonic acid surfactant in a non-aqueous solvent.

6. The method of claim 5, wherein the sulfonic acid surfactant comprises dodecylsulfonic acid, dioctylsulfosuccinic acid or dodecylbenzenesulfonic acid and salts thereof.

7. The method of claim 5, wherein the non-aqueous surfactant solution is 5 wt% dodecylbenzenesulfonic acid in undecane.

8. The method of claim 1, wherein the monosaccharide comprises glucose, fructose or galactose.

9. The method of claim 1, wherein the disaccharide comprises sucrose, trehalose, maltose or lactose.

10. The method of claim 1, wherein the surfactant-containing sugar solution is a sucrose solution having sucrose in a range of 10 to 20 wt% and an alkyl polysaccharide surfactant in a range of 0.05 to 0.1 wt%.

11. The method of claim 1, wherein the carbohydrate solution containing a surfactant is a sucrose solution having sucrose in a range of 10 wt% to 20 wt% and a zwitterionic surfactant in a range of 0.05 wt% to 0.2 wt%.

12. A sequencing method, comprising: applying a washing solution through a sensor device including a semiconductor device including an aperture structure defining an aperture on each of surface electrode structures of the semiconductor device; A sugar coating formed on a surface electrode structure of a semiconductor device; Remove the sugar coating with a washing solution; loading a well of a semiconductor device with a sample of beads capable of binding multiple copies of a target nucleic acid; applying the sensor device to the sequencing system; and Sequencing the target nucleic acid using a sequencing system, The sugar coating is formed by a sugar solution. The sugar solution comprises a sugar in the range of 5 wt % to 30 wt % and a surfactant in the range of 0.01 wt % to 10.0 wt %, the sugar comprising a monosaccharide, a disaccharide or a combination thereof, and the surfactant comprising a nonionic fluorosurfactant, an alkyl polysaccharide surfactant, an alkyl sulfonate surfactant or a zwitterionic surfactant, The semiconductor device includes a field effect transistor having a gate electrode structure, and the surface electrode structure forms at least a part of the gate electrode structure.

13. The method of claim 12, wherein the surfactant-containing sugar solution is a sucrose solution having sucrose in a range of 10 to 20 wt% and an alkyl polysaccharide surfactant in a range of 0.05 to 0.1 wt%.

14. The method of claim 12, wherein the carbohydrate solution containing a surfactant is a sucrose solution having sucrose in a range of 10 wt% to 20 wt% and a zwitterionic surfactant in a range of 0.05 wt% to 0.2 wt%.

15. The method of claim 12, wherein the sensor device comprises an array of chemical field effect transistor (chemFET) sensors.

16. A sensor device comprising: A substrate, a semiconductor device disposed on the substrate, and a flow channel cover, wherein the flow channel is defined between the substrate and the flow channel cover; an integrated unit, the integrated unit comprising a microwell array and a sensor array, which forms a lower wall of a flow chamber of a flow cell; and a protective water-soluble sugar coating formed on the lower wall, wherein the protective water-soluble sugar coating is configured to be removed prior to use of the sensor device, The sugar coating is formed by a sugar solution. The sugar solution comprises a sugar in the range of 5 wt % to 30 wt % and a surfactant in the range of 0.01 wt % to 10.0 wt %, the sugar comprising a monosaccharide, a disaccharide or a combination thereof, and the surfactant comprising a nonionic fluorosurfactant, an alkyl polysaccharide surfactant, an alkyl sulfonate surfactant or a zwitterionic surfactant, The semiconductor device includes a field effect transistor having a gate electrode structure, and the surface electrode structure forms at least a part of the gate electrode structure.

17. The sensor device of claim 16, wherein the sensor array is an array of chemical field effect transistor (chemFET) sensors.

18. A sequencing method comprising: flowing a wash solution through a lower wall of a flow cell of a sensor device comprising a substrate, a semiconductor device disposed on the substrate, and a flow cell cover, the lower wall comprising an integrated unit of a microwell array formed on an array of chemical FET sensors, beads disposed in the microwell array, and a sugar coating formed over the beads; The washing solution removes the sugar coating; Connect the sensor device to a sequencing system comprising: Communications circuitry in electronic communication with the array of chemical FET sensors; and a container and a fluid control member in fluid communication with the flow cell; applying a nucleic acid target to the sensor device; and Using the sequencing system to sequence the nucleic acid target, The sugar coating is formed by a sugar solution. The sugar solution comprises a sugar in the range of 5 wt % to 30 wt % and a surfactant in the range of 0.01 wt % to 10.0 wt %, the sugar comprising a monosaccharide, a disaccharide or a combination thereof, and the surfactant comprising a nonionic fluorosurfactant, an alkyl polysaccharide surfactant, an alkyl sulfonate surfactant or a zwitterionic surfactant, The semiconductor device includes a field effect transistor having a gate electrode structure, and the surface electrode structure forms at least a part of the gate electrode structure.

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