Ukr.Biochem.J. 2012; Volume 84, Issue 1, Jan-Feb, pp. 67-78

Complete conformational family of 2′,3′-didehydro-2′,3′-dideoxyguanosine: quantum chemical and electron density topological study

A. G. Ponomareva1, Ye. P. Yurenko1,2,3, R. O. Zhurakivsky1,2, D. M. Hovorun1,2,3

1Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv;
2Research and educational center “State key laboratory of molecular and cell biology”, Kyiv, Ukraine;
3Taras Shevchenko Kyiv National University, Institute of High Technologies, Ukraine;

Comprehensive conformational analysis of the biologically active nucleoside 2′,3′-didehydro-2′,3′-dideoxyaguanosine (d4G) has been performed at the MP2/6-311++G(d,p)//DFT B3LYP/6-31G(d,p) level of theory. The energetic, geometrical and polar characteristics of twenty d4G conformers as well as their conformational equilibrium were investigated. The electron density topological analysis allowed us to establish that the d4G molecule is stabilized by nine types of intramolecular interactions: O5′H…N3, O5′H…C8, C8H…O5′, C2′H…N3, C5′H1…N3, C5′H2…N3, C8H…H1C5′, С8Н…Н2′С5′ and N2H1…O5′. The obtained results of conformational analysis permit us to think that d4G may be a terminator of the DNA chain synthesis in the 5′-3′ direction. Thus it can be inferred that d4G competes with canonical 2′-deoxyaguanosine in binding an active site of the corresponding enzyme.

Keywords: , , ,

Creative CommonsThis work is licensed under a Creative Commons Attribution 4.0 International License.