Book of Abstracts: Albany 2003

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Conversation 13
Abstract Book
June 17-21 2003

Density Functional Theory Study of Some Conformations of dGpdC and dGpdC?Na+ Complex

As a first step in the investigation of solution conformations of single-stranded nucleic acid fragments, we performed the study of dinucleoside monophosphate dGpdC and its complex with counter ion Na+ by the Density Functional Theory methods using B3LYP functional with 3-21G(d,p), 6-31G and 6-31G(d,p) basis sets and PW91PW91 functional with 3-21G(d,p) and 6-31G(d,p) basis sets. Only the minimal energy conformations close to those of DNA double helix were considered in details. The study demonstrated a tendency for both the base stacking (with substantial overlap of pyrimidine rings of Gua and Cyt), and the formation of base-base and base-sugar hydrogen bonds (with the exception of the 6-31G basis set). A distortion of the planarity of amine groups allows such mutual positions of amine group of one base and carbonyl oxygen of another one (as well as of amine group of Gua and O4? of Cyd), which can be considered as the hydrogen bonds. We suggested, that N-H...O hydrogen bonds are formed when N...O distance is less than 3.2 Å and H...O distance is less than 2.4 Å, simultaneously. Besides, some conformations are stabilized by an additional secondary long-range electrostatic interactions that also involve the hydrogen atoms bonded to ring carbon atoms in the base-phosphate C-H...O contacts. The above-mentioned effects are absent in the calculations with the 6-31G basis set.

The counter ion binds at nearly equal distances from two negatively charged phosphate oxygens. Details of conformation geometry of dGpdC and precise values of Na+...O distances depend on the method, while the general features mentioned above are the same for all the methods used. The torsion angles of sugar-phosphate backbone, the puckering of deoxyribose rings, characteristics of amine groups, and details of base geometries are compared for conformations obtained by DFT methods with different functionals as well as with those available in literature.

A. Les1,*
V.I. Danilov2,*
N.V. Shulyupina3
N.A. Polteva3
V.I. Poltev3,4

1Department of Chemistry
University of Warsaw
Pasteura 1
02-093 Warsaw, Poland
2Institute of Molecular Biology and Genetics
National Academy of Sciences of Ukraine
03143 Ukraine
3Institute of Theoretical and Experimental Biophysics
Russian Academy of Sciences
Pushchino, Moscow Region, 142240 Russia
4Facultad de Ciencias Fisico Matematicas
Benemerita Universidad Autonoma de Puebla
Puebla, 72570 Mexico