INTERACTION OF MUTS PROTEIN WITH THE MAJOR AND MINOR GROOVES OF A HETERODUPLEX DNA

Thermus aquaticus MutS protein is a DNA mismatch repair protein that r ecognizes and binds to heteroduplex DNAs containing mispaired or unpai red bases. Using enzymatic and chemical probe methods, we have examine d the binding of Tag MutS protein to a heteroduplex DNA having a singl e unpaired thymidine residue. DNase I footprinting identifies a symmet rical region of protection 24-28 nucleotides long centered on the unpa ired base. Methylation protection and interference studies establish t hat Tag MutS protein makes contacts with the major groove of the heter oduplex in the immediate vicinity of the unpaired base. Hydroxyl radic al and 1,10-phenanthroline-copper footprinting experiments indicate th at MutS also interacts with the minor groove near the unpaired base. T ogether with the identification of key phosphate groups detected by et hylation interference, these data reveal critical contact points resid ing in the major and minor grooves of the heteroduplex DNA.