Friederich M W, Vacano E, Hagerman P J
Department of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, Denver, CO 80262, USA.
Proc Natl Acad Sci U S A. 1998 Mar 31;95(7):3572-7. doi: 10.1073/pnas.95.7.3572.
The study of RNA structure using x-ray crystallography or NMR has yielded a wealth of detailed structural information; however, such approaches do not generally yield quantitative information regarding long-range flexibility in solution. To address this issue, we describe a solution-based method that is capable of characterizing the global flexibilities of nonhelix elements in RNA, provided that such elements are flanked by helix (e.g., bulges, internal loops, or branches). The "phased tau ratio" method is based on the principle that, for RNA molecules possessing two variably phased bends, the relative birefringence decay times depend on the flexibility of each bend, not simply the mean bend angles. The method is used to examine the overall flexibility of the yeast tRNAPhe core (as unmodified transcript). In the presence of magnesium ions, the tRNA core is not significantly more flexible than an equivalent length of RNA helix. In the absence of divalent ions, the tRNA core gains flexibility under conditions where its secondary structure is likely to be largely preserved. The phased tau ratio approach should be broadly applicable to nonhelix elements in both RNA and DNA and to protein-nucleic acid interactions.
利用X射线晶体学或核磁共振对RNA结构进行的研究已产生了大量详细的结构信息；然而，此类方法通常无法得出有关溶液中远程柔韧性的定量信息。为解决这一问题，我们描述了一种基于溶液的方法，该方法能够表征RNA中非螺旋元件的整体柔韧性，前提是这些元件两侧为螺旋结构（例如，凸起、内环或分支）。“相位τ比率”方法基于这样一个原理：对于具有两个可变相位弯曲的RNA分子，相对双折射衰减时间取决于每个弯曲的柔韧性，而不仅仅取决于平均弯曲角度。该方法用于研究酵母苯丙氨酸转运RNA核心（作为未修饰的转录本）的整体柔韧性。在镁离子存在的情况下，转运RNA核心的柔韧性并不比相同长度的RNA螺旋显著更高。在没有二价离子的情况下，转运RNA核心在其二级结构可能基本保持的条件下获得了柔韧性。相位τ比率方法应广泛适用于RNA和DNA中的非螺旋元件以及蛋白质 - 核酸相互作用。
