Kinetics of renaturation of DNA

James G. Wetmur, Norman Davidson

Research output: Contribution to journalArticlepeer-review

986 Scopus citations

Abstract

The rate of renaturation of fully denatured DNA is kinetically a second-order reaction. The reaction rate increases as the temperature decreases below Tm † Abbreviation used: Tm, temperature for 50% denaturation., reaching a broad flat maximum from 15 to 30 °C below Tm and then decreases with a further decrease in temperature. Let N be the complexity of the DNA or the number of base-pairs in non-repeating sequences per virus or cell for the given DNA, and L the average number of nucleotides 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 × 105 L0.5 N 1. mole-1 sec-1 at (Tm - 25) °C and at [Na+] = 1.0 mole 1.-1 in aqueous solution. The reaction rate increases slightly with the GC content of the DNA. The reaction rate at the temperature maximum (Tm - 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 glycol) or a large (NaClO4) effect on Tm. It is proposed that the mechanism of the reaction involves the joining of short, homologous sites on the two strands followed by a fast, reversible zippering reaction with forward rate constant kt. 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 reaction is hydrodynamically limited. Any simple theory predicts k2 ~ L N; the observed L0.5 length dependence is attributed to an excluded volume or steric hindrance effect, that is, to restricted interpenetration of the two complementary denatured DNA coils.

Original languageEnglish
Pages (from-to)349-370
Number of pages22
JournalJournal of Molecular Biology
Volume31
Issue number3
DOIs
StatePublished - 14 Feb 1968
Externally publishedYes

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