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, Taekjip Ha

Research output: Contribution to journalArticle

Abstract

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
Volume32
Issue number1
DOIs
StatePublished - Feb 2004
Externally publishedYes

Fingerprint

Cruciform DNA
Catalytic Domain
RNA
Molecules
Homologous Recombination
DNA
Structural dynamics
Nucleic Acids
Fluorescence
Observation
hairpin ribozyme

Keywords

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

ASJC Scopus subject areas

  • Biochemistry

Cite this

McKinney, S. A., Tan, E., Wilson, T. J., Nahas, M. K., Déclais, A. C., Clegg, R. M., ... Ha, T. (2004). Single-molecule studies of DNA and RNA four-way junctions. Biochemical Society Transactions, 32(1), 41-45. https://doi.org/10.1042/BST0320041

Single-molecule studies of DNA and RNA four-way junctions. / McKinney, S. A.; Tan, E.; Wilson, T. J.; Nahas, M. K.; Déclais, A. C.; Clegg, R. M.; Lilley, D. M J; Ha, Taekjip.

In: Biochemical Society Transactions, Vol. 32, No. 1, 02.2004, p. 41-45.

Research output: Contribution to journalArticle

McKinney, SA, Tan, E, Wilson, TJ, Nahas, MK, Déclais, AC, Clegg, RM, Lilley, DMJ & Ha, T 2004, 'Single-molecule studies of DNA and RNA four-way junctions', Biochemical Society Transactions, vol. 32, no. 1, pp. 41-45. https://doi.org/10.1042/BST0320041
McKinney SA, Tan E, Wilson TJ, Nahas MK, Déclais AC, Clegg RM et al. Single-molecule studies of DNA and RNA four-way junctions. Biochemical Society Transactions. 2004 Feb;32(1):41-45. https://doi.org/10.1042/BST0320041
McKinney, S. A. ; Tan, E. ; Wilson, T. J. ; Nahas, M. K. ; Déclais, A. C. ; Clegg, R. M. ; Lilley, D. M J ; Ha, Taekjip. / Single-molecule studies of DNA and RNA four-way junctions. In: Biochemical Society Transactions. 2004 ; Vol. 32, No. 1. pp. 41-45.
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