Biopolym. Cell. 1996; 12(6):36-49.
http://dx.doi.org/10.7124/bc.000453
1H-NMR investigation of complex fonnation of ethidium bromide with single-stranded non-complementary deoxytetranucleotide 5'-d(CpGpApA) in aqueous solution
1Veselkov A. N., 1Baranovsky S. F., 1Djimant L. N., 1Petrenko N. V., 1Osetrov S. G., 2Tucker A., 2Davies D. B.
  1. Sevastopol National Technical University
    33, Universytetska Str., Sevastopol, Ukraine, 99053
  2. Birkbeck, University of London
    Malet Str., Bloomsbury, London WC1E 7HX, UK

Abstract

Complex formation between the aromatic dye ethidium bromide (3,8-diamino-6-phenyl-5-ethyl-phenan-thridine) and single-stranded non-complementary deoxytetranucleotide 5'-d(CpGpApA) in aqueous solution has been studied by one- and two-dimensional H-NMR spectroscopy (500 and 600 MHz). Concentration dependences of proton chemical shifts of the interacting molecules were measured at different temperatures T1 – 298 K and T2 – 305 K. Investigations of the self-association of the tetranucleotide molecules have shown that there is a very tow probability of duplex formation at the experimental conditions studied. Itfollows that the complexations of the dye molecules with the monomer of the tetranucleotide play the main rote in the complex equilibrium in solution giving an opportunity to analyze the specificity of interactions of aromatic ligand with the single-stranded DNA. Different schemes of complex formation have been examined, equilibrium reaction constants and limiting chemical shifts of dye protons in different complexes have been determined. Analysis of the relative content of different types of complexes was made and special features of the dynamic equilibrium were revealed as a function of both the dye and tetranucleotide concentrations. The analysis has shown that there is a sequence-specific binding of ethidium bromide with the single-stranded oligonucleotide. The most favorable structures of1:1 complexes of the dye with the single strand of the tetranucleotide corresponding to the drug binding from the opposite aromatic rings of the phenanthridine chromophore were constructed using the calculated values of induced chemical shifts of ethidium bromide protons.
Full text: (PDF, in Russian)

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