Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, D-60438 Frankfurt/Main, Germany.
Acc Chem Res. 2011 Dec 20;44(12):1292-301. doi: 10.1021/ar200137d. Epub 2011 Sep 6.
Among the three major classes of biomacromolecules (DNA, RNA, and proteins) RNA's pronounced dynamics are the most explicitly linked to its wide variety of functions, which include catalysis and the regulation of transcription, translation, and splicing. These functions are mediated by a range of RNA biomachinery, including such varied examples as macromolecular noncoding RNAs, microRNAs, small interfering RNAs, riboswitch RNAs, and RNA thermometers. In each case, the functional dynamics of an interconversion is characterized by an associated rate constant. In this Account, we provide an introduction to NMR spectroscopic characterization of the landscape of RNA dynamics. We introduce strategies for measuring NMR parameters at various time scales as well as the underlying models for describing the corresponding rate constants. RNA exhibits significant dynamic motion, which can be modulated by (i) intermolecular interactions, including specific and nonspecific binding of ions (such as Mg(2+) and tertiary amines), (ii) metabolites in riboswitches or RNA aptamers, and (iii) macromolecular interactions within ribonucleic protein particles, including the ribosome and the spliceosome. Our understanding of the nature of these dynamic changes in RNA targets is now being incorporated into RNA-specific approaches in the design of RNA inhibitors. Interactions of RNA with proteins, other RNAs, or small molecules often occur through binding mechanisms that follow an induced fit mechanism or a conformational selection mechanism, in which one of several populated RNA conformations is selected through ligand binding. The extent of functional dynamics, including the kinetic formation of a specific RNA tertiary fold, is dependent on the messenger RNA (mRNA) chain length. Thus, during de novo synthesis of mRNA, both in prokaryotes and eukaryotes, nascent mRNA of various lengths will adopt different secondary and tertiary structures. The speed of transcription has a critical influence on the functional dynamics of the RNA being synthesized. In addition to modulating the local dynamics of a conformational RNA ensemble, a given RNA sequence may adopt more than one global, three-dimensional structure. RNA modification is one way to select among these alternative structures, which are often characterized by nearly equal stability, but with high energy barriers for conformational interconversion. The refolding of different secondary and tertiary structures has been found to be a major regulatory mechanism for transcription and translation. These conformational transitions can be characterized with NMR spectroscopy, for any given RNA sequence, in response to external stimuli.
在三大生物大分子（DNA、RNA 和蛋白质）中，RNA 的显著动态与其广泛的功能最明显相关，这些功能包括催化以及转录、翻译和剪接的调控。这些功能由一系列 RNA 生物机制介导，包括大分子非编码 RNA、microRNA、小干扰 RNA、核糖开关 RNA 和 RNA 温度计等各种不同的例子。在每种情况下，相互转化的功能动态都由相关的速率常数来表征。在本专题介绍中，我们提供了一种 RNA 动力学的 NMR 光谱特征的介绍。我们介绍了在各种时间尺度下测量 NMR 参数的策略，以及描述相应速率常数的基础模型。RNA 表现出显著的动态运动，这种运动可以通过（i）分子间相互作用进行调节，包括离子（如 Mg2+和叔胺）的特异性和非特异性结合，（ii）核糖开关或 RNA 适体中的代谢物，以及（iii）核糖核蛋白颗粒内的大分子相互作用，包括核糖体和剪接体。我们对 RNA 靶标中这些动态变化性质的理解，现在正被纳入 RNA 特异性抑制剂设计中。RNA 与蛋白质、其他 RNA 或小分子的相互作用通常通过诱导契合机制或构象选择机制发生，在这些机制中，通过配体结合选择几种流行的 RNA 构象之一。功能动力学的程度，包括特定 RNA 三级折叠的动力学形成，取决于信使 RNA (mRNA) 链长。因此，在原核生物和真核生物中，mRNA 的从头合成过程中，各种长度的新生 mRNA 将采用不同的二级和三级结构。转录的速度对正在合成的 RNA 的功能动力学有至关重要的影响。除了调节构象 RNA 整体的局部动力学外，给定的 RNA 序列可能采用不止一种全局的、三维结构。RNA 修饰是在这些替代结构中进行选择的一种方式，这些结构通常具有几乎相等的稳定性，但构象相互转化的能量壁垒很高。不同二级和三级结构的重折叠已被发现是转录和翻译的主要调节机制。这些构象转换可以通过 NMR 光谱学来表征，对于任何给定的 RNA 序列，都可以对外界刺激做出响应。
