van Buuren B N, Overmars F J, Ippel J H, Altona C, Wijmenga S S
Department of Medical Biosciences, Medical Biophysics, Umeâ, S-90187, Sweden.
J Mol Biol. 2000 Dec 1;304(3):371-83. doi: 10.1006/jmbi.2000.4224.
The solution structure of a DNA three-way junction (3H) containing two unpaired thymidine bases at the branch site (3HT2), was determined by NMR. Arms A and B of the 3HT2 form a quasi-continuous stacked helix, which is underwound at the junction and has an increased helical rise. The unstacked arm C forms an acute angle of approximately 55 degrees with the unique arm A. The stacking of the unpaired thymidine bases on arm C resembles the folding of hairpin loops. From this data, combined with the reported stacking behavior of 23 other 3HS2 s, two rules are derived that together correctly reproduce their stacking preference. These rules predict, from the sequence of any 3HS2, its stacking preference. The structure also suggests a plausible mechanism for structure-specific recognition of branched nucleic acids by proteins.
通过核磁共振确定了在分支位点含有两个未配对胸腺嘧啶碱基的DNA三向接头（3H）（3HT2）的溶液结构。3HT2的臂A和臂B形成了一个准连续堆积螺旋，该螺旋在接头处解旋并且螺旋上升增加。未堆积的臂C与独特的臂A形成约55度的锐角。臂C上未配对胸腺嘧啶碱基的堆积类似于发夹环的折叠。根据这些数据，结合其他23种3HS2的报道堆积行为，得出了两条规则，这两条规则共同正确地再现了它们的堆积偏好。这些规则根据任何3HS2的序列预测其堆积偏好。该结构还提出了一种蛋白质对分支核酸进行结构特异性识别的合理机制。
