Process for in vitro creation of recombinant polynucleotide sequences by oriented ligation

• US 6,991,922 B2
• Filed: 04/25/2001
• Issued: 01/31/2006
• Est. Priority Date: 08/12/1998
• Status: Expired due to Fees

• Current Assignee: Proteus Corporation
• Original Assignee: Proteus Corporation
• Inventors: Lefevre, Fabrice, Dupret, Daniel, Masson, Jean-Michel
• Primary Examiner(s): Horlick, Kenneth R.
• Assistant Examiner(s): Kim, Young J.
• Application Number:
  US09/840,861
• Publication Number:
  US 20020160366A1
• Time in Patent Office: 1,742 Days
• Field of Search: 435/6, 435/455, 435/91.2, 435/91.1, 435/5, 435/7.5, 435/91.5, 435/91.52, 536/23.1, 536/24.3
• US Class Current: 435/91.1
• CPC Class Codes: C07H 21/02 with ribosyl as saccharide radical
• CPC Class Codes: C12N 15/1027 by DNA shuffling, e.g. RSR, STEP, RPR

Abstract

The object of this invention is a process for the creation of at least one recombinant polynucleotide sequence comprising a step of oriented ligation of fragments derived from a bank of at least two polynucleotide sequences, and optionally cloning the recombinant polynucleotide sequences, and the selection of polynucleotide sequences offering advantageous characteristics compared to one or several reference sequences.

Claims

1. A ligase-mediated method of recombination, comprising:

providing oligonucleotide fragments derived from each of at least two heterologous polynucleotide sequences of a polynucleotide bank;

hybridizing the fragments to an assembly matrix so that the hybridized fragments are oriented for ligation with each other; and

ligating the hybridized fragments having immediately adjacent ends with a ligase to form random recombinant polynucleotide sequences.

2. The method of claim 1, further comprising at least one repetition of the providing step, the hybridizing step or the ligating step.

3. The method of claim 2, wherein the hybridizing step is repeated, before or after the ligating step, until the ends of more than half of the hybridized fragments are immediately adjacent to each other.

4. The method of claim 3, wherein, before a final ligating step, the ends of all of the hybridized fragments are immediately adjacent to each other.

5. The method of claim 1, wherein any polymerase extension performed during the hybridizing or ligating step, or between the hybridizing and ligating step, consists of gap filling between the hybridized fragments.

6. The method of claim 1, wherein the method is performed without a polymerase.

7. The method of claim 1, wherein the method is performed in vitro.

8. The method of claim 1, wherein, at the providing step, the fragments are cleavage fragments.

9. The method of claim 1, wherein, at the providing step, the fragments are random fragments.

10. The method of claim 1, wherein the method of recombination is a method of random recombination.

11. The method of claim 1, wherein the providing step comprises providing fragments that have been obtained in a manner such that degree of recombination desired and the position of the recombination points have been precisely controlled.

12. The method of claim 1, wherein the providing step comprises fragmenting the at least two heterologous polynucleotide sequences in a manner such that degree of recombination desired and the position of the recombination points have been precisely controlled.

13. The method of claim 1, wherein the at least two heterologous polynucleotide sequences differ from each other at more than one base position.

14. The method of claim 13, wherein the at least two heterologous polynucleotide sequences are derived from at least two distinct genes.

15. The method of claim 14, wherein the at least two heterologous polynucleotide sequences are derived from at least two distinct genes from at least two distinct gene families.

16. The method of claim 14, wherein the at least two heterologous polynucleotide sequences are derived from at least two distinct genes from at least two different species of organism.

17. The method of claim 1, wherein the at least two heterologous polynucleotide sequences are single-stranded.

18. The method of claim 1, wherein at least one assembly matrix is double-stranded and it is first denatured and then added in single-stranded form at the hybridizing step.

19. The method of claim 1, wherein at least one assembly matrix is single-stranded.

20. The method of claim 1, wherein the ligase is a thermostable ligase that is active at temperatures at or above 65°

C.

21. The method of claim 1, wherein the polynucleotide bank comprises a variety of polynucleotide sequences obtained by mutagenesis or by combining genes of close or distinct families.

22. The method of claim 1, wherein, in addition to said fragments and assembly matrix, oligonucleotides of varying length, and single- or double-stranded, are added at the providing or hybridizing step.

23. The method of claim 1, wherein the polynucleotide bank comprises a restricted bank.

24. The method of claim 1, wherein the recombinant polynucleotide formed by the method is a non-naturally occurring polynucleotide.

25. The method of claim 1, further comprising cloning the recombinant polynucleotide sequence.

26. The method of claim 1, wherein a fragment from the providing step is used as the assembly matrix.

27. The method of claim 1, wherein the providing step comprises subjecting the at least two heterologous polynucleotide sequences to hydrolysis by the action of a plurality of different restriction enzymes or by the action of one or more restriction enzymes having a large number of cutting sites on the at least two heterologous polynucleotide sequences.

28. The method of claim 27, wherein a fragment obtained at the providing step by a treatment with restriction enzymes is used as the assembly matrix.

29. The method of claim 1, wherein the providing step further comprises randomly fragmenting the at least two heterologous polynucleotide sequences by treating them with DNAase I.

30. The method of claim 29, wherein a fragment produced by the random fragmenting is used as the assembly matrix at the hybridizing step.

31. The method of claim 1, wherein the hybridizing and ligating steps are performed simultaneously.

32. The method of claim 1, wherein the at least two heterologous polynucleotide sequences are double-stranded and the providing step further comprises denaturing the fragments obtained at the providing step.

33. The method of claim 1, further comprising using the recombinant polynucleotide sequence as a source of fragments or as an assembly matrix during at least one repetition of the providing or hybridizing step.

34. The method of claim 1, further comprising separating the recombinant polynucleotide sequence formed at the ligating step from the assembly matrix.

35. The method of claim 34, wherein the recombinant polynucleotide sequence is separated from the assembly matrix using a marker present on the assembly matrix or on the recombinant polynucleotide sequence.

36. The method of claim 1, further comprising, before the selecting step, using polymerase extension to amplify the number of copies of the recombinant polynucleotide sequence.

37. The method of claim 1, wherein the selected recombinant polynucleotide sequence is used to form a new polynucleotide bank for a repeat of one or more of the providing step, the hybridizing step, the ligating step or the selecting step.

38. The method of claim 1, wherein the selection is performed by in vitro expression of the recombinant polynucleotide sequence.

39. The method of claim 1, further comprising using a degrading enzyme at the hybridizing or ligating step that specifically recognizes and degrades any nonhybridized ends of the fragments when said nonhybridized ends overlap hybridized fragments on the assembly matrix.

40. The method of claim 39, wherein the degrading enzyme is Flap endonuclease.

41. The method of claim 39, wherein the degrading enzyme and the ligase are equally thermostable at temperatures at or above 65°

C.

42. The method of claim 39, wherein the degrading enzyme is an exonuclease that cleaves single-stranded nucleic acids.

44. The method of claim 1, wherein the recombinant polynucleotide sequences comprise at least two recombinant polynucleotide sequences.

43. A ligase-mediated method of recombination, comprising:

hybridizing oligonucleotide fragments derived from each of at least two heterologous polynucleotide sequences to an assembly matrix so that the hybridized fragments are oriented for ligation with each other; and

ligating the hybridized fragments having immediately adjacent ends with a ligase to form random recombinant polynucleotide sequences.