Physicochemical basis of RecA filamentation on single-stranded DNA

Quantitative analysis was performed for the first time for the interaction of Escherichia coli RecA, which plays the central role in homologous recombination, and ssDNA varying in length and structure. DNA recognition was shown to depend on weak additive interactions between RecA monomers of the filament and various structural elements of DNA. Orthophosphate and dNMPs acted as minimal inhibitors of RecA filamentation on d(pN)20. A stepwise increase in homooligonucleotide length by one nucleotide (from 2 to 20 nt) monotonically increased the affinity approximately twofold (factor f) due to weak additive contacts of RecA with each internucleoside phosphate (f ≈ 1.56) and specific interactions with T and C(f ≈ 1.32). In the case of d(pA) n, the RecA filament showed virtually no interaction with bases and interacted more efficiently with internucleoside phosphates of the first than of the next helix turn (n < 10, f ≈ 2.1 vs. n > 10, f ≈ 1.3). The affinity of RecA for d(pN)n and various modified bases proved to depend on the base, the DNA structure, and the conformation of the sugar-phosphate backbone. The affinity considerably increased with bases containing exocyclic proton-accepting groups. Possible causes of the preferential binding of RecA with DNAs of a particular length and composition are considered. Mechanisms are proposed for ssDNA recognition by RecA and for homologous strand exchange. © 2005 Pleiades Publishing, Inc.