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 of 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 °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.