STABILIZATION OF TRIPLE-HELICAL NUCLEIC-ACIDS BY BASIC OLIGOPEPTIDES

Intermolecular tripler DNA is stabilized by metal cations and polyamin es which reduce repulsion between the negatively charged phosphates of the three nucleic acid strands. We use a quantitative chemical-probin g assay involving protection of duplex guanines in a homopyrimidine ho mopurine (Py . Pu) sequence from dimethyl sulfate modification to stud y the effects of basic oligopeptides on the stability of tripler DNA. An intermolecular protonated pyrimidine purine pyrimidine (Py . PuPy) tripler formed readily between a duplex DNA region and a 14-mer pyrim idine triplex-forming oligonucleotide (TFO) at pH 5. The tripler was s tabilized at pH 6 by the addition of magnesium ions. In the presence o f spermine and lysine-rich peptides, the intermolecular tripler was st abilized up to pH 6.5-7.0. The effective peptide concentration require d for stabilization was 10(-5)-10(-2) M. Of the basic peptides studied , pentalysine (Lys-Lys-Lys-Lys-Lys) was the most effective tripler sta bilizer. 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 simi lar to active concentrations of spermine. Basic peptides were more eff ective at stabilizing a Py . PuPy tripler than a pyrimidine purine pu rine (Py . PuPu) tripler. At 1 mM, Lys-Lys-Lys-Lys-Lys stabilized the Py . PuPu tripler at a level comparable to stabilization by Mn2+ and spermine, whereas Lys-Gly-Lys-Gly-Lys and Lys-Ala-Lys-Ala-Lys resulte d in weaker TFO binding. The concentrations of TFOs required to form t ripler DNA were significantly reduced in the presence of peptides. The difference in tripler stability as a function of amino acid compositi on suggests the possibility of tuning the tripler-stabilizing effect b y varying peptide sequence and the fraction of basic amino acid residu es.