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Homologous gene shuffling between DNA promotes genetic diversity and is animportant pathway for DNA repair. For this to occur, homologous genes need tofind and recognize each other. However, despite its central role in homologousrecombination, the mechanism of homology recognition is still an unsolvedpuzzle. While specific proteins are known to play a role at later stages ofrecombination, an initial coarse grained recognition step has been proposed.This relies on the sequence dependence of the DNA structural parameters, suchas twist and rise, mediated by intermolecular interactions, in particularelectrostatic ones. In this proposed mechanism, sequences having the same basepair text, or are homologous, have lower interaction energy than thosesequences with uncorrelated base pair texts; the difference termed therecognition energy. Here, we probe how the recognition energy changes when oneDNA fragment slides past another, and consider, for the first time, homologoussequences in antiparallel alignment. This dependence on sliding was termed therecognition well. We find that there is recognition well for anti-parallel,homologous DNA tracts, but only a very shallow one, so that their interactionwill differ little from the interaction between two nonhomologous tracts. Thisfact may be utilized in single molecule experiments specially targeted to testthe theory. As well as this, we test previous theoretical approximations incalculating the recognition well for parallel molecules against MC simulations,and consider more rigorously the optimization of the orientations of thefragments about their long axes. The more rigorous treatment affects therecognition energy a little, when the molecules are considered rigid. Howeverwhen torsional flexibility of the DNA molecules is introduced, we findexcellent agreement between analytical approximation and simulation.

Which way up? Recognition of homologous DNA segments in parallel and antiparallel alignment