Formation of a stable triplex from a single DNA strand

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Abstract
HOMOPURINE·homopyrimidine DNA sequences have been shown to form triple-stranded structures readily under appropriate conditions1–5. Interest in DNA triplexes arises from potential applications of intermolecular triplexes as antisense inhibitors of gene expression6–8 and from the possibility that intramolecular triplexes may have a role in gene expression and recombination1. We recently presented NMR evidence for triplex formation from the DNA oligonucleotides d(GA)4 and d(TC)4, which showed unambiguously that the second pyrimidine strand is Hoogsteen base paired and the cytosines are protonated at N3 as required9,10. To obtain a more well defined triplex, and to provide a model for in vivo triplex structures, we have designed and synthesized a 28-base DNA oligomer with a sequence that could potentially fold to form a triplex containing both T·A·T and C +·G·C triplets. Our NMR results indicate that the conformation at pH5.5 is an intramolecular triplex and that a significant amount of triplex remains even at pH 8.0.