Biopolym. Cell. 2000; 16(6):468-481.
http://dx.doi.org/10.7124/bc.00058C
Structure and Function of Biopolymers
Molecular basis of the protective action of caffeine on the complexation of intercalating ligands with DNA
1, 2Veselkov D. A., 2Davies D. B., 1Djimant L. N., 1Veselkov A. N.
  1. Sevastopol National Technical University
    33, Universytetska Str., Sevastopol, Ukraine, 99053
  2. Birkbeck, University of London
    Malet Str., Bloomsbury, London WC1E 7HX, UK

Abstract

Molecular mechanism of caffeine (CF) action as a complex-forming agent – interceptor of aromatic ligands intercalating into DNA has been examined using as an example a typical intercalator, the phenanthridinium dye, ethidium bromide (EB). Self-association and hetero-association of CF and EB as well as their complexation with deoxytetranucleotide 5'-d(TpGpCpA) under the same experimental conditions have been studied using one- and two-dimensional 1H-NMR spectroscopy (500 MHz). The concentration dependencies (at 298 K and 308 K) and temperature dependencies of the proton chemical shifts of the molecules in aqueous solution have been measured. Equilibrium constants of self-association and hetero-association of CF and EB as well as equilibrium constants of formation of different complexes between CF, EB and monomer and duplex forms of deoxytetranucleotide d(TGCA) haw been determined. The limiting proton chemical shifts of the aromatic ligands in different associates and complexes have been calculated. The most favourable structures of caffeine dimer and 1:1 CF + EB hetero-complex in aqueous solution have been constructed. The relative content of different types of associates and complexes in the mixed solution containing CF, EB and d(TGCA) has been calculated. Specific features of the dynamic equilibrium between the hetero-associates of CF and EB and their hetero-complexes with d(TGCA), i. e. CF-EB-d(TGCA), have been revealed as a function of concentration of caffeine in the mixed solution. It has been concluded that the decrease in the efficacy of the action of the ligand intercalating into DNA upon the CF addition in the solution is mostly due to the competition for the binding sites of oligonucleotide sequence by caffeine molecules and less – to the formation of CF-EB hetero-association complexes in the mixed solution.
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