Compositions and methods for nonenzymatic ligation of oligonucleotides and detection of genetic polymorphisms

• US 7,033,753 B1
• Filed: 01/14/2000
• Issued: 04/25/2006
• Est. Priority Date: 01/15/1999
• Status: Expired due to Fees

• Current Assignee: University of Rochester
• Original Assignee: University of Rochester
• Inventors: Kool, Eric T.
• Primary Examiner(s): CRANE, LAWRENCE E
• Application Number:
  US09/483,337
• Time in Patent Office: 2,293 Days
• Field of Search: 536/23.1, 536/26.7, 536/26.8, 536/27.3, 536/27.7, 536/27.81, 536/28.5, 536/28.53, 536/25.33, 536/26.5, 536/26.6, 536/24.3, 536/24.5, 435/6
• US Class Current: 435/6.12
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 2523/109 chemical ligation between nucleic acids
• CPC Class Codes: C12Q 2525/101 incorporating non-naturally occurring nucleotides, e.g. inosine
• CPC Class Codes: C12Q 2561/125 Ligase Detection Reaction [LDR]

Abstract

The invention is directed to novel compositions and methods for nonenzymatic ligation of oligonucleotides. In one aspect of the invention, the nonenzymatic ligation is selenium-mediated or tellurium mediated ligation. In another aspect, the invention provides for the use of fluorescence resonance energy transfer (FRET) to detect the nonenzymatic ligation.

Claims

1. A method for detecting a genetic polymorphism in a target nucleic acid comprising:

providing a mutant polymorphism oligonucleotide probe that is complementary to a region on the target nucleic acid that comprises the genetic polymorphism;

providing a universal oligonucleotide probe capable of binding to the target nucleic acid at a region that is conserved in the analogous wild-type nucleic acid;

wherein one oligonucleotide probe constitutes an upstream oligonucleotide having, as its 5′

-end, a ribo- or deoxyribonucleoside wherein the 5′

-hydroxyl group thereof has been replaced by a leaving group, and the other oligonucleotide probe constitutes a downstream oligonucleotide comprising, at its 3′

end, a nucleoside comprising a 3′

functional group selected from the group consisting of 3′

-phosphoroselenoates such that, when both probes are bound to the target nucleic acid, an end of the universal oligonucleotide probe is substantially adjacent to an end of the mutant polymorphism oligonucleotide probe so as to position the 5′

leaving group and the 3′

-functional group in close proximity to one another;

contacting the target nucleic acid with the universal oligonucleotide probe and the mutant polymorphism oligonucleotide probe to yield an autoligated oligonucleotide product comprising the universal oligonucleotide probe and the mutant polymorphism probe; and

detecting the presence of the autoligated oligonucleotide product, wherein the presence of an autoligated product indicates the presence of a genetic polymorphism in the target nucleic acid.

2. The method of claims 1 wherein at least one of the mutant polymorphism oligonucleotide probe and the universal oligonucleotide probe further comprises a detectable label.

3. The method of claim 2 wherein the detectable label is a radiolabel.

4. The method of claim 1 wherein the genetic polymorphism is selected from the group consisting of a single base mutation, a plurality of single base mutations, a deletion, an insertion, and a genetic rearrangement.

5. The method of claim 1 wherein the nucleotide position is not the nucleotide position corresponding to the ligation junction end of the mutant polymorphism probe.

6. The method of claim 1 wherein the target nucleic acid is DNA.

7. The method of claim 1 wherein the target nucleic acid is RNA.