Effect of a water molecule on the sugar puckering of uridine, 2'-deoxyuridine, and 2'-O-methyl uridine inserted in duplexes

The Journal of Physical Chemistry. a
Sophie Barbe, Marc Le Bret

Abstract

We used high-level quantum mechanical calculations to determine the pucker (north type or south type) of various compounds: uridine, 2'-deoxyuridine, and 2'-O-methyl uridine. Although the dihedrals of the backbone are set close to their experimental values in double-stranded nucleic acids, calculations using density functional theory show that, in vacuo or in a continuum mimicking the dielectric properties of water, the south puckering conformations of uridine is favored. This contrasts with experimental data: most ribonucleosides inserted into a duplex have the north puckering. We show here that the north puckering is favored when an explicit water molecule is introduced into the calculation. The orientations of the 2' group and of the water molecule have implications for the prevalence of the north puckering. We studied several orientations of the water molecule binding uracil O2 and the 2' group and estimated the energy barriers in the path between the north-to-south conformations. The north puckering is more favored in 2'-OH than in 2'-OCH3 compounds in the presence of the explicit water molecule.

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Citations

Apr 8, 2011·Journal of the American Society for Mass Spectrometry·Adrien NyakasStefan Schürch
Feb 4, 2016·Journal of Computational Chemistry·You XuLennart Nilsson
Dec 1, 2010·Physical Chemistry Chemical Physics : PCCP·Matthew J TuckerRobin M Hochstrasser
Apr 2, 2010·Physical Chemistry Chemical Physics : PCCP·Ru bo Zhang, Leif A Eriksson
Aug 23, 2019·Journal of the American Society for Mass Spectrometry·C C HeM T Rodgers
Aug 16, 2011·Physical Chemistry Chemical Physics : PCCP·Cassandra D M Churchill, Stacey D Wetmore
Dec 31, 2009·The Journal of Physical Chemistry. B·Jennifer L Przybylski, Stacey D Wetmore
Apr 11, 2009·The Journal of Physical Chemistry. B·Jennifer L Przybylski, Stacey D Wetmore
Jan 30, 2010·The Journal of Physical Chemistry. B·Yoshiaki MasakiMitsuo Sekine

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