Recombinases polymerize along single-stranded DNA (ssDNA) at the end of a broken DNA to form a helical nucleofilament with a periodicity of ∼18 bases. The filament catalyzes the search and checking for homologous sequences and promotes strand exchange with a donor duplex during homologous recombination (HR), the mechanism of which has remained mysterious since its discovery. Here, by inserting mismatched segments into donor duplexes and using single-molecule techniques to catch transient intermediates in HR, we found that, even though 3 base pairs (bp) is still the basic unit, both the homology checking and the strand exchange may proceed in multiple steps at a time, resulting in ∼9-bp large steps on average. More interestingly, the strand exchange is blocked remotely by the mismatched segment, terminating at positions ∼9 bp before the match–mismatch joint. The homology checking and the strand exchange are thus separated in space, with the strand exchange lagging behind. Our data suggest that the strand exchange progresses like a traveling wave in which the donor DNA is incorporated successively into the ssDNA–RecA filament to check homology in ∼9-bp steps in the frontier, followed by a hypothetical transitional segment and then the post-strand-exchanged duplex.

重组酶在断裂的DNA末端沿着单链DNA（ssDNA）聚合，形成螺旋核丝，周期约为18个碱基。细丝催化搜索和检查同源序列，并在同源重组（HR）过程中促进与供体双链的链交换，自发现以来，其机理一直很神秘。在这里，通过将不匹配的片段插入供体双链体并使用单分子技术捕获HR中的瞬时中间体，我们发现，即使3个碱基对（bp）仍然是基本单位，同源性检查和链交换都可能进行一次以多步进行，平均约有9 bp大步。更有趣的是，链交换被不匹配的链段远程阻止，在匹配-不匹配接头之前终止于〜9 bp的位置。同源性检查和链交换因此在空间上分开，而链交换滞后。我们的数据表明，链交换像行进波一样进行，在该行波中，供体DNA被连续掺入ssDNA–RecA细丝中，以约9bp的步长检查边界的同源性，然后是假设的过渡片段，然后是后序列。链交换双链体。