Visualizing single-stranded nucleic acids in solution.
Visualizing single-stranded nucleic acids in solution.
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DOI：
10.1093/nar/gkw1297
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发表时间：
2017-05-19
影响因子：
14.9
通讯作者：
Pollack L
中科院分区：
文献类型：
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作者：
Plumridge A;Meisburger SP;Pollack L
单链核酸 (ssNA) 在许多关键细胞功能中普遍存在。它们的灵活性限制了可用高分辨率结构的数量，仅留下少量蛋白质-ssNA晶体结构，同时迫使解决方案研究报告总体平均值。 ssNA 构象分布的描述对于更全面地表征生物学相关相互作用至关重要。我们将小角度 X 射线散射 (SAXS) 与整体优化方法 (EOM) 相结合，动态构建和细化 ssNA 结构集。通过在代表性二核苷酸步骤中构建候选链并根据 SAXS 数据改进模型，可以获得广泛的结构以匹配不同的溶液条件和链序列。除了大规模结构参数的分布之外，该方法还首次揭示了磷酸盐主链和底层链构象的复杂细节。这些关于未受干扰链的信息将为详细了解一系列问题提供重要信息，包括蛋白质-ssNA 结合、RNA 折叠和 NA 的聚合物性质。此外，该方案将 EOM 选择与迭代精炼池结合起来，以提供对底层结构的信心，可以扩展到其他灵活系统的研究。
Single-stranded nucleic acids (ssNAs) are ubiquitous in many key cellular functions. Their flexibility limits both the number of high-resolution structures available, leaving only a small number of protein–ssNA crystal structures, while forcing solution investigations to report ensemble averages. A description of the conformational distributions of ssNAs is essential to more fully characterize biologically relevant interactions. We combine small angle X-ray scattering (SAXS) with ensemble-optimization methods (EOM) to dynamically build and refine sets of ssNA structures. By constructing candidate chains in representative dinucleotide steps and refining the models against SAXS data, a broad array of structures can be obtained to match varying solution conditions and strand sequences. In addition to the distribution of large scale structural parameters, this approach reveals, for the first time, intricate details of the phosphate backbone and underlying strand conformations. Such information on unperturbed strands will critically inform a detailed understanding of an array of problems including protein–ssNA binding, RNA folding and the polymer nature of NAs. In addition, this scheme, which couples EOM selection with an iteratively refining pool to give confidence in the underlying structures, is likely extendable to the study of other flexible systems.