Double-stranded DNA templates can induce alpha-helical conformation in peptides containing lysine and alanine: functional implications for leucine 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 flexible 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 dichroism measurements showed that 20-bp double-stranded DNA oligonucleotides can act as templates to promote random coil-->alpha-helix transitions in short peptides containing alanine and lysine. This conformational change takes place without altering the structure of the DNA, and neither specific peptide-DNA contacts nor cooperative interactions between peptides are necessary. The conformational change does require (i) double-stranded (but not single-stranded) oligodeoxynucleotides in either the B or the B' conformation and (ii) peptides that can form positively 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 was delta Gex = -0.15 (+/- 0.07) kcal/mol per lysine residue. The implications of these results for the thermodynamics and kinetics of DNA target site selection by basic-leucine zipper and basic-helix-loop-helix regulatory proteins are discussed.