Biochemically activated electronic device

• US 10,605,766 B2
• Filed: 07/14/2015
• Issued: 03/31/2020
• 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:
  US14/798,762
• Publication Number:
  US 20160017416A1
• Time in Patent Office: 1,722 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 of nucleic acid sequencing, comprising:

(a) contacting a nucleic acid molecule to be sequenced with a polymerase attached to a solid support charge sensor with an oligonucleotide tether;

(b) contacting the nucleic acid molecule and the polymerase with different nucleotide types, wherein each of the different nucleotide types is respectively attached to an oligonucleotide capable of hybridizing to a complementary region of the oligonucleotide tether and includes a unique label that can be detected by the solid support charge sensor when the label is in proximity of a screening length of the charge sensor

wherein the polymerase catalyzes incorporation of one of the different nucleotide types to a nascent nucleic acid strand complementary to the nucleic acid molecule and wherein the oligonucleotide of the one of the different nucleotide types hybridizes to the complementary region of the oligonucleotide tether and brings the unique label within proximity of the screening length; and

(c) detecting a distinguishable signal using the charge sensor in response to the incorporation of the one of the different nucleotide types into the nascent nucleic acid strand complementary to the nucleic acid molecule to be sequenced.

2. The method of claim 1, wherein a phosphate of the incorporated one of the different nucleotide types is cleaved by the polymerase after incorporation, and wherein the oligonucleotide of the incorporated one of the different nucleotide types dissociates from the oligonucleotide tether.

3. The method of claim 2, wherein the polymerase catalyzes incorporation of a next of the different nucleotide types to the nascent nucleic acid strand complementary to the nucleic acid molecule, wherein the oligonucleotide of the next of the different nucleotide types hybridizes to its complementary region of the oligonucleotide tether and brings its unique label within proximity of the screening length, and wherein the method further comprises detecting a next distinguishable signal using the charge sensor in response to the incorporation of the next of the different nucleotide types into the nascent nucleic acid strand complementary to the nucleic acid molecule to be sequenced.

4. The method of claim 1, wherein the different nucleotide types comprise four different types of nucleotides, wherein each of the four different types of nucleotides comprises a unique charge label.

5. The method of claim 1, wherein the solid support charge sensor comprises a nanowire field-effect transistor (FET) or a carbon nanotube field-effect transistor (FET).

6. The method of claim 1, wherein the solid support charge sensor is one of a plurality of charge sensors in an array and wherein the polymerase is one of a plurality of polymerases, wherein each of the plurality of charge sensors is tethered to a respective one of the plurality of polymerases, and step (c) comprises detecting distinguishable signals at each of the plurality of charge sensors in response to incorporation of respective nucleotide types into respective nascent complementary strands at each polymerase.

7. The method of claim 1, wherein each of the different nucleotide types is a reversibly terminated nucleotide, wherein the polymerase lacks a 3′

to 5′

exonuclease function, and wherein the method further comprises adding a deblocking agent prior to performing a subsequent sequencing cycle.

8. The method of claim 7, wherein the polymerase comprises the large fragment of Bsu DNA polymerase I.

9. The method of claim 8, wherein the large fragment of Bsu DNA polymerase I is modified to include residues from the O-helix finger domain of Klenow fragment.

10. The method of claim 1, wherein the solid support charge sensor comprises a variable width including a region of substantially narrower width, wherein the region of substantially narrower width is 10% to 75% of a diameter of larger width regions of the solid support charge sensor.

11. The method of claim 10, wherein the polymerase is tethered to the solid support charge sensor by attachment to the region of substantially narrower width.

12. The method of claim 1, wherein the oligonucleotide tether comprises native ribonucleotides or analogs thereof.

13. The method of claim 12, wherein the oligonucleotide capable of hybridizing to the complementary region of the oligonucleotide tether is the unique label, and wherein the unique label comprises native ribonucleotides or analogs thereof.

14. The method of claim 1, wherein the oligonucleotide tether comprises native deoxyribonucleotides or analogs thereof.

15. The method of claim 14, wherein the oligonucleotide tether comprises native deoxyribonucleotides or analogs thereof, wherein the oligonucleotide capable of hybridizing to the complementary region of the oligonucleotide tether is the unique label, and wherein the unique label comprises native deoxyribonucleotides or analogs thereof.

16. The method of claim 1, wherein the different nucleotide types comprise reversible terminator moieties;

wherein the incorporation of the one of the different nucleotide types incorporates a reversibly terminated nucleotide into the nascent nucleic acid strand; and

wherein the method further comprises (d) adding a deblocking agent to render the nascent nucleic acid strand capable of further incorporation of a next nucleotide; and

(e) repeating steps (b) through (d) to obtain a sequence of the nucleic acid molecule to be sequenced.

17. The method of claim 1, wherein the unique label of the one of the different nucleotide types comprises a unique charge tag that is detected by the charge sensor during incorporation of the one nucleotide type into the nascent nucleic acid strand complementary to the nucleic acid molecule to be sequenced.

18. The method of claim 1, wherein the oligonucleotide of each of the different nucleotide types is the unique label, wherein the oligonucleotide of each of the different nucleotide types hybridizes to a different location of the oligonucleotide tether.

19. The method of claim 1, wherein the polymerase is in proximity of less than 10 nm to the charge sensor.

20. A method of detecting incorporation of nucleotides, comprising:

(a) contacting a nucleic acid molecule to be sequenced with a polymerase,

attached to a solid support charge sensor with an oligonucleotide tether;

(b) contacting the nucleic acid molecule and the polymerase with four different nucleotide types, wherein each of the four different nucleotide types is respectively attached to an oligonucleotide capable of hybridizing to a complementary region of the oligonucleotide tether and includes a charge unique label that can be detected by the solid support charge sensor when the unique charge label is in proximity of a screening length of the charge sensor,

wherein the polymerase catalyzes incorporation of one of the four different nucleotide types to a nascent nucleic acid strand complementary to the nucleic acid molecule and wherein the oligonucleotide of the one of the four different nucleotide types hybridizes to the complementary region of the oligonucleotide tether and brings the unique charge label within proximity of the screening length;

(c) detecting a distinguishable signal of the unique charge label using the charge sensor; and

(d) identifying the incorporated one of the four different nucleotide types by the distinguishable signal.