Riddles P W, Lehman I R
J Biol Chem. 1985 Jan 10;260(1):165-9.
During the initial pairing events in the transfer of a strand from a linear duplex to a homologous single-stranded circular DNA by the recA and single-stranded DNA-binding proteins of Escherichia coli, two types of structure are formed that are distinguishable by their stability in the presence of protein denaturants. One type which is resistant to 5.2 M guanidinium chloride is most likely a D-loop that depends only on heteroduplex base pairing for its stability. These D-loops form rapidly when the ends of the linear duplex are homologous with the single-stranded DNA but do not form when the ends are heterologous. The second type appears to require protein, in addition to base pairing, for stability since it is rapidly dissociated by treatment with 5.2 M guanidinium chloride. These unstable structures form even when the ends of the duplex are not homologous with the circular single-stranded DNA. The stability and topological properties of the stable and unstable structures are consistent with those of plectonemic and paranemic joints, respectively (Bianchi, M., Das Gupta, C., and Radding, C. M. (1983) Cell 34, 931-939). The plectonemic joints can be generated in situ from paranemic joints by the addition of a restriction enzyme that cleaves in the region of homology, thus producing free homologous ends. Omission of single-stranded DNA-binding protein results in a large decrease in the rate of formation of both paranemic and plectonemic joints.
在大肠杆菌的recA蛋白和单链DNA结合蛋白将线性双链中的一条链转移到同源单链环状DNA的初始配对过程中，会形成两种类型的结构，这两种结构可通过它们在蛋白质变性剂存在下的稳定性来区分。一种对5.2M氯化胍有抗性的结构很可能是一个D环，其稳定性仅取决于异源双链碱基配对。当线性双链的末端与单链DNA同源时，这些D环迅速形成，但当末端异源时则不形成。第二种类型似乎除了碱基配对外还需要蛋白质来维持稳定性，因为用5.2M氯化胍处理会使其迅速解离。即使双链的末端与环状单链DNA不同源，这些不稳定结构也会形成。稳定和不稳定结构的稳定性和拓扑性质分别与扭结和并列连接的性质一致（Bianchi, M., Das Gupta, C., and Radding, C. M. (1983) Cell 34, 931 - 939）。通过添加在同源区域切割的限制性酶可以从并列连接原位产生扭结连接，从而产生自由的同源末端。省略单链DNA结合蛋白会导致并列连接和扭结连接的形成速率大幅下降。
