Kinetics of renaturation of DNA.

The rate of renaturation of fully denatured DNA is kinetically a second-order reaction. The reaction rate increases as the temperature decreases below T,t, reaching a broad flat maximum from 15 to 30°C below T, and then decreases with a further decrease in temperature. Let N be the complexity of the DNA or the number of base-pairs iu non-repeating sequences per virus or cell for the given DNA, and L the average number of nuoleotides per single strand of the denatured DNA preparation. Then, the second-order renaturation rate constants for all DNA’s are given approximately by k2 = 3 x IO6 Loss/N 1. mole-l sea-l at (T,.26)% aud at ma+] = 1-O mole 1.-l in aqueous solution. The reaction rate increases slightly with the GC content of the DNA. The reaction rate at the temperature maximum (T,25)“C is inversely proportional to solvent viscosity, when the viscosity is changed by the addition of components which either have a small (sucrose, glycerol, ethylene glyool) or a large (NaClOJ effect on T,. It is proposed that the mechanism of the raaotion involves the joining of short, homologous sites on the two strands followed by a fast, reversible zippering reaction with forward rate constant kf. A computer analysis for this model explains the temperature and the GC dependence. To explain the viscosity dependence it is proposed that kf is inversely proportional to viscosity ; that is, the zippering remtion is hydrodynamically limited. Any simple theory predicts k2 N L/N; the observed LO.6 length dependence is attributed to an excluded volume or sterio hindrance effect, that is, to restricted interpenetration of the two complementary denatured DNA coils.