Real-time redox sequencing methods

• US 10,273,537 B2
• Filed: 03/22/2016
• Issued: 04/30/2019
• Est. Priority Date: 10/14/2011
• Status: Active Grant

• Current Assignee: Pacific Bioscience of California Incorporated (L'Oreal SA)
• Original Assignee: Pacific Bioscience of California Incorporated (L'Oreal SA)
• Inventors: Korlach, Jonas, Turner, Stephen, Sun, Lei
• Primary Examiner(s): Zhang, Kaijiang
• Application Number:
  US15/077,770
• Publication Number:
  US 20160319343A1
• Time in Patent Office: 1,134 Days
• Field of Search: None
• 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 1/001 Enzyme electrodes
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2521/101 DNA polymerase
• CPC Class Codes: C12Q 2521/543 Immobilised enzyme(s)
• CPC Class Codes: C12Q 2563/113 the label being electroactive, e.g. redox labels
• CPC Class Codes: C12Q 2563/155 Particles of a defined size, e.g. nanoparticles
• CPC Class Codes: C12Q 2565/607 being a sensor, e.g. electrode
• CPC Class Codes: C40B 60/10 for identifying library members
• CPC Class Codes: G01N 27/00 Investigating or analysing materials by the use of electric, electrochemical, or magnetic means G01N3/00 – G01N25/00 take precedence; measurement or testing of electric or magnetic variables or of electric or magnetic properties of materials G01R
• CPC Class Codes: G01N 27/3277 being a redox reaction, e.g. detection by cyclic voltammetry voltammetry per se G01N27/42, G01N27/48
• CPC Class Codes: G01N 27/3278 involving nanosized elements, e.g. nanogaps or nanoparticles nanopores G01N33/48721; magnetic beads G01N27/745

Abstract

Real time redox sequencing methods, devices, and systems are described. Arrays of redox devices comprising one or two electrodes are used to provide sequence information about a template nucleic acid in a polymerase-template complex bound proximate to the electrode(s). A sequencing reaction mixture comprising nucleotide analogs comprising redox labels is introduced to the array of redox devices under conditions of polymerase mediated nucleic acid synthesis. The time sequence of incorporation of nucleotide analogs is determined by electrochemically identifying the redox labels of the nucleotide analogs that are incorporated into the growing strand.

Claims

1. A method for nucleic acid sequencing comprising:

providing a substrate comprising an oxidizing nanoscale electrode and a reducing nanoscale electrode, the substrate comprising a polymerase enzyme complex comprising a polymerase enzyme and a template nucleic acid, the complex attached to one of the nanoscale redox electrodes or to the substrate proximate to the electrodes;

exposing the polymerase to a plurality of types of nucleotide analogs each comprising a different redox label attached to the phosphate portion of the nucleotide analog through a linker of a length such that the redox label can come into contact with the oxidizing nanoscale electrode and the reducing nanoscale electrode when the nucleotide analog is held in the polymerase enzyme active site under conditions whereby polymerase mediated nucleic acid synthesis occurs, resulting in the growth of a nascent nucleic acid strand;

applying voltages over time at the oxidizing nanoscale electrode and reducing nanoscale electrode, whereby when a nucleotide analog resides in the active site of the enzyme, a redox label is oxidized by the oxidizing nanoscale electrode, and reduced by the reducing nanoscale electrode;

monitoring the current at the oxidizing nanoscale electrode and at the reducing nanoscale electrode over time, whereby the current from multiple oxidations and reductions of a redox label at the electrodes indicates an incorporation event for a nucleotide analog having a specific redox label; and

using the monitored current at the electrodes over time to determine a sequence of the template nucleic acid.

2. The method of claim 1 wherein the voltage of the oxidizing nanoscale electrode and the voltage of the reducing nanoscale electrode are each repeatedly brought to different voltage levels, whereby the current measured at each voltage level is used to identify a specific redox label.

3. The method of claim 1 wherein the voltages applied to the electrodes comprise sine waves, triangular waves or saw tooth waves.

4. The method of claim 1 wherein the polymerase is exposed to four types of nucleotide analogs, corresponding to A, G, C, T, or A, G, C, U, wherein the voltage of the oxidizing nanoscale electrode and the voltage of the reducing nanoscale electrode are each repeatedly brought to at least 4 different voltage levels.

5. The method of claim 1 wherein the amount of current over time is used to identify which type of nucleotide is incorporated.

6. The method of claim 1 wherein the characteristics of the current over time is used to identify which type of nucleotide is incorporated.

7. The method of claim 6 wherein the characteristic of the current over time includes the current oscillation color.

8. The method of claim 1 wherein the enzyme is attached to the substrate between the electrodes.

9. The method of claim 1 wherein the plurality of types of nucleotide analogs comprises four differently labeled nucleotide analogs 1, 2, 3, and 4, wherein nucleotide analogs 1 and 2 each comprise a redox label with a first type of redox moiety, and nucleotide analogs 3 and 4 each comprise redox label with a second type of redox moiety, wherein nucleotide 1 has a different number of redox moieties than nucleotide analog 2, and nucleotide 3 has a different number of redox moities than nucleotide analog 4.

10. A method for nucleic acid sequencing comprising:

providing a substrate comprising a nanoscale redox electrode, the substrate comprising a polymerase enzyme complex comprising a polymerase enzyme and a template nucleic acid, the complex attached to the nanoscale electrode or to the substrate proximate to the nanoscale electrode;

exposing the polymerase to a plurality of types of nucleotide analogs each comprising a different redox label attached to the phosphate portion of the nucleotide analog through a linker of a length such that the redox label can come into contact with the nanoscale redox electrode when the nucleotide analog is held in the polymerase enzyme active site under conditions whereby polymerase mediated nucleic acid synthesis occurs, resulting in the growth of a nascent nucleic acid strand;

wherein the nanoscale electrode is repeatedly brought to a plurality of voltage levels comprising at least one oxidizing voltage and at least one reducing voltage;

applying voltages over time to the nanoscale redox electrode, whereby when a nucleotide analog resides in the active site of the enzyme, the redox label is oxidized and reduced by the nanoscale electrode;

monitoring the current at nanoscale electrode at the plurality of voltages over time, whereby the current from multiple oxidations and reductions of a redox label at the electrode indicates an incorporation event for a nucleotide analog having a specific redox label; and

using the monitored current at the electrode over time to determine a sequence of the template nucleic acid.

11. The method of claim 10 wherein the voltage of the nanoscale electrode is repeatedly brought to different voltage levels, whereby the current measured at each voltage level is used to identify a specific redox label.

12. The method of claim 10 wherein the polymerase is exposed to four types of nucleotide analogs corresponding to A, G, C, T, or A, G, C, U, wherein the voltage of the nanoscale electrode is repeatedly brought to at least 8 different voltage levels.

13. The method of claim 10 wherein the voltages applied to the electrode comprise a sine wave, a triangular wave, or a saw tooth wave.

14. The method of claim 10 wherein the amount of current over time is used to identify which type of nucleotide is incorporated.

15. The method of claim 10 wherein the characteristics of the current over time is used to identify which type of nucleotide is incorporated.

16. The method of claim 15 wherein the characteristic of the current over time includes the current oscillation color.

17. The method of claim 10 wherein the enzyme is attached to the nanoscale redox electrode.