Solution structures of DNA•RNA hybrids with purine-rich and pyrimidine-rich strands:: Comparison with the homologous DNA and RNA duplexes
Solution structures of DNA•RNA hybrids with purine-rich and pyrimidine-rich strands:: Comparison with the homologous DNA and RNA duplexes
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DOI：
10.1021/bi9719713
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发表时间：
1998-01-06
期刊：
影响因子：
2.9
通讯作者：
Brown, T
中科院分区：
文献类型：
--
作者：
Gyi, JI;Lane, AN;Brown, T
d（GAAGAGAAGC）.d（GCTTCTCTTC）、d（GAAGAGAAGC）.r（GCUUCUCUC）、r（GAAGAGAAGC）.d（GCTTCTCTTC）和r（GAAGAGAAGC）.r（GCUUCUUC）的结构已在溶液中根据核磁共振数据确定。在全局上，纯DNA和RNA双链体分别为B和A形式。这两个DNA/RNA杂交体既不是A也不是B，但总体上比B形式更接近A。然而，药物稳定性较低的d（GAAGAGAAGC）.r（GCUCUUC）双链体具有与r（GAAGAGAAGC）.d（GCTTCTCTTC）显著不同的构象。基于NMR数据，使用受限分子动力学计算结构。一种新的方法来治疗的构象平均的先验概率的基础上已被使用。通过将标量耦合数据和NOE时间过程拟合到两态模型来处理核苷酸，所述两态模型包括N和S糖褶皱，每个糖褶皱具有不同的糖苷扭转角和S状态的摩尔分数。构建了分子内N和S态的不同分布的约束集，使得每个核苷酸根据摩尔分数（或先验概率）在系综中加权。个别核苷酸的构象受到强烈的限制，而核苷酸间的限制设置相对宽松。通过比较从系综平均松弛矩阵计算的NOE与实验NOE，生成并评估了构象系综。整体平均值比任何单个成员都更好地解释了实验数据，或者假设单一独特构象计算的结构。这两个杂交体占据不同程度的构象空间。小沟和大沟宽度的一般趋势为d（GAAGAGAAGC）>.d（GCTTCTCTTC），d（GAAGAGAAGC）.r（GCUUCUUC），r（GAAGAGAAGC）.d（GCTTCTCTTC），r（GAAGAGAAGC）.r（GCUUCUUC），总体特征从B样结构到A样结构也有类似的进展。此外，r（GAAGAGAAGC）.d（GCTTCTCTTC）在系综中显示出比d（GAAGAGAAGC）.r（GCUUCUUC）更大的构象分散度，反映了糖的更大的灵活性。如果忽略核苷酸的构象平均，则产生不正确的虚拟结构，然而其能够满足实验数据的大部分。
The structures of d(GAAGAGAAGC).d(GCTTCTCTTC), d(GAAGAGAAGC).r(GCUUCUCUC), r(GAAGAGAAGC).d(GCTTCTCTTC), and r(GAAGAGAAGC).r(GCUUCUCUUC) have been determined in solution from NMR data. Globally, the pure DNA and RNA duplexes were in the B and A forms, respectively. The two DNA RNA hybrids were neither A nor B, but closer globally to the A than the B form. However, the thermodynamically less stable d(GAAGAGAAGC).r(GCUCUCUUC) duplex has a significantly different conformation from r(GAAGAGAAGC).d(GCTTCTCTTC). Structures were calculated based on the NMR data, using restrained molecular dynamics. A new approach to the treatment of conformational averaging based on a priori probabilities has been used. The nucleotides were treated by fitting the scalar coupling data and NOE time courses to a two-state model comprising N and S sugar puckers each with a different glycosidic torsion angle, and the mole fraction of the S state. Restraint sets for different distributions of N and S states within molecules were constructed, such that each nucleotide was weighted in the ensemble according to the mole fractions (or a priori probabilities). The individual nucleotide conformations were strongly restrained, whereas the internucleotide restraints were set relatively loosely. Ensembles of conformations were generated and assessed by comparison of the NOEs calculated from ensemble-averaged relaxation matrices with the experimental NOEs. The ensemble averages accounted for the experimental data much better than any individual member, or for structures calculated assuming a single unique conformation. The two hybrids populated different degrees of conformational space. There was a general trend in minor and major groove widths in the order d(GAAGAGAAGC>.d(GCTTCTCTTC), d(GAAGAGAAGC).r(GCUUCUCUUC), r(GAAGAGAAGC).d(GCTTCTCTTC), r(GAAGAGAAGC).r(GCUUCUCUUC) and a similar progression in global character from B-like to A-like structures. Furthermore, r(GAAGAGAAGC).d(GCTTCTCTTC) showed a greater dispersion of conformations in the ensemble than d(GAAGAGAAGC).r(GCUUCUCUUC), reflecting the greater flexibility of the sugars. :if conformational averaging of the nucleotides is ignored, incorrect virtual structures are produced that nevertheless are able to satisfy a substantial fraction of the experimental data.