Methods of analysis and manipulation of DNA utilizing mismatch repair systems

A method for detecting a base pair mismatch in a DNA duplex, comprising the steps of:

• contacting at least one strand of a first DNA molecule with the complimentary strand of a second DNA molecule under conditions such that base pairing occurs;
• contacting a DNA duplex potentially containing a base pair mismatch with a mispair recognition protein under conditions suitable for said protein to form a specific complex only with said DNA duplex having a base pair mismatch, and not with a DNA duplex with conventional Watson-Crick base pairing,
• detecting any DNA:protein complexes as a measure of the presence of a base pair mismatch in said DNA duplex by comparing the electrophoretic mobility of said DNA:protein complexes to that of uncomplexed DNA.

A method for detecting a base pair mismatch in a DNA duplex, comprising the steps of:

• contacting at least one strand of a first DNA molecule with the complimentary strand of a second DNA molecule under conditions such that base pairing occurs;
• contacting a DNA duplex potentially containing a base pair mismatch with a mispair recognition protein under conditions suitable for said protein to form a specific complex only with said DNA duplex having a base pair mismatch, and not with a DNA duplex with conventional Watson-Crick base pairing,
• detecting any DNA:protein complexes as a measure of the presence of a base pair mismatch in said DNA duplex by utilizing an antibody specific for said base mispair recognition protein.

A method for detecting and localizing a base pair mismatch in a DNA duplex, comprising the steps of

• contacting at least one strand of a first DNA molecule with the complementary strand of a second DNA molecule under conditions such that base pairing occurs;
• contacting the resulting double-stranded DNA duplexes with a mispair recognition protein under conditions such that the protein forms specific complexes with mispairs and thereby directs modification of at least one strand of the DNA in the resulting DNA:protein complexes in the vicinity of the DNA:protein complex, and
• determining the location of the resulting DNA modification.

A method for detecting and localizing a base pair mismatch within a DNA duplex, comprising the steps of:

• contacting at least one strand of a first DNA molecule with a complementary strand of a second DNA molecule under conditions such that base pairing occurs;
• contacting resultant duplex DNA molecules with a mispair recognition protein able to cleave DNA, under conditions such that the protein forms specific complexes with a mispair and thereby directs cleavage of at least one strand of the DNA in the resulting DNA protein complexes in the vicinity of the DNA protein complex, and
• determining the location of the cleavage of the DNA.

A method for detecting and localizing A--G mispairs in a DNA duplex, comprising the steps of:

• contacting at least one strand of the first DNA molecule with the complementary strand of the second DNA molecule under conditions such that base pairing occurs;
• contacting resultant duplex DNA molecules with a mispair recognition protein that recognizes A--G mispairs and an apurinic endonuclease or lyase under conditions such that in the presence of a mismatch an endonucleolytic incision is introduced in the duplex molecule, and
• determining the location of the incision.

Assay kit for detecting and localizing individual base sequence differences within homologous regions of two DNA molecules comprising:

• an aliquot of a mispair recognition protein attached to a hydroxyl radical cleaving function or attached to a DNA endonuclease.

Assay kit for detecting and localizing an A--G mispair within a DNA duplex comprising one or more of the following components;

• an aliquot of an A--G mispair recognition protein;
• and
• an aliquot of an apurinic endonuclease or lyase.