Method for nucleic acid detection using voltage enhancement

• US 9,551,026 B2
• Filed: 12/27/2011
• Issued: 01/24/2017
• Est. Priority Date: 12/03/2007
• Status: Active Grant

• Current Assignee: Complete Genomics Incorporated (BGI Genomics Co., Ltd.)
• Original Assignee: Complete Genomics Incorporated (BGI Genomics Co., Ltd.)
• Inventors: Fernandez, Andres, Staker, Bryan, Drmanac, Radoje
• Primary Examiner(s): CROW, ROBERT THOMAS
• Application Number:
  US13/337,968
• Publication Number:
  US 20120122721A1
• Time in Patent Office: 1,855 Days
• Field of Search: None
• US Class Current: 1/1
• CPC Class Codes: C12Q 1/6825 Nucleic acid detection involving sensors
• CPC Class Codes: C12Q 1/6832 Enhancement of hybridisation reaction
• CPC Class Codes: C12Q 2523/307 Denaturation or renaturation by electric current/voltage
• CPC Class Codes: C12Q 2565/501 being an array of oligonucleotides
• CPC Class Codes: C12Q 2565/607 being a sensor, e.g. electrode

Abstract

Methods are provided for carrying out DNA sequencing on a device having upper and lower conductive layers separated by an insulative layer. Holes in the upper conductive layer create discrete attachment sites for DNA fragments. Voltage is applied to the surface to control affinity between the attachment sites and the DNA fragments, and to compact the DNA fragments for discrete optical detection.

Claims

1. A method of discrete analysis of individual nucleic acid constructs in an array, said method comprising:

(a) providing a device comprising a substrate comprising a surface and a plurality of nucleic acid macromolecules disposed on the surface at localized discrete attachment sites;

(b) hybridizing a probe of known sequence having an optically detectable label to each of at least some of the nucleic acid macromolecules under conditions that permit formation of perfectly matched duplexes between the probe and complementary sequences in the nucleic acid macromolecules;

(c) applying a positive charge to the substrate surface to promote compacting of the macromolecules for discrete optical detection; and

(d) optically detecting the labeled duplexes while the positive voltage is applied, thereby identifying a nucleotide sequence in at least some of the nucleic acid macromolecules.

2. The method according to claim 1, comprising:

hybridizing an oligonucleotide anchor to at least some of the nucleic acid macromolecules;

hybridizing a probe of known sequence to each of at least some of the nucleic acid macromolecules at a position that is adjacent to an oligonucleotide anchor under conditions that permit formation of perfectly matched duplexes between the probes and complementary sequences in the nucleic acid macromolecules; and

ligating at least some of the probes to an oligonucleotide anchor hybridized at an adjacent position.

3. The method according to claim 1, further comprising applying a negative voltage to the substrate surface to promote relaxation of the nucleic acid macromolecules;

and then removing the probes from the nucleic acid macromolecules.

4. The method according to claim 1, wherein the nucleic acid macromolecules are singly disposed on the substrate surface at the localized discrete attachment sites that are separated by a distance of 0.3 μ

m to 10 μ

m.

5. The method of claim 1, wherein at least 80% of the localized discrete attachment sites are occupied by a single nucleic acid macromolecule, and the positive voltage compacts each nucleic acid macromolecule into its own discrete attachment site.

6. The method of claim 5, wherein the single nucleic acid macromolecules occupying at least 80% of the localized discrete attachment sites are amplicons.

7. The method of claim 1, wherein said probes of known sequence are each labeled with a fluorescent tag, and probes hybridized to the nucleic acid macromolecules are identified in step (d) by detecting fluorescence.

8. The method of claim 1, wherein the device comprises a dielectric layer disposed between two conductive layers, and the positive voltage is applied in step (c) between the two conductive layers.

9. The method of claim 8, wherein the substrate surface is a dielectric layer disposed on the lower conductive layer.

10. The method of claim 8, wherein the discrete attachment sites are defined areas of the substrate surface exposed through holes etched in the upper conductive layer, and wherein a topside layer that resists binding of nucleic acid macromolecules is disposed upon the upper conductive layer.

11. The method of claim 8, wherein one of the two conductive layers is a single layer below the surface, and the other layer is a single layer above the surface with openings around the discrete attachment sites,

whereby the positive voltage is applied to the discrete attachment sites by applying a voltage between the two conductive layers.

12. A method of preparing nucleic acid macromolecules in an array, said method comprising:

providing a device comprising a substrate comprising a surface and a plurality of nucleic acid macromolecules to be analyzed singly disposed on the surface at localized discrete attachment sites, said substrate surface having a positive electric charge at the discrete attachment sites;

reducing but not removing the positive charge on the discrete attachment sites so as to relax the attached macromolecules in preparation for hybridizing probes of known sequence to the nucleic acid macromolecules at the attachment sites; and

hybridizing the probes to the nucleic acid macromolecules under conditions that permit formation of perfectly matched duplexes between the probes and complementary sequences in the nucleic acid macromolecules; and

compacting the nucleic acid molecules by increasing the positive charge on the discrete attachment sites after hybridizing the probes,

wherein hybridization of each probe is indicative of a sequence in the nucleic acid macromolecule to which it is hybridized.

13. The method of claim 12 further comprising removing the probes from the nucleic acid macromolecules.

14. The method of claim 12, wherein at least 80% of the localized discrete attachment sites are occupied by a single nucleic acid macromolecule, and the positive charge compacts each nucleic acid macromolecule into its own discrete attachment site.

15. The method of claim 12, wherein the positive electric charge results from applying voltage between a lower conductive layer beneath the substrate surface and an upper conductive layer surrounding the attachment sites, wherein the device comprises a dielectric layer disposed between two conductive layers, and the positive electric charge results from applying voltage between the two conductive layers.

16. The method of claim 15, wherein at least 80% of the localized discrete attachment sites are occupied by a single nucleic acid macromolecule, and the positive electric charge compacts each nucleic acid macromolecule into its own discrete attachment site.

17. The method of claim 15, wherein one of the two conductive layers is a single layer below the surface, and the other layer is a single layer above the surface with openings around the discrete attachment sites,

whereby the positive voltage is applied to the discrete attachment sites by applying a voltage between the two conductive layers.

18. The method of claim 12, wherein the discrete attachment sites are 30 nm to 1000 nm in size.

19. The method of claim 12, wherein the discrete attachment sites are 200 nm to 500 nm in size.

20. A method of compacting individual nucleic acid constructs in an array for discrete analysis, said method comprising:

providing a device comprising a plurality of different nucleic acid macromolecules to be analyzed that are singly disposed on a substrate surface at localized discrete attachment sites that are separated by a distance of 0.3 μ

m to 10 μ

m;

hybridizing labeled probes of known sequence to the nucleic acid macromolecules under conditions that permit formation of perfectly matched duplexes between the probes and complementary sequences in the nucleic acid macromolecules, wherein hybridization of the probe is indicative of a sequence in the nucleic acid macromolecule(s) to which it is hybridized;

applying a positive voltage to the substrate surface after hybridizing the probes such that the nucleic acid macromolecules are compacted for discrete analysis.

21. The method of claim 20, wherein at least 80% of the localized discrete attachment sites are occupied by a single nucleic acid macromolecule, and the positive charge compacts each nucleic acid macromolecule into its own discrete attachment site.

22. The method of claim 20, wherein the device comprises a dielectric layer disposed between two conductive layers, and the positive voltage is applied between the two conductive layers.

23. The method of claim 22, wherein one of the two conductive layers is a single layer below the surface, and the other layer is a single layer above the surface with openings around the discrete attachment sites,

whereby the positive voltage is applied to the discrete attachment sites by applying a voltage between the two conductive layers.

24. The method of claim 20, wherein the discrete attachment sites are 30 nm to 500 nm in size.