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Sequence-dependent folding of DNA three-way junctions

Record type: Article

Three-way DNA junctions can adopt several different conformers, which differ in the coaxial stacking of the arms. These structural variants are often dominated by one conformer, which is determined by the DNA sequence. In this study we have compared several three-way DNA junctions in order to assess how the arrangement of bases around the branch point affects the conformer distribution. The results show that rearranging the different arms, while retaining their base sequences, can affect the conformer distribution. In some instances this generates a structure that appears to contain parallel coaxially stacked helices rather than the usual anti-parallel arrangement. Although the conformer equilibrium can be affected by the order of purines and pyrimidines around the branch point, this is not sufficient to predict the conformer distribution. We find that the folding of three-way junctions can be separated into two groups of dinucleotide steps. These two groups show distinctive stacking properties in B-DNA, suggesting there is a correlation between B-DNA stacking and coaxial stacking in DNA junctions.

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Citation

Assenberg, Rene, Weston, Anthony, Cardy, Don L.N. and Fox, Keith R. (2002) Sequence-dependent folding of DNA three-way junctions Nucleic Acids Research, 30, (23), pp. 5142-5150.

More information

Published date: December 2002

Identifiers

Local EPrints ID: 56575
URI: http://eprints.soton.ac.uk/id/eprint/56575
ISSN: 0305-1048
PURE UUID: 96da73a9-b559-47a8-9cdb-c432e865cbe5
ORCID for Keith R. Fox: ORCID iD orcid.org/0000-0002-2925-7315

Catalogue record

Date deposited: 08 Aug 2008
Last modified: 17 Jul 2017 14:30

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Contributors

Author: Rene Assenberg
Author: Anthony Weston
Author: Don L.N. Cardy
Author: Keith R. Fox ORCID iD

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