Methods and kits for fractionating a population of DNA molecules based on the presence or absence of a base-pair mismatch utilizing mismatch repair systems

A method of genomic mismatch scanning, wherein heterohybrid DNA molecules containing base pair mismatches are removed, without the use of exonuclease III, comprising the steps of:

• contacting a population of heterohybrid DNA molecules potentially containing a base pair mismatch with a DNA mismatch repair system in the presence of one or more dideoxynucleoside triphosphates such that a single-stranded region is generated in a DNA molecule that contained a base pair mismatch, without the use of exonuclease III, and,
• removing said molecule containing a single-stranded region from the population.

A method for fractionating a population of DNA molecules based upon a mismatch in a subset of said molecules, wherein a heterohybrid DNA molecule containing a base pair mismatch is separated from non-mismatch-containing molecules, without the use of exonuclease III, comprising the steps of:

• contacting a population of heterohybrid DNA molecules potentially containing a base pair mismatch with a DNA mismatch repair system and biotinylated nucleotide triphosphates, in the absence of exonuclease III, such that biotinylated nucleotides are incorporated into DNA molecules that contained a base pair mismatch and,
• separating said molecule containing biotinylated nucleotides from those not containing said nucleotides by binding to avidin.

A method for removing DNA duplex molecules containing base pair mismatches in a population of heteroduplex DNA molecules produced from different sources, comprising the steps of:

• contacting said population of DNA duplex molecules potentially containing base pair mismatches with some or all components of a mismatch repair system and biotinylated nucleotides such that said nucleotides are incorporated into duplex molecules that contain a base pair mismatch and not into DNA duplex molecules lacking a base pair mismatch, and
• removing said duplexes with incorporated biotinylated nucleotides by binding to avidin.