Department of Chemistry and Biochemistry, University of California-Los Angeles, CA 90095, USA.
RNA. 2012 Feb;18(2):284-99. doi: 10.1261/rna.027557.111. Epub 2011 Dec 21.
Single-stranded RNAs (ssRNAs) longer than a few hundred nucleotides do not have a unique structure in solution. Their equilibrium properties therefore reflect the average of an ensemble of structures. We use cryo-electron microscopy to image projections of individual long ssRNA molecules and characterize the anisotropy of their ensembles in solution. A flattened prolate volume is found to best represent the shapes of these ensembles. The measured sizes and anisotropies are in good agreement with complementary determinations using small-angle X-ray scattering and coarse-grained molecular dynamics simulations. A long viral ssRNA is compared with shorter noncoding transcripts to demonstrate that prolate geometry and flatness are generic properties independent of sequence length and origin. The anisotropy persists under physiological as well as low-ionic-strength conditions, revealing a direct correlation between secondary structure asymmetry and 3D shape and size. We discuss the physical origin of the generic anisotropy and its biological implications.
单链 RNA（ssRNA）长度超过几百个核苷酸时在溶液中没有独特的结构。因此，它们的平衡性质反映了结构的整体平均值。我们使用冷冻电子显微镜对单个长 ssRNA 分子的投影进行成像，并对其在溶液中的整体各向异性进行了特征描述。发现扁长的旋转体形状最能代表这些整体的形状。通过使用小角度 X 射线散射和粗粒分子动力学模拟进行互补测定，所测量的大小和各向异性与实验结果吻合较好。我们将长病毒 ssRNA 与较短的非编码转录物进行了比较，证明了扁长的几何形状和平坦度是通用特性，与序列长度和来源无关。在生理和低离子强度条件下，各向异性仍然存在，这揭示了二级结构不对称性与 3D 形状和大小之间的直接相关性。我们讨论了通用各向异性的物理起源及其生物学意义。
