Single nucleotide RNA choreography

Nucleic Acids Research
Chiaolong HsiaoLoren Dean Williams

Abstract

New structural analysis methods, and a tree formalism re-define and expand the RNA motif concept, unifying what previously appeared to be disparate groups of structures. We find RNA tetraloops at high frequencies, in new contexts, with unexpected lengths, and in novel topologies. The results, with broad implications for RNA structure in general, show that even at this most elementary level of organization, RNA tolerates astounding variation in conformation, length, sequence and context. However the variation is not random; it is well-described by four distinct modes, which are 3-2 switches (backbone topology variations), insertions, deletions and strand clips.

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Citations

Sep 21, 2013·Journal of Chemical Information and Modeling·Jeffrey R Van Voorst, Barry C Finzel
Aug 24, 2010·Journal of the American Chemical Society·Srividya MohanLoren Dean Williams
Mar 16, 2007·Nature Reviews. Molecular Cell Biology·Jung-Hoon HanJane Clarke
Aug 30, 2011·Bioinformatics·Ying ShenZhiwen Yu
Jul 25, 2009·Molecular Biology and Evolution·Chiaolong HsiaoLoren Dean Williams
Jan 23, 2009·Nucleic Acids Research·Alberto ApostolicoLoren Dean Williams
Mar 13, 2009·Nucleic Acids Research·Chiaolong Hsiao, Loren Dean Williams
Feb 18, 2010·Nucleic Acids Research·Karen Sargsyan, Carmay Lim
Jun 19, 2013·Nucleic Acids Research·Anton S PetrovLoren Dean Williams
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Dec 3, 2014·Biochimica Et Biophysica Acta·Carolina EstarellasJiří Sponer
Apr 17, 2015·Journal of Molecular Evolution·Anton S Petrov, Loren Dean Williams
Jul 19, 2016·Biochemistry·Kathryn A LanierLoren Dean Williams
Jul 21, 2016·Journal of Chemical Theory and Computation·Petra KührováPavel Banáš
Dec 22, 2016·RNA·Luigi D'AscenzoPascal Auffinger
Nov 20, 2016·Wiley Interdisciplinary Reviews. RNA·Jiří ŠponerMichal Otyepka
Aug 27, 2009·The Journal of Physical Chemistry. B·Srividya MohanLoren Dean Williams
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Jan 4, 2018·Chemical Reviews·Jiří ŠponerMichal Otyepka
Nov 21, 2020·Journal of Chemical Theory and Computation·Klaudia MrázikováJiří Šponer
Mar 22, 2019·Journal of Chemical Theory and Computation·Petra KührováPavel Banáš
Apr 9, 2013·Journal of Chemical Theory and Computation·Petra KührováMichal Otyepka
Nov 13, 2019·Biochemistry·Katherine E RichardsonBrent M Znosko
Dec 12, 2007·The Journal of Physical Chemistry. B·Alessandra VillaGerhard Stock

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