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Published June 14, 1995 | public
Journal Article

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.

Additional Information

© 1995 American Chemical Society. Received January 28, 1994. Revised Manuscript Received July 18, 1994. All peptides and oligonucleotides were synthesized using the facilities at the Biopolymer Synthesis Center at Caltech. This research was supported by a grant from the Biological and Chemical Technologies Research (BCTR) of the Department of Energy (DOE). The facilities of the Materials and Process Simulation Center (MSC) are also supported by grants from the National Science Foundation (CHE-91100284 and ASC-9217368), Allied Chemical, Asahi Chemical, Asahi Glass, Chevron Petroleum Technology Co., BF Goodrich, BP America, Teijin LTD, Vestar, Xerox, and Beckman Institute.

Additional details

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