Single-stranded noncoding regulatory RNAs, as exemplified by bacterial riboswitches, are highly dynamic. The conformational dynamics allow the riboswitch to reach maximum switching efficiency under appropriate conditions. Here we characterize the conformational dynamics of preQ₁ riboswitches from mesophilic and thermophilic bacterial species at various temperatures. With the integrative use of small-angle X-ray scattering, NMR, and molecular dynamics simulations, we model the ensemble-structures of the preQ₁ riboswitch aptamers without or with a ligand bound. We show that the preQ₁ riboswitch is sufficiently dynamic and fluctuating among multiple folding intermediates only near the physiological temperature of the microorganism. The hierarchical folding dynamics of the RNA involves the docking of 3′-tail to form a second RNA helix and the helical stacking to form an H-type pseudoknot structure. Further, we show that RNA secondary and tertiary dynamics can be modulated by temperature and by the length of an internal loop. The coupled equilibria between RNA folding intermediates are essential for preQ₁ binding, and a four-state exchange model can account for the change of ligand-triggered switching efficiency with temperature. Together, we have established a relationship between the hierarchical dynamics and riboswitch function, and illustrated how the RNA adapts to high temperature.

如细菌核糖开关所举例说明的，单链非编码调控RNA是高度动态的。构象动力学允许核糖开关在适当条件下达到最大开关效率。在这里，我们表征了在不同温度下嗜温和嗜热细菌物种的preQ ₁核糖开关的构象动力学。通过小角度X射线散射，NMR和分子动力学模拟的综合使用，我们对没有或带有配体结合的preQ ₁核糖开关适体的整体结构进行了建模。我们证明了preQ ₁核糖开关是足够动态的，并且仅在微生物的生理温度附近才在多种折叠中间体之间波动。RNA的分层折叠动力学涉及3'-尾对接以形成第二个RNA螺旋，以及螺旋堆叠以形成H型假结结构。此外，我们表明RNA二级和三级动力学可以通过温度和内部环的长度进行调节。RNA折叠中间体之间的偶联平衡对于preQ ₁结合至关重要，并且四态交换模型可以说明配体触发的转换效率随温度的变化。我们共同建立了层次动力学与核糖开关功能之间的关系，并说明了RNA如何适应高温。