The structural basis for RNA-mediated gene regulation and for the de novo design of riboswitches: The example of the synthetic neomycin-sensing riboswitch

合成的新霉素感应核糖开关是迄今为止描述的最小的具有体内活性的核糖开关。将含有rna元件的33个核苷酸插入到mRNA的5 '非翻译区，可在结合配体时有效下调基因表达。结合遗传学、生物化学和核磁共振光谱技术，我们将阐明这种基因开关的结构和调控机制的分子基础。在我们的研究中，我们将不仅仅使用功能性核糖开关RNA。此外，我们还发现了结构相似的RNA，它们保留了结合新霉素的能力，但不再具有调节活性，以及与新霉素相关的氨基糖苷，它们仍然以高亲和力结合核糖体开关，但RNA结合不会导致基因表达的调节。这些变异的比较分析将产生一个详细的画面的分子决定因素的调节活性的核蛋白开关，以及一个合理的结构优化和核蛋白开关的从头设计的起点。

The synthetic neomycin-sensing riboswitch is the smallest riboswitch with in vivo activity described to date. The insertion of this 33 nucleotide containing RNA-element into the 5’-untranslated region of an mRNA leads to an efficient down-regulation of gene expression upon binding of the ligand. By combining genetic, biochemical and NMR-spectroscopic techniques we will elucidate the structure and the molecular basis for the regulatory mechanism of this genetic switch. For our studies we will not only use the functional riboswitch RNA. In addition, we found structurally similar RNAs which retained the ability to bind neomycin but are no longer regulatory active as well as aminoglycosides related to neomycin which still bind to the riboswitch with high affinity but where RNA binding does not result in the regulation of gene expression. The comparative analysis of these variants will yield a detailed picture of the molecular determinants of the regulatory activity of this riboswitch as well as starting points for a rational structure based optimization and the de novo design of riboswitches.