Book of Abstracts: Albany 2003

category image Albany 2003
Conversation 13
Abstract Book
June 17-21 2003

Possible Mutual Arrangements of Guanine and Cytosine Bases. Comparison of the Results Obtained by Molecular Mechanics and Quantum Mechanics Calculations

The calculations of interaction energy between nucleic acid bases Gua and Cyt in various mutual positions have been performed by Molecular Mechanics (MM) and quantum mechanical (QM) density functional DFT/PW91PW91 methods. The results obtained are discussed in relation to conformations of dinucleoside monophosphates in solutions and to nucleic acid functioning. The comparison is made with other calculations and experimental data available in the literature. This combination of bases is of special interest because it can appear as one of Watson-Crick pairs, and the most stable pair of natural bases. An importance of detailed consideration of Gua-Cyt interactions is also due to a more pronounced polarity of these bases as compared to base pairs formed by Ade, Thy or Ura.

Both MM and DFT computations predict three types of interaction energy minima. The first type corresponds to nearly in-plane base ring arrangements and formation of three, two or single N-H?N and/or N-H?O hydrogen bonds. The second type corresponds to base stacking, i.e. to nearly parallel base arrangement one above another. These two types of mutual base arrangements had been studied extensively in the past via computational methods of various complexities. One more type of energy minima has been revealed recently and it has not been examined in details before. This type corresponds to nearly perpendicular (?T-shape?) base arrangement with one or two hydrogen bonds.

The mutual positions of bases corresponding to the first type of minima are nearly the same as revealed by different MM and QM methods. Minor differences in inter-base H-bond lengths and interaction energies are discussed. The dependence of mutual base positions corresponding to stacking minima on method of calculations is more pronounced. Amine groups of the bases are not coplanar with the base rings in all such minima obtained by DFT method. In some minima of the third type, the base positions and interaction energies, obtained by MM method, do not correspond to minima predicted by DFT method.

Our calculations show that the planar structures with two and three H bonds are the most stable ones. The most stable stacking and ?perpendicular? minima differ in energy less than 1 kcal/mol.

V. I. Poltev1,2
V. I. Danilov3
A. Les4
A. Jurkiewicz4
A. S. Deriabina1
E. Gonzalez1

1Facultad de Ciencias Fisico Matemáticas
Benemerita Universidad Autonoma de Puebla
Puebla, 72570 Mexico
2Institute of Theoretical and Experimental Biophysics
Russian Academy of Sciences
Pushchino, Moscow Region
142240 Russia
3Institute of Molecular Biology and Genetics
National Academy of Sciences of Ukraine
Kiev-143, 003143 Ukraine
4Department of Chemistry
University of Warsaw
Pasteura 1
02-093 Warsaw, Poland