DOUBLE-STRANDED DNA TEMPLATES CAN INDUCE ALPHA-HELICAL CONFORMATION IN PEPTIDES CONTAINING LYSINE AND ALANINE - FUNCTIONAL IMPLICATIONS FORLEUCINE-ZIPPER AND HELIX-LOOP-HELIX TRANSCRIPTION FACTORS

Transcription factors of the basic-leucine zipper and basic-helix-loop -helix families specifically recognize DNA by means of intrinsically f lexible peptide domains that assume an alpha-helical conformation upon binding to target DNA sequences. We have investigated the nonspecific interactions that underlie specific DNA recognition. Circular dichroi sm measurements showed that 20-bp double-stranded DNA oligonucleotides can act as templates to promote random coil --> alpha-helix transitio ns in short peptides containing alanine and lysine. This conformationa l change takes place without altering the structure of the DNA, and ne ither specific peptide-DNA contacts nor cooperative interactions betwe en peptides are necessary. The conformational change does require (i) double-stranded (but not single-stranded) oligodeoxynucleotides in eit her the B or the B' conformation and (ii) peptides that can form posit ively charged amphipathic alpha-helices. In 10 mM Na2HPO4 (pH 7.5; 10 degrees C), the excess free-energy contribution of the DNA template to the stability of the alpha-helical form of the oligopeptides tested w as Delta G(ex) = -0.15 (+/- 0.07) kcal/mol per lysine residue. The imp lications of these results for the thermodynamics and kinetics of DNA target site selection by basic-leucine zipper and basic-helix-loop-hel ix regulatory proteins are discussed.