The strand-exchange reaction is central to homologous recombination. It is catalysed by the RecA family of ATPases, which form a helical filament with single-stranded DNA (ssDNA) and ATP. This filament binds to a donor double-stranded DNA (dsDNA) to form synaptic filaments, which search for homology and then catalyse the exchange of the complementary strand, forming either a new heteroduplex or—if homology is limited—a D-loop 1 , 2 . How synaptic filaments form, search for homology and catalyse strand exchange is poorly understood. Here we report the cryo-electron microscopy analysis of synaptic mini-filaments with both non-complementary and partially complementary dsDNA, and structures of RecA–D-loop complexes containing a 10- or a 12-base-pair heteroduplex. The C-terminal domain of RecA binds to dsDNA and directs it to the RecA L2 loop, which inserts into and opens up the duplex. The opening propagates through RecA sequestering the homologous strand at a secondary DNA-binding site, which frees the complementary strand to sample pairing with the ssDNA. At each RecA step, there is a roughly 20% probability that duplex opening will terminate and the as-yet-unopened dsDNA portion will bind to another C-terminal domain. Homology suppresses this process, through the cooperation of heteroduplex pairing with the binding of ssDNA to the secondary site, to extend dsDNA opening. This mechanism locally limits the length of ssDNA sampled for pairing if homology is not encountered, and could allow for the formation of multiple, widely separated synapses on the donor dsDNA, which would increase the likelihood of encountering homology. These findings provide key mechanistic insights into homologous recombination. Cryo-electron microscopy structures of the bacterial recombination protein RecA with DNA, and of RecA–D-loop complexes, provide insights into the double-stranded DNA opening, homology search and strand-exchange processes of homologous recombination.

中文翻译：

---

RecA-DNA突触和D环结构的链交换机制

链交换反应是同源重组的核心。它由 ATP 酶的 RecA 家族催化，该家族与单链 DNA (ssDNA) 和 ATP 形成螺旋丝。该细丝与供体双链 DNA (dsDNA) 结合形成突触细丝，突触细丝寻找同源性，然后催化互补链的交换，形成新的异源双链，或者——如果同源性受到限制——形成 D 环 1， 2. 突触丝是如何形成的，寻找同源性和催化链交换的方式知之甚少。在这里，我们报告了具有非互补和部分互补 dsDNA 的突触微丝的低温电子显微镜分析，以及含有 10 或 12 碱基对异源双链体的 RecA-D 环复合物的结构。RecA 的 C 端结构域与 dsDNA 结合并将其引导至 RecA L2 环，它插入并打开双工。开口通过 RecA 传播，将同源链隔离在二级 DNA 结合位点，从而释放互补链以与 ssDNA 进行样品配对。在每个 RecA 步骤中，双工开放终止的概率约为 20%，而尚未开放的 dsDNA 部分将与另一个 C 端域结合。同源性抑制这个过程，通过异源双链配对与 ssDNA 与二级位点的结合的合作，以延长 dsDNA 的开放。如果没有遇到同源性，这种机制会局部限制采样用于配对的 ssDNA 的长度，并且可以允许在供体 dsDNA 上形成多个广泛分离的突触，这将增加遇到同源性的可能性。这些发现为同源重组提供了关键的机制见解。细菌重组蛋白 RecA 与 DNA 以及 RecA-D 环复合物的冷冻电子显微镜结构提供了对双链 DNA 开放、同源性搜索和同源重组的链交换过程的见解。