SHORT PEPTIDE-FRAGMENTS DERIVED FROM HMG-I Y PROTEINS BIND SPECIFICALLY TO THE MINOR-GROOVE OF DNA/

Short peptides derived from chromosomal proteins have previously been proposed to bind specifically to the minor groove of A,T-rich DNA [for a review, see M. E. A. Churchill and A. A, Travers (1991) Trends Bioc hem. Sci. 16, 92-97]. Using NMR spectroscopy, we investigated the DNA binding of SPRKSPRK, which is one such A,T-specific motif. Under the c onditions studied SPRKSPRK interacts only nonspecifically with d(CGCAA AAAAGGC).d(GCCTTTTTTGCG). The peptides TPKRPRGRPKK, PRGRPKK, and PRGRP derived from the non-histone chromosomal protein HMG-I/Y, however, bi nd specifically to the central A,T sites of d(CGCAAATTTGCG)(2) and d(C GCGAATTCGCG)(2). 2D NOE measurements show that the RGR segment of each peptide is in contact with the minor groove. The arginine side chains and the peptide backbone are buried deep in the minor groove, in a fa shion generally similar to the antibiotic netropsin. Under the same co nditions the-peptide PKGKP does not interact with the same oligonucleo tide duplexes, indicating that the arginine guanidinium groups are maj or determinants of the A,T specificity.