Unique structural and stabilizing roles for the individual pseudouridine residues in the 1920 region of Escherichia coli 23S rRNA.

Meroueh M, Grohar PJ, Qiu J, SantaLucia J, Scaringe SA, Chow CS
Nucleic Acids Res. 2000 28 (10): 2075-83

PMID: 10773075 · PMCID: PMC105375 · DOI:10.1093/nar/28.10.2075

The synthesis of a 5'-O-BzH-2'- O -ACE-protected pseudouridine phosphoramidite is reported [BzH, benzhydryloxy-bis(trimethylsilyloxy)silyl; ACE, bis(2-acetoxyethoxy)methyl]. The availability of the phosphoramidite allows for reliable and efficient syntheses of hairpin RNAs containing single or multiple pseudouridine modifications in the stem or loop regions. Five 19-nt hairpin RNAs representing the 1920-loop region (G(1906)-C(1924)) of Escherichia coli 23S rRNA were synthesized with pseudouridine residues located at positions 1911, 1915 and 1917. Thermodynamic parameters, circular dichroism spectra and NMR data are presented for all five RNAs. Overall, three different structural contexts for the pseudouridine residues were examined and compared with the unmodified RNA. Our main findings are that pseudouridine modifications exhibit a range of effects on RNA stability and structure, depending on their locations. More specifically, pseudouridines in the single-stranded loop regions of the model RNAs are slightly destabilizing, whereas a pseudo-uridine at the stem-loop junction is stabilizing. Furthermore, the observed effects on stability are approximately additive when multiple pseudouridine residues are present. The possible relationship of these results to RNA function is discussed.

MeSH Terms (12)

Base Sequence Circular Dichroism Escherichia coli Models, Molecular Nuclear Magnetic Resonance, Biomolecular Nucleic Acid Conformation Oligoribonucleotides Organophosphorus Compounds Pseudouridine RNA, Bacterial RNA, Ribosomal, 23S Thermodynamics

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