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 a 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.

Základní údaje

Originální název

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

Název česky

P-31 Chemicke posuny v pateri RNA a DNA. DFT studium konformacni zavislosti a jeji dusledky pro NMR aplikace.

Autoři

PŘECECHTĚLOVÁ, Jana, Petr PADRTA, Markéta MUNZAROVÁ a Vladimír SKLENÁŘ

Vydání

43rd Symposium on Theoretical Chemistry: Large, Non-Biological Systems, 2007

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Další údaje

Jazyk

angličtina

Typ výsledku

Konferenční abstrakt

Obor

10403 Physical chemistry

Stát vydavatele

Česká republika

Utajení

není předmětem státního či obchodního tajemství

Organizační jednotka

Přírodovědecká fakulta

Klíčová slova anglicky

DFT calculations; P-31 chemical shifts; NMR ; DNA; RNA

Štítky

DFT calculations, DNA, NMR, P-31 chemical shifts, RNA

Příznaky

Mezinárodní význam

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Anotace

V originále

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.

Česky

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.

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Návaznosti

GD204/03/H016, projekt VaV	Název: Strukturní biofyzika makromolekul Investor: Grantová agentura ČR, Strukturní biofyzika makromolekul
LC06030, projekt VaV	Název: Biomolekulární centrum Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Biomolekulární centrum
MSM0021622413, záměr	Název: Proteiny v metabolismu a při interakci organismů s prostředím Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Proteiny v metabolismu a při interakci organismů s prostředím