Polyamine effects on purine-purine-pyrimidine triple helix formation by phosphodiester and phosphorothioate oligodeoxyribonucleotides

Abstract

Utilization of oligodeoxyribonucleotides to Inhibit specific gene transcription In vivo (antigene strategy) requires the efficient formation of triple helices under physiological conditions. However, pyrlmldlne-mottf triplexes are not favored at physiological pH, and physiological concentrations of potassium cations hamper purine-motrf triplex formation. Here we investigated the effects of polyamines on promoting triplex formation by G/T-rich oligodeoxyribonucleotides containing either phosphodiester or a diastereomeric mixture of phosphorothioate linkages. Compared with Mg2+, equimolar concentrations of polyamines greatly facilitated purine-motrf triplex formation with the following order of effectiveness: spermine > spermidlne > putrescine. At low polyamine concentrations, phosphorothioate oligonucleotides were better at triplex formation than the corresponding phosphodiester oligonucleotides. Kinetic studies indicated that polyamines facilitated triplex formation by increasing the rate of oiigonucleotide-duptex DNA association. However, triplex accumulation with either oligonucleotide was still low under physiological conditions (140 mM K+, 10 mM Mg2+, 1 mM spermine). The Inhibitory effects of K+ could be partially overcome with high concentrations of Mg2+ or spermine, with phosphodiester oligonucleotides being better able to form triplexes than phosphorothioates under these conditions. © 1995 Oxford University Press.