Kinetics of the helix‐coil transition in DNA

Abstract The kinetics of the helix‐coil transition have been investigated for T2 and T7 phage DNA in a formamide‐water‐salt mixed solvent using a slow temperature perturbation technique (applicable to kinetic processes with rate constants ⩽ 3 min −1 ). In this solvent degradation of the DNA is effectively suppressed. Complex kinetic curves are observed by absorbance and viscosity measurements for the response to denaturing perturbations in the transition region. Analysis of the decay curves indicates that the denaturation reaction in this time range can be treated as a first‐order reaction with a variable first‐order rate parameter, k , the derivative of the logarithm of the absorbance or viscosity change with respect to time. In the approach to denaturation equilibrium in the transition region, the rate parameter is determined only by the instantaneous extent of denaturation of the molecules. Near equilibrium, the rate parameter assumes a constant value characteristic of the equilibrium state. In this region, where the denaturation reaction proceeds as a simple first‐order process, both the decay of absorbance (reflected local conformational change) and the decay of solution viscosity (reflecting macromolecular conformational change) are characterized by the same constant value of k . In 83% formamide, 0.3 M Na + , the rate parameter k for T2 DNA decreases from an extrapolated value of 2.0 min −1 at 0% denaturation to 0.11 min −1 at 90% denaturation. Rate parameters determined for T7 DNA at the same counterion concentration and fraction of denaturation are approximately five times as large as those cited for T2 DNA, indicating an inverse proportionality of rate constant to molecular length. On the other hand, simple first‐order kinetic responses with constant k are obtained for renaturing perturbations within the transition, indicating that the mechanism of rewinding differs, in most cases, from that of unwinding. Only in the limit of very small perturbations about a given equilibrium position are the rate constants k obtained from denaturing and renaturing perturbations equal. For perturbations of finite size, it appears possible that an intramolecular initiation or nucleation event may precede rewinding and limit the rate of this reaction. The rate parameters again are approximately inversely proportional to molecular weight. The one exception to the first‐power dependence on molecular weight appears when temperature jumps are made upward into the post‐transition region. Here the molecular‐weight dependence is second power, but complications arising from the different strand‐separation properties of T2 and T7 DNA's make interpretation difficult. The previously used model of friction‐limited unwinding appears to fit all the observations except for the molecular‐weight dependence.