Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
Nucleic Acids Res. 2010 Jul;38(13):4458-65. doi: 10.1093/nar/gkq159. Epub 2010 Mar 9.
Oligonucleotide models of ribosomal RNA domains are powerful tools to study the binding and molecular recognition of antibiotics that interfere with bacterial translation. Techniques such as selective chemical modification, fluorescence labeling and mutations are cumbersome for the whole ribosome but readily applicable to model RNAs, which are readily crystallized and often give rise to higher resolution crystal structures suitable for detailed analysis of ligand-RNA interactions. Here, we have investigated the HX RNA construct which contains two adjacent ligand binding regions of helix h44 in 16S ribosomal RNA. High-resolution crystal structure analysis confirmed that the HX RNA is a faithful structural model of the ribosomal target. Solution studies showed that HX RNA carrying a fluorescent 2-aminopurine modification provides a model system that can be used to monitor ligand binding to both the ribosomal decoding site and, through an indirect effect, the hygromycin B interaction region.
寡核苷酸核糖体 RNA 结构域模型是研究与细菌翻译过程干扰的抗生素结合和分子识别的有力工具。对于整个核糖体来说，选择性化学修饰、荧光标记和突变等技术很繁琐，但很容易应用于模型 RNA，这些 RNA 很容易结晶，并且通常会产生更高分辨率的晶体结构，适合于详细分析配体-RNA 相互作用。在这里，我们研究了 HX RNA 构建体，它包含了 16S 核糖体 RNA 中 h44 螺旋的两个相邻配体结合区。高分辨率晶体结构分析证实，HX RNA 是核糖体靶标的忠实结构模型。溶液研究表明，携带荧光 2-氨基嘌呤修饰的 HX RNA 提供了一个模型系统，可用于监测与核糖体解码位点的结合，并且通过间接效应，监测潮霉素 B 相互作用区域。
