The relation between genetic recombination and base sequence complementarity

A non-sliding and sliding model of illegitimate recombination utilizing recent experimentally determined free energies are presented. In each model two random sequences of nucleotide bases were brought into contact and the free energy of stabilization was computed.Combinatorial and Monte-Carlo versions were developed to investigate the role of base sequence complementarity in regions of non-homology over varying lengths. It was found that short sequences of complementarity enhanced the frequency of recombination. When the energy threshold wasequivalent to ten contiguous base pairs, the results conformed to experimental recombination frequencies. Recombination is slightly enhanced by increasing the size of exposed contact regions. Skewing the G-C composition does not significantly effect recombination. There was a significant difference in frequencies between sliding and non-sliding models. Application of the models to other genetic events such as nonhomologous sticking of circular DNA and hair-pin formation indicate that these events are essentially non-random processes.