Dodecamer DNA duplex formation is characterized by second-order kinetics, positive activation energies, and a dependence on sequence and Mg2+ ion concentration.

This study provides quantitative information about the kinetics of formation of a complex between DNA oligomers having 12 bp. The DNA dodecamers were designed in such a way as to avoid the formation of hairpins or slipped duplex structures within single strands. The hybridization was carried out employing stopped-flow techniques. The reaction was studied in different buffers (phosphate or cacodylate), in the presence and absence of Mg2+ ions, and at different temperatures. Under all conditions, the reaction followed second-order kinetics. The association rate constants were on the order of 106 M(-1) s(-1) and were found to increase with an increase in temperature. Both the rate constants and the positive activation energies of the two dodecamers, which differ only by the presence of the TAGG tetrad either at the 3'end or at the 5' end, turned out to be significantly different. The presence of Mg2+ ions had a profound influence on the kinetics of association of either compound by substantially decreasing the activation energy of the process. The dependence on sequence of the kinetics of hybridization was manifest in all parameters under all the experimental conditions.