DESIGN AND SYNTHESIS OF A NEW PEPTIDE RECOGNIZING A SPECIFIC 16-BASE-PAIR SITE OF DNA

We designed a peptide to recognize a new 16-base pair site (about 1.5 turns) of DNA by stitching together three peptides of the v-Jun basic region in a specified order. The binding site consists of three five-base-pair half-sites each of which is recognized by a different segment bf the peptide. DNase I footprinting shows that the new peptide specifically recognizes the proposed site, and gel retardation shows that the dissociation constant is about 5 nM at 4 degrees C. Gel retardation shows that the new peptide does recognize the proposed trimer binding site about 10 times stronger than the dimer binding sites [having two half sites for two arms]. These results also provide information about the relationship between specific and nonspecific binding in the recognition between protein and DNA.