Searching genomes for sequences with the potential to form intrastrand triple helices

Paula Rodrigues Hoyne, Lindsay M. Edwards, Alain Viari, L. James Maher

Research output: Contribution to journalArticlepeer-review

27 Scopus citations


The canonical double-helix form of DNA is thought to predominate both in dilute solution and in living cells. Sequence-dependent fluctuations in local DNA shape occur within the double helix. Besides these relatively modest variations in shape, more extreme and remarkable structures have been detected in which some bases become unpaired. Examples include unusual three-stranded structures such as H-DNA. Certain RNA and DNA strands can also fold onto themselves to form intrastrand triplexes. Although they have been extensively studied in vitro, it remains unknown whether nucleic acid triplexes play natural roles in cells. If natural nucleic acid triplexes were identified in cells, much could be learned by examining the formation, stabilization, and function of such structures. With these goals in mind, we adapted a pattern-recognition program to search genetic databases for a type of potential triplex structure whose presence in genomes has not been previously investigated. We term these sequences Potential Intrastrand Triplex (PIT) elements. The formation of an intrastrand triplex requires three consecutive sequence domains with appropriate symmetry along a single nucleic acid strand. It is remarkable that we discovered multiple copies of sequence elements with the potential to form one particular class of intrastrand triplexes in the fully sequenced genomes of several bacteria. We then focused on the characterization of the 25 copies of a particular ~37 nt PIT sequence detected in Escherichia coli. Through biochemical studies, we demonstrate that an isolated DNA strand from this family of E. coli PIT elements forms a stable intrastrand triplex at physiological temperature and pH in the presence of physiological concentrations of Mg2+. (C) 2000 Academic Press.

Original languageEnglish (US)
Pages (from-to)797-809
Number of pages13
JournalJournal of Molecular Biology
Issue number4
StatePublished - Sep 29 2000


  • Box C
  • Escherichia coli
  • Intrastrand triplexes
  • Palingol
  • Repetitive element

ASJC Scopus subject areas

  • Molecular Biology
  • Biophysics
  • Structural Biology


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