General recognition of U‑G, U‑A, and C‑G pairs by double-stranded RNA-binding PNAs incorporated with an artificial nucleobase

• Main Authors: Ong, Alan Ann Lerk, Toh, Desiree-Faye Kaixin, Patil, Kiran M., Meng, Zhenyu, Yuan, Zhen, Krishna, Manchugondanahalli S., Devi, Gitali, Haruehanroengra, Phensinee, Lu, Yunpeng, Xia, Kelin, Okamura, Katsutomo, Sheng, Jia, Chen, Gang
• Other Authors: Interdisciplinary Graduate School (IGS)
• Format: Article
• Language: English
• Published: 2021
• Subjects: Science::Biological sciences; Peptide Nucleic-acids; Triplex-forming Oligonucleotides
• Online Access: https://hdl.handle.net/10356/151002
• Institution: Nanyang Technological University

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.