NMR structure of a 2',5' RNA favors A type duplex with compact C2'endo nucleotide repeat

Biochemical and Biophysical Research Communications
B J PremrajN Yathindra

Abstract

In order to provide a structural basis for the unusual properties of 2',5' nucleic acids, especially their unsuitability as information molecules, we report here a high resolution NMR structure of a 2',5' RNA fragment r(GCCGCGGC). It forms an A type duplex with C2'endo compact nucleotide repeat, instead of the familiar C3'endo compact nucleotide (seen in RNA) supporting the deductions made earlier from stereochemical considerations. This data together with the observation that 2',5' nucleic acids require mandatory slide and displacement for duplex and triplex structure formation suggest their reluctance to form the biologically relevant B type duplex. It is argued that this lack of flexibility for helical polymorphism and other inadequacies as a consequence of this may be a contributing factor for the rejection of 2',5' links by nature. The structure exhibits interesting features such as the syn glycosyl conformation for the terminal guanine and a hydrogen bond between O3' hydroxyl and anionic oxygen of the phosphate.

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Citations

Feb 18, 2009·Journal of the American Chemical Society·Jason N Pitt, Adrian R Ferré-D'Amaré
Jan 28, 2006·Nucleosides, Nucleotides & Nucleic Acids·Rami N Hannoush, Masad J Damha
Feb 12, 2014·Proceedings of the National Academy of Sciences of the United States of America·Jia ShengJack W Szostak
Feb 16, 2016·The Journal of Physical Chemistry. B·Xing CheYi Qin Gao
Jul 6, 2004·European Journal of Biochemistry·Bernard J PremrajNarayanarao Yathindra
Feb 7, 2014·Journal of the American Chemical Society·Li Li, Jack W Szostak
Feb 23, 2011·Chemical Communications : Chem Comm·Namrata ErandeVaijayanti A Kumar
Nov 4, 2015·Angewandte Chemie·Christopher CozensPhilipp Holliger
Dec 31, 2016·Nucleic Acids Research·Fusheng ShenJia Sheng
Mar 25, 2009·Journal of the American Chemical Society·Eric D HorowitzNicholas V Hud
Nov 30, 2006·Journal of the American Chemical Society·Eric D Horowitz, Nicholas V Hud
Sep 18, 2003·Journal of the American Chemical Society·Alexei Yu DenisovMasad J Damha

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