Thermodynamic description of oligonucleotide self-association in DNA concatamer structures

Abstract

A scheme of the formation of concatamer structures consisting of two different oligonucleotides has been considered. It was shown that, in the general case, the dependence of the concentration of oligonucleotide components on temperature cannot be found in the analytic form. Therefore, it is impossible to find the thermodynamic parameters of the formation of concatamer complexes (deltaH0, deltaS0) and melting temperature by analyzing the profiles of thermal denaturation of oligonucleotide complexes. An algorithm of the numerical solution of implicit dependences has been developed. A number of approaches have been considered that simplify the analysis of thermal denaturation curves of concatamer complexes. It was shown that the analytical dependence of the efficiency of the concatamer formation on temperature can be described when duplex fragments have close stability and there is no cooperativity at the helix-helix interface. In this case, the dependence of melting temperature on thermodynamic parameters and oligonucleotide concentration has the same form as in the case of the duplex structure formed by a pair of noncomplementary oligonucleotides. The capacity of various model approaches to describe the experimental curves of thermal denaturation of concatamer structures has been evaluated. For the case of concatamer structures used as signal amplifiers in DNA hybridization analysis, a function was introduced that shows a relative contribution of a concatamer of a fixed length to the magnitude of signal amplification. The dependence of the maximum of this function on the concentration of oligonucleotides, the thermodynamic characteristics of their complexes, and temperature has been determined. It was shown by the gel shift assay that the function of the length distribution of concatamers qualitatively correlates with the experimental dependences.