Leija-Martínez Nehemías, Casas-Flores Sergio, Cadena-Nava Rubén D, Roca Joan A, Mendez-Cabañas José A, Gomez Eduardo, Ruiz-Garcia Jaime
Biological Physics Laboratory, Physics Institute, Universidad Autónoma de San Luis Potosí, Alvaro Obregon 64, San Luis Potosí, S.L.P. 78290, México.
División de Biología Molecular, IPICYT, Camino a la Presa San Jose s/n, San Luis Potosí, SLP 78216, México.
Nucleic Acids Res. 2014 Dec 16;42(22):13963-8. doi: 10.1093/nar/gku1249. Epub 2014 Nov 26.
RNA molecules play different roles in coding, decoding and gene expression regulation. Such roles are often associated to the RNA secondary or tertiary structures. The folding dynamics lead to multiple secondary structures of long RNA molecules, since an RNA molecule might fold into multiple distinct native states. Despite an ensemble of different structures, it has been theoretically proposed that the separation between the 5' and 3' ends of long single-stranded RNA molecules (ssRNA) remains constant, independent of their base content and length. Here, we present the first experimental measurements of the end-to-end separation in long ssRNA molecules. To determine this separation, we use single molecule Fluorescence Resonance Energy Transfer of fluorescently end-labeled ssRNA molecules ranging from 500 to 5500 nucleotides in length, obtained from two viruses and a fungus. We found that the end-to-end separation is indeed short, within 5-9 nm. It is remarkable that the separation of the ends of all RNA molecules studied remains small and similar, despite the origin, length and differences in their secondary structure. This implies that the ssRNA molecules are 'effectively circularized' something that might be a general feature of RNAs, and could result in fine-tuning for translation and gene expression regulation.
RNA分子在编码、解码和基因表达调控中发挥着不同的作用。这些作用通常与RNA的二级或三级结构相关。折叠动力学导致长RNA分子具有多种二级结构，因为一个RNA分子可能折叠成多个不同的天然状态。尽管存在多种不同的结构，但从理论上提出，长单链RNA分子（ssRNA）5'端和3'端之间的距离保持恒定，与它们的碱基含量和长度无关。在此，我们展示了长ssRNA分子中端到端距离的首次实验测量结果。为了确定这个距离，我们使用了单分子荧光共振能量转移技术，该技术应用于长度从500到5500个核苷酸的荧光标记末端的ssRNA分子，这些分子来自两种病毒和一种真菌。我们发现端到端距离确实很短，在5 - 9纳米范围内。值得注意的是，尽管所研究的所有RNA分子的来源、长度以及二级结构存在差异，但其两端的距离仍然很小且相似。这意味着ssRNA分子“有效地环化了”，这可能是RNA的一个普遍特征，并可能导致翻译和基因表达调控的微调。
