Attaching a stem-loop oligonucleotide to a double stranded DNA molecule

• US 8,728,737 B2
• Filed: 02/13/2013
• Issued: 05/20/2014
• Est. Priority Date: 08/02/2005
• Status: Active Grant

• Current Assignee: Takara Bio Usa, Inc. (Ningbo Junsheng Investment Group Co., Ltd.)
• Original Assignee: Rubicon Genomics, Inc
• Inventors: Makarov, Vladimir L., Kamberov, Emmanuel, Tarrier, Brendan J.
• Primary Examiner(s): HORLICK, KENNETH R
• Application Number:
  US13/766,607
• Publication Number:
  US 20130303407A1
• Time in Patent Office: 461 Days
• Field of Search: 435/6.12, 435/91.1, 435/91.2
• US Class Current: 435/6.12
• CPC Class Codes: C12N 15/1068 Template (nucleic acid) mediated chemical library synthesis, e.g. chemical and enzymatical DNA-templated organic molecule synthesis, libraries prepared by non ribosomal polypeptide synthesis [NRPS], DNA/RNA-polymerase mediated polypeptide synthesis
• CPC Class Codes: C12P 19/34 Polynucleotides, e.g. nucleic acids, oligoribonucleotides
• CPC Class Codes: C12Q 1/6853 using modified primers or templates
• CPC Class Codes: C12Q 1/6855 Ligating adaptors
• CPC Class Codes: C12Q 1/686 Polymerase chain reaction [PCR]
• CPC Class Codes: C12Q 1/6865 Promoter-based amplification, e.g. nucleic acid sequence amplification [NASBA], self-sustained sequence replication [3SR] or transcription-based amplification system [TAS]
• CPC Class Codes: C12Q 2521/301 Endonuclease
• CPC Class Codes: C12Q 2521/501 Ligase
• CPC Class Codes: C12Q 2525/119 incorporating abasic sites
• CPC Class Codes: C12Q 2525/191 incorporating an adaptor
• CPC Class Codes: C12Q 2525/301 Hairpin oligonucleotides

Abstract

The present invention concerns preparation of DNA molecules, such as a library, using a stem-loop oligonucleotide. In particular embodiments, the invention employs a single reaction mixture and conditions. In particular, at least part of the inverted palindrome is removed during the preparation of the molecules to facilitate amplification of the molecules. Thus, in specific embodiments, the DNA molecules are suitable for amplification and are not hindered by the presence of the palindrome.

Claims

1. A method of preparing a nucleic acid molecule, comprising:

providing a double stranded nucleic acid DNA molecule; and

attaching one strand of a stem-loop oligonucleotide comprising an inverted repeat and a loop to the double stranded nucleic acid molecule to produce an oligonucleotide-attached nucleic acid molecule, wherein the stem-loop oligonucleotide comprises at least one deoxy-uridine.

2. The method of claim 1, wherein the attaching is further defined as attaching the oligonucleotide to the double stranded nucleic acid molecule under conditions to produce a non-covalent junction in the oligonucleotide-attached nucleic acid molecule.

3. The method of claim 2, wherein the non-covalent junction comprises a nick, a gap, or a 5′

flap structure.

4. The method of claim 1, wherein the attaching is further defined as ligating.

5. The method of claim 1, further comprising displacing one strand of the oligonucleotide from the oligonucleotide-attached nucleic acid molecule by strand displacement or by nick translation polymerization.

6. The method of claim 1, further comprising amplifying at least part of the oligonucleotide-attached nucleic acid molecule.

7. The method of claim 6, wherein the at least part of the oligonucleotide-attached nucleic acid molecule is amplified by polymerase chain reaction.

8. The method of claim 6, wherein the at least part of the oligonucleotide-attached nucleic acid molecule is amplified by RNA transcription.

9. The method of claim 6, wherein the at least part of the oligonucleotide-attached nucleic acid molecule is amplified by strand displacement.

10. The method of claim 1, further comprising amplifying the oligonucleotide-attached nucleic acid molecule, wherein at least part of the inverted repeat is excluded from the amplified oligonucleotide-attached nucleic acid molecule.

11. The method of claim 4, wherein the ligating is further defined as comprising:

generating ligatable ends on the double stranded nucleic acid molecule;

generating a ligatable end on the stem-loop oligonucleotide; and

ligating one strand of the ligatable end of the stem-loop oligonucleotide to one strand of an end of the nucleic acid molecule, thereby generating a non-covalent junction in the oligonucleotide-attached nucleic acid molecule.

12. The method of claim 1, further defined as comprising:

generating blunt ends on the nucleic acid molecule;

generating a blunt end on the stem-loop oligonucleotide; and

ligating one strand of the blunt end of the stem-loop oligonucleotide to one strand of a blunt end of the nucleic acid molecule, thereby generating a nick in the oligonucleotide-ligated nucleic acid molecule.

13. The method of claim 1, wherein said stem-loop oligonucleotide comprises a defined sequence.

14. The method of claim 1, wherein said stem-loop oligonucleotide comprises a transcription regulatory sequence.

15. The method of claim 1, further comprising:

digesting the DNA molecule with one or more endonucleases to produce DNA fragments;

producing blunt ends on the DNA fragments;

producing a blunt end on the stem-loop oligonucleotide; and

ligating one strand of the blunt end of a stem-loop oligonucleotide to one strand of a blunt end of a DNA fragment, thereby generating a nick in a oligonucleotide-ligated DNA fragment.

16. The method of claim 15, wherein the endonuclease is a restriction endonuclease, DNAse I, or an apoptotic endonuclease.

17. The method of claim 16, wherein the restriction endonuclease is methylation-specific or methylation-sensitive.

18. The method of claim 1, wherein the oligonucleotide-attached nucleic acid molecule comprises a nick having a 3′

hydroxy group.

19. The method of claim 5, wherein the strand displacement or nick translation polymerization is further defined as polymerization that ceases at a non-replicable base or region in the loop or in a region of the stem adjacent to the loop.

20. The method of claim 1, further comprising the step of digesting the double stranded DNA molecule with an endonuclease to generate DNA fragments.

21. The method of claim 1, wherein the stem-loop oligonucleotide is further defined as comprising a further non-replicable base or sequence in addition to the at least one deoxy-uridine.

22. The method of claim 21, wherein at least part of the non-replicable base or sequence is present in the loop of the oligonucleotide or in a sequence of the stem adjacent to the loop.

23. The method of claim 21, wherein the non-replicable base or sequence comprises an abasic site or sequence, hexaethylene glycol, or a bulky chemical moiety attached to the sugar-phosphate backbone or the base.

24. The method of claim 23, wherein the non-replicable base or sequence comprises an abasic site or sequence that is introduced by one or more enzymes.

25. The method of claim 1, wherein the loop of the stem-loop oligonucleotide comprises at least one deoxy-uridine.

26. The method of claim 5, wherein the strand displacement or nick translation polymerization of the oligonucleotide-attached nucleic acid molecule generates an endonuclease site.

27. The method of claim 26, wherein the endonuclease site is a site-specific restriction endonuclease site and wherein at least part of the inverted repeat is removed by cleavage with said restriction endonuclease.

28. The method of claim 26, wherein the endonuclease site resides within the stem and loop regions.

29. The method of claim 26, wherein the endonuclease site resides within the loop region.

30. The method of claim 26, wherein the endonuclease site resides within the stem region.

31. The method of claim 26, wherein the endonuclease site is a homing endonuclease site.

32. The method of claim 14, further comprising initiating RNA transcription from the transcription regulatory sequence, thereby producing at least one transcribed polynucleotide.

33. The method of claim 32, wherein the transcribed polynucleotide is replicated by a reverse transcriptase.

34. The method of claim 33, wherein reverse transcription is initiated by hybridization of an oligonucleotide complementary to the 3′

end of the transcribed polynucleotide.

35. The method of claim 1, wherein the stem-loop oligonucleotide further comprises a recognition sequence for a nicking endonuclease and wherein the oligonucleotide-attached nucleic acid molecule is amplified by strand displacement synthesis and second strand synthesis.

36. The method of claim 35, wherein the recognition sequence for a nicking endonuclease resides at least in part within the stem of the stem-loop oligonucleotide.

37. The method of claim 35, wherein the recognition sequence for a nicking endonuclease resides at least in part within the loop of the stem-loop oligonucleotide.

38. The method of claim 1, wherein a 5′

end of the stem-loop oligonucleotide lacks a phosphate.

39. The method of claim 1, further comprising incorporating the nucleic acid molecule into a vector.

40. The method of claim 39, wherein the nucleic acid is incorporated at ends in the modified molecule generated by endonuclease cleavage sites within the inverted repeat.

41. The method of claim 1, wherein the method is carried out in a single suitable solution.

42. The method of claim 41, wherein the method is carried out at one temperature.

43. The method of claim 41, wherein the solution comprises one or more of the following:

ligase;

DNA polymerase;

one or more endonucleases;

RNA polymerase;

reverse transcriptase;

RNase H;

deoxy-uridine glycosylase;

nickase;

thermophilic DNA polymerase;

ATP;

rNTPs; and

dNTPs.

44. The method of claim 6, wherein the method is carried out in a single suitable solution.

45. The method of claim 1, wherein the oligonucleotide-attached nucleic acid molecule is immobilized to a solid support.

46. The method of claim 45, wherein the molecule is immobilized non-covalently.

47. The method of claim 45, wherein the molecule is immobilized covalently.

48. The method of claim 1, wherein the stem-loop oligonucleotide comprises more than one deoxy-uridines.