Circular site-directed mutagenesis

• US 5,789,166 A
• Filed: 12/08/1995
• Issued: 08/04/1998
• Est. Priority Date: 12/08/1995
• Status: Expired due to Term

• Current Assignee: Agilent Technologies, Inc., Children's Medical Center Corporation
• Original Assignee: Stratagene California (Agilent Technologies, Inc.)
• Inventors: Bauer, John C., Wright, Dowain A., Geha, Raif S., Braman, Jeffrey Carl
• Primary Examiner(s): Jones, W. Gary
• Assistant Examiner(s): Atzel, Amy
• Application Number:
  US08/567,881
• Time in Patent Office: 970 Days
• Field of Search: 435/6, 435/91.1, 435/91.2, 435/810
• US Class Current: 435/6.18
• CPC Class Codes: C12N 15/102 Mutagenizing nucleic acids
• CPC Class Codes: C12Q 1/6806 Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6853 using modified primers or templates
• CPC Class Codes: C12Q 2521/101 DNA polymerase
• CPC Class Codes: C12Q 2521/319 Exonuclease
• CPC Class Codes: C12Q 2521/331 Methylation site specific nuclease
• CPC Class Codes: C12Q 2525/185 incorporating bases where the precise position of the bases in the nucleic acid string is important
• CPC Class Codes: C12Q 2525/307 Circular oligonucleotides
• CPC Class Codes: C12Q 2531/125 Rolling circle
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: Y10S 435/81 Packaged device or kit

Abstract

The invention provides improved methods of introducing site-directed mutations into circular DNA molecules of interest by means of mutagenic primer pairs. The mutagenic primer pairs are also selected so as to be either completely complementary or partially complementary to each other, wherein the mutation site (or sites) is located within the region of complementarity. A mutagenic primer pair is annealed to opposite strands of a circular DNA molecule containing the DNA sequence to be mutagenized. After annealing, first and second mutagenized DNA strands, each incorporating a member of the mutagenic oligonucleotide primer pair is synthesized by a linear cyclic amplification reaction. After the linear cyclic amplification mediated synthesis step is completed, the reaction mixture is treated with a selection enzyme that digests the parental template strands. After the digesting step, a double-stranded circular DNA intermediate is formed. The double-stranded circular DNA intermediates is transformed in suitable competent host cells and closed circular double-stranded DNA corresponding to the parental template molecules, but containing the desired mutation or mutations of interest, may be conveniently recovered from the transformed cells. The invention also provide kits for site-directed mutagenesis in accordance with methods of the present invention.

Claims

1. A method of introducing a specific mutation into a methylated circular double-stranded DNA molecule comprising the steps of:

annealing a first mutagenic primer and a second mutagenic primer to said methylated DNA molecule, wherein said first mutagenic primer comprises a region that is complementary to the second mutagenic primer, and wherein said first and second mutagenic primers contain at least one mutation site with respect to said methylated DNA molecule, and wherein said mutation site(s) is located within the region of complementarity between said first and second mutagenic primers, thereby forming an annealed mixture;

subjected said annealed mixture to a linear cyclic amplification reaction, thereby producing an amplified mixture containing a first mutagenized DNA strand comprising said first mutagenic primer, and a second mutagenized DNA strand comprising said second mutagenic primer, wherein said first and second mutagenized DNA strands form a double-stranded mutagenized circular DNA intermediate; and

digesting said amplified mixture by adding a restriction endonuclease that selectively cleaves said methylated DNA molecule at methylated sites therein.

2. The method of claim 1 wherein said methylated circular double-stranded DNA molecule is methylated in vivo.

3. The method of claim 1 wherein said methylated circular double-stranded DNA molecule is methylated in vitro.

4. The method of claim 1, wherein said restriction endonuclease is DpnI.

5. A kit for introducing a specific mutation into a methylated circular double-stranded DNA molecule, said kit comprising,

a DNA polymerase,

DpnI restriction endonuclease,

a control methylated circular double-stranded DNA molecule, and

control first and second mutagenic primers, wherein said first mutagenic primer comprises a region that is complementary to the second mutagenic primer, and wherein said first and second mutagenic primers contain at least one mutation site with respect to said methylated DNA molecule, and wherein said mutation site(s) is located within the region of complementarity between said first and second mutagenic primers.