[Interaction of single-stranded DNA with the second DNA-binding site of RecA nucleoprotein filament].

RecA protein first forms filament on single-stranded (ss) DNA forming the first DNA-binding site for interaction with this ssDNA a formation of the second site for interaction with double-stranded DNA occurs in parallel. Then the formed nucleoprotein filament interacts with molecules of double-stranded (ds) DNA but can also recognize ssDNA. The formed complex realizes a search of homology and exchange of homologous strands. We have studied recently the mechanism of RecA filamentation on ssDNA. Here a study of interaction of different DNAs with the second site of RecA filament using a method of stepwise increase of the ligand complicity was performed. The second site under recognition interacts with every nucleotide units of DNA-ligand forming contact with both internucleotide phosphate groups and bases of DNA. Pyrimidinic d(pC)n [Russian character: see text d(pT)n oligonucleotides interact with the second site of the RecA filament more effectively than with d(pA)n oligonucleotides. This occurs due to a more effective interaction of the RecA filament with 5'-terminal unit of pyrimidinic DNAs and to a difference in specific conformational changes of nucleoprotein filaments in the complex with purinic and pyrimidinic DNAs. A comparison of thermodynamic characteristics of DNA recognition by the first and the second sites of DNA recognition is carried out. It was shown that at n >10 d(pC)n d(pN)n interact with the second site weaker, that with the first site. The complexation of the second site with d(pA)n at n >20 is more effective than with the first site. The difference in the affinity of d(pA)n to the fist and second sites is increased monotonically with the enhancement of their length. Possible mechanisms of RecA-dependent search of homology and strand exchange are discussed.

[Physico-chemical basis of RecA nucleo-protein filament formation on single].

The analysis of RecA protein playing a central role in homologous recombination of E. coli with single-stranded DNAs of various structure and length on quantitative level is carried out for the first time. It was shown that weak additive interactions between protein monomers of filament and different structural elements of DNA provide DNA recognition. Orthophosphate and dNMPs (I50 = 12-20 mM) were shown to be the minimal inhibitors of RecA filamentation on d(pN)20. The lengthening of homooligonucleotides from d(pN)2 to d(pN)20 by one unit leads to monotonic increase in the affinity by a factor approximately 2 (factor f) due to weak additive contacts of RecA with every internucleoside phosphate group of DNA (f = 1.56) and specific interactions with each of T and C bases (f = 1.32). RecA filament does not practically interact with bases of d(pA)n, but contacts with internucleoside phosphate groups of the first turn (n < 10; f = 2.1) more effective than with additional turns of d(pA)n (n > 10; f = 1.3). The affinity of RecA protein for d(pN)n, containing typical and a number of different modified bases depends on a type of base, peculiarities of DNA structure and conformation of its sugar-phosphate backbone. The affinity is increased significantly if the bases contain exocyclic proton accepting groups. The possible reasons of preferable complexation of RecA with DNA of definite structure and length are analyzed. The mechanism of single-stranded DNA recognition by RecA and hypothetical mechanism of homological DNA strands exchange are proposed.