Talbott John M, Tessier Brandon R, Harding Emily E, Walby Grant D, Hess Kyle J, Baskevics Vladislavs, Katkevics Martins, Rozners Eriks, MacKay James A
Department of Chemistry and Biochemistry, Elizabethtown College, Elizabethtown, PA 17022, USA.
Department of Chemistry, Binghamton University, Binghamton, NY 13902, USA.
Chemistry. 2023 Nov 16;29(64):e202302390. doi: 10.1002/chem.202302390. Epub 2023 Oct 2.
Four new isoorotamide (Io)-containing PNA nucleobases have been designed for A-U recognition of double helical RNA. New PNA monomers were prepared efficiently and incorporated into PNA nonamers for binding A-U in a PNA:RNA triplex. Isothermal titration calorimetry and UV thermal melting experiments revealed slightly improved binding affinity for singly modified PNA compared to known A-binding nucleobases. Molecular dynamics simulations provided further insights into binding of Io bases in the triple helix. Together, the data revealed interesting insights into binding modes including the notion that three Hoogsteen hydrogen bonds are unnecessary for strong selective binding of an extended nucleobase. Cationic monomer Io8 additionally gave the highest affinity observed for an A-binding nucleobase to date. These results will help inform future nucleobase design toward the goal of recognizing any sequence of double helical RNA.
为了实现对双螺旋RNA中A-U碱基对的识别，设计了四种含新异罗他胺（Io）的肽核酸（PNA）核碱基。新型PNA单体被高效合成，并被并入PNA九聚体中，用于在PNA:RNA三链体中结合A-U碱基对。等温滴定量热法和紫外热变性实验表明，与已知的A结合核碱基相比，单修饰PNA的结合亲和力略有提高。分子动力学模拟进一步深入了解了Io碱基在三链螺旋中的结合情况。综合这些数据，揭示了关于结合模式的有趣见解，包括对于一个延伸核碱基的强选择性结合而言，三个Hoogsteen氢键并非必需这一观点。阳离子单体Io8还给出了迄今为止所观察到的A结合核碱基的最高亲和力。这些结果将有助于为未来的核碱基设计提供参考，以实现识别双螺旋RNA任何序列的目标。
