Stabilization of intramolecular triple/single-strand structure by cationic peptides.

For better comprehension of possible physiological roles of triple-helical DNA structures, it is important to understand if the proteins can stabilize intramolecular triplex (H-DNA). One plausible mode of stabilization is through the neutralization of electrostatic repulsion of negatively charged phosphates in the three DNA strands by positively charged arginine and lysine residues of a bound protein. To gain an insight into interactions between H-DNA and cationic protein domains, we examined the effect of Lys- and Arg-rich oligopeptides on the B-DNA to H-DNA transition. These oligopeptides as well as another type of polycation, spermine, shifted the equilibrium toward H-DNA. These polycations introduced little change in DNA superhelicity, so that an increase in torsional stress was not responsible for facilitated H-DNA formation. Competing influences of polycations and monovalent cations suggest a significant involvement of electrostatic interactions in H-DNA stabilization. The Arg-rich peptides are more effective in H-DNA stabilization than the Lys-rich ones. However, as inferred from experiments on intermolecular complexes, this is not due to a better stabilization of triple helix or destabilization of double helix. It is possible that Arg-rich peptides interact with the unpaired single strand in H-DNA and stabilize its unpaired conformation.