Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055;
Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290; and.
Proc Natl Acad Sci U S A. 2014 Jul 1;111(26):9485-90. doi: 10.1073/pnas.1407969111. Epub 2014 Jun 16.
Using on- and off-resonance carbon and nitrogen R1ρ NMR relaxation dispersion in concert with mutagenesis and NMR chemical shift fingerprinting, we show that the transactivation response element RNA from the HIV-1 exists in dynamic equilibrium with a transient state that has a lifetime of ∼2 ms and population of ∼0.4%, which simultaneously remodels the structure of a bulge, stem, and apical loop. This is accomplished by a global change in strand register, in which bulge residues pair up with residues in the upper stem, causing a reshuffling of base pairs that propagates to the tip of apical loop, resulting in the creation of three noncanonical base pairs. Our results show that transient states can remodel distant RNA motifs and possibly give rise to mechanisms for rapid long-range communication in RNA that can be harnessed in processes such as cooperative folding and ribonucleoprotein assembly.
利用碳和氮的局域和非局域 R1ρ NMR 弛豫分散实验，结合诱变和 NMR 化学位移指纹图谱分析，我们发现 HIV-1 的反式激活反应元件 RNA 与其瞬变态处于动态平衡中，其半衰期约为 2 毫秒，丰度约为 0.4%，该瞬变态能够同时重塑一个凸起、茎部和顶端环的结构。这是通过链寄存器的全局变化来实现的，其中凸起残基与上茎部的残基配对，导致碱基对的重新排列传播到顶端环的尖端，从而产生三个非canonical 碱基对。我们的结果表明，瞬变态可以重塑远距离的 RNA 基序，并可能为 RNA 中快速长程通讯提供机制，这些机制可以用于协同折叠和核糖核蛋白组装等过程。
