Conformational states of 2′-C-methylpyrimidine nucleosides in single and double nucleic acid stranded structures

The hybridization performance of a set of 12-mer RNA:RNA duplexes containing 2′-C-methyluridine, 5-bromo-2′-C-methyluridine, or (2′S)-2′-deoxy-2′-C-methyluridine was analyzed. Melting point temperatures of the modified duplexes showed an important ΔTm decrease (-8.9 to -12.5 C), while circular dichr...

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Autores principales:	Robaldo, Laura, Pontiggia, Rodrigo Martín, Estrin, Dario Ariel, Iribarren, Adolfo Marcelo
Publicado:	2013
Materias:	Computer simulation Molecular dynamics RNA Conformational state DNAzyme Melting point temperature Molecular dynamics simulations Stem-loop structures Structural knowledge Biomolecules
Acceso en línea:	https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_15206106_v117_n1_p57_Robaldo http://hdl.handle.net/20.500.12110/paper_15206106_v117_n1_p57_Robaldo
Aporte de:	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) de Universidad de Buenos Aires

id	paper:paper_15206106_v117_n1_p57_Robaldo
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spelling	paper:paper_15206106_v117_n1_p57_Robaldo2023-06-08T16:19:07Z Conformational states of 2′-C-methylpyrimidine nucleosides in single and double nucleic acid stranded structures Robaldo, Laura Pontiggia, Rodrigo Martín Estrin, Dario Ariel Iribarren, Adolfo Marcelo Computer simulation Molecular dynamics RNA Conformational state DNAzyme Melting point temperature Molecular dynamics simulations Stem-loop structures Structural knowledge Biomolecules The hybridization performance of a set of 12-mer RNA:RNA duplexes containing 2′-C-methyluridine, 5-bromo-2′-C-methyluridine, or (2′S)-2′-deoxy-2′-C-methyluridine was analyzed. Melting point temperatures of the modified duplexes showed an important ΔTm decrease (-8.9 to -12.5 C), while circular dichroism experiments indicated that the helix was still A-type, suggesting a localized disturbance disorder. Molecular dynamics simulations using AMBER were carried out in order to gain structural knowledge about the effect of the 2′-C-methyl modification in double stranded environments. On the other hand, in an attempt to explain the behavior of the 2′-deoxy-2′-C-methyl nucleosides in single stranded environments, like the 10-23 DNAzyme core, molecular dynamic simulations were performed, incorporating the modified analogues into single stranded reported stem-loop structures, studding the sugar conformations along the MD trajectories. It was observed that, despite their preferential conformational states, the 2′-C-methyl analogues are flexible enough to adopt a different puckering in single stranded environments. © 2012 American Chemical Society. Fil:Robaldo, L. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Pontiggia, R. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Estrin, D.A. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Iribarren, A.M. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. 2013 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_15206106_v117_n1_p57_Robaldo http://hdl.handle.net/20.500.12110/paper_15206106_v117_n1_p57_Robaldo
institution	Universidad de Buenos Aires
institution_str	I-28
repository_str	R-134
collection	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA)
topic	Computer simulation Molecular dynamics RNA Conformational state DNAzyme Melting point temperature Molecular dynamics simulations Stem-loop structures Structural knowledge Biomolecules
spellingShingle	Computer simulation Molecular dynamics RNA Conformational state DNAzyme Melting point temperature Molecular dynamics simulations Stem-loop structures Structural knowledge Biomolecules Robaldo, Laura Pontiggia, Rodrigo Martín Estrin, Dario Ariel Iribarren, Adolfo Marcelo Conformational states of 2′-C-methylpyrimidine nucleosides in single and double nucleic acid stranded structures
topic_facet	Computer simulation Molecular dynamics RNA Conformational state DNAzyme Melting point temperature Molecular dynamics simulations Stem-loop structures Structural knowledge Biomolecules
description	The hybridization performance of a set of 12-mer RNA:RNA duplexes containing 2′-C-methyluridine, 5-bromo-2′-C-methyluridine, or (2′S)-2′-deoxy-2′-C-methyluridine was analyzed. Melting point temperatures of the modified duplexes showed an important ΔTm decrease (-8.9 to -12.5 C), while circular dichroism experiments indicated that the helix was still A-type, suggesting a localized disturbance disorder. Molecular dynamics simulations using AMBER were carried out in order to gain structural knowledge about the effect of the 2′-C-methyl modification in double stranded environments. On the other hand, in an attempt to explain the behavior of the 2′-deoxy-2′-C-methyl nucleosides in single stranded environments, like the 10-23 DNAzyme core, molecular dynamic simulations were performed, incorporating the modified analogues into single stranded reported stem-loop structures, studding the sugar conformations along the MD trajectories. It was observed that, despite their preferential conformational states, the 2′-C-methyl analogues are flexible enough to adopt a different puckering in single stranded environments. © 2012 American Chemical Society.
author	Robaldo, Laura Pontiggia, Rodrigo Martín Estrin, Dario Ariel Iribarren, Adolfo Marcelo
author_facet	Robaldo, Laura Pontiggia, Rodrigo Martín Estrin, Dario Ariel Iribarren, Adolfo Marcelo
author_sort	Robaldo, Laura
title	Conformational states of 2′-C-methylpyrimidine nucleosides in single and double nucleic acid stranded structures
title_short	Conformational states of 2′-C-methylpyrimidine nucleosides in single and double nucleic acid stranded structures
title_full	Conformational states of 2′-C-methylpyrimidine nucleosides in single and double nucleic acid stranded structures
title_fullStr	Conformational states of 2′-C-methylpyrimidine nucleosides in single and double nucleic acid stranded structures
title_full_unstemmed	Conformational states of 2′-C-methylpyrimidine nucleosides in single and double nucleic acid stranded structures
title_sort	conformational states of 2′-c-methylpyrimidine nucleosides in single and double nucleic acid stranded structures
publishDate	2013
url	https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_15206106_v117_n1_p57_Robaldo http://hdl.handle.net/20.500.12110/paper_15206106_v117_n1_p57_Robaldo
work_keys_str_mv	AT robaldolaura conformationalstatesof2cmethylpyrimidinenucleosidesinsingleanddoublenucleicacidstrandedstructures AT pontiggiarodrigomartin conformationalstatesof2cmethylpyrimidinenucleosidesinsingleanddoublenucleicacidstrandedstructures AT estrindarioariel conformationalstatesof2cmethylpyrimidinenucleosidesinsingleanddoublenucleicacidstrandedstructures AT iribarrenadolfomarcelo conformationalstatesof2cmethylpyrimidinenucleosidesinsingleanddoublenucleicacidstrandedstructures
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Conformational states of 2′-C-methylpyrimidine nucleosides in single and double nucleic acid stranded structures

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