P-31 Chemical Shift Tensors in RNA and DNA Backbone. A DFT Study of Conformational Dependence and Its Implications for NMR Studies.

PŘECECHTĚLOVÁ, Jana, Petr PADRTA, Markéta MUNZAROVÁ and Vladimír SKLENÁŘ. P-31 Chemical Shift Tensors in RNA and DNA Backbone. A DFT Study of Conformational Dependence and Its Implications for NMR Studies. In 43rd Symposium on Theoretical Chemistry: Large, Non-Biological Systems. 2007.

Basic information

• Original name: P-31 Chemical Shift Tensors in RNA and DNA Backbone. A DFT Study of Conformational Dependence and Its Implications for NMR Studies.
• Name in Czech: P-31 Chemicke posuny v pateri RNA a DNA. DFT studium konformacni zavislosti a jeji dusledky pro NMR aplikace.
• Authors: PŘECECHTĚLOVÁ, Jana, Petr PADRTA, Markéta MUNZAROVÁ and Vladimír SKLENÁŘ.
• Edition: 43rd Symposium on Theoretical Chemistry: Large, Non-Biological Systems, 2007.

Other information

• Original language: English
• Type of outcome: Conference abstract
• Field of Study: 10403 Physical chemistry
• Country of publisher: Czech Republic
• Confidentiality degree: is not subject to a state or trade secret
• Organization unit: Faculty of Science
• Keywords in English: DFT calculations; P-31 chemical shifts; NMR ; DNA; RNA
• Tags: DFT calculations, DNA, NMR, P-31 chemical shifts, RNA
• Tags: International impact

Abstract

P-31 chemical shift anisotropy (CSA) tensors in DNA and RNA backbone conformations have been studied at the DFT level using hexahydrated dimethyl phosphate as a model. The set of conformations inspected includes canonical A-RNA, A-DNA, B-DNA, and Z-DNA as well as non-canonical structures of both DNA and RNA. The P-31 chemical shift tensors obtained are discussed in terms of characteristics common for gauche-gauche (gg) and gauche-trans-conformations (gt) around the P-O bonds. Our calculations reveal a dominant effect of backbone torsion angles alpha and zeta on the isotropic chemical shift delta_iso and the delta^CSA_11 component of the traceless chemical shift tensor that results in separated ranges of both delta_iso and delta^CSA_11 for the gg- and gt-conformers, respectively. No such clear distinction between the two conformation types has been found for components delta^CSA_22 and delta^CSA_33, which is attributed to their different directional properties in the molecule favoring the influence of coupled changes in all torsion angles (alpha, zeta, beta, epsilon). The values of P-31 CSA tensor components display large spans of 16 ppm for delta^CSA_11 and ~22 ppm for delta^CSA_22 and delta^CSA_33. The considerable variations in tensor components among conformations has important implications for experimental P-31 NMR studies. We examine the effect on the predicted values of chemical shift changes upon partial alignment as well as on CSA order parameters derived from relaxation measurements. The goal of the study is to assess the consequences of using a uniform P-31 CSA tensor for nucleic acid structure refinement and for the interpretation of P-31 NMR relaxation data.

Abstract (in Czech)

P-31 chemical shift anisotropy (CSA) tensors in DNA and RNA backbone conformations have been studied at the DFT level using hexahydrated dimethyl phosphate as a model. The set of conformations inspected includes canonical A-RNA, A-DNA, B-DNA, and Z-DNA as well as non-canonical structures of both DNA and RNA. The P-31 chemical shift tensors obtained are discussed in terms of characteristics common for gauche-gauche (gg) and gauche-trans-conformations (gt) around the P-O bonds. Our calculations reveal a dominant effect of backbone torsion angles alpha and zeta on the isotropic chemical shift delta_iso and the delta^CSA_11 component of the traceless chemical shift tensor that results in separated ranges of both delta_iso and delta^CSA_11 for the gg- and gt-conformers, respectively. No such clear distinction between the two conformation types has been found for components delta^CSA_22 and delta^CSA_33, which is attributed to their different directional properties in the molecule favoring the influence of coupled changes in all torsion angles (alpha, zeta, beta, epsilon). The values of P-31 CSA tensor components display large spans of 16 ppm for delta^CSA_11 and ~22 ppm for delta^CSA_22 and delta^CSA_33. The considerable variations in tensor components among conformations has important implications for experimental P-31 NMR studies. We examine the effect on the predicted values of chemical shift changes upon partial alignment as well as on CSA order parameters derived from relaxation measurements. The goal of the study is to assess the consequences of using a uniform P-31 CSA tensor for nucleic acid structure refinement and for the interpretation of P-31 NMR relaxation data.

Links

• GD204/03/H016, research and development project: Name: Strukturní biofyzika makromolekul

Investor: Czech Science Foundation, Structural biophysics of macromolecules

• LC06030, research and development project: Name: Biomolekulární centrum

Investor: Ministry of Education, Youth and Sports of the CR, Biomolecular centre

• MSM0021622413, plan (intention): Name: Proteiny v metabolismu a při interakci organismů s prostředím

Investor: Ministry of Education, Youth and Sports of the CR, Proteins in metabolism and interaction of organisms with the environment