Biochemically activated electronic device

• US 10,545,115 B2
• Filed: 12/12/2017
• Issued: 01/28/2020
• Est. Priority Date: 07/15/2014
• Status: Active Grant

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: Boyanov, Boyan, Mandell, Jeffrey G., Bai, Jingwei, Gunderson, Kevin L., Chen, Cheng-Yao, Perbost, Michel
• Primary Examiner(s): Sisson, Bradley L.
• Application Number:
  US15/839,795
• Publication Number:
  US 20180112265A1
• Time in Patent Office: 777 Days
• Field of Search: None
• CPC Class Codes: B01J 2219/00653 the compounds being bound to electrodes embedded in or on the solid supports
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B82Y 15/00 Nanotechnology for interacting, sensing or actuating, e.g. quantum dots as markers in protein assays or molecular motors
• CPC Class Codes: C12Q 1/6825 Nucleic acid detection involving sensors
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2521/101 DNA polymerase
• CPC Class Codes: C12Q 2523/307 Denaturation or renaturation by electric current/voltage
• CPC Class Codes: C12Q 2523/319 Photocleavage, photolysis, photoactivation
• CPC Class Codes: C12Q 2525/197 incorporating a spacer/coupling moiety
• CPC Class Codes: C12Q 2535/122 Massive parallel sequencing
• CPC Class Codes: C12Q 2563/113 the label being electroactive, e.g. redox labels
• CPC Class Codes: C12Q 2563/116 electrical properties of nucleic acids, e.g. impedance, conductivity or resistance
• CPC Class Codes: C12Q 2565/107 Alteration in the property of hybridised versus free label oligonucleotides
• CPC Class Codes: C12Q 2565/607 being a sensor, e.g. electrode
• CPC Class Codes: C12Q 2565/629 being a microfluidic device
• CPC Class Codes: G01N 27/4145 specially adapted for biomolecules, e.g. gate electrode with immobilised receptors

Abstract

A method of nucleic acid sequencing. The method can include the steps of (a) providing a polymerase tethered to a solid support charge sensor; (b) providing one or more nucleotides, whereby the presence of the nucleotide can be detected by the charge sensor; and (c) detecting incorporation of the nucleotide into a nascent strand complementary to a template nucleic acid.

Claims

1. A method for attaching a single polymerase to a single charge sensor, comprising:

(a) providing a solid support comprising a plurality of charge sensors, wherein each of the charge sensors has a capacity to attach a plurality of polymerases;

(b) providing a liquid comprising a plurality of polymerases, wherein each polymerase is bound to a nucleic acid repellant moiety and bound to a tether; and

(c) contacting the solid support with the liquid under conditions wherein

(i) the plurality of polymerases are in fluid communication with the plurality of charge sensors,

(ii) a greater number of polymerases are in the fluid than the number of charge sensors on the solid support,

(iii) polymerases from the liquid attach to the charge sensors via the tether, wherein a single polymerase attaches to a single charge sensor, and

(iv) the nucleic acid repellant moiety bound to each of the polymerases prevents more than one of the polymerases from attaching to each of the charge sensors.

2. The method of claim 1, wherein the polymerases are DNA polymerases.

3. The method of claim 2 wherein the DNA polymerases are selected from the group consisting of DNA polymerases in Family A, DNA polymerases in Family B, DNA polymerases in Family C, DNA polymerases in Family D, DNA polymerases in Family X, DNA polymerases in Family Y, and DNA polymerases in Family RT.

4. The method of claim 1, wherein the tether has a nucleic acid sequence.

5. The method of claim 1, wherein the nucleic acid repellant moiety comprises a compacted nucleic acid with a ball or globular structure having an average diameter ranging from 0.1 μ

m to 5 μ

m.

6. The method of claim 1, wherein the polymerases comprise at least two different types of polymerases, wherein the different types of polymerases attach to individual charge sensors of the solid support.

7. The method of claim 6, wherein the different types of polymerases produce mutually distinguishable signals detectable by the charge sensors when incorporating the same type of nucleotide into a nascent nucleic acid strand.

8. The method of claim 1, wherein the nucleic acid repellant moiety occupies a volume of space that sterically hinders more than one of the polymerases from attaching to each of the charge sensors.

9. The method of claim 1, wherein the nucleic acid repellant moiety comprises a charge polarity that electrostatically hinders more than one of the polymerases from attaching to each of the charge sensors.

10. The method of claim 1, wherein each of the charge sensors has a capacity to attach more than two of the polymerases.

11. The method of claim 1, further comprising removing the bound nucleic acid repellant moiety from the polymerases after the polymerases attach to the charge sensors.

12. The method of claim 11, wherein the liquid is removed from the solid support before the removing of the bound nucleic acid repellant moiety and after the polymerases attach to the charge sensors.

13. The method of claim 1, wherein the tethers are conducting tethers selected from the group consisting of doped polythiophene, poly(3,4-ethylenedioxythiophene), polyacetylene, polypyrrole, polyaniline, polyfluorene, polyphenylene, polypyrene, polyazulene, polynaphthalenes, polycarbazole, polyindole, and polyazepine.

14. The method of claim 1, wherein the polymerase lacks a 3′

to 5′

exonuclease function.

15. The method of claim 14, wherein the polymerase comprises the large fragment of Bsu DNA polymerase I.

16. The method of claim 15, wherein the large fragment of Bsu DNA polymerase I is modified to include amino acid residues from the O-helix finger domain of Klenow fragment.

17. The method of claim 1, wherein the tether has a nucleic acid sequence of native ribonucleotides or analogs thereof.

18. The method of claim 1, wherein the tether has a nucleic acid sequence of native deoxyribonucleotides or analogs thereof.

19. The method of claim 1, wherein the charge sensor comprises a field-effect transistor (FET) selected from the group consisting of a silicon nanowire, a carbon nanotube, a single walled carbon nanotube, and a graphene nanoribbon.

20. The method of claim 1 wherein the polymerases are RNA polymerases selected from the group consisting of T7 RNA polymerase, RNA polymerase I, RNA polymerase II, RNA polymerase III, RNA polymerase IV, RNA polymerase V, and Archaea RNA polymerase.

21. The method of claim 3 wherein the DNA polymerases are the DNA polymerases in Family A and are selected from the group consisting of T7 DNA polymerase, eukaryotic mitochondrial DNA Polymerase γ

, E. coli DNA Pol I, Thermus aquaticus Pol I, and Bacillus stearothermophilus Pol I.

22. The method of claim 3 wherein the DNA polymerases are the DNA polymerases in Family B and are selected from the group consisting of eukaryotic DNA polymerase α

, eukaryotic DNA polymerase δ

, eukaryotic DNA polymerase ε

, T4 DNA polymerase, Phi29 DNA polymerase, and RB69 bacteriophage.

23. The method of claim 3 wherein the DNA polymerases are the DNA polymerases in Family C and includes E. coli DNA polymerase III alpha subunit.

24. The method of claim 3 wherein the DNA polymerases are the DNA polymerases in Family D and includes polymerases derived from Euryarchaeota subdomain of Archaea.

25. The method of claim 3 wherein the DNA polymerases are the DNA polymerases in Family X and are selected from the group consisting of eukaryotic polymerases Pol β

, eukaryotic polymerases Pol σ

, eukaryotic polymerases Pol λ

, eukaryotic polymerases Pol μ

, and S. cerevisiae Pol4.

26. The method of claim 3 wherein the DNA polymerases are the DNA polymerases in Family Y and are selected from the group consisting of Pol η

, Pol iota, Pol kappa, E. coli Pol IV, and E. coli Pol V.

27. The method of claim 3 wherein the DNA polymerases are the DNA polymerases in Family RT and are selected from the group consisting of retrovirus reverse transcriptases and eukaryotic telomerases.

28. A method for attaching a single polymerase to a single charge sensor, comprising:

(a) providing a solid support comprising a plurality of charge sensors, wherein each of the charge sensors has a capacity to attach a plurality of polymerases;

(b) providing a liquid comprising a plurality of polymerases, wherein each polymerase is bound to a tether; and

(c) contacting the solid support with the liquid; and

(d) applying an electric field, wherein

the plurality of polymerases are in fluid communication with the plurality of charge sensors,

a greater number of polymerases are in the fluid than the number of charge sensors on the solid support,

polymerases from the fluid attach to the charge sensors via the tether, wherein a single polymerase attaches to a single charge sensor, and

the electric field actively transports the polymerases to the charge sensors.