Single-molecule studies of DNA and RNA four-way junctions

S. A. McKinney, E. Tan, T. J. Wilson, M. K. Nahas, A. C. Déclais, R. M. Clegg, D. M.J. Lilley, T. Ha

Research output: Contribution to journalArticlepeer-review


Branched helical junctions are common in nucleic acids. In DNA, the four-way junction (Holliday junction) is an essential intermediate in homologous recombination and is a highly dynamic structure, capable of stacking conformer transitions and branch migration. Our single-molecule fluorescence studies provide unique insight into the energy landscape of Holliday junctions by visualizing these processes directly. In the hairpin ribozyme, an RNA four-way junction is an important structural element that enhances active-site formation by several orders of magnitude. Our single-molecule studies suggest a plausible mechanism for how the junction achieves this remarkable feat; the structural dynamics of the four-way junction bring about frequent contacts between the loops that are needed to form the active site. The most definitive evidence for this is the observation of three-state folding in single-hairpin ribozymes, the intermediate state of which is populated due to the intrinsic properties of the junction.

Original languageEnglish (US)
Pages (from-to)41-45
Number of pages5
JournalBiochemical Society transactions
Issue number1
StatePublished - Feb 2004
Externally publishedYes


  • Branch migration
  • Fluorescence resonance energy transfer (FRET)
  • Hairpin ribozyme
  • Holliday junction
  • RNA folding
  • Single-molecule spectroscopy

ASJC Scopus subject areas

  • Biochemistry


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