基于形状的化学探针研究活菌中preQ1-RNA相互作用

IF 3.8 2区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY
José A Reyes Franceschi, Emilio L Cárdenas, Brandon J C Klein, Chase A Weidmann, Amanda L Garner
{"title":"基于形状的化学探针研究活菌中preQ1-RNA相互作用","authors":"José A Reyes Franceschi, Emilio L Cárdenas, Brandon J C Klein, Chase A Weidmann, Amanda L Garner","doi":"10.1021/acschembio.5c00548","DOIUrl":null,"url":null,"abstract":"<p><p>Interrogating RNA-small molecule interactions inside cells is critical for advancing RNA-targeted drug discovery. In particular, chemical probing technologies that both identify small molecule-bound RNAs and define their binding sites in the complex cellular environment will be key to establishing the on-target activity necessary for successful hit-to-lead campaigns. Using the small molecule metabolite preQ<sub>1</sub> and its cognate riboswitch RNA as a model, herein we describe a chemical probing strategy for filling this technological gap. Building on well-established RNA acylation chemistry employed by <i>in vivo</i> click-selective 2'-hydroxyl acylation analyzed by primer extension (icSHAPE) probes, we developed an icSHAPE-based preQ<sub>1</sub> probe that retains biological activity in a preQ<sub>1</sub> riboswitch reporter assay and successfully enriches the preQ<sub>1</sub> riboswitch from living bacterial cells. Further, we map the preQ<sub>1</sub> binding site on probe-modified riboswitch RNA by mutational profiling (MaP). As the need for rapid profiling of on- and off-target small molecule interactions continues to grow, this chemical probing strategy offers a method to interrogate cellular RNA-small molecule interactions and supports the future development of RNA-targeted therapeutics.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.8000,"publicationDate":"2025-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"SHAPE-Based Chemical Probes for Studying preQ<sub>1</sub>-RNA Interactions in Living Bacteria.\",\"authors\":\"José A Reyes Franceschi, Emilio L Cárdenas, Brandon J C Klein, Chase A Weidmann, Amanda L Garner\",\"doi\":\"10.1021/acschembio.5c00548\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Interrogating RNA-small molecule interactions inside cells is critical for advancing RNA-targeted drug discovery. In particular, chemical probing technologies that both identify small molecule-bound RNAs and define their binding sites in the complex cellular environment will be key to establishing the on-target activity necessary for successful hit-to-lead campaigns. Using the small molecule metabolite preQ<sub>1</sub> and its cognate riboswitch RNA as a model, herein we describe a chemical probing strategy for filling this technological gap. Building on well-established RNA acylation chemistry employed by <i>in vivo</i> click-selective 2'-hydroxyl acylation analyzed by primer extension (icSHAPE) probes, we developed an icSHAPE-based preQ<sub>1</sub> probe that retains biological activity in a preQ<sub>1</sub> riboswitch reporter assay and successfully enriches the preQ<sub>1</sub> riboswitch from living bacterial cells. Further, we map the preQ<sub>1</sub> binding site on probe-modified riboswitch RNA by mutational profiling (MaP). As the need for rapid profiling of on- and off-target small molecule interactions continues to grow, this chemical probing strategy offers a method to interrogate cellular RNA-small molecule interactions and supports the future development of RNA-targeted therapeutics.</p>\",\"PeriodicalId\":11,\"journal\":{\"name\":\"ACS Chemical Biology\",\"volume\":\" \",\"pages\":\"\"},\"PeriodicalIF\":3.8000,\"publicationDate\":\"2025-10-10\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"ACS Chemical Biology\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1021/acschembio.5c00548\",\"RegionNum\":2,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"BIOCHEMISTRY & MOLECULAR BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"ACS Chemical Biology","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1021/acschembio.5c00548","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
引用次数: 0

摘要

探究细胞内rna与小分子的相互作用对于推进rna靶向药物的发现至关重要。特别是,化学探测技术既能识别小分子结合rna,又能在复杂的细胞环境中定义它们的结合位点,这将是建立成功的靶向靶向活动的关键。利用小分子代谢物preQ1及其同源核糖开关RNA作为模型,我们描述了一种化学探测策略来填补这一技术空白。利用引物延伸(icSHAPE)探针分析体内点击选择性2'-羟基酰化的RNA酰化化学,我们开发了一种基于icSHAPE的preQ1探针,该探针在preQ1核糖开关报告实验中保留了生物活性,并成功地富集了活细菌细胞中的preQ1核糖开关。此外,我们通过突变谱(map)绘制了探针修饰的核糖开关RNA上的preQ1结合位点。随着对靶向和脱靶小分子相互作用快速分析的需求不断增长,这种化学探测策略提供了一种询问细胞rna -小分子相互作用的方法,并支持rna靶向治疗的未来发展。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
SHAPE-Based Chemical Probes for Studying preQ1-RNA Interactions in Living Bacteria.

Interrogating RNA-small molecule interactions inside cells is critical for advancing RNA-targeted drug discovery. In particular, chemical probing technologies that both identify small molecule-bound RNAs and define their binding sites in the complex cellular environment will be key to establishing the on-target activity necessary for successful hit-to-lead campaigns. Using the small molecule metabolite preQ1 and its cognate riboswitch RNA as a model, herein we describe a chemical probing strategy for filling this technological gap. Building on well-established RNA acylation chemistry employed by in vivo click-selective 2'-hydroxyl acylation analyzed by primer extension (icSHAPE) probes, we developed an icSHAPE-based preQ1 probe that retains biological activity in a preQ1 riboswitch reporter assay and successfully enriches the preQ1 riboswitch from living bacterial cells. Further, we map the preQ1 binding site on probe-modified riboswitch RNA by mutational profiling (MaP). As the need for rapid profiling of on- and off-target small molecule interactions continues to grow, this chemical probing strategy offers a method to interrogate cellular RNA-small molecule interactions and supports the future development of RNA-targeted therapeutics.

求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
来源期刊
ACS Chemical Biology
ACS Chemical Biology 生物-生化与分子生物学
CiteScore
7.50
自引率
5.00%
发文量
353
审稿时长
3.3 months
期刊介绍: ACS Chemical Biology provides an international forum for the rapid communication of research that broadly embraces the interface between chemistry and biology. The journal also serves as a forum to facilitate the communication between biologists and chemists that will translate into new research opportunities and discoveries. Results will be published in which molecular reasoning has been used to probe questions through in vitro investigations, cell biological methods, or organismic studies. We welcome mechanistic studies on proteins, nucleic acids, sugars, lipids, and nonbiological polymers. The journal serves a large scientific community, exploring cellular function from both chemical and biological perspectives. It is understood that submitted work is based upon original results and has not been published previously.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:604180095
Book学术官方微信