NUCLEIC ACID ARRAY HAVING FIXED NUCLEIC ACID ANTI-PROBES AND COMPLEMENTARY FREE NUCLEIC ACID PROBES

• US 20080044821A1
• Filed: 08/21/2006
• Published: 02/21/2008
• Est. Priority Date: 08/21/2006
• Status: Abandoned Application

• Current Assignee: Cnvgenes Incorporated
• Original Assignee: Cnvgenes Incorporated
• Inventors: Zainiev, Gafur, Zainiev, Inlik
• Application Number:
  US11/465,870
• Publication Number:
  US 20080044821A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 2537/161 A competitive reaction step

Abstract

A process for identifying a complementary nucleic acid probe to a target nucleic acid involves forming an array of spots where each spot of the array has an immobilized nucleic acid anti-probe to which is hybridized a nucleic acid probe. The array of the anti-probe-probe complex is denatured. The nucleic acid probes are then moved into a target chamber that includes a target nucleic acid. Hybridization conditions are established to form double-stranded complexation between the target nucleic acid and nucleic acid probes in instances where the target nucleic acid has a sequence complementary. The nucleic acid probes noncomplementary to the target nucleic acid are allowed to rehybridize with anti-probes. Determining whether the anti-probe spots exposed to nucleic acid probes noncomplementary to the target nucleic acid are single stranded after exposure to noncomplementary nucleic acid probes provides information as to target nucleic acid sequence.

Claims

1. A process for identifying a complementary nucleic acid probe to a target nucleic acid comprising:

forming an array of spots, each spot comprising a nucleic acid probe, a nucleic acid probe hybridized to a respective immobilized oligonucleotide anti-probe to yield a double-stranded anti-probe-nucleic acid probe complex;

placing said array in a solution filled array chamber;

denaturing said double-stranded oligonucleotide anti-probe-nucleic acid probe complex;

moving said nucleic acid probe electrophoretically into a target chamber comprising a target nucleic acid;

establishing hybridization conditions in said target chamber to form a target nucleic acid-nucleic acid probe double-stranded complex when the target nucleic acid has a complementary sequence to said nucleic acid probe;

transporting a nucleic acid probe noncomplementary to the target nucleic acid into contact with a series of immobilized anti-probes;

hybridizing each of said nucleic acid probes noncomplementary to the target nucleic acid to one of said series of immobilized anti-probes; and

determining whether each of said series of immobilized anti-probes exist as present as a single strand.

2. The process of claim 1 wherein said anti-probe is a strand.

3. The process of claim 1 wherein moving said nucleic acid probe electrophoretically into the target chamber occurs through a gel.

4. The process of claim 1 wherein the target nucleic acid within said target chamber is untethered.

5. The process of claim 1 wherein the target nucleic acid within said target chamber is bound to a particle.

6. The process of claim 5 wherein said particle is paramagnetic.

7. The process of claim 1 wherein the target nucleic acid within said target chamber is embedded within gel.

8. The process of claim 1 wherein the target nucleic acid within said target chamber is adhered.

9. The process of claim 1 wherein said series of immobilized anti-probes include said anti-probe within said array of spots.

10. The process of claim 1 wherein said series of immobilized anti-probes extend from an egress pathway in fluid communication with said target chamber.

11. The process of claim 10 wherein determining whether one of said series of immobilized anti-probes exists in single-strand form as determined by time of flight between each spot and a detector.

12. The process of claim 1 further comprising denaturing said target nucleic acid-nucleic acid probe double-stranded complex and returning said nucleic acid probe to which said target nucleic acid has the complementary sequence to said array chamber, and rehybridizing said array of spots to return each spot of said array of spots to the form of the double-stranded oligonucleotide anti-probe-nucleic acid probe complex.

13. The process of claim 10 further comprising recycling effluent from said egress pathway to said array of spots.

14. The process of claim 1 further comprising exposing under hybridization conditions the target nucleic acid to a second series of nucleic acid probes, said second series of nucleic acid probes originating from a second array of spots, each spot of said second array of spots comprising a second nucleic acid probe hybridized to a respective second immobilized nucleic acid anti-probe.

15. The process of claim 1 further comprising exposing said nucleic acid from said array of spots to a second target chamber comprising a second target nucleic acid.

16. The process of claim 1 wherein determining whether each spot of said series of immobilized complementary anti-probes is single stranded comprises:

creating a high pH solution environment;

deactivating an electrode proximal to each spot of said series of immobilized complementary anti-probes to denature any double-stranded complex associated with each spot; and

detecting the passage of nucleic acid probe as a function of time of flight.

17. A nucleic acid assay assemblage comprising:

an array chamber containing nucleic acid probes each immobilized to a complementary nucleic acid anti-probe in the form of a double-stranded complex;

a target chamber containing a target nucleic acid;

a channel permeable to said nucleic acid probes in fluid communication between said array chamber and said target chamber; and

a fixture for coupling an electrophoretic electrode to said assay chamber and a second electrophoretic electrode to said target chamber.

18. The assemblage of claim 17 wherein the channel comprises a gel permeable to said nucleic acid probes.

19. The assemblage of claim 17 further comprising an egress pathway in fluid communication with said target chamber.

20. The assemblage of claim 17 further comprising a detector operating on time of flight.

21. The assemblage of claim 19 wherein said egress pathway further comprises multiple electrophoretic electrodes along a pathway length.

22. The assemblage of claim 19 further comprising a return pathway between said egress pathway and said array chamber independent of said target chamber.