Collect. Czech. Chem. Commun. 2000, 65, 631-643

Modelling of DNA Complexes with Distamycin Analogues Using an ab initio Continuum Solvent Model

Petr Bouřa,b,* and Vladimír Králb

a Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
b Department of Analytical Chemistry, Prague Institute of Chemical Technology, Technická 5, 166 28 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.

References: 29 live references.