Methods and apparatus for detecting molecular interactions using FET arrays

• US 8,349,167 B2
• Filed: 06/26/2009
• Issued: 01/08/2013
• 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 M., Hinz, Wolfgang
• Primary Examiner(s): Le, Thao
• Assistant Examiner(s): GORDON, MATTHEW E
• Application Number:
  US12/492,844
• Publication Number:
  US 20100282617A1
• Time in Patent Office: 1,292 Days
• Field of Search: 205/777.5, 257/253, 257/E23.08, 438/10
• US Class Current: 205/777.5
• 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 an analyte in a sample comprising

providing a sample analyzer comprising an array of at least 10⁵ sensors formed in the substrate, the sensors having a pitch distance of not more than 10 microns, the sensors further comprising a field-effect transistor having a gate oxide with a characteristic thickness, a floating gate, and a characteristic threshold voltage;

disposing one or more nucleic acid species in proximity to or in contact with at least a portion of the sensors of the array;

disposing a sample in proximity to or in contact with at least a portion of the sensors of the array wherein an interaction between the analyte in the sample and the one or more nucleic acid species effectuates a change in at least one electrical property of at least one sensor of the array to produce one or more outputs reflective of the one or more sensors for which interactions were detected, and

registering the one or more outputs from the one or more sensors in the array after contact with the sample as an indicator of analyte presence.

2. The method of claim 1, wherein the analyte is a nucleic acid, a polynucleotide, or a single nucleotide species.

3. The method of claim 1, wherein the analyte is a protein, an amino acid, an enzyme, an antibody, a receptor, or a compound or molecule at least a portion of which comprises a protein or amino acid.

4. The method of claim 1, wherein the nucleic acids are less than approximately 1000 bases in length.

5. The method of claim 1, wherein the nucleic acids are single stranded.

6. The method of claim 1, wherein the nucleic acids are double stranded.

7. The method of claim 1, wherein the nucleic acids are DNA, RNA, mRNA, siRNA or cDNA.

8. The method of claim 1, wherein the nucleic acids are aptamers.

9. The method of claim 1, wherein the nucleic acids are covalently attached to the chemFET array.

10. The method of claim 1, wherein the interaction between analyte and the nucleic acids causes a change in the concentration of an ionic species in proximity to the chemFET.

11. The method of claim 1, wherein the field-effect transistor is a chemFET.

12. The method of claim 1, wherein the field-effect transistor is an ion-sensitive field-effect transistor.

13. A method for detecting an analyte in a sample comprising

providing an apparatus comprising a plurality of nucleic acids attached to a field-effect transistor array comprising 10⁴ field-effect transistors wherein each field-effect transistor includes a floating gate;

disposing nucleic acids in proximity to or in contact with at least a portion of the field-effect transistor array;

disposing a sample in proximity to or in contact with at least a portion of the sensor array, and

identifying interactions between the nucleic acids and an analyte present in the sample by detecting changes in electrical output of a field-effect transistor of the field-effect transistor array representative of a change in a diffusion rate of an ionic species in proximity to the field-effect transistor due to the presence of the analyte.

14. The method of claim 13, wherein the field-effect transistor is a chemFET.

15. The method of claim 13, wherein the field-effect transistor is an ion-sensitive field-effect transistor.

16. The method of claim 13, wherein the analyte is a nucleic acid, a polynucleotide, or a single nucleotide species.

17. The method of claim 13, wherein the analyte is a protein, an amino acid, an enzyme, an antibody, a receptor, or a compound or molecule at least a portion of which comprises a protein or amino acid.

18. The method of claim 13, wherein the nucleic acids are less than 1000 bases in length.

19. The method of claim 13, wherein the nucleic acids are single stranded.

20. The method of claim 13, wherein the nucleic acids are double stranded.

21. The method of claim 13, wherein the nucleic acids are DNA, RNA, mRNA, siRNA, or cDNA.

22. The method of claim 13, wherein the nucleic acids are aptamers.

23. The method of claim 13, wherein the nucleic acids are covalently attached to the chemFET array.