Qin Peter Z, Iseri Jennifer, Oki Arisa
Department of Chemistry, University of Southern California, Los Angeles, CA 90089-0744, USA.
Biochem Biophys Res Commun. 2006 Apr 28;343(1):117-24. doi: 10.1016/j.bbrc.2006.02.138. Epub 2006 Mar 3.
In RNA site-directed spin labeling (SDSL) studies, structural and dynamic information at the individual RNA nucleotide level is derived from the observed electron paramagnetic resonance spectrum of a covalently attached nitroxide. A systematic approach for RNA SDSL is to establish a library that categorizes observed spectral lineshapes based on known RNA structures, thus enabling lineshape-based structure identification at any RNA site. To establish the first RNA SDSL library, selective secondary structure elements have been systematically engineered into a model RNA. Nitroxide lineshapes reporting features specific to each element were obtained utilizing a new avidin-tethering scheme for suppressing spectral effects due to uniform RNA tumbling. The data demonstrated two key features required for a SDSL library with a predicting power: (i) spectral divergence--distinctive lineshape for different elements; and (ii) spectral convergence--similar lineshape for the same element in different contexts. This sets the foundation for further RNA SDSL library development.
在RNA定点自旋标记（SDSL）研究中，单个RNA核苷酸水平的结构和动力学信息来自于共价连接的氮氧化物的观测电子顺磁共振谱。RNA SDSL的一种系统方法是建立一个库，该库根据已知的RNA结构对观测到的光谱线形进行分类，从而能够在任何RNA位点进行基于线形的结构识别。为了建立第一个RNA SDSL库，已将选择性二级结构元件系统地工程化到一个模型RNA中。利用一种新的抗生物素蛋白连接方案抑制由于RNA均匀翻滚引起的光谱效应，获得了报告每个元件特异性特征的氮氧化物线形。数据证明了具有预测能力的SDSL库所需的两个关键特征：（i）光谱发散——不同元件的独特线形；（ii）光谱收敛——同一元件在不同背景下的相似线形。这为进一步开发RNA SDSL库奠定了基础。
