Nucleic acid concatenation

• US 20080124707A1
• Filed: 06/09/2006
• Published: 05/29/2008
• Est. Priority Date: 06/09/2006
• Status: Abandoned Application

• Current Assignee: Agency For Science Technology and Research
• Original Assignee: Agency For Science Technology and Research
• Inventors: Lee, Yen Ling, Ruan, Yijun, Ng, Patrick, Fullwood, Melissa Jane
• Application Number:
  US11/449,872
• Publication Number:
  US 20080124707A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/6804 Nucleic acid analysis using immunogens immunoassay G01N33/53
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 2525/131 incorporating a restriction site
• CPC Class Codes: C12Q 2525/151 repeat or repeated sequences, e.g. VNTR, microsatellite, concatemer
• CPC Class Codes: C12Q 2539/103 Serial analysis of gene expression [SAGE]

Abstract

The present invention provides a method of manipulating nucleic acids. In particular, of length-controlled concatenating of nucleotide fragments, the method comprising: (a) providing at least two nucleotide fragments, wherein each fragment has one ligatable end and one non-ligatable end; and (b) allowing the two fragments to ligate at the ligatable ends to form an oligonucleotide comprising at least two concatenated nucleotide fragments. The present invention also provides an isolated oligonucleotide comprising at least two nucleotide fragments, wherein each fragment has at least one ligatable end and and one non-ligatable end, and the fragments are ligated at the ligatable ends to form the oligonucleotide.

Claims

1. A method of length-controlled concatenating nucleotide fragments, the method comprising:

(a) providing at least two nucleotide fragments, wherein each fragment has one ligatable end and one non-ligatable end; and

(b) allowing the two fragments to ligate at the ligatable ends to form at least one oligonucleotide comprising at least two concatenated nucleotide fragments.

2. The method according to claim 1, wherein the ligatable end of each fragment is a palindromic cohesive end.

3. The method according to claim 1, wherein the ligatable end and/or the non-ligatable end is located in at least one adaptor.

4. The method according to claim 3, wherein the adaptor is part of a plasmid or vector.

5. The method according to claim 1, wherein the nucleotide fragments are amplified.

6. The method according to claim 5, wherein the amplification is by bacterial amplification, by rolling circle amplification, and/or by polymerase chain reaction.

7. The method according to claim 1, further comprising the steps of treating the at least one oligonucleotide to produce at least one oligonucleotide having one ligatable end and one non-ligatable end, and allowing the oligonucleotide to ligate with a further oligonucleotide or a nucleotide fragment to form an oligonucleotide comprising more than two concatenated nucleotide fragments.

8. The method according to claim 7, wherein the steps are repeated one or more times.

9. The method according to claim 7, wherein the ligatable end of each oligonucleotide or of the nucleotide fragment is a palindromic cohesive end.

10. The method according to claim 1, further comprising treating the at least one oligonucleotide to produce at least one oligonucleotide with two ligatable ends and allowing the oligonucleotide to self-circularize at the ligatable ends.

11. The method according to claim 10, wherein the ligatable ends are palindromic cohesive ends.

12. The method according to claim 10, wherein the ligatable ends are obtained from two adaptors, each adaptor linked to each end of the oligonucleotide.

13. The method according to claim 10, further comprising selecting the at least one circularized oligonucleotide and/or amplifying the oligonucleotide.

14. The method according to claim 13, further comprising treating the at least one circularized and/or amplified oligonucleotide to produce at least one oligonucleotide having one ligatable end and one non-ligatable end, and allowing the oligonucleotide to ligate with at least a further oligonucleotide at their ligatable ends to form at least two concatenated oligonucleotides.

15. The method according to claim 1, further comprising:

(a) treating the at least one oligonucleotide to produce at least one oligonucleotide having two ligatable ends, and allowing the oligonucleotide to self-circularize at its ligatable ends;

(b) selecting the at least one self-circularized oligonucleotide;

(c) optionally amplifying the selected oligonucleotide;

(d) treating the oligonucleotide to produce at least one oligonucleotide with one ligatable end and one non-ligatable end; and

(e) allowing the oligonucleotide to ligate with a further oligonucleotide at their ligatable ends to form at least two concatenated oligonucleotides.

16. The method according to claim 15, comprising repetition of the steps (a) to (e) one or more times.

17. The method according to claim 1, wherein the at least one nucleotide fragment comprises at least one ditag, the ditag comprising at least one first tag comprising a 5′

terminus and at least one second tag comprising a 3′

terminus of a polynucleotide.

18. The method according to claim 1, wherein each nucleotide fragment of the concatemer has orientation opposite to the orientation of a nucleotide fragment positioned upstream and/or downstream.

19. The method according to claim 1, further comprising sequencing the concatenated nucleotide fragments.

20. The method according to claim 19, wherein the sequencing is by pyrosequencing and/or by serial analysis of gene expression.

21. A method of length-controlled concatenating nucleotide fragments, the method comprising the steps of:

(a) providing at least one oligonucleotide comprising at least one nucleotide fragment, wherein the oligonucleotide has ligatable ends;

(b) allowing the at least one oligonucleotide to self-circularize at its ligatable ends;

(c) selecting the at least one self-circularized oligonucleotide;

(d) treating the selected circularized oligonucleotide with at least one restriction enzyme to obtain at least one oligonucleotide with one ligatable end and one non-ligatable end; and

(e) concatenating at least two oligonucleotides at the ligatable ends to form a concatenated oligonucleotide comprising at least two nucleotide fragments.

22. The method according to claim 21, wherein the provided oligonucleotide in step (a) comprises at least two concatenated nucleotide fragments, and the obtained concatenated oligonucleotide in step (e) comprises at least four concatenated nucleotide fragments.

23. The method according to claim 21, wherein the nucleotide fragment comprises at least one ditag, the ditag comprising at least one first tag comprising a 5′

terminus and at least one second tag comprising a 3′

terminus of a polynucleotide.

24. The method according to claim 21, wherein the ligatable ends are palindromic cohesive ends.

25. The method according to claim 21, wherein step (e) concatenation is repeated one or more times.

26. The method according to claim 25, wherein each repeat of concatenation results in a doubling of the number of concatenated nucleotide fragments.

27. The method according to claim 21, wherein the ligatable ends are obtained from adaptors.

28. The method according to claim 21, wherein step (c) further comprises amplification of the oligonucleotide.

29. The method according to claim 28, wherein the amplification is by rolling circle amplification, and/or by polymerase chain reaction.

30. The method according to claim 21, the method further comprising sequencing the concatenated oligonucleotide.

31. The method according to claim 21, wherein each nucleotide fragment of the oligonucleotide has orientation opposite to the orientation of a nucleotide fragment positioned upstream and/or downstream.

32. An isolated oligonucleotide comprising at least two nucleotide fragments, wherein each fragment has at least one ligatable end and and one non-ligatable end, and the fragments are ligated at the ligatable ends to form the oligonucleotide.

33. The oligonucleotide according to claim 32, wherein the ligatable ends are palindromic cohesive ends.

34. The oligonucleotide according to claim 32, wherein the fragment comprises at least one ditag, the ditag comprising at least one first tag comprising a 5′

terminus and at least one second tag comprising a 3′

terminus of a polynucleotide.

35. The oligonucleotide according to claim 34, wherein each nucleotide fragment of the oligonucleotide has orientation opposite to the orientation of a nucleotide fragment positioned upstream and/or downstream.

36. The oligonucleotide according to claim 34, wherein the oligonucleotide is inserted into a plasmid or vector.