RNA. 2014 Mar;20(3):331-47. doi: 10.1261/rna.042747.113. Epub 2014 Jan 17.
Folding mechanisms of functional RNAs under idealized in vitro conditions of dilute solution and high ionic strength have been well studied. Comparatively little is known, however, about mechanisms for folding of RNA in vivo where Mg(2+) ion concentrations are low, K(+) concentrations are modest, and concentrations of macromolecular crowders and low-molecular-weight cosolutes are high. Herein, we apply a combination of biophysical and structure mapping techniques to tRNA to elucidate thermodynamic and functional principles that govern RNA folding under in vivo-like conditions. We show by thermal denaturation and SHAPE studies that tRNA folding cooperativity increases in physiologically low concentrations of Mg(2+) (0.5-2 mM) and K(+) (140 mM) if the solution is supplemented with physiological amounts (∼ 20%) of a water-soluble neutral macromolecular crowding agent such as PEG or dextran. Low-molecular-weight cosolutes show varying effects on tRNA folding cooperativity, increasing or decreasing it based on the identity of the cosolute. For those additives that increase folding cooperativity, the gain is manifested in sharpened two-state-like folding transitions for full-length tRNA over its secondary structural elements. Temperature-dependent SHAPE experiments in the absence and presence of crowders and cosolutes reveal extent of cooperative folding of tRNA on a nucleotide basis and are consistent with the melting studies. Mechanistically, crowding agents appear to promote cooperativity by stabilizing tertiary structure, while those low molecular cosolutes that promote cooperativity stabilize tertiary structure and/or destabilize secondary structure. Cooperative folding of functional RNA under physiological-like conditions parallels the behavior of many proteins and has implications for cellular RNA folding kinetics and evolution.
在稀溶液和高离子强度的理想化体外条件下,功能性 RNA 的折叠机制已经得到了很好的研究。然而,在体内条件下,RNA 的折叠机制相对知之甚少,因为体内的 Mg(2+) 离子浓度低,K(+) 浓度适中,并且大分子拥挤剂和低分子量共溶剂的浓度也很高。在这里,我们应用生物物理和结构映射技术的组合来研究 tRNA,以阐明在类似于体内条件下控制 RNA 折叠的热力学和功能原理。我们通过热变性和 SHAPE 研究表明,如果在生理浓度(0.5-2 mM)的 Mg(2+) 和 K(+) 溶液中补充生理量(约 20%)的水溶性中性大分子拥挤剂(如 PEG 或葡聚糖),tRNA 的折叠协同性会增加。低分子量共溶剂对 tRNA 折叠协同性的影响各不相同,具体取决于共溶剂的种类,会增加或减少协同性。对于那些增加折叠协同性的添加剂,其增益表现为全长 tRNA 与其二级结构元件之间的二级结构转变更加明显。在拥挤剂和共溶剂存在或不存在的情况下进行的温度依赖性 SHAPE 实验,揭示了 tRNA 在核苷酸基础上的协同折叠程度,与熔融研究一致。从机制上讲,拥挤剂似乎通过稳定三级结构来促进协同性,而那些促进协同性的低分子量共溶剂则稳定三级结构和/或破坏二级结构。功能性 RNA 在类似于生理条件下的协同折叠与许多蛋白质的行为相似,这对细胞内 RNA 折叠动力学和进化具有重要意义。