Methods and apparatus for measuring analytes using polymerase in large scale molecular electronics sensor arrays

Patent metadata

Field	Value
Publication number	US-11624725-B2
Application number	US-201716073693-A
Country	US
Kind code	B2
Filing date	Jan 27, 2017
Priority date	Jan 28, 2016
Publication date	Apr 11, 2023
Grant date	Apr 11, 2023

Abstract

In various embodiments of the present disclosure, a molecular electronics sensor array chip comprises: (a) an integrated circuit semiconductor chip; and (b) a plurality of molecular electronic sensor devices disposed thereon, each of said sensor devices comprising: (i) a pair of nanoscale source and drain electrodes separated by a nanogap; (ii) a gate electrode; and (iii) a bridge and/or probe molecule spanning the nanogap and connecting the source and drain electrodes, wherein the molecular electronic sensor devices are organized into an electronically addressable, controllable, and readable array of sensor pixels.

First claim

We claim:

1. A molecular electronics sensor array chip comprising:
(a) an integrated circuit semiconductor chip; and
(b) a plurality of molecular electronic sensor devices disposed thereon, each sensor device comprising:
(i) a pair of nanoscale source and drain electrodes separated by a nanogap,
(ii) a gate electrode;
(iii) a peptide alpha-helix bridge molecule comprising an amino acid sequence according to SEQ ID NO:1 spanning the nanogap and connecting the source and drain electrodes, wherein the peptide alpha-helix comprises a coupling group having a central lysine modified to include biotin on a linker for binding of a neutravidin protein; and
(iv) a polymerase enzyme coupled to the central lysine of the peptide alpha-helix bridge molecule by a linker conjugated to the polymerase and connected to the coupling group of the bridge molecule by a biotin-neutravidin binding reaction;

wherein the sensor devices are organized into an array of sensor pixels.

2. The molecular electronics sensor array chip of claim 1 , wherein the linker conjugated to the polymerase enzyme comprises a biotin-maleimide linker conjugated to a surface cysteine on the polymerase.

3. The molecular electronics sensor array chip of claim 1 , wherein the chip comprises at least 100 sensor devices.

4. The molecular electronics sensor array chip of claim 1 , wherein device voltages are used to monitor and/or facilitate molecular self-assembly of each bridge molecule to each source and drain electrode pair and/or a molecular self-assembly of each probe molecule to each bridge molecule, including the use of a voltage-directed reset to restore the sensor to pre-molecular state as needed for successive trials.

5. The molecular electronics sensor array chip of claim 1 , wherein the source and drain electrodes comprise gold contacts on electrodes comprising chromium.

6. The molecular electronics sensor array chip of claim 5 , wherein the peptide alpha-helix bridge molecule comprising SEQ ID NO:1 has cysteine amino acids at the terminal for thiol-gold coupling to the gold contacts on the electrodes.

7. The molecular electronics sensor array chip of claim 1 , wherein the polymerase enzyme comprises a DNA polymerase.

8. The molecular electronics sensor array chip of claim 1 , wherein the polymerase enzyme comprises a E. Coli Klenow fragment of a DNA polymerase.

9. The molecular electronics sensor array chip of claim 1 , wherein each sensor pixel further comprises a readout capacitor or readout resistor connected to each sensor device.

10. The molecular electronics sensor array chip of claim 9 , wherein each sensor pixel further comprises a transistor-based output switch.

11. The molecular electronics sensor array chip of claim 10 , wherein each sensor pixel further comprises a transistor-based reset switch.

12. The molecular electronics sensor array chip of claim 11 , wherein each sensor pixel further comprises a row select line and a column readout line connected thereto, and the array of sensor pixels comprises an integrated row select column-readout array architecture, whereby the row select lines energize the sensor pixels.

13. The molecular electronics sensor array chip of claim 12 , wherein the row select lines control the output switches.

14. The molecular electronics sensor array chip of claim 13 , wherein each sensor pixel further comprises a row-reset line and a column-reset line for controlling each reset switch.

15. The molecular electronics sensor array chip of claim 14 , wherein each reset switch is controlled by a combination of the row select line and the column-reset line, such as to provide direct control over the reset of each sensor pixel.

16. A process for measuring signals of incorporation for a multiplicity of replicate primed DNA fragments applied to a chip, said process comprising:
providing at least one molecular electronics sensor array chip of claim 1 ;
applying a mixture of deoxynucleotide triphosphates and specific base terminators to the molecular electronics sensor array chip; and
measuring the specific base locations along the DNA fragments.

17. The process of claim 16 , wherein at least four (4) molecular electronics sensor array chips are utilized, one for each base reaction.

18. The process of claim 16 , used to perform a digital fragment length assay.

19. A chip-based analyzer system for sample analysis, said system comprising:
at least one molecular electronics sensor array chip of claim 1 ;
a motherboard in which the at least one molecular electronics sensor array chip is integrated;
a liquid handling system configured to control introduction of at least the sample to the plurality of molecular electronic sensor devices;
at least one signal processor; and
a CPU.

20. The chip-based analyzer system of claim 19 , wherein the chip-based analyzer is integrated into a multi-modality bio-analyzer, thereby producing a multi-modality integrated report from the sample.

21. The chip-based analyzer system of claim 19 , configured as a hand-held, wearable, or implantable system.

22. A process of analyzing a bio-sample, said method rising the steps of:
providing the chip-based analyzer system of claim 19 ;
collecting the bio-sample from a subject;
processing the bio-sample through the chip-based analyzer system to obtain data relevant to an analysis of the bio-sample; and
transferring the data to a storage server or cloud.

23. The process of claim 22 , wherein the bio-sample is collected from a subject in conjunction with information pertaining to the subject, and analyzed to produce an integrated report comprising both the information.

24. A molecular electronics sensor array chip comprising:
a) an integrated circuit semiconductor chip; and
b) a plurality of molecular electronic sensor devices disposed thereon, each sensor device comprising:
(i) a pair of nanoscale source and drain electrodes separated by a nanogap,
(ii) a gate electrode;
(iii) a peptide alpha-helix bridge molecule spanning the nanogap and connecting the source and drain electrodes, wherein the peptide alpha-helix comprises a coupling group having an amino acid modified to include biotin on a linker to support binding of a neutravidin protein; and
(iv) a polymerase coupled to an amino acid of the peptide alpha-helix bridge molecule by a linker conjugated to a surface amino acid on the polymerase and connected to the coupling group of the bridge molecule by a biotin-neutravidin binding reaction;
wherein the sensor devices are organized into an array of sensor pixels.

25. The molecular electronics sensor array chip of claim 24 , wherein the peptide alpha-helix bridge molecule is approximately 9 nm in length.

Assignees

• Roswell Biotechnologies Inc
• Roswell Blotechnologies Inc

Inventors

• Merriman Barry L
• Mola Paul W
• Choi Chulmin

Classifications

• H10W10/021

  of air gaps · CPC title

• H10W10/20

  Air gaps · CPC title

• H10D64/20

  Electrodes characterised by their shapes, relative sizes or dispositions · CPC title

• H10D62/10

  Shapes, relative sizes or dispositions of the regions of the semiconductor bodies; Shapes of the semiconductor bodies · CPC title

• H10D64/251

  Source or drain electrodes for field-effect devices · CPC title