Calculation of Scalar Couplings in the Backbone of Nucleic Acid
V. Sychrovský1, Z. Vokáčová1, J. Šponer2, N. Špačková2 and B. Schneider1
1 Institute of Organic Chemistry and Biochemistry,v.v.i.,
2 Institute of
Global architecture of nucleic acids corresponds to conformation of nucleic acid backbone. Structure of the backbone is usually described by the torsion angles measured along the backbone, a, b, g, d, e, z. Calculation of scalar coupling constants between the 31P, 13C, and 1H nuclei correlate strongly with the backbone torsion angles.
Distinct patterns of RNA backbone by x-ray crystallography at the dinucleotide level  were used as structural models for the theoretical calculation of all relevant scalar couplings. It was shown that the calculated scalar couplings can facilitate their accurate and reliable structural interpretation . In particular: i) proposed computational strategy allows for the determination of the multidimensional character for scalar couplings, i.e. for example the effect of sugar pucker (d-torsion) on the scalar couplings correlated only with the neighboring g-torsion, ii) new correlation of the 2J(P,C) couplings indicative of the trans, gauge+, and gauge- conformations of the a- and z-torsion was calculated, iii) the stepwise procedure for assignment of different scalar couplings in torsion space for nucleic acid backbone was proposed.
1. B. Schneider, Z. Morávek, H.M. Berman, RNA, 32 (5) 2004, 1666-1677.
2. V. Sychrovský, Z. Vokáčová, J. Šponer, N. Špačková, B. Schneider, J. Phys. Chem. B, 110 (45), 2006, 22894-22902