Stabilization of triple-helical nucleic acids by basic oligopeptides.

Intermolecular triplex 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 effects of basic oligopeptides on the stability of triplex DNA. An intermolecular protonated pyrimidine.purine.pyrimidine (Py.Pu*Py) triplex formed readily between a duplex DNA region and a 14-mer pyrimidine triplex-forming oligonucleotide (TFO) at pH 5. The triplex was stabilized at pH by the addition of magnesium ions. In the presence of spermine and lysine-rich peptides, the intermolecular triplex 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 triplex 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 triplex than a pyrimidine.purine.purine (Py.Pu*Pu) triplex. At 1 mM, Lys-Lys-Lys-Lys-Lys stabilized the Py.Pu*Pu triplex 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 concentration of TFOs required to form triplex DNA were significantly reduced in the presence of peptides.(ABSTRACT TRUNCATED AT 250 WORDS)