A more complete kinetic theory of DNA renaturation

We develop here a more complete theory of DNA renaturation kinetics which differs from the Wetmur and Davidson theory mainly in the assumption that nucleation is not necessarily the rate−limiting step. Thus, the theory includes the several first order zipping steps. Our assumption that zipping is much slower than previously thought appears to be due to the presence of secondary structure in reacting single strands. The theory explains several anomalies seen in renaturation kinetic experiments followed by optical density. Specifically, it explains quantitatively (1) the deviations from linearity in reciprocal−second−order (RSO) plots, (2) the variation with concentration of rate constants obtained from the early−time linear region of an RSO plot, and (3) the high values of complexity calculated for viral DNAs using bacterial DNAs as the known standard. Renaturation kinetic experiments followed by hydroxypatite chromatography do not show these anomalies, since hydroxyapatite presumably ’’sees’’ only nucleation. In this paper the theory is derived and compared with experiments on bacterial and bacteriophage DNA. The implications of the theory for other biologically oriented experiments will be explained elsewhere.