STRANDEDNESS DISCRIMINATION IN PEPTIDE-POLYNUCLEOTIDE COMPLEXES

Preferential binding to single- or double-stranded nucleic acids is im portant for the activity of many proteins that process RNA and DNA. We have investigated the mechanism of strandedness discrimination with p eptides derived from the putative DNA-binding domain of the RecA prote in, a bacterial recombinase that modulates its affinity for single-str anded DNA by means of ATP binding and hydrolysis. Contributions of ele ctrostatic and non-electrostatic interactions to binding of these pept ides with polynucleotides were evaluated by fluorescence spectroscopy as a function of salt concentration and peptide charge. Binding of the se peptides to single- and double-stranded nucleic acids was dominated by non-electrostatic interactions. Small electrostatic contributions selectively enhanced peptide complexation with single-stranded nucleic acids. Similar results were observed in control experiments carried o ut with tripeptides containing charged and aromatic amino acid residue s, It was possible to modify the strandedness preference of peptide-po lynucleotide complexes by changing electrostatic contributions to the binding free energy. These observations suggest a mechanism whereby so me proteins that interact with DNA or RNA might determine and regulate their relative affinity for single- and double-stranded nucleic acids .