Recognition of double helical DNA by alternate strand triple helix formation

Peter A. Beal, Peter B. Dervan

Research output: Contribution to journalArticlepeer-review

88 Scopus citations


The triplet specificities and required strand orientations of two classes of DNA triple can be compined to target double helical sequences contaning all four base pairs by alternate strand triple helix formation. This allows for the use of oligonucleotides contaning only natural 3′-5′ phosphodiester linkages to simultaneously bind both stands of double helical DNA in the major groove. The stabilities and structures of these alternate strand triple helices depend on whether the binding site sequence is 5′-(purine)n-3′ was targeted with an olignucleotide consisting of a pyrimidine domain and a purine domain linked by a 3′-5′ phosphodiester. To bind the duplex sequence type 5′-(pyrimidine)m(purine)n-3′, the third strand requires at least two nucleotides linking binding domains at the site of crossover in the major groove. A new class of oligonucleotides capable of binding mixed duples sequences by crossovers in the major groove may be possible.

Original languageEnglish (US)
Pages (from-to)4976-4982
Number of pages7
JournalJournal of the American Chemical Society
Issue number13
StatePublished - 1992
Externally publishedYes

ASJC Scopus subject areas

  • Chemistry(all)


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