Compositions, kits, and methods for effecting adenine nucleotide modulation of DNA mismatch recognition proteins

A method of detecting a difference between a sample nucleotide sequence and a reference nucleotide sequence, the method comprising

• a) annealing a first DNA strand and a second DNA strand to form a duplex DNA,
• i) wherein the first DNA strand has the sample nucleotide sequence
• ii) wherein the second DNA strand has a nucleotide sequence which is complementary to the reference nucleotide sequence, and
• iii) whereby if there is a difference between the sample nucleotide sequence and the reference nucleotide sequence then the duplex DNA is a mismatched duplex DNA;
• b) thereafter contacting the duplex DNA and an MSH dimer in the presence of a binding solution comprising ADP and optionally ATP, wherein the concentration of ATP, if present, in the binding solution is less than about 3 micromolar, whereby the MSH dimer binds ADP, and ADP-bound MSH dimer binds the duplex DNA if the duplex DNA is a mismatched duplex DNA;
• and
• c) determining whether the MSH dimer is associated with the duplex DNA molecule, whereby association of the MSH dimer with the duplex DNA molecule is an indication that there is a difference between the sample nucleotide sequence and the reference nucleotide sequence.

A method of determining whether a mammal is predisposed for carcinogenesis, the method comprising

• a) annealing a first DNA strand and a second DNA strand to form a duplex DNA,
• i) wherein the first DNA strand has the nucleotide sequence of at least a portion of a gene selected from the group consisting of an oncogene and a tumor suppressor gene of the mammal, and
• ii) wherein the second DNA strand has a nucleotide sequence which is complementary to the nucleotide sequence of the gene portion,
• iii) whereby if there is a sequence difference between the first DNA strand and the second DNA strand then the duplex DNA is a mismatched duplex DNA;
• b) thereafter contacting the duplex DNA and an MSH dimer in the presence of a binding solution comprising ADP and otionally ATP, wherein the concentration of ATP, if present, in the binding solution is less than about 3 micromolar, whereby the MSH dimer binds ADP, and ADP-bound MSH dimer binds the duplex DNA if the duplex DNA is a mismatched duplex DNA;
• and
• c) determining whetler the MSH dimer is associated with the duplex DNA, whereby association of the MSH dimer with the duplex DNA is an indication that the mammal is predisposed for carcinogenesis.

A method of determining whether the nucleotide sequence of a first copy of a genomic sequence differs from the nucleotide sequence of a second copy of the genomic sequence, the method comprising

• amplifying a region of each of the first copy and the second copy of the genomic sequence to yield amplified first copies and amplified second copies;
• mixing and denaturing the amplified first copies and the amplified second copies to form a first mixture;
• annealing the nucliec acids in the first mixture to form a second mixture comprising duplex DNAs, whereby if the nucleotide sequence of the first copy and the nucleotide sequence of the second copy of the genomic sequence differ then at least some of the duplex DNAs are mismatched duplex DNAs;
• contacting the second mixture with an MSH dimer in a binding solution comprising ADP and optionally ATP, wherein the concentration of ATP, if present, in the binding solution is less than about 3 micromolar, whereby the MSH dimer binds ADP, and ADP-bound MSH dimer binds the mismatched duplex DNAs;
• and
• determining whether the MSH dimer is associated with at least some of the duplex DNAs, whereby association of the MSH dimer with at least some of the duplex DNAs is an indication that the nucleotide sequence of the first copy of the genomic sequence differs from the nucleotide sequence of the second copy of the genomic sequence.

A kit for screening a genomic region for a nucleotide sequence which differs from a reference nucleotide sequence, the kit comprising

• a pair of primers complementary to the ends of the region for amplifying the region;
• ADP;
• a DNA strand having the reference nuclcotide sequence;
• at least two MutS homologs;
• and
• an instructional material which describes contacting the MutS homologs and annealed DNA in the presence of a binding solution comprising ADP, wherein the concentration of ATP in the binding solution is less tan about 3 micromolar, whereby in at least two of the MutS homologs dimerize in the binding solution, the dimer binds ADP, and ADP-bound dimer binds duplex DNA formed of the reference DNA and a complementary DNA if the duplex DNA is a mismatched duplex DNA.