Non-Watson-Crick base pairs modulate homologous alignments in RecA pairing reactions

Abstract

Complementary pairing by RecA was examined in vitro to investigate how homology is deciphered from non-homology. Somewhere in a window of 40–50% sequence complementarity, RecA pairing begins to manifest the specificity of homology. Quantitation reveals a hierarchy among non-Watson-Crick mispairs: RecA reaction treats six out of 12 possible mispairs as good ones and three each of the remaining ones as moderate and bad pairs. The mispairs seem to function as independent pairing units free of sequence context effects. The overall strength of pairing is simply the sum of the constituent units. RecA mediated gradation of mispairs, free of sequence context effects, might offer a general thumb-rule for predicting the pairing strength of any alignment that carries multiple mispairs.