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Chemical Shifts in Nucleic Acids Studied by Density Functional Theory Calculations and Comparison with Experiment

NMR chemical shifts are highly sensitive probes of local molecular conformation and environment and form an important source of structural information. In this study, the relationship between the NMR chemical shifts of nucleic acids and the glycosidic torsion angle, χ, has been investigated for the two commonly occurring sugar conformations. We have calculated by means of DFT the chemical shifts of all atoms in the eight DNA and RNA mono-nucleosides as a function of these two variables. From the DFT calculations, structures and potential energy surfaces were determined by using constrained geometry optimizations at the BP86/TZ2P level of theory. The NMR parameters were subsequently calculated by single-point calculations at the SAOP/TZ2P level of theory. Comparison of the 1H and 13C-NMR shifts calculated for the mono-nucleosides with the shifts determined by NMR spectroscopy for nucleic acids demonstrates that the theoretical shifts are valuable for the characterization of nucleic acid conformation. For example, a clear distinction can be made between χ angles in the anti and syn domains. Furthermore, a quantitative determination of the χ angle in the syn domain is possible, in particular when 13C and 1H chemical shift data are combined. The approximate linear dependence of the C1’ shift on the χ angle in the anti domain provides a good estimate of the angle in this region. It is also possible to derive the sugar conformation from the chemical shift information. The DFT calculations reported herein were performed on mono-nucleosides, but examples are also provided to estimate intramolecularly induced shifts as a result of hydrogen bonding, polarization effects, or ring-current effects

We thank the following organizations for financial support: the Netherlands organization for Scientific Research (NWO-CW and NWO-NCF), the Spanish Ministerio de Ciencia e Innovacion (MICINN projects CTQ2005-08797-C02-01/BQU, CTQ2008-06532/BQU, and CTQ2011-25086/BQU), the Catalan Ministry of Universities, Research and the Information Society (DURSI projects 2005SGR-00238 and 2009SGR528)

Wiley-VCH Verlag

Director: Ministerio de Educación y Ciencia (Espanya)
Ministerio de Ciencia e Innovación (Espanya)
Generalitat de Catalunya. Agència de Gestió d’Ajuts Universitaris i de Recerca
Autor: Fonville, Judith M.
Swart, Marcel
Vokáčová, Zuzana
Sychrovský, Vladimír
Šponer, Judit E.
Šponer, Jiří
Hilbers, Cornelis W.
Bickelhaupt, F. Matthias
Wijmenga, Sybren S.
Data: 24 setembre 2012
Resum: NMR chemical shifts are highly sensitive probes of local molecular conformation and environment and form an important source of structural information. In this study, the relationship between the NMR chemical shifts of nucleic acids and the glycosidic torsion angle, χ, has been investigated for the two commonly occurring sugar conformations. We have calculated by means of DFT the chemical shifts of all atoms in the eight DNA and RNA mono-nucleosides as a function of these two variables. From the DFT calculations, structures and potential energy surfaces were determined by using constrained geometry optimizations at the BP86/TZ2P level of theory. The NMR parameters were subsequently calculated by single-point calculations at the SAOP/TZ2P level of theory. Comparison of the 1H and 13C-NMR shifts calculated for the mono-nucleosides with the shifts determined by NMR spectroscopy for nucleic acids demonstrates that the theoretical shifts are valuable for the characterization of nucleic acid conformation. For example, a clear distinction can be made between χ angles in the anti and syn domains. Furthermore, a quantitative determination of the χ angle in the syn domain is possible, in particular when 13C and 1H chemical shift data are combined. The approximate linear dependence of the C1’ shift on the χ angle in the anti domain provides a good estimate of the angle in this region. It is also possible to derive the sugar conformation from the chemical shift information. The DFT calculations reported herein were performed on mono-nucleosides, but examples are also provided to estimate intramolecularly induced shifts as a result of hydrogen bonding, polarization effects, or ring-current effects
We thank the following organizations for financial support: the Netherlands organization for Scientific Research (NWO-CW and NWO-NCF), the Spanish Ministerio de Ciencia e Innovacion (MICINN projects CTQ2005-08797-C02-01/BQU, CTQ2008-06532/BQU, and CTQ2011-25086/BQU), the Catalan Ministry of Universities, Research and the Information Society (DURSI projects 2005SGR-00238 and 2009SGR528)
Format: application/pdf
Accés al document: http://hdl.handle.net/10256/11455
Llenguatge: eng
Editor: Wiley-VCH Verlag
Col·lecció: info:eu-repo/semantics/altIdentifier/doi/10.1002/chem.201103593
info:eu-repo/semantics/altIdentifier/issn/0947-6539
info:eu-repo/semantics/altIdentifier/eissn/1521-3765
info:eu-repo/grantAgreement/MICINN//CTQ2008-06532/ES/REACTIVIDAD Y ENLACE QUIMICO EN BIOMEDICINA Y QUIMICA (BIO)INORGANICA/
info:eu-repo/grantAgreement/MICINN//CTQ2011-25086/ES/MODELIZACION MULTIESCALAR EN (BIO)QUIMICA/
MEC/PN 2005-2008/CTQ2005-08797-C02-01
AGAUR/2005-2008/2005SGR 00238
Drets: Tots els drets reservats
Matèria: Funcional de densitat, Teoria del
Density functionals
Espectroscòpia de ressonància magnètica nuclear
Nuclear magnetic resonance spectroscopy
Àcids nucleics
Nucleic acids
Títol: Chemical Shifts in Nucleic Acids Studied by Density Functional Theory Calculations and Comparison with Experiment
Tipus: info:eu-repo/semantics/article
Repositori: DUGiDocs

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