Recognition of RNA secondary structures with a programmable peptide nucleic acid-based platform

• Main Authors: Lu, Rongguang, Deng, Liping, Lian, Yun, Ke, Xin, Yang, Lixia, Xi, Kun, Ong, Alan Ann Lerk, Chen, Yanyu, Zhou, Hanting, Meng, Zhenyu, Lin, Ruiyu, Fan, Shijian, Liu, Yining, Toh, Desiree-Faye Kaixin, Zhan, Xuan, Krishna, Manchugondanahalli S., Patil, Kiran M., Lu, Yunpeng, Liu, Zheng, Zhu, Lizhe, Wang, Hongwei, Li, Guobao, Chen, Gang
• Other Authors: School of Physical and Mathematical Sciences
• Format: Article
• Language: English
• Published: 2024
• Subjects: Chemistry; Double-stranded RNA; miRNA precursor
• Online Access: https://hdl.handle.net/10356/181785
• Institution: Nanyang Technological University

RNA secondary structures comprise double-stranded (ds) and single-stranded (ss) regions. Antisense peptide nucleic acids (asPNAs) enable the targeting of ssRNAs and weakly formed dsRNAs. Nucleobase-modified dsRNA-binding PNAs (dbPNAs) allow for dsRNA targeting. A programmable RNA-structure-specific targeting strategy is needed for the simultaneous recognition of dsRNAs and ssRNAs. Here, we report on combining dbPNAs and asPNAs (designated as daPNAs) for the targeting of dsRNA-ssRNA junctions. Our data suggest that combining traditional asPNA (with a 4-letter code: T, C, A, and G) and dbPNA (with a 4-letter code: T or s2U, L, Q, and E) scaffolds facilitates RNA-structure-specific tight binding (nM to μM). We further apply our daPNAs in substrate-specific inhibition of Dicer acting on precursor miRNA (pre-miR)-198 in a cell-free assay and regulating ribosomal frameshifting induced by model hairpins in both cell-free and cell culture assays. daPNAs would be a useful platform for developing chemical probes and therapeutic ligands targeting RNA.