Thermodynamic analysis of conformational transitions in oligonucleotide complexes in presence of Na(+) and Mg(2+) ions, using "staggering zipper" model.

Curves of transitions in double (2-->1 transition) and triple (3-->2 transition) complexes of oligonucleotides dA(N1)with dT(N2) in solutions with Na(+) and Mg(2+) are calculated for the case of oligomer lengths from 10 to 500 nucleotides in the wide range of ion concentrations. The calculated curves of transitions and their differential analogs reflect rather exactly the position and form of experimental curves and describe dependences of transition temperatures on the length of molecules, their concentration, and ionic conditions. Values of the nucleation parameter beta for the systems studied are determined by comparison of the calculated and experimental data obtained in a number of works.