NUCLEIC ACID ARRAY WITH RELEASEABLE NUCLEIC ACID PROBES

• US 20080044822A1
• 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, Zainieva, Inlik
• Application Number:
  US11/465,875
• Publication Number:
  US 20080044822A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: B01J 2219/00358 electrode driven
• CPC Class Codes: B01J 2219/00644 the porous medium being present in discrete locations, e.g. gel pads
• 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: B01L 3/5027 by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip B01L3/5023 takes precedence; micromixers B01F33/30; microreactors for synthesis B01J19/0093; microcapillary devices in general B81B1/00
• CPC Class Codes: C12Q 1/6813 Hybridisation assays
• CPC Class Codes: C12Q 2537/149 Sequential reactions
• CPC Class Codes: C12Q 2547/107 Use of permeable barriers, e.g. waxes
• CPC Class Codes: C12Q 2565/125 Electrophoretic separation

Abstract

A process is provided for identifying a complementary target nucleic acid. The process includes the hybridization of a nucleic acid probe to a carrier to form a nucleic acid probe-carrier complex. The complex is placed in a compartment bounded by a media permeable to the nucleic acid probe and exclusive of both the carrier and the complex. The complex is then denatured, with the nucleic acid probe transported through the media and into contact with the target nucleic acid. The nucleic acid probe hybridizes to the complementary target nucleic acid to yield a probe-target double stranded complex. A non-complementary nucleic acid probe, independent probe-target complex is returned to the compartment and given an opportunity to rehybridize to the carrier. A determination as to whether at least one of the complementary target nucleic acid or the carrier is present as a complex provides information as to probe sequences complementary to the target nucleic acid.

Claims

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

hybridizing a nucleic acid probe complementary to the complementary target nucleic acid to a carrier yield a probe-carrier complex;

placing said probe-carrier complex into a compartment bounded by a first side of media permeable to said nucleic acid probe and exclusive of said carrier and said complex;

denaturing said complex;

allowing said nucleic acid probe to migrate through said media to a second side;

bringing the complementary target nucleic acid into contact with said nucleic acid probe;

providing hybridization conditions such that said nucleic acid probe has an opportunity to hybridize to the complementary target nucleic acid to yield a probe-target complex;

allowing said nucleic acid probe the opportunity to rehybridize to said carrier when said nucleic acid probe is not part of said probe-target complex; and

determining whether at least one of the complementary target nucleic acid or said carrier is present as said probe-carrier complex or said probe-target complex to identify a probe sequence to complementary target nucleic acid.

2. The process of claim 1 further comprising denaturing said probe-target complex and returning all of said nucleic acid probe to the first side of said media to reform said probe-carrier complex.

3. The process of claim 1 wherein said nucleic acid probe migrates to the second side of said media via solution flow from said carrier compartment through said media.

4. The process of claim 1 wherein said nucleic acid probe migrates to the second side of said media by establishing an electrophoretic potential across said media.

5. The process of claim 1 wherein said carrier is monitored through the presence of said probe-carrier complex with fluorescence subsequent to providing hybridization conditions for said nucleic acid probe and the complementary target nucleic acid to yield the probe-target complex.

6. The process of claim 1 wherein the complementary target nucleic acid is attached to a paramagnetic particle.

7. The process of claim 1 wherein the complementary target nucleic acid is bound within a gel.

8. The process of claim 1 wherein said carrier is a strand hybridized to multiple copies of said nucleic acid probe.

9. The process of claim 1 wherein said nucleic acid probe is attached to a detectable label.

10. The process of claim 1 further comprising repetition with the steps of claim 1 simultaneously in a plurality of isolated carrier compartments each containing a single nucleic acid probe that varies in identity from said nucleic acid probe.

19. The array of claim 1I wherein said plurality of channels extend in three dimensions.

11. A reusable nucleic acid hybridization array channel comprising a carrier for a nucleic acid probe immobilized in a carrier compartment in fluid communication with a target nucleic acid compartment;

a media permeable to single strand nucleic acid probes intermediate between said carrier compartment and said target nucleic acid compartment; and

an apparatus for selectively driving said single strand nucleic acid probes between said carrier compartment and said target nucleic acid compartment.

12. The channel of claim 11 wherein at least one of said carrier compartment and said target nucleic acid compartment comprises a gel.

13. The channel of claim 11 wherein said carrier is immobilized within said carrier compartment in a form selected from the group consisting of:

adhered to a surface and incorporated into a gel.

14. The channel of claim 11 wherein said carrier is a linear strand hybridizing to multiple copies of said nucleic acid probe.

15. The channel of claim 11 wherein said carrier compartment and said target nucleic acid compartment are bounded by a pair of electrodes and said source is a power supply.

16. The channel of claim 15 further comprising a second electrode pair forming a potential gradient only within said carrier compartment.

17. The channel of claim 11 wherein said apparatus is a pump transferring solution between said carrier compartment and said target nucleic acid compartment,

18. A reusable nucleic acid array comprising:

a plurality of channels according to claim 11 extending in two dimensions.

20. A process for duplicating a nucleic acid array comprising:

forming multiple copies of the nucleic acid within a gel filled chamber bounded by an electrode;

placing said chamber in contact with a second chamber filled with gel and bounded by a second electrode;

inducing electrophoretic migration of a portion of the nucleic acid from said first chamber to said second chamber; and

separating said second chamber from said first chamber.

21. The process of claim 20 further comprising amplifying the portion of nucleic acid within said second chamber to form multiple copies of the portion of the nucleic acid.

22. The process of claim 21 wherein the amplification is by polymerase chain reaction.