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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" (2013) Journal of Physical Chemistry B. 117(1):57-69
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Abstract:

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.

Registro:

Documento: Artículo
Título:Conformational states of 2′-C-methylpyrimidine nucleosides in single and double nucleic acid stranded structures
Autor:Robaldo, L.; Pontiggia, R.; Di Lella, S.; Estrin, D.A.; Engels, J.W.; Iribarren, A.M.; Montserrat, J.M.
Filiación:INGEBI (CONICET), Vuelta de Obligado 2490, Buenos Aires (1428), Argentina
Departamento de Quimica Inorganica, Analitica y Quimica Fisica-INQUIMAE, Fac. de Cs. Exactas y Naturales, UBA, Ciudad Universitaria, Cap. Fed., Argentina
Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
Laboratorio de Biotransformaciones, Universidad Nacional de Quilmes, Roque Saenz Peña 352, (1876) Bernal, Prov. de Bs. As., Argentina
Instituto de Ciencias, Universidad Nacional de Gral. Sarmiento, J. M. Gutierrez 1150, Los Polvorines (B1613GSX), Prov. de Bs. As., Argentina
Departamento de Quimíca Biologíca-IQUIBICEN (CONICET), Fac. de Cs. Exactas y Naturales, UBA, Ciudad Universitaria, Cap. Fed., Argentina
Palabras clave:Computer simulation; Molecular dynamics; RNA; Conformational state; DNAzyme; Melting point temperature; Molecular dynamics simulations; Stem-loop structures; Structural knowledge; Biomolecules
Año:2013
Volumen:117
Número:1
Página de inicio:57
Página de fin:69
DOI: http://dx.doi.org/10.1021/jp3081645
Título revista:Journal of Physical Chemistry B
Título revista abreviado:J Phys Chem B
ISSN:15206106
CODEN:JPCBF
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_15206106_v117_n1_p57_Robaldo

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Citas:

---------- APA ----------
Robaldo, L., Pontiggia, R., Di Lella, S., Estrin, D.A., Engels, J.W., Iribarren, A.M. & Montserrat, J.M. (2013) . Conformational states of 2′-C-methylpyrimidine nucleosides in single and double nucleic acid stranded structures. Journal of Physical Chemistry B, 117(1), 57-69.
http://dx.doi.org/10.1021/jp3081645
---------- CHICAGO ----------
Robaldo, L., Pontiggia, R., Di Lella, S., Estrin, D.A., Engels, J.W., Iribarren, A.M., et al. "Conformational states of 2′-C-methylpyrimidine nucleosides in single and double nucleic acid stranded structures" . Journal of Physical Chemistry B 117, no. 1 (2013) : 57-69.
http://dx.doi.org/10.1021/jp3081645
---------- MLA ----------
Robaldo, L., Pontiggia, R., Di Lella, S., Estrin, D.A., Engels, J.W., Iribarren, A.M., et al. "Conformational states of 2′-C-methylpyrimidine nucleosides in single and double nucleic acid stranded structures" . Journal of Physical Chemistry B, vol. 117, no. 1, 2013, pp. 57-69.
http://dx.doi.org/10.1021/jp3081645
---------- VANCOUVER ----------
Robaldo, L., Pontiggia, R., Di Lella, S., Estrin, D.A., Engels, J.W., Iribarren, A.M., et al. Conformational states of 2′-C-methylpyrimidine nucleosides in single and double nucleic acid stranded structures. J Phys Chem B. 2013;117(1):57-69.
http://dx.doi.org/10.1021/jp3081645