RecA balances genomic stability and evolution using many successive mismatch tolerant homology tests

A double-strand break (DSB) must usually be repaired with as little alteration to the genome as possible, though some rare alterations provide valuable genomic evolution. In E . coli , a DSB undergoes resection to give 3’ ssDNA tails. These invading strand tails are loaded with RecA protein and then rapidly search the genome for the corresponding (allelic) partner. Thus, a searching ssDNA/RecA filament must almost never make stable non-allelic contact; therefore, it has been puzzling that RecA forms stable products that join partially homologous sequences. Homology testing by RecA family proteins begins with an 8-bp test, followed by successive homology tests of base pair triplets. Here we introduce a highly simplified homology recognition model to highlight how mismatch sensitivity could affect non-allelic pairing in bacterial genomes. The model predicts that even if each triplet test accepts 2 mismatches, RecA can have ∼ 95% probability of establishing allelic pairing after a DSB in E. coli ; however, that accuracy requires homology testing ⪆50 contiguous base pairs, consistent with the homology lengths probed in vivo . In contrast, if no mismatches are accepted testing 14 bp is sufficient, and testing more base pairs does not reduce non-allelic pairing because bacterial genomes contain long repeats. ### Competing Interest Statement The authors have declared no competing interest.