The structure of intramolecular triplex DNA: Atomic force microscopy study

William J. Tiner, Vladimir N. Potaman, Richard R. Sinden, Yuri L. Lyubchenko

Research output: Contribution to journalArticlepeer-review

59 Scopus citations


We applied atomic force microscopy (AFM) for direct imaging of intramolecular triplexes (H-DNA) formed by mirror-repeated purine-pyrimidine repeats and stabilized by negative DNA supercoiling. H-DNA appears in atomic force microscopy images as a clear protrusion with a different thickness than DNA duplex. Consistent with the existing models, H-DNA formation results in a kink in the double helix path. The kink forms an acute angle so that the flanking DNA regions are brought in close proximity. The mobility of flanking DNA arms is limited compared with that for cruciforms and three-way junctions. Structural properties of H-DNA may be important for promoter-enhancer interactions and other DNA transactions.

Original languageEnglish (US)
Pages (from-to)353-357
Number of pages5
JournalJournal of Molecular Biology
Issue number3
StatePublished - Nov 30 2001
Externally publishedYes


  • Alternative DNA structures
  • Atomic force microscopy
  • DNA supercoiling
  • H-DNA
  • Intramolecular triplexes

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology


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