Methods for generating polynucleotides having desired characteristics by iterative selection and recombination

• US 6,277,638 B1
• Filed: 01/15/1999
• Issued: 08/21/2001
• Est. Priority Date: 02/17/1994
• Status: Expired due to Term

• Current Assignee: Codexis, Inc.
• Original Assignee: Maxygen Inc.
• Inventors: Stemmer, Willem P. C.
• Primary Examiner(s): WHISENANT, ETHAN C
• Application Number:
  US09/232,863
• Time in Patent Office: 949 Days
• Field of Search: 435/6, 435/76, 435/77, 435/78, 536/440, 536/23.1, 536/24.3
• US Class Current: 506/1
• CPC Class Codes: C07K 14/43595 from coelenteratae, e.g. medusae
• CPC Class Codes: C07K 14/545 IL-1
• CPC Class Codes: C07K 16/00 Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies antibodies with enzymatic activity, e.g. abzymes C12N9/0002
• CPC Class Codes: C07K 2317/565 Complementarity determining region [CDR]
• CPC Class Codes: C07K 2317/622 Single chain antibody (scFv)
• CPC Class Codes: C12N 15/1027 by DNA shuffling, e.g. RSR, STEP, RPR
• CPC Class Codes: C12N 15/1034 Isolating an individual clone by screening libraries
• CPC Class Codes: C12N 15/1037 Screening libraries presented on the surface of microorganisms, e.g. phage display, E. coli display
• CPC Class Codes: C12N 9/2471 Beta-galactosidase (3.2.1.23), i.e. exo-(1-->4)-beta-D-galactanase
• CPC Class Codes: C12N 9/86 acting on amide bonds in cyclic amides, e.g. penicillinase (3.5.2)
• CPC Class Codes: C12Q 1/68 involving nucleic acids
• CPC Class Codes: C12Q 1/6811 Selection methods for production or design of target specific oligonucleotides or binding molecules
• CPC Class Codes: C12Y 302/01023 Beta-galactosidase (3.2.1.23), i.e. exo-(1-->4)-beta-D-galactanase
• CPC Class Codes: C12Y 305/02006 Beta-lactamase (3.5.2.6)
• CPC Class Codes: C40B 40/02 Libraries contained in or displayed by microorganisms, e.g. bacteria or animal cells; Libraries contained in or displayed by vectors, e.g. plasmids; Libraries containing only microorganisms or vectors
• CPC Class Codes: C40B 40/08 Libraries containing RNA or DNA which encodes proteins, e.g. gene libraries
• CPC Class Codes: C40B 50/06 Biochemical methods, e.g. using enzymes or whole viable microorganisms

Abstract

A method for DNA reassembly after random fragmentation, and its application to mutagenesis of nucleic acid sequences by in vitro or in vivo recombination is described. In particular, a method for the production of nucleic acid fragments or polynucleotides encoding mutant proteins is described. The present invention also relates to a method of repeated cycles of mutagenesis, shuffling and selection which allow for the directed molecular evolution in vitro or in vivo of proteins.

Claims

1. A method of evolving a polynucleotide toward a desired functional property comprising:

(a) providing a plurality of polynucleotides comprising two or more species variants;

(b) shuffling said plurality of polynucleotides to form a population of recombinant polynucleotides;

(c) selecting or screening said population of recombinant polynucleotides for recombinant polynucleotides that have evolved toward the desired functional property,

(d) repeating steps (b) and (c) with the plurality of polynucleotides in step (b) comprising the recombinant polynucleotides selected or screened in step (c) until a recombinant polynucleotide is obtained which has acquired the desired functional property, wherein at least one shuffling cycle comprises conducting a mult-cyclic polynucleotide extension process on partially annealed polynucleotide strands having sequences from the plurality of polynucleotides, the plurality of polynucleotides having regions of similarity and regions of heterology with each other and the partially annealed polynucleotide strands being partially annealed through the regions of similarity, under conditions whereby one strand serves as a template for extension of another strand with which it is partially annealed to generate said recombinant polynucleotides.

2. The method of claim 1, wherein the partially-annealed polynucleotide strands are produced by providing overlapping single-stranded segments of the plurality of polynucleotides and incubating said overlapping single-stranded segments under annealing conditions to form the partially annealed polynucleotide strands.

3. The method of claim 2 wherein the overlapping single-stranded segments are random segments of the plurality of polynucleotides.

4. The method of claim 2 wherein the overlapping single-stranded segments are nonrandom segments of the plurality of polynucleotides.

5. The method of claim 2 wherein the overlapping single stranded segments are produced by cleaving the plurality of polynucleotides to produce a population of double-stranded fragments and denaturing the double-stranded fragments to produce the overlapping single-stranded segments.

6. The method of claim 5 wherein the polynucleotide variants are DNA and the cleavage is by DNAse I digestion.

7. The method of claim 2 wherein the overlapping single-stranded polynucleotide segments are produced by a DNA synthesizer.

8. The method of claim 1 wherein at least one of the plurality of polynucleotides is naturally occurring.

9. The method of claim 8 wherein at least one of the plurality of polynucleotide is obtained from a source in nature.

10. The method of claim 1 wherein the plurality of polynucleotides encode an enzyme.

11. The method of claim 1 wherein the plurality of polynucleotides encode a therapeutic protein.

12. The method of claim 1 wherein the plurality of polynucleotides encode an antibody.

13. The method of claim 1 wherein said plurality of polynucleotides are bacterial.

14. The method of claim 2, wherein at least one of the plurality of polynucleotides encode natural polypeptide.

15. The metod of claim 2, wherein at least one of the plurality of polynucleotides has been mutagenized prior to the first shuffling cycle.

16. The method of claim 15, wherein said mutagenesis is conducted by error-prone PCR.

17. The method of claim 15, wherein said mutagenesis is conducted by oligonucleotide-directed mutagenesis.

18. The method of claim 15, wherein said mutagenesis is conducted by chemical mutagenesis.

19. The method of claim 15, wherein said mutagenesis is random mutagenesis.

20. The method of claim 14 wherein at least one of the plurality of polynucleotides is obtained from a source in nature.

21. The method of claim 2, wherein the sequences of the plurality of variant polynucleotides are unknown.

22. The method of claim 2, wherein synthetic polynucleotides and/or PCR fragments are added to the shuffling reaction mixture.

23. The method of claim 2, wherein said desired functional property is the ability to bind a receptor.

24. The method of claim 2, wherein said functional property is drug resistance.

25. The method of claim 2, wherein the desired functional property is suitability of the recombinant polynucleotide as an agent for gene therapy.

26. The method of claim 2, wherein the desired functional property is suitability of the recombinant polynucleotide or an expression product thereof as an agent for anti-neoplastic therapy.

27. The method of claim 2, wherein the desired functional proprety is suitabilit of the recombinant polynucleotide as an agent for DNA-based vaccination.

28. The method of claim 2, wherein the polynucleotides encode variants of an antibody.

29. The method of claim 2, wherein the plurality of polynucleotides encode variants of an enzyme.

30. The method of claim 2, wherein the plurality of polynucleotides encode variants of a therapeutic protein.

31. The method of claim 30, wherein said therapeutic protein is IL-1beta.

32. The method of claim 2, wherein the plurality of polynucleotides comprise animal polynucleotides.

33. The method of claim 32, wherein the plurality of polynucleotides comprise a mouse polynucleotide.

34. The method of claim 32, wherein the plurality of polynucleotides comprise a human polynucleotide.

35. The method of claim 32, wherein the plurality of polynucleotides comprise a mouse and a human polynucleotide.

36. The method of claim 2, wherein the plurality of polynucleotides comprise bacterial polynucleotides.

37. The method of claim 2, wherein the pluality of polynucleotides comprise plant polynucleotides.

38. The method of claim 2, wherein the plurality of polynucleotides comprise fungal polynucleotides.

39. The method of claim 2, wherein the plurality of polynucleotides comprise viral polynucleotides.

40. A method of obtaining a recombinant polynucleotide having a desired functional property comprising:

a) treating a sample comprising species variants of a polynucleotide wherein the species variants of the polynucleoytide contain regions of similarity, under conditions whereby overlapping double-stranded segments of the species variants of the polynucleotide are formed;

b) denaturing the resultant overlapping double-standed segments of the species variants of the polynucleotide into single-stranded segments;

c) incubating said single-stranded segments under conditions which provide for the annealing of the single-stranded segments at the areas of simlarity to form pairs of annealed segments and extending the annealed segments with a polymerase, wherein said areas of similarity are sufficient for one member of a pair to prime replication of the other thereby forming recombinant double-stranded polynucleotide sequences;

d) repeating steps b) and c) for at least two cycles wherein the resultant mixture in step b) of a cycle comprises the recombinant double-stranded polynucleotide sequences formed in step c) of the previous cycle and the further cycle forms further recombinant sequences whereby the average length of the recombinant polynucleotide sequences increases in each cycle; and

e) screening or selecting recombinant polynucleotide sequences formed in step d) to identify a recombinant polynucleotide having the desired functional property.

41. The method of claim 40 wherein said overlapping double-stranded segments are random segments.

42. The method of claim 40 wherein said overlapping double-standed segments are non-random segments.

43. The method of claim 40 wherein said overlapping double-stranded segments are produced by cleavage of the species variants of the polynucleotide.

44. The method of claim 43 wherein said species variants of a polynucleotide are DNA and cleavage is by digestion with DNAse I.

45. The method of claim 40 wherein the overlapping double-stranded segments of step a) comprise recombinant sequences obtained by synthesizing oligonucleotides having sequences fom the plurality of polynucleotides and by annealing said oligonucleotides in thc presence of a polymerase.

46. The method of claim 40 wherein at least one of the species variants of a polynucleotide is naturally-occurring.

47. The method of claim 46 wherein at least one of the species variants of a polynucleotide is obtained from a source in nature.

48. The method of claim 40 wherein at least one of the species variants of the polynucleotide has been mutagenized prior to te first shuffling cycle.

49. The method of claim 48 wherein said mutagenesis is conducted by error-prone PCR.

50. The method of claim 48 wherein said mutagenesis is conducted by oligonucleotide-directed mutagenesis.

51. The method of claim 48 wherein said mutagenesis is conducted by chemical mutagenesis.

52. The method of claim 48 wherein said mutagenesis is random mutagenesis.

53. The method of claim 52 wherein said random mutagenesis is affected by irradiation.

54. The method of claim 40 wherein the sequence of at least one of the species variants of the polyucleotide is unknown.

55. The method of claim 40 wherein synthetic polynucleotides and/or PCR fragments are added to the reaction mixture of step b).

56. The method of claim 40 wherein said desired functional property is the ability to bind a receptor.

57. The method of claim 40 wherein the species variants of the polynucleotide encode an antibody molecule.

58. The method of claim 40 wherein the species variants of the polynucleotide encode an enzyme.

59. The method of claim 40 wherein the species variants of a polynucleotide encode a therapeutic protein.

60. The method of claim 59 wherein said therapeutic protein is IL-1beta.

61. The method of claim 40 wherein the species variants of a polynucleotide comprise animal polynucleotides.

62. The method of claim 61 wherein the species variants of a polynucleotide comprise a mouse polynucleotide.

63. The method of claim 62 wherein the species variants of a polynucleotide comprise a human polynucleotide.

64. The method of claim 40 wherein the species variants of a polynucleotide comprise bacterial polynucleotides.

65. The method of claim 40 wherein the species variants of a polynucleotide comprise plant polynucleotides.

66. The method of claim 40 wherein the species variants of a polynucleotide comprise fungal polynucleotides.

67. The method of claim 40 wherein the species variants of a polynucleotide comprise viral polynucleotides.

68. The method of claim 40 wherein the region of similarity is a region of identity between two or more species of the polynucleotide.

69. The method of claim 40 wherein step e) comprises:

a) introducing the recombinant polynucleotide to be screened or selected into a population of cells;

b) expressing the the recombinnt polynucleotides in said population of cells; and

c) selecting or screening the population of cells for the desired functional property.

70. The method of claim 40 further comprising formulating the recombinant polynucleotide having the desired property or an expression product thereof as pharmaceutical.

71. The method of claim 40 wherein the size of the double-stranded overlapping segments is from 5 base pairs to 5 kilobases.

72. The method of claim 71 wherein the size of the double-stranded overlapping segments is from 10 to 1000 base pairs.

73. The method of claim 72 wherein the size of the double-stranded overlapping segments is from 20 to 500 base pairs.