Structural effects on ss- and dsDNA recognition by a beta-hairpin peptide.

FORM DEFINES FUNCTION: The effects of beta-hairpin structure on the binding affinity and selectivity for ssDNA versus dsDNA were investigated; this provided insights into the factors that contribute to the selective recognition of both ss- and dsDNA and suggested new approaches for designing biomimetic receptors. Binding studies showed that 1) folding is crucial for binding to both ss- and dsDNA, and 2) chirality affects binding for duplex but not for ssDNA.The interactions involved in the binding of a designed beta-hairpin dimer to single-stranded and duplex DNA have been explored. Previously the peptide dimer had been found to bind ssDNA with a dissociation constant of 3 micromicro through a combination of aromatic and electrostatic interactions, whereas binding to duplex DNA was primarily driven by electrostatic interactions. In this report, the effects of folding and chirality were studied to determine the factors that contribute to affinity and selectivity for ssDNA versus dsDNA. Binding studies showed that 1) folding is crucial for binding to both ss- and dsDNA, and 2) chirality affects binding for duplex DNA but not for ssDNA. Taken together, these studies reveal different modes of binding for ss- and duplex DNA, with different driving forces, but in each case peptide structure contributes significantly to binding.