Biopolym. Cell. 2004; 20(3):215-223.
Structure and Function of Biopolymers
Thermodynamics of complexation of aromatic ligand with single-stranded deoxyoligonucleotide and a hairpin loop of the same nucleotide content
1Baranovsky S. F., 1Rogova O. V., 2Hernandez Santiago A. A., 1Zavyalova O. S., 1Veselkov A. N.
  1. Sevastopol National Technical University
    33, Universytetska Str., Sevastopol, Ukraine, 99053
  2. Autonomous University of Puebla
    Puebla, Mexico, 72570

Abstract

Comparative analysis of the thermodynamical parameters of interaction of phenanthridine dye, ethidium bromide (EB) with deoxyheptanucleotide d(GpCpGpApApGpC), capable to form a hairpin structure, and a single-stranded deoxytetranucleotide d(GpApApG), being a component element of the heptamer sequence, has been made using 1NMR spectroscopy (500/600 MHz). Thermodynamical parameters (ΔH, DS) of complexation of EB with oligonucleotides have been calculated from the experimental temperature dependences of proton chemical shifts using a model of dynamic equilibrium between different conformational states of oligomers in solution. For example, monomer, hairpin and dimer forms have been considered as the heptamer conformational states in aqueous solution. The calculated enthalpy of complexation of EB with single-stranded tetranucleotide d(GAAG) is similar, within the error limits, to the value of complex formation between the dye molecule and the hairpin loop d(GAA). Analysis of the results obtained enables to conclude that single-stranded non-self-complementery oligonucleotides of the same nucleotide content as in the hairpin loop may be used as model systems for the investigation of complexation of aromatic ligands with hairpin structures in solution.

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