Single-strand DNA triple-helix formation

Abstract

Chemical modification studies provide evidence that single-stranded oligodeoxyribonucleotides can form stable intrastrand triple helices. Two oligonucleotides of opposite polarity were synthesized, each composed of a homopurine-homopyrimidine hairpin stem linked to a pyrimidine sequence which is capable of folding back on the hairpin stem and forming specific Hoogsteen hydrogen bonds. Using potassium permanganate as a chemical modification reagent, we have found that two oligodeoxyribonucleotides of sequence composition type 5'-(purine)_8(N)_4(pyrimidine)_8(N)_6(pyrimidine)_8-3' and 5'-(pyrimidine)_8N_6(pyrimidine)_8N_4(purine)_8-3' undergo dramatic structural changes consistent with intrastrand DNA triple-helix formation induced by lowering the pH or raising the Mg^(2+) concentration. The intrastrand DNA triple helix is sensitive to base mismatches.

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