Conserved sequence preference in DNA binding among recombination proteins:an effect of ssDNA secondary structure

Repetitive sequences have been proposed to be recombinogenic elements in eu karyotic chromosomes, We tested whether dinucleotide repeats sequences are preferential sites for recombination because of their high affinity for rec ombination enzymes. We compared the kinetics of the binding of the scRad51, hsRad51 and ecRecA proteins to oligonucleotides with repeats of dinucleoti des GT, CA, CT, GA, GC or AT, Since secondary structures in single-stranded DNA (ssDNA) act as a barrier to complete binding we measured whether these oligonucleotides are able to form stable secondary structures. We show tha t the preferential binding of recombination proteins is conserved among the three proteins and is influenced mainly by secondary structures in ssDNA.