Going beyond base-pairs: topology-based characterization of base-multiplets in RNA

RNA
Sohini BhattacharyaAbhijit Mitra

Abstract

Identification and characterization of base-multiplets, which are essentially mediated by base-pairing interactions, can provide insights into the diversity in the structure and dynamics of complex functional RNAs, and thus facilitate hypothesis driven biological research. The necessary nomenclature scheme, an extension of the geometric classification scheme for base-pairs by Leontis and Westhof, is however available only for base-triplets. In the absence of information on topology, this scheme is not applicable to quartets and higher order multiplets. Here we propose a topology-based classification scheme which, in conjunction with a graph-based algorithm, can be used for the automated identification and characterization of higher order base-multiplets in RNA structures. Here, the RNA structure is represented as a graph, where nodes represent nucleotides and edges represent base-pairing connectivity. Sets of connected components (of n nodes) within these graphs constitute subgraphs representing multiplets of "n" nucleotides. The different topological variants of the RNA multiplets thus correspond to different nonisomorphic forms of these subgraphs. To annotate RNA base-multiplets unambiguously, we propose a set of topology-bas...Continue Reading

References

Dec 1, 1974·Proceedings of the National Academy of Sciences of the United States of America·S H KimA RICH
Dec 11, 1999·Nucleic Acids Research·U NagaswamyG E Fox
Apr 11, 2001·Proceedings of the National Academy of Sciences of the United States of America·P NissenT A Steitz
May 10, 2001·RNA·N B Leontis, E Westhof
Aug 3, 2001·The EMBO Journal·D J KleinT A Steitz
Dec 26, 2001·Nucleic Acids Research·Uma NagaswamyGeorge E Fox
Jul 12, 2002·Nature·Jennifer A Doudna, Thomas R Cech
Jan 10, 2003·Nucleic Acids Research·John WestbrookHelen M Berman
Jul 2, 2003·Current Opinion in Structural Biology·Neocles B Leontis, Eric Westhof
Jan 2, 2004·Journal of Computer-aided Molecular Design·Anne-Marie HarrisonPeter J Artymiuk
Feb 14, 2004·Bioinformatics·Hin Hark GanTamar Schlick
Aug 20, 2004·Journal of Biomolecular Structure & Dynamics·Filip RázgaJirí Sponer
May 9, 2006·Nucleic Acids Research·Sébastien Lemieux, François Major
May 18, 2006·Annual Review of Microbiology·Anette Schneemann
Jul 15, 2006·The Journal of Physical Chemistry. a·Judit E SponerJirí Sponer
Jul 21, 2006·The Journal of Physical Chemistry. B·Judit E SponerJirí Sponer
Jul 21, 2006·The Journal of Physical Chemistry. B·Judit E SponerJirí Sponer
Aug 25, 2006·Journal of Biomolecular Structure & Dynamics·Jhuma DasDhananjay Bhattacharyya
Dec 14, 2006·ACS Chemical Biology·Dipali G Sashital, Samuel E Butcher
Sep 7, 2007·Cell·Charles E DannWade C Winkler
Jan 22, 2008·Nature Structural & Molecular Biology·Sunny D GilbertRobert T Batey
Mar 7, 2008·Nature·Marc Parisien, François Major
Apr 11, 2008·Journal of Biomolecular Structure & Dynamics·Purshotam SharmaDhananjay Bhattacharyya
Jul 17, 2008·Comparative and Functional Genomics·Neocles B Leontis, Eric Westhof
Oct 11, 2008·Nucleic Acids Research·Yurong Xin, Wilma K Olson
Oct 30, 2008·RNA·Mahassine Djelloul, Alain Denise
Jan 15, 2009·Genes & Development·Tina M Henkin
Jan 20, 2009·The Journal of Physical Chemistry. B·Arnost MládekJudit E Sponer
Feb 24, 2009·Nature Structural & Molecular Biology·Daniel J KleinAdrian R Ferré-D'Amaré
Feb 26, 2009·Nucleic Acids Research·Jesse StombaughNeocles B Leontis
Aug 8, 2009·Journal of Molecular Biology·Christian LaingTamar Schlick
Sep 16, 2011·Nucleic Acids Research·Christian LaingTamar Schlick
Oct 18, 2011·The Journal of Physical Chemistry. B·Kamila RéblováJiří Šponer
Nov 5, 2011·Nucleic Acids Research·Amal S Abu AlmakaremNeocles B Leontis
Jul 12, 2012·Journal of the American Chemical Society·Giulia BiffiShankar Balasubramanian

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Citations

Jul 15, 2020·Journal of Biomolecular Structure & Dynamics·Ashita OhriPurshotam Sharma
Oct 8, 2019·Bioinformatics·Mariusz PopendaMarta Szachniuk

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