Methods and apparatus for detecting molecular interactions using FET arrays

• US 8,540,865 B2
• Filed: 09/08/2011
• Issued: 09/24/2013
• Est. Priority Date: 12/14/2006
• Status: Active Grant

• Current Assignee: Life Technologies Corporation (Thermo Fisher Scientific Incorporated)
• Original Assignee: Life Technologies Corporation (Thermo Fisher Scientific Incorporated)
• Inventors: Rothberg, Jonathan, Hinz, Wolfgang
• Primary Examiner(s): Ball, J. Christopher
• Application Number:
  US13/228,058
• Publication Number:
  US 20120061255A1
• Time in Patent Office: 747 Days
• Field of Search: 257/253, 205/789, 205/792, 205/793.5, 422 8201- 8203, 435/6, 435/285.1, 435/287.1, 435/287.3, 436103-105, 436/150, 436/182, 506/1, 506/9, 204/403.01, 204/416, 204/433
• US Class Current: 205/793.5
• CPC Class Codes: C12Q 1/6825 Nucleic acid detection involving sensors
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: G01N 27/26 by investigating electrochemical variables; by using electrolysis or electrophoresis
• CPC Class Codes: G01N 27/4145 specially adapted for biomolecules, e.g. gate electrode with immobilised receptors
• CPC Class Codes: G01N 27/4148 Integrated circuits therefor, e.g. fabricated by CMOS processing CMOS processing per se H01L21/82
• CPC Class Codes: G01N 33/54373 involving physiochemical end-point determination, e.g. wave-guides, FETS, gratings
• CPC Class Codes: G01N 33/6818 Sequencing of polypeptides
• CPC Class Codes: H01L 29/78 with field effect produced by an insulated gate H01L29/7725, H01L29/775, H01L29/778 take precedence
• CPC Class Codes: H01L 29/788 with floating gate H01L29/78391 takes precedence
• CPC Class Codes: H01L 2924/01006 Carbon [C]

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

1. A method for detecting biomolecular binding interactions 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 a nucleic acid sample in proximity to or in contact with at least a portion of the sensors of the array;

providing at least one metabolite in proximity to or in contact with at least a portion of the sensors of the array wherein metabolite interactions with the nucleic acid sample effectuate changes in at least one electrical property of at least a portion of the sensors of the array; and

identifying binding interactions between the at least one metabolite and the nucleic acid sample by detecting the changes in electrical properties of at least a portion of the sensors of the array.

2. The method of claim 1, wherein the sensors of the array are associated with or capacitively coupled to at least one reaction chamber containing the nucleic acid sample and the at least one metabolite.

3. The method of claim 1, wherein the nucleic acid sample comprises RNA species, DNA species, nucleic acid analog species or combinations thereof.

4. The method of claim 1, wherein the nucleic acid sample or the at least one metabolite is immobilized, bound to, or coupled with the sensors of the array.

5. The method of claim 4, wherein the nucleic acid sample or the at least one metabolite is covalently or non-covalently bound to or coupled with at least a portion of the sensors of the array.

6. The method of claim 1, wherein the nucleic acid sample or the at least one metabolite is bound to or coupled with the passivation layer.

7. The method of claim 1, wherein the changes in electrical properties of the sensors of the array comprise changes in voltage or current.

8. The method of claim 1, wherein the nucleic acid sample and the at least one metabolite are unlabeled or unmodified.

9. A method of determining a binding interaction between a nucleic acid sample and at least one metabolite, the method comprising:

providing a chemical-sensitive field effect transistor (chemFET) array comprising at least 10⁵ chemFETs formed in a substrate and a nucleic acid sample or at least one metabolite associated therewith, the chemFETs 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;

contacting the chemFET array with the at least one metabolite when the nucleic acid sample is associated therewith or contacting the chemFET array with the nucleic acid sample when the at least one metabolite is associated with the chemFET array;

providing suitable conditions for association or coupling between the nucleic acid sample and the at least one metabolite;

washing the chemFET array to at least partially remove unassociated or uncoupled nucleic acid sample or metabolite; and

detecting changes in the electrical properties of the chemFET array indicative of interactions between the nucleic acid sample and the at least one metabolite.

10. The method of claim 9, wherein the nucleic acid sample comprises RNA species, DNA species, nucleic acid analog species or combinations thereof.

11. The method of claim 10, wherein the chemFET array is contacted with a plurality of nucleic acid samples or metabolites.

12. The method of claim 9, wherein the floating gate of each chemFET has substantially zero trapped charge, thereby reducing variations in sensitivity between the chemFETs.

13. The method of claim 9, wherein the nucleic acid sample or the at least one metabolite is immobilized, bound or coupled to at least a portion of the chemFETs of the chemFET array.

14. The method of claim 9, wherein the changes in electrical properties of the chemFET array comprises changes in voltage or current.

15. An apparatus for determining a binding interaction between a nucleic acid sample and a metabolite, the apparatus comprising:

a chemical-sensitive field effect transistor (chemFET) array comprising at least 10⁵ chemFETs formed in a substrate and a nucleic acid sample or a metabolite disposed thereon or associated therewith, the chemFETs 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;

a fluidics assembly comprising;

a reaction assembly for contacting the chemFET with the metabolite when the nucleic acid sample is disposed on or associated with the chemFET or an assembly for contacting the chemFET with the nucleic acid sample when the metabolite is disposed on or associated therewith the chemFET;

a washing assembly for removing at least a portion of unbound metabolite or nucleic acid sample from the chemFET; and

a detection system for detecting an electrical output from the chemFET,

wherein the electrical output is indicative of a binding interaction between the nucleic acid sample and the metabolite.

16. The apparatus of claim 15, wherein the floating gate of each chemFET has substantially zero trapped charge, thereby reducing variations in sensitivity between the chemFETs.

17. A method for detecting biomolecular activity comprising:

providing a sample analyzer comprising a plurality of chemical-sensitive field effect transistors (chemFETs), the chemFETs comprising 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 a biological sample in proximity to or in contact with at least a portion of the chemFETs;

providing at least one chemical compound in proximity to or in contact with at least a portion of the chemFETs wherein interactions or reactions with the biological sample effectuate changes in at least one electrical property of at least a portion of the chemFETs; and

identifying interactions or reactions between the at least one chemical compound and the biological sample by detecting the changes in electrical properties of at least a portion of the chemFETs.

18. The method of claim 17, wherein the biological sample comprises at least one protein molecule, nucleic acid molecule, or combination thereof.