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

RNA介导的基因调控和核糖开关从头设计的结构基础：合成新霉素感应核糖开关的例子

• 批准号: 127262111
• 负责人: Professorin Dr. Beatrix Süß
• 金额: --
• 依托单位: Institut für Molekulare Biowissenschaften
• 依托单位国家: 德国
• 项目类别: Research Grants
• 财政年份: 2009
• 资助国家: 德国
• 起止时间: 2008-12-31 至 2014-12-31
• 项目状态: 已结题
• 来源: https://gepris.dfg.de/gepris/projekt/127262111?language=en
• 关键词: structural; basis; RNA; mediated; gene

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.

合成新霉素感应核糖开关是最小的核糖开关，迄今为止描述的体内活性。将33个核元素插入mRNA的5'-非翻译区域，导致配体结合后基因表达的有效下调。通过结合遗传学，生化和NMR-谱镜技术，我们将阐明该遗传转换调节机制的结构和分子基础。对于我们的研究，我们不仅将使用功能性核糖开关RNA。此外，我们发现结构相似的RNA保留了结合新霉素的能力，但不再是与新霉素相关的调节性和氨基糖苷，这些氨基霉素仍然与具有高亲和力的核糖开关结合，但RNA结合并不导致基因表达的调节。这些变体的比较分析将产生该核糖开关调节活性的分子确定因素的详细图片，以及基于理性结构优化的起点和核糖开关的从头设计。

项目成果

Sequence Elements Distal to the Ligand Binding Pocket Modulate the Efficiency of a Synthetic Riboswitch

• DOI: 10.1002/cbic.201402067
• 发表时间: 2014-07
• 期刊: ChemBioChem
• 影响因子: 3.2
• 作者: J. Weigand;Sina R. Gottstein‐Schmidtke;Shemsi Demolli;Florian Groher;E. Duchardt-Ferner;J. Wöhnert;B. Suess

Building a stable RNA U-turn with a protonated cytidine

• DOI: 10.1261/rna.043083.113
• 发表时间: 2014-08-01
• 期刊: RNA
• 影响因子: 4.5
• 作者: Gottstein-Schmidtke, Sina R.;Duchardt-Ferner, Elke;Woehnert, Jens
• 通讯作者: Woehnert, Jens