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, L., Pontiggia, R., Di Lella, S., Estrin, D.A., Engels, J.W., Iribarren, A.M., Montserrat, J.M.
Formato: JOUR
Materias:
Computer simulation
Molecular dynamics
RNA
Conformational state
DNAzyme
Melting point temperature
Molecular dynamics simulations
Stem-loop structures
Structural knowledge
Biomolecules
Acceso en línea:http://hdl.handle.net/20.500.12110/paper_15206106_v117_n1_p57_Robaldo
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Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) de Universidad de Buenos Aires
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spelling todo:paper_15206106_v117_n1_p57_Robaldo2023-10-03T16:20:25Z Conformational states of 2′-C-methylpyrimidine nucleosides in single and double nucleic acid stranded structures Robaldo, L. Pontiggia, R. Di Lella, S. Estrin, D.A. Engels, J.W. Iribarren, A.M. Montserrat, J.M. 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. JOUR info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/2.5/ar 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, L.
Pontiggia, R.
Di Lella, S.
Estrin, D.A.
Engels, J.W.
Iribarren, A.M.
Montserrat, J.M.
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.
format JOUR
author Robaldo, L.
Pontiggia, R.
Di Lella, S.
Estrin, D.A.
Engels, J.W.
Iribarren, A.M.
Montserrat, J.M.
author_facet Robaldo, L.
Pontiggia, R.
Di Lella, S.
Estrin, D.A.
Engels, J.W.
Iribarren, A.M.
Montserrat, J.M.
author_sort Robaldo, L.
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
url http://hdl.handle.net/20.500.12110/paper_15206106_v117_n1_p57_Robaldo
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