METHODS AND COMPOSITIONS COMPRISING NUCLEIC ACID POLYMERIZATION ENHANCERS

• US 20110282043A1
• Filed: 03/11/2011
• Published: 11/17/2011
• Est. Priority Date: 03/12/2010
• Status: Abandoned Application

• Current Assignee: Cenetron Diagnostics, LLC
• Original Assignee: Cenetron Diagnostics, LLC
• Inventors: Dubois, Dwight
• Application Number:
  US13/046,325
• Publication Number:
  US 20110282043A1
• Time in Patent Office: Days
• US Class Current: 536/23.1
• CPC Class Codes: C12Q 1/6848 characterised by the means for preventing contamination or increasing the specificity or sensitivity of an amplification reaction
• CPC Class Codes: C12Q 1/686 Polymerase chain reaction [PCR]
• CPC Class Codes: C12Q 2525/186 incorporating a non-extendable or blocking moiety
• CPC Class Codes: C12Q 2525/204 specific length of the oligonucleotides

Abstract

Embodiments of the invention are directed to compositions and methods that use non-extendable oligonucleotides to enhance or improve synthesis or amplification of nucleic acids.

Claims

1. A non-extendable nucleic acid for enhancing or increasing the yield of nucleic acid amplification or synthesis comprising a non-extendable nucleic acid of 5 or more nucleotides comprising a nucleotide sequence of ggxgg, ccxcc, gcxcg, gcxcg, aaxaa, ttxtt, atxta, taxat, xggxgg, xccxcc, xgcxcg, xgcxcg, xaaxaa, xttxtt, xatxta, xtaxat, or nucleotide analogs thereof, wherein x is any nucleotide or nucleotide analog.

2. The non-extendable nucleic acid of claim 1, wherein the non-extendable nucleic acid does not form a double stranded nucleic acid by either intra-oligonucleotide or inter-oligonucleotide hybridization at 20°

C. or above.

3. The non-extendable nucleic acid of claim 1, further comprising a modified 3′

hydroxyl of the 3′

terminal nucleotide.

4. The non-extendable nucleic acid of claim 3, wherein an H, alkyl, arylalkyl, group replaces or is covalently attached to the 3′

hydroxyl group of the 3′

nucleotide.

5. The non-extendable nucleic acid of claim 1, further comprising a modified 5′

position of the 5′

nucleotide.

6. The non-extendable nucleic acid of claim 1, wherein the 5′

position comprises a mono-phosphate, a H, or an alkyl group.

7. The non-extendable nucleic acid of claim 1, wherein the oligonucleotide is an RNA oligonucleotide.

8. The non-extendable nucleic acid of claim 1, further comprising a detectable label.

9. The non-extendable nucleic acid of claim 8, wherein the detectable label is selected from the group consisting of fluorescers, chemiluminescers, dyes, biotin, haptens, enzymes, enzyme substrates, enzyme cofactors, enzyme inhibitors, enzyme subunits, metal ions, electron-dense reagents, and radioactive isotopes.

10. A method for amplifying a target nucleic acid sequence comprising:

contacting the target nucleotide sequence under hybridizing conditions with;

(a) an oligonucleotide primer;

(b) an amplification enhancer comprising a non-extendable oligonucleotide of 5 or more nucleotides comprising a nucleotide sequence of ggxgg, ccxcc, gcxcg, gcxcg, aaxaa, ttxtt, atxta, taxat, xggxgg, xccxcc, xgcxcg, xgcxcg, xaaxaa, xttxtt, xatxta, xtaxat, or nucleotide analogs thereof, wherein x is any nucleotide or nucleotide analog wherein x is any nucleotide or nucleotide analog; and

(c) an agent for polymerization of the nucleotides.

11. The method of claim 10, wherein the oligonucleotide does not form a double stranded oligonucleotide by either intra-oligonucleotide or inter-oligonucleotide hybridization at 20°

C. or above

12. The method of claim 10, wherein the oligonucleotide is an RNA or an RNA analog.

13. The method of claim 10, further comprising a detectable label.

14. The method of claim 13, wherein the detectable label is selected from the group consisting of fluorescers, chemiluminescers, dyes, biotin, haptens, enzymes, enzyme substrates, enzyme cofactors, enzyme inhibitors, enzyme subunits, metal ions, electron-dense reagents, and radioactive isotopes.

15. The method of claim 10, wherein the target nucleic acid is a microbial DNA or RNA.

17. The method of claim 10, wherein the agent for polymerization is a DNA polymerase or a DNA ligase.

19. The method of claim 10, wherein the agent for polymerization is an RNA polymerase or an RNA reverse transcriptase.

16. The method of claim 16, wherein the microbial DNA or RNA is a viral DNA or RNA.

18. (canceled)

20. -25. (canceled)

26. An amplicon formed by amplifying a nucleic acid in the presence of a non-extendable oligonucleotide of 5 or more nucleotides comprising a nucleotide sequence of ggxgg, ccxcc, gcxcg, gcxcg, aaxaa, ttxtt, atxta, taxat, xggxgg, xccxcc, xgcxcg, xgcxcg, xaaxaa, xttxtt, xatxta, xtaxat, or nucleotide analogs thereof, wherein x is any nucleotide or nucleotide analog;

wherein the oligonucleotide does not form a double stranded oligonucleotide by either intra-oligonucleotide or inter-oligonucleotide hybridization at 20°

C. or above.

27. (canceled)

28. A kit for amplifying nucleic acids comprising a non-extendable oligonucleotide of 5 or more nucleotides comprising a nucleotide sequence of ggxgg, ccxcc, gcxcg, gcxcg, aaxaa, ttxtt, atxta, taxat, xggxgg, xccxcc, xgcxcg, xgcxcg, xaaxaa, xttxtt, xatxta, xtaxat, or nucleotide analogs thereof, wherein x is any nucleotide or nucleotide analog.

29. -35. (canceled)