Correlating the P-31 NMR Chemical Shielding Tensor and the (2)J(P,C) Spin-Spin Coupling Constants with Torsion Angles zeta and alpha in the Backbone of Nucleic Acids

0379080 - ÚOCHB 2013 RIV US eng J - Journal Article
Benda, Ladislav - Sochorová Vokáčová, Zuzana - Straka, Michal - Sychrovský, Vladimír
Correlating the P-31 NMR Chemical Shielding Tensor and the (2)J(P,C) Spin-Spin Coupling Constants with Torsion Angles zeta and alpha in the Backbone of Nucleic Acids.
Journal of Physical Chemistry B. Roč. 116, č. 12 (2012), s. 3823-3833. ISSN 1520-6106. E-ISSN 1520-5207
R&D Projects: GA ČR GAP205/10/0228; GA ČR GPP208/10/P398; GA ČR GA203/09/2037
Institutional research plan: CEZ:AV0Z40550506
Keywords : nucleic acids * phosphorus NMR * NMR calculations * cross-correlated relaxation * spin–spin coupling constants
Subject RIV: CF - Physical ; Theoretical Chemistry
Impact factor: 3.607, year: 2012

Determination of nucleic acid (NA) structure with NMR spectroscopy is limited by the lack of restraints on conformation of NA phosphate. In this work, the P-31 chemical shielding tensor, the Gamma(P,C5'H5'1) and Gamma(P,C5'H5'2) cross-correlated relaxation rates, and the (2)J(P,C3'), (2)J(P,C5'), and (3)J(P,C4') coupling constants were calculated in dependence on NA backbone torsion angles zeta and alpha. While the orientation of the P-31 chemical shielding tensor was almost independent of the NA phosphate conformation, the principal tensor components varied by up to similar to 40 ppm. This variation and the dependence of the phosphate geometry on torsion angles zeta and alpha had only a minor influence on the calculated Gamma(P,C5'H5'1) and Gamma(P,C5'H5'2) cross-correlated relaxation rates, and therefore, the so-called rigid tensor approximation was here validated. For the first time, the (2)J(P,C) spin-spin coupling constants were correlated with the conformation of NA phosphate. Although each of the two J-couplings was significantly modulated by both torsions zeta and alpha, the (2)J(P,C3'), coupling could be structurally assigned to torsion zeta and the (2)J(P,C5') coupling to torsion alpha. We propose qualitative rules for their structural interpretation as loose reStraints on torsion angles zeta and alpha. The (3)J(P,C4') coupling assigned to torsion angle beta was found dependent also on torsions zeta and alpha, implying that the uncertainty in determination of beta with standard Karplus curves could be as large as similar to 25 degrees. The calculations provided a unified picture of NMR parameters applicable for the determination of NA phosphate conformation.
Permanent Link: http://hdl.handle.net/11104/0007102