SINGLE-STRAND DNA TRIPLE-HELIX FORMATION

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)8N6(pyrimidine)8N4(purine)8-3′ undergo dramatic structural changes consistent with intrastrand DNA triple-helix formation induced by lowering the pH or raising the Mg2+ concentration. The intrastrand DNA triple helix is sensitive to base mismatches. © 1990, American Chemical Society. All rights reserved.