METHOD FOR NUCLEIC ACID DETECTION USING VOLTAGE ENHANCEMENT

• US 20120122721A1
• Filed: 12/27/2011
• Published: 05/17/2012
• 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
• Granted Patent: US 9,551,026 B2
• Time in Patent Office: Days
• US Class Current: 506/9
• 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 nucleic acid analysis, including sequence identification, employing voltage and/or controlled electric charge to enhance operation. A device comprises substrates for nucleic acid analysis, a first electrically conductive layer, a first electrically insulative layer of dielectric material on the first conductive layer, a second electrically conductive layer disposed upon the first insulative layer in a pattern to define discrete attachment sites for macromolecules on the first insulative layer, the second conductive layer provided with means for resisting affinity for the macromolecules to impede their attachment to sites on the second conductive layer, and terminals for the first and second conductive layers for applying a voltage pattern between the first and the second conductive layers to control affinity between the macromolecules and the discrete attachment sites.

Claims

1. A method for identifying a nucleotide sequence of a nucleic acid macromolecule, said method comprising:

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

(b) applying a more positive voltage to the substrate to promote enhanced affinity of the macromolecules to the attachment sites;

thereafter

(c) reducing the positive charge on the substrate surface to relax the attached macromolecules in preparation for hybridization of probes to the macromolecules attached at the attachment sites;

(d) hybridizing probes of known sequence to the macromolecules under conditions that permit formation of perfectly matched duplexes between the probes and complementary sequences on the nucleic acid macromolecules;

thereafter

(d) increasing the positive charge on the substrate surface to promote compacting of the macromolecules for discrete optical detection;

(d) identifying said hybridized probes by optical observation,

wherein hybridization of the probes is indicative of a sequence in the nucleic acid macromolecule.

2. The method according to claim 1 wherein said hybridization step further includes ligating probes to hybridized portions the nucleic acid macromolecules.

3. The method according to claim 1 further comprising:

thereafter reducing the positive voltage to relax the macromolecules at the attachment sites; and

providing a chemical stripping agent for interaction with the macromolecules to promote release of the probes at the attachment sites.

4. A method for use in a nucleotide sequence identification process applied to a nucleic acid macromolecule, said method comprising:

providing a device comprising a plurality of nucleic acid macromolecules to be analyzed disposed on a substrate surface at localized discrete attachment sites;

applying a positive voltage to the substrate to promote enhanced affinity of the macromolecules to the attachment sites.

5. A method for use in a nucleotide sequence identification process applied to a nucleic acid macromolecule, said method comprising:

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

reducing the positive charge on the substrate surface to relax the attached macromolecules in preparation for hybridization of probes to the macromolecules at the attachment sites; and

hybridizing probes of known sequence to the macromolecules under conditions that permit formation of perfectly matched duplexes between the probes and complementary sequences on the nucleic acid macromolecules, wherein hybridization of the probes is indicative of a sequence in the nucleic acid macromolecule.

6. The method according to claim 5 further including the step of

increasing the positive charge on the substrate surface to promote compacting of the macromolecules for discrete optical detection.

7. A method for use in a nucleotide sequence identification process applied to a nucleic acid macromolecule, said method comprising:

providing a device comprising a plurality of nucleic acid macromolecules to be analyzed disposed on a substrate surface at localized discrete attachment sites;

reducing the positive voltage to relax the macromolecules at the attachment sites; and

providing a chemical stripping agent for interaction with the macromolecules to promote release of the probes at the attachment sites.

8. A method for use in a nucleotide sequence identification process applied to a nucleic acid macromolecule, said method comprising:

providing a device comprising a plurality of nucleic acid macromolecules to be analyzed disposed on a substrate surface at localized discrete attachment sites;

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

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

wherein hybridization of the probes is indicative of a sequence in a nucleic acid macromolecule.