Ukr.Biochem.J. 2011; Volume 83, Issue 2, Mar-Apr, pp. 74-84

Conformational capacity of 2′,3′-didehydro-2′,3′-dideoxyadenosine as a key to understanding its biological activity: results of quantum chemical modelling


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

1Institute of Molecular Biology and Genetics, National Academy
of Sciences of Ukraine, Kyiv;
2Institute of High Technologies, Taras Shevchenko Kyiv
National University, Ukraine

Comprehensive conformational analysis of the biologically active nucleoside 2′,3′-didehydro-2′,3′-dideoxyadenosine (d4A) 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 one d4A conformers as well as their conformational equilibrium were investigated. The electron density topological analysis allowed us to establish that the d4A molecule is stabilized by eight types of intramolecular interactions: O5′H…N3, O5′H…C8, C8H…O5′, C2′H…N3, C5′H1…N3, C5′H2…N3 та C8H…H1/2C5′. The obtained results of conformational analysis lead us to think that d4A may be a terminator of the DNA chain sythesis in the 5′-3′ direction. Thus it can be inferred that d4A competes with canonical 2′-deoxyadenosine in binding an active site of the corresponding enzyme.

Keywords: , , , ,

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