FOLDING OF AN IMMOBILE DNA BRANCHED JUNCTION

霍利迪连接是一个四链DNA分子，其中 四股线成对形成四个双螺旋臂 分支点，即遗传过程中的中心中间体 重组 自然发生的分支点的位置 假日路口是不稳定的，因为它两侧是双重的 （同源）序列对称性，允许连接重新定位 通过称为分支迁移的异构化。 存在下 Mg阳离子，结折叠成一个结构，其中四个 臂彼此成对堆叠，以形成两个双螺旋结构域; H两股采用大致螺旋结构， H链在两个结构域之间交叉。 在没有Mg的情况下， 阳离子，四个臂采用四重对称排列。 的 羟基自由基裂解模式对折叠的 在Mg的存在下的结。相对于它们的线性模式 双链DNA中，两条交叉链受到保护，免受攻击 双畴结构。 同样，在分支的3'端的四个核苷酸 因此，螺旋线显示出保护作用，因为它们 在那里互相拥抱。 这两种保护似乎都在减少， 缺乏镁。 因此，这是一个系统， 该关键中间体的折叠动力学是可测量的 通过Hthese reporter保护differences差异. 剂量反应 在H同步加速器的实验已经完成， 条件H对于42个碱基的靶需要100毫秒的曝光 顺序

The Holliday junction is a four-stranded DNA molecule, in which the four strands pair to form four double helical arms that flank a branch point, that is a central intermediate in the process of genetic recombination. The site of the branch point in naturally occurring Holiday junctions is unstable, because it is flanked by twofold (homologous) sequence symmetry that permits the junction to relocate through an isomerization known as branch migration. In the presence of Mg cations, the junction folds into a structure in which the four arms stack on each other pairwise, to form two double helical domains; Htwo strands adopt a roughly helical structure, and the other two Hstrands cross over between the two domains. In the absence of Mg cations, the four arms adopt a fourfold symmetric arrangement. The hydroxyl radical cleavage pattern is sensitive to the folding of the junction in the presence of Mg. Relative to their pattern in linear duplex DNA, the two crossover strands are protected from attack in the Htwo-domain structure. Likewise, four nucleotides 3' to the branch Hpoint, the helical strands demonstrate protection, because they Hocclude each other there. Both protections appear to be lessened in Hthe absence of magnesium. Hence, this is a system whereby the Hkinetics of the folding of this key intermediate is measurable through Hthese reporter protection differences. Dose response experiments at Hthe synchrotron have been completed and footprinting conditions Hrequired 100 milliseconds of exposure for a 42 base target sequence.