Effect of DNA sequence divergence on homologous recombination as analyzed by a random-walk model

A point connecting a pair of homologous regions of DNA duplexes moves along the homology in a reaction intermediate of the homologous recombination. F ormulating this movement as a random walk, we were previously successful at explaining the dependence of the recombination frequency on the homology l ength. Recently, the dependence of the recombination frequency on the DNA s equence divergence in the homologous region was investigated experimentally ; if the methyl-directed mismatch repair (MMR) system is active, the logari thm of the recombination frequency decreases very rapidly with an increase of the divergence in a low-divergence regime. Beyond this regime, the logar ithm decreases slowly and linearly with the divergence. This "very rapid dr op-off" is not observed when the MMR system is defective. In this article, we show that our random-walk model call explain these data in a straightfor ward way. When a connecting point encounters a diverged base pair, it is as sumed to he destroyed with a probability that depends on the level of MMR a ctivity.