Two distinct mismatch binding activities are detected using bandshift
assays with human cell extracts and DNA with mispairs at defined posit
ions. One requires hMSH2 protein and is absent from extracts of LoVo c
ells, which contain a partial deletion of the hMSH2 gene. The second a
ctivity is independent of hMSH2 and is present at normal levels in LoV
o and three other cell lines, which are defective in in vitro hMSH2-de
pendent binding. The two mismatch recognition activities are distingui
shed by their sensitivity to polycations and can be resolved by chroma
tography on MonoQ. hMSH2-independent activity has been purified extens
ively from wild-type cells and from a cell line deficient in hMSH2-dep
endent binding. The purified material preferentially recognizes A . C,
some pyrimidine pyrimidine mismatches, and certain slipped mispaired
structures. Binding exhibits some sequence preferences. The similar pr
operties of the two mismatch binding activities suggest that they both
contribute to mismatch repair.