Effect of nonplanarity on 3J-couplings in nucleic acid bases


Z. Vokáčová1, L. Trantírek2, V. Sychrovský1


1Institute of Organic Chemistry and Biochemistry, Academy of Science of the Czech Republic, Praha, Czech Republic

2Department of Chemistry, Utrecht University, The Netherlands



The glycosidic torsion angle c is used as a measure of the nucleobase orientation with respect to sugar ribose in nucleosides and it is one of the major determinants of nucleic acid structure. The deformations from planar geometry arrangement in the deoxy-adenosine (dA), deoxy-cytidine (dC), deoxy-guanosine, and deoxy-thymidine (dT) nucleosides due to variation of the glycosidic bond orientation were investigated with the computational methods and the calculated trends were correlated with the X-ray data [1].

One of the methods often used for determination of the c torsion is NMR spectroscopy. Correlation between value of 3J-coupling and corresponding torsion angle is described by Karplus equation [2]. Our study showed that angular argument of Karplus equations for the 3J(C8/6-H1’) and 3J(C4/2-H1’) couplings assigned to the c torsion, must reflect deformation from ideal tetrahedric and planar spatial arrangement of atoms around carbon C1’ and/or nitrogen N9/1 involving in the c torsion, respectively (Conception of ideal tetrahedric and planar spatial arrangement consist in using of constant phase shift in Karplus equation.[3]). Whereas, the calculated magnitude of the deformations revealed to be large at the side of the glycosidic nitrogen N9/1 (pyramidalization), the deformation of the arrangement around the carbon C1’ (sugar side) was relatively smaller. The pyramidalization depends significantly on the c torsion, namely the orientation of the pyramidalization (up and down). The magnitude of pyramidalization is also slightly different for molecules with different sugar conformation.

The deformation of the spatial arrangement of atoms around the carbon C1’ and degree and orientation of the pyramidalization at the glycosidic nitrogen N9/1 affect mostly the phase factor in the Karplus equation for structural interpretation of the 3J(C8/6-H1’) coupling. The 3J(C4-H1’) coupling is effected slightly and only by deformation at the C1’ arrangement.

The calculated dependence of pyramidalization on c torsion for all deoxy-nucleosides shows similar behaviour, including the trends due to the sugar pucker.



1.     V. Sychrovský, S. Foldýnová-Trantírková, N. Špačková, K. Robeyns, L. Van Meervelt, W. Blankenfeldt, Z. Vokáčová, J. Šponer, L. Trantírek, Nucleic Acid Res., 37, (2009), 7321.

2.     M. Karplus, J.Am.Chem.Soc., 85, (1963), 2870.

2.     S. S. Wijmenga, B. N. M. van Buuren, Prog. NMR Spectrosc., 32, (1998), 287.



This work was supported by the Grant Agency of the Czech Republic, grants no. P208/10/P398 and P205/10/0228.