Polynucleotide sequence variants
First Claim
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1. A method for preparing a variant polynucleotide having a different nucleotide sequence from at least two parent polynucleotides comprising;
- preparing at least one heteroduplex between at least said two parent polynucleotides, cleaving at least one polynucleotide strand in said heteroduplex at a mismatch site to form a cleavage site, replacing at least one nucleotide on at least one polynucleotide strand at or near the cleavage site, wherein at least one of said polynucleotide strands has a different nucleotide sequence from either of said at least two parent polynucleotides.
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Abstract
We describe here an in vitro method of redistributing sequence variations between non-identical polynucleotide sequences, by making a heteroduplex polynucleotide from two non-identical polynucleotides; introducing a nick in one strand at or near a base pair mismatch site; removing mismatched base(s) from the mismatch site where the nick occurred; and using the opposite strand as template to replace the removed base(s) with bases that complement base(s) in the first strand. By this method, information is transferred from one strand to the other at sites of mismatch.
44 Citations
41 Claims
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1. A method for preparing a variant polynucleotide having a different nucleotide sequence from at least two parent polynucleotides comprising;
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preparing at least one heteroduplex between at least said two parent polynucleotides, cleaving at least one polynucleotide strand in said heteroduplex at a mismatch site to form a cleavage site, replacing at least one nucleotide on at least one polynucleotide strand at or near the cleavage site, wherein at least one of said polynucleotide strands has a different nucleotide sequence from either of said at least two parent polynucleotides. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 32, 33)
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9. A method for obtaining a polynucleotide sequence encoding a desired functional property comprising;
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preparing at least one heteroduplex from at least two parent polynucleotides;
cleaving at least one polynucleotide strand in said heteroduplex at a mismatch site to form a cleavage site, replacing at least one nucleotide on at least one polynucleotide strand at or near the cleavage site, wherein a plurality of variant polynucleotide strands are formed which have different nucleotide sequences from either of said at least two parent polynucleotides, and screening or selecting a population of variants for the desired functional property. - View Dependent Claims (10, 11, 12)
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13. A method of identifying a reasserted DNA molecule with a desired functional property, comprising:
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a) providing at least one single-stranded modified polynucleotide, which single-stranded modified polynucleotide, or a complementary strand thereto has or encodes the desired functional property, wherein said modified polynucleotide is capable of hybridization but not amplification;
b) providing one or a plurality of non-identical single-stranded DNA molecules capable of hybridizing to the single-stranded modified polynucleotide, wherein said DNA molecules have or encode at least one additional variant;
contacting the single-stranded modified polynucleotide with at least one single-stranded DNA molecule of step (b), thereby producing an annealed DNA molecule;
incubating the annealed DNA molecule with a mismatch endonuclease, proofreading enzyme and a ligase, thereby producing a recombined DNA strand annealed to the single stranded modified polynucleotide; and
screening or selecting the population of reasserted DNA molecules to identify those that encode the desired functional property, thereby identifying one or more DNA molecules(s) that encode a polypeptide with the desired functional property. - View Dependent Claims (14, 15, 34, 35)
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16. A method of identifying a recombined DNA molecule with a desired functional property, comprising:
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forming an annealed double stranded molecule between at least a. at least one single-stranded modified polynucleotide, which single-stranded modified polynucleotide, or a complementary strand thereto, wherein the modified polynucleotide is capable of hybridization but not amplification, and b. at least one non-identical single-stranded DNA capable of hybridizing to the single-stranded modified polynucleotide, wherein said DNA molecules have or encode at least one additional variant;
cleaving at least the DNA strand of the annealed double stranded molecule to form a cleavage site, and replacing a nucleotide at or near the cleavage site, thereby producing a recombined DNA strand annealed to the modified polynucleotide;
wherein said recombined DNA strand has a different nucleotide sequence from either polynucleotide of said annealed double stranded molecule, andscreening or selecting the population of recombined DNA molecules to identify those that have or encode the desired functional property, thereby identifying one or more DNA molecules(s) that have or encode the desired functional property. - View Dependent Claims (17, 18, 19)
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- 20. A composition for a method of making sequence variants in vitro from at least one heteroduplex polynucleotide where said heteroduplex has at least two non-complementary nucleotide base pairs, said composition comprises effective amounts of an agent or agents with exonuclease activity, polymerase activity and mismatch strand cleavage activity.
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22. The composition for a method of making sequence variants in vitro from at least one heteroduplex polynucleotide where said heteroduplex has at least two non-complementary nucleotide base pairs, said composition comprises effective amounts of an agent or agents with 3′
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proofreading exonuclease activity, polymerase activity and strand cleavage activity. - View Dependent Claims (23)
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- 24. A kit used for making sequence variants in vitro from at least one heteroduplex polynucleotide where said heteroduplex has at least two non-complementary nucleotide base pairs, wherein said kit comprises a plurality of vessels containing an effective amount of an agent or agents with exonuclease activity, polymerase activity and strand cleavage activity.
- 26. A nicked circular heteroduplex which has at least two non-complementary nucleotide base pairs and a nick located at at least one of the two non-complementary nucleotide base pairs.
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28. A method for altering the length of polynucleic acid sequences resolved within a heteroduplex comprising;
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a. preparing at least one heteroduplex polynucleotide;
b. combining said heteroduplex polynucleotide with an effective amount of an agent or agents with at least exonuclease activity, polymerase activity, ligase activity and strand cleavage activity; and
c. allowing sufficient time for the percentage of complementarity between strands of said heteroduplex polynucleotide to increase, wherein the ratio of polymerase activity to ligase activity is altered to obtain a desired length of resolution between the polynucleotide strands of the heteroduplex. - View Dependent Claims (29)
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30. A method of generating mutations in a zone around a particular nucleotide within a desired polynucleotide comprising;
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a. preparing at least one partially complementary polynucleotide having at least one non-complementary nucleotide within the zone around the desired polynucleotide, b. forming at least one heteroduplex between said desired polynucleotide and said partially complementary polynucleotide;
c. combining said heteroduplex with at least one nucleotide analogue, effective amount of an agent or agents with exonuclease activity, polymerase activity, and mismatch strand cleavage activity; and
d. allowing sufficient time for the nucleotide analogue to be incorporated into either said desired polynucleotide, said partially complementary polynucleotide or both. - View Dependent Claims (31, 36, 37)
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38. A non-naturally occurring variant polynucleotide comprising at least two parts, a first nucleotide sequence and a second nucleotide sequence,
wherein the first nucleotide sequence is identical to or complementary to part of a first naturally occurring polynucleotide, and not identical to and not complementary to a corresponding part of a second naturally occurring polynucleotide, wherein the second nucleotide sequence is identical to or complementary to part of a second naturally occurring polynucleotide, and not identical to and not complementary to a corresponding part of a first naturally occurring polynucleotide.
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40. A non-naturally occurring variant polypeptide comprising at least two parts, a first peptide sequence and a second peptide sequence,
wherein the first peptide sequence is identical to or complementary to part of a first naturally occurring polypeptide, and not identical to and not complementary to a corresponding part of a second naturally occurring polypeptide, wherein the second peptide sequence is identical to or complementary to part of a second naturally occurring polypeptide, and not identical to and not complementary to a corresponding part of a first naturally occurring polypeptide.
Specification