Cyano Modification on Uridine Decreases Base-Pairing Stability and Specificity through Neighboring Disruption in RNA Duplex
Cyano Modification on Uridine Decreases Base-Pairing Stability and Specificity through Neighboring Disruption in RNA Duplex
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尿苷的氰基修饰通过 RNA 双链体中的相邻破坏降低碱基配对的稳定性和特异性
DOI：
10.1002/cbic.201800399
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发表时间：
2018
期刊：
影响因子：
3.2
通讯作者：
Sheng, Jia
中科院分区：
文献类型：
--
作者：
Mao, Song;Ranganathan, Srivathsan V.;Tsai, Hsu-Chun;Haruehanroengra, Phensinee;Shen, Fusheng;Valsangkar, Vibhav A.;Han, Bo;Hassan, Abdalla E.;Chen, Alan;Sheng, Jia
合成了两种尿苷类似物5-氰基甲基尿苷（cnm 5 U）和5-氰基尿苷（cn 5 U），并将其掺入RNA寡核苷酸中。RNA双链体的碱基配对稳定性和特异性研究表明，cnm 5 U略微降低了双链体的稳定性，但保留了碱基配对偏好。相比之下，cn 5 U显著降低了U：A与其他非经典U：G、U：U和U：C对之间的碱基配对稳定性和特异性。此外，在RNA双链体的情况下，发现cn 5 U：G对比cn 5 U：A对和其他错配对更强;这意味着cn 5 U可能比A稍微更喜欢识别G。我们通过分子模拟的机制研究表明，cn 5 U修饰并不直接影响亲本核苷酸的碱基配对;相反，它削弱了RNA双链体中修饰的5′侧的相邻碱基对。 与模拟数据一致，在5′相邻位点将Watson-Crick A：U对替换为错配的C：U对不会影响双链体的总体稳定性。我们的工作揭示了吸电子氰基在天然tRNA系统中的重要性，并为构建基于RNA的疗法提供了两个新的构建模块。
5‐Cyanomethyluridine (cnm5U) and 5‐cyanouridine (cn5U), the two uridine analogues, were synthesized and incorporated into RNA oligonucleotides. Base‐pairing stability and specificity studies in RNA duplexes indicated that cnm5U slightly decreased the stability of the duplex but retained the base‐pairing preference. In contrast, cn5U dramatically decreased both base‐pairing stability and specificity between U:A and other noncanonical U:G, U:U, and U:C pairs. In addition, the cn5U:G pair was found to be stronger than the cn5U:A pair and the other mismatched pairs in the context of a RNA duplex; this implied that cn5U might slightly prefer to recognize G over A. Our mechanistic studies by molecular simulations showed that the cn5U modification did not directly affect the base pairing of the parent nucleotide; instead, it weakened the neighboring base pair in the 5′ side of the modification in the RNA duplexes. Consistent with the simulation data, replacing the Watson–Crick A:U pair to a mismatched C:U pair in the 5′‐neighboring site did not affect the overall stability of the duplex. Our work reveals the significance of the electron‐withdrawing cyano group in natural tRNA systems and provides two novel building blocks for constructing RNA‐based therapeutics.