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.
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Conference Article|
February 01 2004
Single-molecule studies of DNA and RNA four-way junctions
S.A. McKinney;
S.A. McKinney
*Department of Physics, University of Illinois, Urbana-Champaign, Urbana, IL 61801, U.S.A.
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E. Tan;
E. Tan
*Department of Physics, University of Illinois, Urbana-Champaign, Urbana, IL 61801, U.S.A.
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T.J. Wilson;
T.J. Wilson
†Cancer Research UK Nucleic Acid Structure Research Group, Department of Biochemistry, The University of Dundee, Dundee DD1 5EH, U.K.
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M.K. Nahas;
M.K. Nahas
*Department of Physics, University of Illinois, Urbana-Champaign, Urbana, IL 61801, U.S.A.
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A.-C. Déclais;
A.-C. Déclais
†Cancer Research UK Nucleic Acid Structure Research Group, Department of Biochemistry, The University of Dundee, Dundee DD1 5EH, U.K.
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R.M. Clegg;
R.M. Clegg
*Department of Physics, University of Illinois, Urbana-Champaign, Urbana, IL 61801, U.S.A.
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D.M.J. Lilley;
D.M.J. Lilley
†Cancer Research UK Nucleic Acid Structure Research Group, Department of Biochemistry, The University of Dundee, Dundee DD1 5EH, U.K.
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T. Ha
T. Ha
1
*Department of Physics, University of Illinois, Urbana-Champaign, Urbana, IL 61801, U.S.A.
1To whom correspondence should be addressed (e-mail tjha@uiuc.edu).
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Publisher: Portland Press Ltd
Online ISSN: 1470-8752
Print ISSN: 0300-5127
© 2004 Biochemical Society
2004
Biochem Soc Trans (2004) 32 (1): 41–45.
Citation
S.A. McKinney, E. Tan, T.J. Wilson, M.K. Nahas, A.-C. Déclais, R.M. Clegg, D.M.J. Lilley, T. Ha; Single-molecule studies of DNA and RNA four-way junctions. Biochem Soc Trans 1 February 2004; 32 (1): 41–45. doi: https://doi.org/10.1042/bst0320041
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