CCCC 2000, Volume 65, Issue 5, Abstracts pp. 631-643

Collection
of Czechoslovak Chemical Communications

Abstracts: 2000, 65(5), 631-643; doi:10.1135/cccc20000631

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MODELLING OF DNA COMPLEXES WITH DISTAMYCIN ANALOGUES USING AN ab initio CONTINUUM SOLVENT MODEL

Petr BOUR^a,b,* and Vladimir KRAL^a
^a Department of Analytical Chemistry, Prague Institute of Chemical Technology, Technicka 5, 166 28 Prague 6, Czech Republic
^b Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic

Model systems related to non-covalent minor groove DNA complexes with distamycin analogues were investigated using the Turbomole and Gaussian quantum chemical packages. The role of molecular shape, electrostatic field and conformer energies in the complex formation was discussed. The ab initio calculations included the COSMO solvent model. If compared to vacuum computations, polar solvent significantly destabilizes such complexes and increases conformational flexibility of distamycin. The DNA complex formation appears to be driven mainly by entropy lowering and complementarity of molecular shapes. The NH moiety of the amide group preferably points to the base pair according to the computations, in agreement with experimental data.
Keywords: Ab initio calculations; DFT; DNA; COSMO; Distamycin; Amides; Solvation; Minor groove.

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