Saon Md Sharear, Douds Catherine A, Veenis Andrew J, Pearson Ashley N, Yennawar Neela H, Bevilacqua Philip C
bioRxiv. 2025 Jan 2:2024.12.31.630957. doi: 10.1101/2024.12.31.630957.
RNA can serve as an enzyme, small molecule sensor, and vaccine, and it may have been a conduit for the origin of life. Despite these profound functions, RNA is thought to have quite limited molecular diversity. A pressing question, therefore, is whether RNA can adopt novel molecular states that enhance its function. Covalent modifications of RNA have been demonstrated to augment biological function, but much less is known about non-covalent alterations such as novel protonated or tautomeric forms. Conventionally, a G•U wobble has the U shifted into the major groove. We used a cheminformatic approach to identify four structural families of shifted G•U wobbles in which the G instead resides in the major groove of RNA, which requires alternative tautomeric states of either base, or an anionic state of the U. We provide experimental support for these shifted G•U wobbles via the potent, and unconventional, reactivity of the U with dimethylsulfate (DMS) in three organisms. These shifted wobbles may play important functional roles and could serve as drug targets. Our cheminformatics approach is general and can be applied to identify alternative protonation states in other RNA motifs, as well as in DNA and proteins.
RNA可作为一种酶、小分子传感器和疫苗，它可能是生命起源的一个渠道。尽管具有这些重要功能，但人们认为RNA的分子多样性相当有限。因此，一个紧迫的问题是RNA是否能呈现出增强其功能的新分子状态。RNA的共价修饰已被证明可增强生物学功能，但对于非共价改变，如新型质子化或互变异构形式，人们了解得要少得多。传统上，G•U摆动碱基对中U会移至大沟中。我们采用化学信息学方法，识别出了四种移位G•U摆动碱基对的结构家族，其中G反而位于RNA的大沟中，这需要碱基处于互变异构状态，或者U处于阴离子状态。我们通过在三种生物体中U与硫酸二甲酯（DMS）发生的强效且非常规的反应，为这些移位G•U摆动碱基对提供了实验支持。这些移位摆动碱基对可能发挥重要的功能作用，并可作为药物靶点。我们的化学信息学方法具有通用性，可用于识别其他RNA基序以及DNA和蛋白质中的替代质子化状态。
