Sequence-dependent folding of DNA three-way junctions


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), 5142-5150.

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Description/Abstract

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.

Item Type: Article
ISSNs: 0305-1048 (print)
Related URLs:
Subjects: Q Science > QH Natural history > QH301 Biology
Divisions: University Structure - Pre August 2011 > School of Biological Sciences
ePrint ID: 56575
Date Deposited: 08 Aug 2008
Last Modified: 27 Mar 2014 18:39
URI: http://eprints.soton.ac.uk/id/eprint/56575

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