DESIGN OF DE-NOVO DNA-BINDING PEPTIDES WITH THE BETA-STRAND-TURN-BETA-STRAND MOTIF FOR DNA-SEQUENCE RECOGNITION

Citation
An. Surovaya et al., DESIGN OF DE-NOVO DNA-BINDING PEPTIDES WITH THE BETA-STRAND-TURN-BETA-STRAND MOTIF FOR DNA-SEQUENCE RECOGNITION, Molecular biology, 28(6), 1994, pp. 859-868
Citations number
49
Categorie Soggetti
Biology
Journal title
ISSN journal
00268933
Volume
28
Issue
6
Year of publication
1994
Part
2
Pages
859 - 868
Database
ISI
SICI code
0026-8933(1994)28:6<859:DODDPW>2.0.ZU;2-B
Abstract
Hereby we report the design and solid-phase synthesis of de novo 26-re sidue linear and cyclic peptides with the beta-strand-turn-beta-strand motif for DNA sequence recognition; the only difference was the cycli c counterpart being conformationally restricted by a sulfhydryl bridge . Another product was a 28-residue peptide with N-terminal copper-chel ating Gly-Gly-His, a potential DNA-cleaving agent. Binding of these pe ptides to natural DNAs, an endonuclease restriction fragment, and synt hetic polydeoxyribonucleotides was examined by CD spectroscopy, fluore scence assays, and DNase I footprinting. The CD data showed the 26-res idue linear and cyclic peptides to be in largely random and partly bet a-conformation in water-or 20% trifluroethanol, but to assume a partly alpha-helical conformation in 50% TFE. Both the linear and the cyclic peptides were shown to bind to DNA, with saturation at one peptide pe r 3-4 bp. The antibiotic distamycin A, binding at the DNA minor groove , was found to compete with the peptides for the binding sites on poly (dA). poly(dT). The CD analysis revealed conformational alterations in the peptides upon binding to DNA, while the DNA structure underwent n o appreciable changes. The CD difference spectra of the DNA-peptide mi xture minus free DNA were distinct from those of the free peptide, and their shape was consistent with the random-to-beta-like conformationa l transition in the peptides upon binding to DNA. The DNase footprints showed that the linear and cyclic peptides specifically protected nuc leotide sequences at the periphery of operators O(R)1, O(R)2, O(R)3 an d pseudooperators in the phage 434 cro gene.