Conformational Flexibility of Four-way Junctions in RNA

Sungchul Hohng, Timothy J. Wilson, Elliot Tan, Robert M. Clegg, David M.J. Lilley, Taekjip Ha

Research output: Contribution to journalArticlepeer-review

Abstract

Helical junctions are common architectural features in RNA. They are particularly important in autonomously folding molecules, as exemplified by the hairpin ribozyme. We have used single-molecule fluorescence spectroscopy to study the dynamic properties of the perfect (4H) four-way helical junction derived from the hairpin ribozyme. In the presence of Mg2+, the junction samples parallel and antiparallel conformations and both stacking conformers, with a bias towards one antiparallel stacking conformer. There is continual interconversion between the forms, such that there are several transitions per second under physiological conditions. Our data suggest that interconversion proceeds via an open intermediate with reduced cation binding in which coaxial stacking between helices is disrupted. The rate of interconversion becomes slower at higher Mg2+ concentrations, yet the activation barrier decreases under these conditions, indicating that entropic effects are important. Transitions also occur in the presence of Na+ only; however, the coaxial stacking appears incomplete under these conditions. The polymorphic and dynamic character of the four-way RNA junction provides a source of structural diversity, from which particular conformations required for biological function might be stabilised by additional RNA interactions or protein binding.

Original languageEnglish (US)
Pages (from-to)69-79
Number of pages11
JournalJournal of Molecular Biology
Volume336
Issue number1
DOIs
StatePublished - Feb 6 2004

Keywords

  • Fluorescence resonance energy transfer
  • Hairpin ribozyme
  • RNA structures
  • Single molecule spectroscopy

ASJC Scopus subject areas

  • Biophysics
  • Structural Biology
  • Molecular Biology

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