STABILIZATION OF TRIPLE-HELICAL NUCLEIC-ACIDS BY BASIC OLIGOPEPTIDES

Intermolecular tripler DNA is stabilized by metal cations and polyamines which reduce repulsion between the negatively charged phosphates of the three nucleic acid strands. We use a quantitative chemical-probing assay involving protection of duplex guanines in a homopyrimidine homopurine (Py . Pu) sequence from dimethyl sulfate modification to study the effects of basic oligopeptides on the stability of tripler DNA. An intermolecular protonated pyrimidine purine pyrimidine (Py . Pu*Py) tripler formed readily between a duplex DNA region and a 14-mer pyrimidine triplex-forming oligonucleotide (TFO) at pH 5. The tripler was stabilized at pH 6 by the addition of magnesium ions. In the presence of spermine and lysine-rich peptides, the intermolecular tripler was stabilized up to pH 6.5-7.0. The effective peptide concentration required for stabilization was 10(-5)-10(-2) M. Of the basic peptides studied, pentalysine (Lys-Lys-Lys-Lys-Lys) was the most effective tripler stabilizer. It was effective at concentrations which are lower than those required for Lys-Gly-Lys-Gly-Lys and Lys-Ala-Lys-Ala-Lys and are similar to active concentrations of spermine. Basic peptides were more effective at stabilizing a Py . Pu*Py tripler than a pyrimidine purine purine (Py . Pu*Pu) tripler. At 1 mM, Lys-Lys-Lys-Lys-Lys stabilized the Py . Pu*Pu tripler at a level comparable to stabilization by Mn2+ and spermine, whereas Lys-Gly-Lys-Gly-Lys and Lys-Ala-Lys-Ala-Lys resulted in weaker TFO binding. The concentrations of TFOs required to form tripler DNA were significantly reduced in the presence of peptides. The difference in tripler stability as a function of amino acid composition suggests the possibility of tuning the tripler-stabilizing effect by varying peptide sequence and the fraction of basic amino acid residues.