Determination of structure of RNA via NMR is complicated in large part by the lack of a precise parameterization linking the observed chemical shifts to the underlying geometric parameters. In contrast to proteins, where numerous high-resolution crystal structures serve as coordinate templates for this mapping, such models are rarely available for smaller oligonucleotides accessible via NMR, or they exhibit crystal packing and counter-ion binding artifacts that prevent their use for the chemical shifts analysis. On the other hand, NMR-determined structures of RNA often are not solved at the density of restraints required to precisely define the variable degrees of freedom. In this study we sidestep the problems of direct parameterization of the RNA chemical shifts/structure relationship, and examine the effects of imposing local fragmental coordinate similarity restraints based on similarities of the experimental secondary ribose 13C/1H chemical shifts instead. The effect of such chemical shift similarity (CSS) restraints on the structural accuracy is assessed via residual dipolar coupling (RDC)-based cross-validation. Improvements in the coordinate accuracy are observed for all of the six RNA constructs considered here as test cases, which argues for routine inclusion of these terms during NMR-based oligonucleotide structure determination. Such accuracy improvements are expected to facilitate derivation of the chemical shift/structure relationships for RNA.

中文翻译：

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基于化学位移的相似性限制提高了通过 NMR 确定的 RNA 结构的准确性

通过 NMR 确定 RNA 的结构在很大程度上是复杂的，因为缺乏将观察到的化学位移与潜在几何参数联系起来的精确参数化。与蛋白质相比，许多高分辨率晶体结构用作此映射的坐标模板，此类模型很少适用于可通过 NMR 访问的较小寡核苷酸，或者它们表现出晶体堆积和反离子结合伪影，阻止它们用于化学变化分析。另一方面，核磁共振确定的 RNA 结构通常无法在精确定义可变自由度所需的约束密度下解决。在这项研究中，我们回避了 RNA 化学位移/结构关系的直接参数化问题，并检查基于实验二级核糖 13C/1H 化学位移的相似性施加局部碎片坐标相似性限制的效果。这种化学位移相似性 (CSS) 限制对结构精度的影响通过基于残余偶极耦合 (RDC) 的交叉验证进行评估。在此处作为测试案例的所有六种 RNA 构建体都观察到坐标精度的改进，这表明在基于 NMR 的寡核苷酸结构确定期间常规包含这些术语。这种准确性的提高有望促进 RNA 化学位移/结构关系的推导。这种化学位移相似性 (CSS) 限制对结构精度的影响通过基于残余偶极耦合 (RDC) 的交叉验证进行评估。在此处作为测试案例的所有六种 RNA 构建体都观察到坐标精度的改进，这表明在基于 NMR 的寡核苷酸结构确定期间常规包含这些术语。这种准确性的提高有望促进 RNA 化学位移/结构关系的推导。这种化学位移相似性 (CSS) 限制对结构精度的影响通过基于残余偶极耦合 (RDC) 的交叉验证进行评估。在此处作为测试案例的所有六种 RNA 构建体都观察到坐标精度的改进，这表明在基于 NMR 的寡核苷酸结构确定期间常规包含这些术语。这种准确性的提高有望促进 RNA 化学位移/结构关系的推导。