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首页> 美国卫生研究院文献>Nucleic Acids Research >DNA tri- and tetra-loops and RNA tetra-loops hairpins fold as elastic biopolymer chains in agreement with PDB coordinates
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DNA tri- and tetra-loops and RNA tetra-loops hairpins fold as elastic biopolymer chains in agreement with PDB coordinates

机译：DNA三环和四环和RNA四环发夹折叠成与PDB坐标一致的弹性生物聚合物链

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摘要

The biopolymer chain elasticity (BCE) approach and the new molecular modelling methodology presented previously are used to predict the tri- dimensional backbones of DNA and RNA hairpin loops. The structures of eight remarkably stable DNA or RNA hairpin molecules closed by a mispair, recently determined in solution by NMR and deposited in the PDB, are shown to verify the predicted trajectories by an analysis automated for large numbers of PDB conformations. They encompass: one DNA tetraloop, -GTTA-; three DNA triloops, -AAA- or -GCA-; and four RNA tetraloops, -UUCG-. Folding generates no distortions and bond lengths and bond angles of main atoms of the sugar–phosphate backbone are well restored upon energy refinement. Three different methods (superpositions, distance of main chain atoms to the elastic line and RMSd) are used to show a very good agreement between the trajectories of sugar–phosphate backbones and between entire molecules of theoretical models and of PDB conformations. The geometry of end conditions imposed by the stem is sufficient to dictate the different characteristic DNA or RNA folding shapes. The reduced angular space, consisting of the new parameter, angle Ω, together with the χ angle offers a simple, coherent and quantitative description of hairpin loops.
机译：先前介绍的生物聚合物链弹性（BCE）方法和新的分子建模方法可用于预测DNA和RNA发夹环的三维骨架。最近通过NMR在溶液中测定并沉积在PDB中的8个由错配关闭的非常稳定的DNA或RNA发夹分子的结构已显示，可通过自动分析大量PDB构象来验证预测的轨迹。它们包括：一个DNA四环，-GTTA-；三个DNA三环，-AAA-或-GCA-；和四个RNA四环-UUCG-。折叠不产生任何扭曲，糖-磷酸盐主链的主要原子的键长和键角在能量精制后可以很好地恢复。三种不同的方法（叠加，主链原子到弹性线的距离和RMSd）被用来显示糖磷酸盐骨架的轨迹之间，理论模型的整个分子与PDB构象之间的很好的一致性。茎施加的末端条件的几何形状足以决定不同的特征性DNA或RNA折叠形状。由新参数角度Ω和χ角度组成的减小的角度空间提供了对发夹环的简单，连贯和定量的描述。

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