Complementary pairing by RecA vc;as examined in vitro to investigate h
ow homology is deciphered from non-homology. Somewhere in a window of
40-50% sequence complementarity, RecA pairing begins to manifest the s
pecificity of homology. Quantitation reveals a hierarchy among non-Wat
son-Crick; mispairs: RecA reaction treats sis out of 12 possible mispa
irs 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 s
imply the sum of the constituent units, RecA mediated gradation of mis
pairs, free of sequence contest effects, might offer a general thumb-r
ule for predicting the pairing strength of any alignment that carries
multiple mispairs. (C) 1998 Federation of European Biochemical Societi
es.