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首页> 美国卫生研究院文献>Nucleic Acids Research >Biopolymer Chain Elasticity: a novel concept and a least deformation energy principle predicts backbone and overall folding of DNA TTT hairpins in agreement with NMR distances
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Biopolymer Chain Elasticity: a novel concept and a least deformation energy principle predicts backbone and overall folding of DNA TTT hairpins in agreement with NMR distances

机译：生物聚合物链弹性：一个新概念和最小变形能原理预测了DNA TTT发夹的骨架和整体折叠与NMR距离一致

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摘要

A new molecular modelling methodology is presented and shown to apply to all published solution structures of DNA hairpins with TTT in the loop. It is based on the theory of elasticity of thin rods and on the assumption that single-stranded B-DNA behaves as a continuous, unshearable, unstretchable and flexible thin rod. It requires four construction steps: (i) computation of the tri-dimensional trajectory of the elastic line, (ii) global deformation of single-stranded helical DNA onto the elastic line, (iii) optimisation of the nucleoside rotations about the elastic line, (iv) energy minimisation to restore backbone bond lengths and bond angles. This theoretical approach called ‘Biopolymer Chain Elasticity’ (BCE) is capable of reproducing the tri-dimensional course of the sugar–phosphate chain and, using NMR-derived distances, of reproducing models close to published solution structures. This is shown by computing three different types of distance criteria. The natural description provided by the elastic line and by the new parameter, Ω, which corresponds to the rotation angles of nucleosides about the elastic line, offers a considerable simplification of molecular modelling of hairpin loops. They can be varied independently from each other, since the global shape of the hairpin loop is preserved in all cases.
机译：提出了一种新的分子建模方法，并显示了该方法可应用于环已含TTT的DNA发夹的所有公开溶液结构。它基于细棒的弹性理论，并基于单链B-DNA表现为连续，不可剪切，不可拉伸和柔性细棒的假设。它需要四个构建步骤：（i）计算弹性线的三维轨迹，（ii）单链螺旋DNA在弹性线​​上的整体变形，（iii）优化围绕弹性线的核苷旋转， （iv）最小化能量以恢复骨架键长和键角。这种称为“生物聚合物链弹性”（BCE）的理论方法能够再现糖-磷酸盐链的三维过程，并利用NMR得出的距离，可以再现与已发布溶液结构接近的模型。通过计算三种不同类型的距离标准可以看出这一点。弹性线和新参数Ω（对应于核苷围绕弹性线的旋转角度）提供的自然描述极大地简化了发夹环的分子建模。它们可以彼此独立地变化，因为发夹环的整体形状在所有情况下都得以保留。

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