Biopolymers and cell. Volume 20. № 3. 215-223.

S. F. Baranovsky, O. V. Rogova, A. A. Hernandez Santiago, O. S. Zavyalova, A. N. Veselkov

Thermodynamics of complexation of aromatic ligand with single-stranded deoxyoligonucleotide and a hairpin loop of the same nucleotide content

Summary

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 1 NMR spectroscopy (500/600 MHz). Thermodynamical parameters (DH, 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.