CD studies of interaction of a bZIP oligopeptide model with DNA

A leucine zipper (bZIP) binding peptide BP1 was constructed based on the DN A binding sequence of the GCN4 protein, slightly modified to make it more s imilar to the sequence of other bZIP proteins (Jun) with related DNA bindin g specificity. Selfcomplementary DNA hexadecanucleotides containing modifie d ATF/CRE target sites were used to study peptide-DNA complex formation. Fo ur oligonucleotides contained substitutions of two GC or AT pairs by IC pai rs in the ATF/CRE target sequence. In two other oligonucleotides there was a substitution of A by I in two AT pairs (mismatch IT pairs were presumably formed in the duplex) and one oligonucleotide contained I instead of C in two base pairs (IG mismatch in the duplex). Conformation changes of BP1 that occur on complex formation were studied by circular dichroism spectroscopy. The binding of peptide BP1 to oligonucleo tides is accompanied by an increase of the alpha-helix content, which depen ds strongly on the oligonucleotide sequence. The substitution of two GC pai rs within the specific binding site has either none or only a small effect. However, the substitution of two AT pairs within the binding site by IC st rongly decreases the specificity of binding to a level observed with an oli gonucleotide containing the C/EBP binding site, differing from the ATF/CRE site at four positions (Votavova et al., J. Biomol. Struct. Dyn. 3 (1997) 5 87). Similar results were obtained also with an oligonucleotide containing I instead of C in two base pairs (IG mismatch in the duplex). Two oligonucl eotides with two substitutions of A by I but with unchanged T in the AT pai rs (IT mismatch) showed smaller decrease in the alpha-helix formation on pe ptide binding than oligonucleotides, in which the whole AT pair was replace d by IC. The effect of such a substitution depends on the position of the o riginal AT pairs in the target sequence, but the presence of T appears to b e essential for specific peptide binding. (C) 1999 Elsevier Science B.V. Al l rights reserved.