Symmetric Holliday junction crossover isomers

The Holliday junction is a four-stranded branched DNA structure found as an intermediate in genetic recombination. Naturally occurring Holliday junctions have homologous (2-fold) sequence symmetry; this symmetry renders the site of the branch unstable, because the molecules can undergo an isomerization called branch migration. For the past decade, these molecules have been modeled in non-migrating "immobile" branched junctions lacking this symmetry. The solution structure derived from immobile branched junctions is a two-domain DNA structure, in which a particular pair of strands forms the crossover between domains, and the other pair of strands has a structure similar to that seen in DNA double helices; reversal of these roles has not been apparent. We investigate here whether this bias ("crossover preference") for particular strands to be the crossover pair extends to structures that contain symmetric sequences flanking the branch point. We employ nicked symmetric immobile junctions in a competition assay to determine the extent of crossover preference. We have measured all six of the 2-fold symmetric dinucleotide sequences that can flank a branch point, and find small preferences (< 650 cal/mol) at 4 degrees C. The largest preference decreases when the 2-fold symmetry is extended to tetranucleotides. The system contains an internal control on systematic errors, because there are 4-fold symmetric dinucleotide sequences that should show no bias; the preferences we measure for them are below or similar to our estimated errors. We have calibrated our experiment by measuring the crossover preferences for a previously characterized immobile junction; the preference is slightly larger than the largest preference seen for a symmetric crossover. We conclude that large crossover preferences are not characteristic of junctions with extensive symmetry, and are thus unlikely to have important consequences for genetic recombination.