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
zuzana.vokacova@uochb.cas.cz
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.
References
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.
Acknowledgements.
This work was supported by the Grant
Agency of the Czech Republic, grants no. P208/10/P398 and P205/10/0228.