2004
DOI: 10.1042/bst0320041
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Single-molecule studies of DNA and RNA four-way junctions

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 a… Show more

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Cited by 32 publications
(23 citation statements)
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“…Our data do not indicate whether Ded1 (without ATP) accelerates the putative branch migration process, but we note that branch migrations can occur spontaneously, as has been observed in other systems. 22,23 Irrespective of the actual mode of transition from the tripartite species to the final RNA structure, our results suggest that RNA structure conversions can be facilitated through stabilization of inherently unstable RNA species. While stabilization of the weak RNA-RNA interactions by proteins may be important throughout RNA metabolism, 1,2,[24][25][26] such structure stabilization has never been observed directly for a DEAD-box protein.…”
Section: Discussionmentioning
confidence: 79%
“…Our data do not indicate whether Ded1 (without ATP) accelerates the putative branch migration process, but we note that branch migrations can occur spontaneously, as has been observed in other systems. 22,23 Irrespective of the actual mode of transition from the tripartite species to the final RNA structure, our results suggest that RNA structure conversions can be facilitated through stabilization of inherently unstable RNA species. While stabilization of the weak RNA-RNA interactions by proteins may be important throughout RNA metabolism, 1,2,[24][25][26] such structure stabilization has never been observed directly for a DEAD-box protein.…”
Section: Discussionmentioning
confidence: 79%
“…This observation lends further support to the hypothesis that the spliceosome and group II introns share a common molecular ancestor. Secondly, four-way junctions form coaxial helical stacks that could juxtapose catalytically essential elements, as observed in the hairpin ribozyme [23]. We utilized the crystal structure of a hairpin ribozyme four-way junction [24] to model such an interaction [20], and the resulting model was satisfying in that it predicted a close proximity between the U6 ISL metal-binding site and the intron-binding regions of U2 and U6 ( Figure 2B).…”
Section: Structural Analysis Of U2-u6 Rnamentioning
confidence: 95%
“…Dynamic characteristics of NAs can be studied using this technique. Recent examples including hairpin ribozymes, Holliday junctions, Gquadruplexes, Rep helicase and reverse transcriptases have been reviewed [36,280].…”
Section: Probing Structures and Distances Between Specific Labeled Simentioning
confidence: 99%