Complementary oligonucleotide invasion into (CA/TG) 31-repetitive region of linear and circular DNA duplexes
Gasanova, V.K.; Riadninskaia, N.V.; Gaillard, C.; Strauss, F.; Belitskiĭ, G.A.; Iakubovskaia, M.G.
Molekuliarnaia Biologiia 44(3): 520-528
2010
ISSN/ISBN: 0026-8984 PMID: 20608177 Document Number: 640861
(CA/TG)n-repeats belong to microsatellite DNA and are the most widespread among dinucleotide repeats in mammalian genomes, occupying 0.25% of the genome. These repeats are known to be recombination "hot spots", however the molecular mechanisms of this effect are not known. We proposed that the high frequency of recombination in the repetitive regions may be due to duplex conformational characteristics resulting from a special geometry of base-stacking contacts, which permits the initiation of an invasion process of single-stranded DNA into the duplex homologous region. Here we show for the first time a DNA-DNA interaction of oligonucleotides d(CA)10 and d(TG)10 with linear and circular duplexes containing (CA/TG)31-repeats, upon incubation at 37 degrees C in the absence of proteins. Using radioactively labeled oligonucleotides, we showed that duplex-oligonucleotide interaction intensities depend on their molar ratio at a duplex concentration 30 nM. Decreasing the duplex concentration to 3 nM did not influence the intensity of oligonucleotide invasion. It was shown that more than 1%, but much less than 10% of the duplexes participate in the interaction with oligonucleotides, assuming that one molecule of the duplex interacts with one molecule of the oligonucleotide. Analysis of the kinetics of the process reveals invasion of d(CA)10 at the first minute of its incubation with the duplex, while d(TG)10 interacts with the duplex at an even higher rate. We discuss the role of DNA conformation plasticity of (CA/TG)n-repeats in the phenomenon observed, as well as its biological significance, in particular the role of CA-microsatellites in the initiation of homologous recombination.