期刊
BIOCHEMISTRY
卷 58, 期 10, 页码 1319-1331出版社
AMER CHEMICAL SOC
DOI: 10.1021/acs.biochem.8b01313
关键词
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资金
- NTU start-up grant
- Singapore Ministry of Education (MOE) Tier 1 grants [RGT3/13, RG42/15, RG152/17]
- MOE Tier 2 grants [MOE2013-T2-2-024, MOE2015-T2-1-028]
- MOE Tier 1 [RG126/16, RG31/18]
- MOE Tier 2 [MOE2018-T2-1-033]
Chemically modified peptide nucleic acids (PNAs) show great promise in the recognition of RNA duplexes by major-groove PNA center dot 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 SC-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.
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