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首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >DNA A-tract bending in three dimensions: Solving the dA_4T_4 vs. dT_4A_4 conundrum
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DNA A-tract bending in three dimensions: Solving the dA_4T_4 vs. dT_4A_4 conundrum

机译：DNA A方向弯曲的三个维度：解决dA_4T_4与dT_4A_4难题

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摘要

DNA A-tracts have been defined as four or more consecutive AT base pairs without a TpA step. When inserted in phase with the DNA helical repeat, bending is manifested macroscopically as anomalous migration on polyacrylamide gels, first observed >20 years ago. An unsolved conundrum is why DNA containing in-phase A-tract repeats of A_4T_4 are bent, whereas T_4A_4 is straight. We have determined the solution structures of the DNA duplexes formed by d(GCAAAATTT-TGC) [A4T4] and d(CGTTTTAAAACG) [T4A4] with NH_4~+ counterions by using NMR spectroscopy, including refinement with residual dipolar couplings. Analysis of the structures shows that the ApT step has a large negative roll, resulting in a local bend toward the minor groove, whereas the TpA step has a positive roll and locally bends toward the major groove. For A4T4, this bend is nearly in phase with bends at the two A-tract junctions, resulting in an overall bend toward the minor groove of the A-tract, whereas for T4A4, the bends oppose each other, resulting in a relatively straight helix. NMR-based structural modeling of d(CAAAATTTTG)_(15) and d(GTTTTAAAAC)_(15) reveals that the former forms a left-handed superhelix with a diameter of ≈110 A and pitch of 80 A, similar to DNA in the nucleosome, whereas the latter has a gentle writhe with a pitch of >250 A and diameter of ≈50 A. Results of gel electrophoretic mobility studies are consistent with the higher-order structure of the DNA and furthermore depend on the nature of the monovalent cation present in the running buffer.
机译：DNA A序列已被定义为四个或更多个连续的AT碱基对，没有TpA步骤。当与DNA螺旋重复序列同相插入时，弯曲在宏观上表现为聚丙烯酰胺凝胶上的异常迁移，最早在20多年前就观察到了。一个未解之谜是为什么含有A_4T_4的A相同相A重复序列的DNA会弯曲而T_4A_4却是直的。我们已经确定了由d（GCAAAATTT-TGC）[A4T4]和d（CGTTTTAAAACG）[T4A4]与NH_4〜+抗衡离子形成的DNA双链体的溶液结构，包括使用残留偶极偶合的精制。结构分析表明，ApT步骤具有较大的负向弯曲，导致朝向次要凹槽的局部弯曲，而TpA步骤具有正向的弯曲并朝着主要凹槽的局部弯曲。对于A4T4，此弯曲几乎与两个A形管结处的弯曲同相，从而导致朝A形管的小凹槽整体弯曲，而对于T4A4，这些弯曲彼此相对，从而产生相对笔直的螺旋。基于NMR的d（CAAAATTTTG）_（15）和d（GTTTTAAAAC）_（15）的结构建模表明，前者形成了一个左旋超螺旋，直径约为≈110A，螺距为80 A，类似于DNA中的DNA。核小体，螺线管柔和，节距> 250 A，直径≈50A。凝胶电泳迁移率研究的结果与DNA的高阶结构一致，而且还取决于单价分子的性质。阳离子存在于运行缓冲液中。

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