Thermodynamic analysis of conformational transitions in oligonucleotide complexes in presence of Na+ and Mg2+ 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 Mg2+ 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. The average beta value equal to 10(-3) l/mole is in an agreement with values reported for similar systems earlier. It is shown that disordering of duplex and triplex ends ("end fraying") has an essential influence on the form of melting curves, their asymmetry and the increase of the transition interval. (c) 2007 Wiley Periodicals, Inc.