Calculation of Scalar Couplings in the Backbone of Nucleic Acid

V. Sychrovský^{1},
Z. Vokáčová^{1}, J. Šponer^{2}, N. Špačková^{2} and B. Schneider^{1}

^{1 }Institute of Organic Chemistry and Biochemistry,v.v.i.,

^{2} Institute of
Biophysics,

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 [1] 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 [2]. 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.

**References**

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