RECOGNITION OF DNA INSERTION DELETION MISMATCHES BY AN ACTIVITY IN SACCHAROMYCES-CEREVISIAE

An activity in nuclear extracts of S. cerevisiae binds specifically to heteroduplexes containing four to nine extra bases in one strand. The specificity of this activity (IMR, for insertion mismatch recognition ) in band shift assays was confirmed by competition experiments. IMR i s biochemically and genetically distinct from the MSH2 dependent, sing le base mismatch binding activity. The two activities migrate differen tly during electrophoresis, they are differentially competable and the ir spectra of mispair binding are distinct. Furthermore, IMR activity is observed in extracts from an msh(2-) msh3(-) msh4(-) strain. IMR ex hibits specificity for insertion mispairs in two different sequence co ntexts. Binding is influenced by the structure of the mismatch since a n insertion with a hairpin configuration is not recognized by this act ivity. IMR does not result from single-strand binding because single-s tranded probes do not yield IMR complex and single-stranded competitor s are unable to displace insertion heteroduplexes from the complex. Si milar results with intrinsically bent duplexes make it unlikely that r ecognition is conferred by a bend alone. Heteroduplexes bound by IMR d o not contain any obvious damage. These findings are consistent with t he idea that yeast contains a distinct recognition factor, IMR, that i s specific for insertion/deletion mismatches.