# US 8,540,866 B2 · Methods and apparatus for detecting molecular interactions using FET arrays > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 8,540,866 B2 - Document ID: US8540866B2 - Status: Granted - Kind: B2 - Application number: 13/229,402 - Filed: 2011-09-09 - Published: 2012-04-12 - Granted: 2013-09-24 - Earliest claimed: 2006-12-14 - Assignees: Life Technologies Corporation - Applicants: Jonathan Rothberg; Wolfgang Hinz - Inventors: Jonathan Rothberg; Wolfgang Hinz - Web page: https://patentgrep.com/patent/US8540866B2 ## CPC - C12Q 1/6825: Nucleic acid detection involving sensors - C12Q 1/6874: involving nucleic acid arrays, e.g. sequencing by hybridisation - G01N 27/26: by investigating electrochemical variables; by using electrolysis or electrophoresis - G01N 27/4145: {specially adapted for biomolecules, e.g. gate electrode with immobilised receptors} - G01N 27/4148: {Integrated circuits therefor, e.g. fabricated by CMOS processing} - G01N 33/54373: {involving physiochemical end-point determination, e.g. wave-guides, FETS, gratings} - G01N 33/6818: {Sequencing of polypeptides} - H10D 30/60: Insulated-gate field-effect transistors [IGFET] (H10D30/40 takes precedence) - H10D 30/68: Floating-gate IGFETs - C12Q 1/6869: Methods for sequencing - C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES - G01N: INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES (measuring or testing apparatus or processes other than immunoassay, involving enzymes or microorganisms C12M, C12Q) - H10D: INORGANIC ELECTRIC SEMICONDUCTOR DEVICES ## Abstract Methods and apparatuses relating to large scale FET arrays for analyte detection and measurement are provided. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes. ## Claims ### Claim 1 A method for detecting bimolecular interactions, the method comprising: providing a sample analyzer comprising an array of at least 105 sensors formed in a substrate, the sensors comprising a field-effect transistor including a gate oxide, a floating gate comprising conductors formed in a plurality of conductor layers and electrically coupled to one another, and a passivation layer overlying the floating gate, the sample analyzer further comprising signal lines for the sensors within at least one of the conductor layers; disposing at least one antibody in proximity to or in contact with at least a portion of the sensors of the array; disposing at least one antigen in proximity to or in contact with at least a portion of the sensors of the array wherein interactions between the at least one antibody and the at least one antigen effectuate changes in at least one electrical property of at least a portion of the sensors of the array; and identifying interactions between the at least one antibody and the at least one antigen by detecting the changes in electrical properties of at least a portion of the sensors of the array. ### Claim 2 (depends on 1) The method of claim 1, wherein the at least one antibody or the at least one antigen is immobilized, bound to, or coupled with the portion of the sensors of the array. ### Claim 3 (depends on 1) The method of claim 1, wherein the at least one antibody or the at least one antigen is bound to or coupled with the passivation layer. ### Claim 4 (depends on 1) The method of claim 1, wherein the changes in electrical properties of the sensors of the array comprise changes in voltage or current. ### Claim 5 (depends on 1) The method of claim 1, wherein the at least one antibody and the at least one antigen are unlabeled or unmodified. ### Claim 6 (depends on 1) The method of claim 1, wherein the gate of each sensor has substantially zero trapped charge, thereby reducing variations in sensitivity between the sensors of the array. ### Claim 7 A method for detecting bimolecular interactions, the method comprising: providing a sample analyzer comprising a plurality of sensors formed in a substrate, the sensors comprising a field-effect transistor having a gate oxide, a floating gate comprising conductors formed in a plurality of conductor layers and electrically coupled to one another, and a passivation layer overlying the floating gate, the sample analyzer further comprising signal lines for the sensors within at least one of the conductor layers; disposing at least one first protein species in proximity to or in contact with at least a portion of the sensors of the array; disposing at least one second protein species in proximity to or in contact with at least a portion of the sensors of the array wherein interactions between the at least one first protein species and the at least one second protein species effectuate changes in at least one electrical property of at least a portion of the sensors of the array; and identifying interactions between the at least one first protein species and the at least one second protein species by detecting the changes in electrical properties of at least a portion of the sensors of the array. ### Claim 8 (depends on 7) The method of claim 7, wherein the at least one first protein species or the at least one second protein species is immobilized, bound to, or coupled with the portion of the sensors of the array. ### Claim 9 (depends on 7) The method of claim 7, the at least one first protein species or the at least one second protein species is bound to or coupled with the passivation layer. ### Claim 10 (depends on 7) The method of claim 7, wherein the changes in electrical properties of the sensors of the arrays comprise changes in voltage or current. ### Claim 11 (depends on 7) The method of claim 7, wherein the at least one first protein species and the at least one second protein species are unlabeled or unmodified. ### Claim 12 (depends on 7) The method of claim 7, wherein the floating gate of each sensor of the array has substantially zero trapped charge, thereby reducing variations in sensitivity between the chemFETs. ### Claim 13 A method for detecting molecular interactions, the method comprising: providing a sample analyzer comprising an array of at least 105 sensors formed in a substrate, the sensors comprising a field-effect transistor having a gate oxide, a floating gate comprising conductors formed in a plurality of conductor layers and electrically coupled to one another, and a passivation layer overlying the floating gate, the sample analyzer further comprising signal lines for the sensors within at least one of the conductor layers; disposing at least one first molecular species in proximity to or in contact with at least a portion of the sensors of the array; disposing at least one second molecular species in proximity to or in contact with at least a portion of the sensors of the array wherein interactions between the at least one first molecular species and the at least one second molecular species effectuate changes in at least one electrical property of at least a portion of the sensors of the array; and identifying interactions or reactions between the at least one first molecular species and the at least one second molecular species by detecting the changes in electrical properties of at least a portion of the chemFETs. ### Claim 14 (depends on 13) The method of claim 13, wherein the molecular interaction or reaction between the at least one first molecular species and the at least one second molecular species is a binding or coupling interaction. ### Claim 15 (depends on 13) The method of claim 13, wherein the at least one first molecular species and the at least one second molecular species are members of a binding or coupling pair. ### Claim 16 (depends on 13) The method of claim 13, wherein the molecular interaction or reaction between the at least one first molecular species and the at least one second molecular species is a hybridization or affinity interaction. ### Claim 17 (depends on 13) The method of claim 13, wherein the change in at least one electrical property of at least a portion of the sensors of the array is the voltage or current change produced by a change in ion concentration or ion localization resulting from the interaction or reaction of the at least one first molecular species with the at least one second molecular species. ### Claim 18 (depends on 13) The method of claim 13, wherein the first molecular species comprises an enzyme, the second molecular species comprises a substrate for the enzyme, and the enzyme reacts with the substrate to effectuate a chance in the at least one electrical property of the sensors of the array. ### Claim 19 A method for detecting molecular interactions, the method comprising: providing a sample analyzer comprising a plurality of chemical-sensitive field effect transistors (chemFETs); disposing at least one first molecular species comprising an enzyme in proximity to or in contact with at least a portion of the chemFETs; disposing at least one second molecular species comprising a substrate for the enzyme in proximity to or in contact with at least a portion of the chemFETs wherein the enzyme reacts with the substrate to form a reaction intermediate, the reaction intermediate effectuates changes in at least one electrical property of at least a portion of the chemFETs; and identifying reactions between the at least one first molecular species and the at least one second molecular species by detecting the reaction intermediate through changes in electrical properties of at least a portion of the chemFETs. ### Claim 20 (depends on 19) The method of claim 19, wherein a product or byproduct from the reaction of the enzyme and the substrate is detectable by the chemFETs. ### Claim 21 A method for detecting molecular interactions, the method comprising: providing a sample analyzer comprising a plurality of chemical-sensitive field effect transistors (chemFETs); disposing at least one first molecular species comprising an enzyme in proximity to or in contact with at least a portion of the chemFETs; disposing at least one second molecular species comprising an inhibitor of the enzyme in proximity to or in contact with at least a portion of the chemFETs wherein inhibition of enzyme activity effectuates changes in at least one electrical property of at least a portion of the chemFETs; and identifying inhibition of enzyme activity through changes in electrical properties of at least a portion of the chemFETs. ### Claim 22 (depends on 21) The method of claim 21, wherein the interaction of the enzyme and the inhibitor is indirectly detected.