DNA mismatch binding by an extensively purified hMutS alpha mismatch r
ecognition complex was investigated using a bandshift assay. The compl
ex bound to G . T mispairs and to looped structures containing an unpa
ired single or two adjacent bases. A CA loop was preferentially recogn
ised if the unpaired bases formed part of a repeated sequence. In gene
ral, single base loops were also more favourably recognised by hMutS a
lpha when present in monotonic runs of two to five. In one series of s
ubstrates, based on a known hotspot for frameshift mutations in the hy
poxanthine-guanine phosphoribosyltransferase gene, in which different
length G, A, C or T tracts were flanked by closely similar sequences,
an A loop was bound preferentially in the absence of adjacent As and a
C loop in the absence of adjacent Cs. This preferential binding was i
nfluenced by the base immediately 5' to the loop. Thus, while repeated
regions generally favour recognition of single base loops by hMutS al
pha, other factors related to local sequence may influence this intera
ction. (C) 1998 Elsevier Science B.V. All rights reserved.