DESIGN OF SEQUENCE-SPECIFIC DNA-BINDING LIGANDS THAT USE A 2-STRANDEDPEPTIDE MOTIF FOR DNA-SEQUENCE RECOGNITION

The design and DNA binding activity of P-structure-forming peptides an d netropsin-peptide conjugates are reported. It is found that a pair o f peptides - S,S'-bis(Lys-Gly-Val-Cys-Val-NH-NH-Dns) - bridged by an S -S bond binds at least 10 times more strongly to poly(dG). poly(dC) th an to poly(dA). poly(dT). This peptide can also discriminate between 5 '-GpG-3' and 5'-GpC-3' steps in the DNA minor groove. Based on these o bservations, new synthetic ligands, bis-netropsins, were constructed i n which two netropsin-like fragments were attached by means of short l inkers to a pair of peptides - Gly-Cys-Gly- or Val-Cys-Val - bridged b y S-S bonds. These compounds possess a composite binding specificity: the peptide chains recognize 5'-GpG-3' steps on DNA, whereas the netro psin-like fragments bind preferentially to runs of 4 AT base pairs. Ou r data indicate that combining the AT-base-pair specific properties of the netropsin-type structure with the 5'-GpG-3'-specific properties o f certain oligopeptides offers a new approach to the synthesis of liga nds capable of recognizing mixed sequences of AT- and GC-base pairs in the DNA minor groove. These compounds are potential models for DNA-bi nding domains in proteins which specifically recognize base pair seque nces in the minor groove of DNA.