Relaxation kinetics of dimer formation by self complementary oligonucleotides

Abstract

We report relaxation measurements on the kinetics of dimer formation by self complementary oligoribonucleotides of the form A(pA) n−1 (pU) n , 4 ≤ n ≤ 7. The two strands combine with a bimolecular rate constant of about 2 × 10 6 liters per mole of strands per second. One relaxation accounts for most of the optical change, with a time constant varying from 100 μsec to 1 second, depending on conditions. Additional effects are much faster and arise mainly from unstacking of bases in the separated strands. We interpret the results with a two-state equilibrium model, an all-or-none transition between the dissociated strands and the fully bonded helix. The rate constant for dimerization decreases with increasing temperature. Consequently the kinetic model requires a transient steady-state intermediate with several bases paired before the rate-limiting step of helix growth to the fully bonded dimer. When the temperature is raised, this species melts out and the rate of dimer formation decreases. According to our analysis the critical transient intermediate has 2 or 3 base pairs; longer helices grow more rapidly than they dissociate (at the temperature of our experiments). Careful analysis of the transition curves allows estimation of the concentration of the intermediate, from which we further calculate a rate constant for the helix growth step of between 1 × 10 6 and 2 × 10 7 sec −1. This is the rate constant for adding a base pair to the end of an existing helical segment. The rate constant for dimer dissociation is strongly dependent on oligomer size and on temperature, with an activation energy roughly proportional to chain length.