Methods and apparatus for detecting molecular interactions using FET arrays

• US 9,039,888 B2
• Filed: 09/23/2013
• Issued: 05/26/2015
• 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:
  US14/033,934
• Publication Number:
  US 20140080719A1
• Time in Patent Office: 610 Days
• Field of Search: 257/235, 205/789, 205/792, 205/793.5, 422 8201- 8203, 435/6, 435/285.1, 435/287.1, 435/287.2, 436103-105, 506/1, 506/9
• 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 sequencing a polypeptide, comprising:

disposing a plurality of polypeptides into each of a plurality of reaction chambers, at least one reaction chamber of the plurality of reaction chambers coupled to at least one chemical-sensitive field effect transistor (chemFET) having a floating gate;

sequentially introducing amino acyl synthetases into the at least one reaction chamber, the amino acyl synthetase operable to bind to a specific amino acid when present at a free end of the polypeptide;

detecting the presence of an amino acyl synthetase bound to the free end of the polypeptide; and

cleaving the amino acid from the free end of the polypeptide.

2. The method of claim 1, wherein detecting the presence of the amino acyl synthetase includes detecting a detection moiety conjugated to the amino acyl synthetase.

3. The method of claim 2, wherein the detection moiety includes an enzyme.

4. The method of claim 3, wherein the detecting the detection moiety includes measuring a change in the electrical properties of the chemFET in response to a reaction catalyzed by the enzyme.

5. The method of claim 1, wherein the plurality of polypeptides are bound to a bead, and at least one bead is disposed into each of the plurality of reaction chambers.

6. The method of claim 1, further comprising denaturing the polypeptide.

7. The method of claim 1, wherein cleaving further includes cleaving the amino acid using a protease conjugated to the amino acyl synthetase.

8. The method of claim 1, wherein cleaving further includes cleaving the amino acid using a limited Edmond degradation or a proximity based radical cleavage.

9. The method of claim 1, wherein the floating gate of the at least one chemFET is coupled to the at least one reaction chamber via a passivation layer sensitive to hydrogen ions.

10. A method for sequencing a polypeptide, comprising:

disposing a plurality of polypeptides into at least one of a plurality of reaction chambers, at least one reaction chamber of the plurality of reaction chambers coupled to at least one chemical-sensitive field effect transistor (chemFET) having a floating gate;

sequentially cleaving amino acids from an end of the polypeptide;

sequentially detecting the identity of the amino acids by a change in an electrical property of the at least one chemFET having the floating gate.

11. The method of claim 10, wherein a center-to-center distance between adjacent reaction chambers is selected from a range of about 1 μ

m to about 10 μ

m.

12. The method of claim 10, wherein the plurality of reaction chambers includes at least 10⁵ reaction chambers.

13. The method of claim 10, wherein the floating gate of the at least one chemFET is coupled to the at least one reaction chamber via a passivation layer sensitive to hydrogen ions.

14. The method of claim 10, wherein the change in the electrical property is due to a change in threshold voltage of the at least one chemFET resulting from a change in ion concentration related to a chemical reaction catalyzed by a detection moiety.

15. The method of claim 10, wherein the detection moiety is conjugated to an amino acyl synthetase specific for the amino acid being detected.

16. The method of claim 15, wherein the detection moiety is a hydrogen peroxidase.

17. A method for sequencing a polypeptide, comprising:

disposing a plurality of polypeptides into at least one of a plurality of reaction chambers, at least one reaction chamber of the plurality of reaction chambers coupled to at least one chemical-sensitive field effect transistor (chemFET) having a floating gate;

sequentially cleaving amino acids from an end of the polypeptide;

detecting a change in the level of a reaction product of a detection moiety conjugated to an amino acyl synthetase as an indicator of the identity of the amino acid.

18. The method of claim 17, wherein the amino acyl synthetase is bound to the amino acid and is specific for the amino acid.

19. The method of claim 17, wherein the change in the level of the reaction product comprises detecting a threshold voltage of the at least one chemFET.

20. The method of claim 17, wherein cleaving amino acids from the end of the polypeptide involves a protease conjugated to the amino acyl synthetase.