锥虫动基体DNA弯曲位点序列定向曲率的分子动力学研究
Molecular Dynamics Studies of Sequence-directed Curvature in Bending Locus of Trypanosome Kinetoplast DNA
摘要：
由规则重复的腺嘌呤束（A-tracts）在双螺旋B-DNA中诱导的宏观曲率在DNA的结构研究中起着特殊的作用，因为这种效应提供了序列特异性构象调制的最有据可查的例子。最近，一个新的假说，其物理起源已被提出，基于分子动力学模拟的结果，一个25-mer的片段与三个A-束相的螺旋螺杆。然而，它的序列在实验研究中从未遇到过，而是根据经验构建的，以便在特定的计算条件下最大限度地提高弯曲的幅度。在这里，我们报告了另一个25聚体B-DNA片段的类似调查的结果，现在有一个天然的碱基对序列中发现的一个微环DNA的弯曲位点。结果表明，静态曲率的一个相当大的幅度和稳定的方向走向小沟的A-道自发出现的条件下，不包括任何初始偏见，除了碱基对序列。这两个DNA片段的弯曲动力学的比较揭示了定性的相似性和有趣的差异。结果表明，在模拟中获得的A道诱导弯曲再现的自然现象，并验证了早期的结论，其可能的机制。
英文摘要：
The macroscopic curvature induced in the double helical B-DNA by regularly repeated adenine tracts (A-tracts) plays an exceptional role in structural studies of DNA because this effect presents the most well-documented example of sequence specific conformational modulations. Recently, a new hypothesis of its physical origin has been put forward, based upon the results of molecular dynamics simulations of a 25-mer fragment with three A-tracts phased with the helical screw. Its sequence, however, had never been encountered in experimental studies, but was constructed empirically so as to maximize the magnitude of bending in specific computational conditions. Here we report the results of a similar investigation of another 25-mer B-DNA fragment now with a natural base pair sequence found in a bent locus of a minicircle DNA. It is shown that the static curvature of a considerable magnitude and stable direction towards the minor grooves of A-tracts emerges spontaneously in conditions excluding any initial bias except the base pair sequence. Comparison of the bending dynamics of these two DNA fragments reveals both qualitative similarities and interesting differences. The results suggest that the A-tract induced bending obtained in simulations reproduces the natural phenomenon and validates the earlier conclusions concerning its possible mechanism.
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