Jana Přecechtělová, Markéta L. Munzarová and Vladimír Sklenář


National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-611 37 Brno, Czech Republic


     Density functional theory has been applied to explore the dependence of  13C and 15N chemical shifts in deoxyribonucleosides on various structural features such as the orientation about the glycosidic bond, the CH2OH group conformation, the sugar pucker, and the hydrogen bonding. Geometry optimizations have been performed with sugar-phosphate backbone dihedral angles frozen to their average experimental values in BI-DNA. Results obtained in NMR parameter calculations have been compared to available experimental data for C1`, C2` and N9.

     The effect of the glycosidic torsion angle c has already been studied [1] but we wished to involve the relaxation of the geometry after changing c, which has not been considered in the previous work [1]. C1`, C2` and N1/N9 chemical shifts appeared to be influenced most by the base orientation. The trends uncovered in chemical shifts are significantly different from those reported previously [1] and the absolute chemical shift values are in the case of C2` approximately the same for all deoxyribonucleosides, except for the anti orientation of the base. On the contrary, for C1` and N1/N9 the trends for purine nucleosides differ from those for pyrimidine nucleosides and the absolute N1 chemical shifts in deoxycytidine are found upfield relative to deoxythymidine.

     Besides the influence of varying the glycosidic torsion angle, we wanted to assess the effect of the sugar puckering and the hydroxymethyl rotation, both of which were studied on deoxyguanosine. N9 experienced the largest changes, namely 10 or 8 ppm difference  between the south and north conformation in both the syn and anti region, respectively. The N9 chemical  shift for deoxyguanosine (S, anti, gg) differed significantly from the other two  CH2OH-rotamers.

      The comparison with the experiment has been carried out using the data from BMRB database [2] (C1`, C2`) and the data for the [d(G4T4G4)]2 quadruplex (C1`, N9) [3], on which changes upon the hydrogen bonding have also been studied.


1.                  X.-P. Xu, S. C. F. Au-Yeung, J. Phys. Chem. B, 104 (2002) 5641-5650

2.                  http://www.bmrb.wisc.edu

3.                   L. Trantírek, R. Štefl, J. E. Masse, J. Feigon, V. Sklenář, J. Biomol. NMR,

             23 (2002) 1-12