Methods of analysis and manipulating of DNA utilizing mismatch repair systems

A method for removing DNA duplex molecules containing one or more 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 under conditions such that said component or components form a complex with DNA duplex molecules containing a base pair mismatch, and not with DNA duplex molecules lacking a base pair mismatch, and
• removing DNA molecules containing said complex or the product of said complex from said population of heteroduplex DNA molecules without the use of an additional agent capable of enzymatic digestion of said DNA duplexes which is not a component of said mismatch repair system prior to said removal.

Assay kit for eliminating DNA molecules containing one or more base pair mismatches from a population of heterohybrid duplex molecules formed by base pairing of single-stranded DNA molecules obtained from a first and a second source comprising:

• an aliquot of proteins of a mismatch repair system,
• an aliquot of a recombinase protein whose ability to catalyze duplex formation is inhibited by said proteins of a mismatch repair system, and
• a means for removing said DNA molecules containing one or more base pairing mismatches.