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
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.