Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371.
Temasek Life Science Laboratory, 1 Research Link, National University of Singapore , Singapore 117604.
Biochemistry. 2019 Sep 10;58(36):3777-3788. doi: 10.1021/acs.biochem.9b00608. Epub 2019 Aug 28.
Recognition of RNAs under physiological conditions is important for the development of chemical probes and therapeutic ligands. Nucleobase-modified dsRNA-binding PNAs (dbPNAs) are promising for the recognition of dsRNAs in a sequence and structure specific manner under near-physiological conditions. Guanidinium is often present in proteins and small molecules for the recognition of G bases in nucleic acids, in cell-penetrating carriers, and in bioactive drug molecules, which might be due to the fact that guanidinium is amphiphilic and has unique hydrogen bonding and stacking properties. We hypothesized that a simple guanidinium moiety can be directly incorporated into PNAs to facilitate enhanced molecular recognition of G-C pairs in dsRNAs and improved bioactivity. We grafted a guanidinium moiety directly into a PNA monomer (designated as R) using a two-carbon linker as guided by computational modeling studies. The synthetic scheme of the PNA R monomer is relatively simple compared to that of the previously reported L monomer. We incorporated the R residue into various dbPNAs for binding studies. dbPNAs incorporated with R residues are excellent in sequence specifically recognizing G-C pairs in dsRNAs over dsDNA and ssRNAs. We demonstrated that the R residue is compatible with unmodified T and C and previously developed modified L and Q residues in dbPNAs for targeting model dsRNAs, the influenza A viral panhandle duplex structure, and the HIV-1 frameshift site RNA hairpin. Furthermore, R residues enhance the cellular uptake of PNAs.
在生理条件下识别 RNA 对于化学探针和治疗配体的开发非常重要。在接近生理条件下，核苷碱基修饰的双链 RNA 结合肽核酸（dbPNA）以序列和结构特异性的方式识别双链 RNA，具有很大的应用潜力。胍基通常存在于蛋白质和小分子中，用于识别核酸中的 G 碱基，在细胞穿透载体和生物活性药物分子中也是如此，这可能是因为胍基具有两亲性，并且具有独特的氢键和堆积性质。我们假设可以将简单的胍基部分直接掺入 PNA 中，以促进对双链 RNA 中 G-C 对的增强分子识别并提高生物活性。我们使用双碳链接，根据计算建模研究的指导，直接将胍基部分接枝到 PNA 单体（指定为 R）上。与之前报道的 L 单体相比，PNA R 单体的合成方案相对简单。我们将 R 残基掺入各种 dbPNA 中进行结合研究。与 dsDNA 和 ssRNA 相比，掺入 R 残基的 dbPNA 非常出色地在序列特异性上识别双链 RNA 中的 G-C 对。我们证明，R 残基与未修饰的 T 和 C 以及 dbPNA 中以前开发的修饰 L 和 Q 残基兼容，可用于靶向模型 dsRNA、甲型流感病毒柄状双链结构和 HIV-1 框架移位位点 RNA 发夹。此外，R 残基增强了 PNA 的细胞摄取。
