Methods and apparatus for detecting molecular interactions using FET arrays

• US 8,540,866 B2
• Filed: 09/09/2011
• 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:
  US13/229,402
• Publication Number:
  US 20120088682A1
• Time in Patent Office: 746 Days
• Field of Search: 257/253, 205/789, 205/792, 205/793.5, 422 8201- 8203, 435/6, 435/285.1, 435/287.1, 435/287.2, 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 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.

2. 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.

3. 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.

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

5. The method of claim 1, wherein the at least one antibody and the at least one antigen are unlabeled or unmodified.

6. 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.

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.

8. 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.

9. 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.

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

11. 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.

12. 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.

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.

14. 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.

15. 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.

16. 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.

17. 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.

18. 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.

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.

20. The method of claim 19, wherein a product or byproduct from the reaction of the enzyme and the substrate is detectable by the chemFETs.

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.

22. The method of claim 21, wherein the interaction of the enzyme and the inhibitor is indirectly detected.