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Title: General recognition of U‑G, U‑A, and C‑G pairs by double-stranded RNA-binding PNAs incorporated with an artificial nucleobase
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
Keywords: Science::Biological sciences
Issue Date: 2019
Source: Ong, A. A. L., Toh, D. K., Patil, K. M., Meng, Z., Yuan, Z., Krishna, M. S., Devi, G., Haruehanroengra, P., Lu, Y., Xia, K., Okamura, K., Sheng, J. & Chen, G. (2019). General recognition of U‑G, U‑A, and C‑G pairs by double-stranded RNA-binding PNAs incorporated with an artificial nucleobase. Biochemistry, 58(10), 1319-1331.
Project: RGT3/13
Journal: Biochemistry
Abstract: 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.
ISSN: 0006-2960
DOI: 10.1021/acs.biochem.8b01313
Rights: © 2019 American Chemical Society. All rights reserved.
Fulltext Permission: none
Fulltext Availability: No Fulltext
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