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首页> 外文期刊>Journal of Biomolecular Structure and Dynamics >The intrinsic curvature of a 51 bp K-DNA fragment of Leishmania tarentolae: a molecular model.
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The intrinsic curvature of a 51 bp K-DNA fragment of Leishmania tarentolae: a molecular model.

机译：塔氏Leishmania tarentolae 51 bp K-DNA片段的内在曲率：分子模型。

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DNA intrinsic structure and curvature is a subject of debate because of the importance of these attributes in processes such as DNA packaging, transcription, and gene regulation. X-ray crystallography of DNA single crystals has provided a wealth of information about the local, short range conformational features of DNA. On the other hand, gel electrophoresis analysis of DNA has not only uncovered the macroscopic curvature of DNA but it also provides most of the available data on DNA intrinsic curvature. However, gel electrophoresis can not identify features of DNA structure at the nucleotide or atomic level. In order to address the problem of DNA intrinsic curvature in an attempt to bridge the gap between X-ray crystallography and gel electrophoresis, we use the computational method of molecular dynamics (MD). In this study, we report the results of 2.0 ns MD simulations on a 51 bp fragment of the K-DNA of Leishmania tarentolae containing several A-tracts. The K-DNA double helix is very stable and remains in an intermediate state between the canonical A and B forms of the duplex. The magnitude of global curvature (75 degrees) agrees well with the experimental estimate (72 degrees) available. Analysis of local (every base triplet) and sublocal (every helix turn) curvature shows that the 51 bp K-DNA fragment has curvature features also present in the Wedge, Junction and Calladine's models of DNA intrinsic curvature. We further characterize the flexibility of individual nucleotides in the molecule and find the sugar flexibility within the A-tracts to be strongly correlated with the pattern of A-tract cleavage by the hydroxyl radical. Differential curvature and flexibility at the 5' and 3'junctions between A-tracts and general-sequence DNA are found to modulate the global curvature of the K-DNA fragment.
机译：由于这些属性在DNA包装，转录和基因调控等过程中的重要性，因此DNA固有的结构和曲率成为争论的话题。 DNA单晶的X射线晶体学提供了有关DNA的局部，短程构象特征的大量信息。另一方面，DNA的凝胶电泳分析不仅揭示了DNA的宏观曲率，而且还提供了有关DNA固有曲率的大多数可用数据。但是，凝胶电泳无法在核苷酸或原子水平上鉴定DNA结构的特征。为了解决DNA固有曲率的问题，以试图弥补X射线晶体学和凝胶电泳之间的差距，我们使用分子动力学（MD）的计算方法。在这项研究中，我们报告了含有几个A谱的塔氏Leishmania tarentolae K-DNA的51 bp片段的2.0 ns MD模拟结果。 K-DNA双螺旋非常稳定，并保持双链体的规范A和B形式之间的中间状态。整体曲率的大小（75度）与可用的实验估计值（72度）非常吻合。对局部（每个碱基三重态）和亚局部（每个螺旋转角）曲率的分析表明，在Wedge，Junction和Calladine的DNA固有曲率模型中也存在51 bp的K-DNA片段具有曲率的特征。我们进一步表征分子中单个核苷酸的柔韧性，并发现A束中的糖柔韧性与羟自由基切割A束的模式密切相关。发现在A序列和一般序列DNA之间的5'和3'交界处不同的曲率和柔韧性可调节K-DNA片段的整体曲率。

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