NTU Institute for Health Technologies (HeathTech NTU), Interdisciplinary Graduate School , Nanyang Technological University , 50 Nanyang Drive , Singapore 637553.
Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371.
Biochemistry. 2019 Mar 12;58(10):1319-1331. doi: 10.1021/acs.biochem.8b01313. Epub 2019 Mar 1.
Chemically modified peptide nucleic acids (PNAs) show great promise in the recognition of RNA duplexes by major-groove PNA·RNA-RNA triplex formation. Triplex formation is favored for RNA duplexes with a purine tract within one of the RNA duplex strands, and is severely destabilized if the purine tract is interrupted by pyrimidine residues. Here, we report the synthesis of a PNA monomer incorporated with an artificial nucleobase S, followed by the binding studies of a series of S-modified PNAs. Our data suggest that an S residue incorporated into short 8-mer dsRNA-binding PNAs (dbPNAs) can recognize internal Watson-Crick C-G and U-A, and wobble U-G base pairs (but not G-C, A-U, and G-U pairs) in RNA duplexes. The short S-modified PNAs show no appreciable binding to DNA duplexes or single-stranded RNAs. Interestingly, replacement of the C residue in an S·C-G triple with a 5-methyl C results in the disruption of the triplex, probably due to a steric clash between S and 5-methyl C. Previously reported PNA E base shows recognition of U-A and A-U pairs, but not a U-G pair. Thus, S-modified dbPNAs may be uniquely useful for the general recognition of RNA U-G, U-A, and C-G pairs. Shortening the succinyl linker of our PNA S monomer by one carbon atom to have a malonyl linker causes a severe destabilization of triplex formation. Our experimental and modeling data indicate that part of the succinyl moiety in a PNA S monomer may serve to expand the S base forming stacking interactions with adjacent PNA bases.
化学修饰的肽核酸（PNA）在通过主沟 PNA·RNA-RNA 三聚体形成识别 RNA 双链方面显示出巨大的应用前景。三聚体的形成有利于 RNA 双链中一条 RNA 双链链上存在嘌呤链，并且如果嘌呤链被嘧啶残基打断，则会严重失稳。在这里，我们报告了一种带有人工碱基 S 的 PNA 单体的合成，随后对一系列 S 修饰的 PNA 进行了结合研究。我们的数据表明，掺入短 8 聚体 dsRNA 结合 PNA（dbPNA）中的 S 残基可以识别 RNA 双链中的内部 Watson-Crick C-G 和 U-A，以及摆动 U-G 碱基对（但不是 G-C、A-U 和 G-U 对）。短 S 修饰的 PNA 对 DNA 双链或单链 RNA 没有明显的结合。有趣的是，用 5-甲基 C 替换 S·C-G 三螺旋中的 C 残基会破坏三螺旋，可能是由于 S 和 5-甲基 C 之间的空间位阻。先前报道的 PNA E 碱基显示出对 U-A 和 A-U 对的识别，但不对 U-G 对。因此，S 修饰的 dbPNA 可能特别有助于对 RNA U-G、U-A 和 C-G 对的一般识别。将我们的 PNA S 单体中的琥珀酰基连接体缩短一个碳原子以形成丙二酰基连接体，会导致三聚体形成严重失稳。我们的实验和建模数据表明，PNA S 单体中的琥珀酰基部分可能有助于 S 碱基展开堆积相互作用与相邻的 PNA 碱基。
