Solution structures of 5-fluorouracil-substituted RNA duplexes containing G-U wobble base pairs

Biochemistry
P V Sahasrabudhe, W H Gmeiner

Abstract

The structures and stabilities of three RNA duplexes that differed only in the position of 5-fluorouridine (FUrd) substitution were elucidated using NMR spectroscopy and UV hyperchromicity studies to determine if FUrd substitution altered the structure or stability of RNA duplexes that contained G-U base pairs. The duplexes investigated corresponded to the region of the U4-U6 snRNA complex that contained the 5' terminus of U4 snRNA. The control duplex contained a G-U wobble base pair and also a G-A mismatched base pair. FUrd was substituted in one duplex at the G-U wobble base pair and in the second duplex at an A-U base pair adjacent to the wobble base pair. FUrd substitution slightly destabilized the duplex that contained a G-FU base pair but stabilized the duplex that contained an A-FU base pair. NOESY spectra were used to determine interproton distances, and these distance constraints were used in a restrained molecular dynamics protocol to determine the three-dimensional structures of these RNA duplexes. Analyses of helical parameters, backbone torsion angles, and rms deviations between the final structures revealed no systematic differences due to FUrd substitution in RNA duplexes that contained G-U base pairs. The G-FU b...Continue Reading

Citations

May 8, 2000·Journal of Biomolecular Structure & Dynamics·J R Arnold, J Fisher
Jun 10, 1998·Nucleic Acids Research·W H GmeinerJ Liu
Oct 5, 2002·Nucleic Acids Research·Mikołaj OlejniczakRyszard W Adamiak
May 7, 2002·Nucleosides, Nucleotides & Nucleic Acids·Wei Cui, William H Gmeiner
Feb 9, 2012·Chemical Research in Toxicology·Hai HuangMichael P Stone
Jun 2, 2015·Chemical Communications : Chem Comm·Shigetaka Nakamura, Kenzo Fujimoto
Aug 6, 2020·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·William H Gmeiner
Nov 10, 2007·Journal of the American Chemical Society·Mirko HennigJames R Williamson
Apr 3, 2018·The Journal of Physical Chemistry. B·Saeed K Amini

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