Nucleic Acids Research, 2002, Vol. 30, No. 23 5142-5150
© 2002 Oxford University Press
Sequence-dependent folding of DNA three-way junctions
1 Cytocell Limited, Banbury Business Park, Adderbury, Banbury OX17 3SN, UK and 2 Division of Biochemistry and Molecular Biology, School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK
*To whom correspondence should be addressed. Tel: +44 23 8059 4374; Fax: + 44 23 8059 4459; Email k.r.fox{at}soton.ac.uk
Present address:
René Assenberg, Oxford Protein Production Facility, Wellcome Trust Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK
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.