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Kinetics of reactions involving DNA containing stress‐induced single‐stranded regions

The theoretical kinetics are analyzed for reactions between torsionally stressed DNA and another compound which reacts at different rates with portions of the substrate molecule which are in different conformational states. These reactions are assumed to obey Michaelis‐Menten kinetics, so no cooperative effects occur. The DNA is regarded as being susceptible to a stress‐induced local conformational transition as described recently by Benham. Briefly, alterations in torsional stress consequent on superhelicity effectively change the relative concentrations of the two conformational states of the substrate, thereby influencing the course of the reaction. This theory is developed for transition between the B‐form helix and the single‐stranded, random‐coil states. To illustrate the influence of posited stress‐induced melting on kinetics, calculations are made on simple models of two biochemical phenomena. First, the variations in initial nicking rates of single‐strand‐specific endonucleases with substrate superhelicity are interpreted as arising from changes in the concentration of (stress‐induced) single‐stranded binding sites. Second, the observed dependence of the transcription rate of RNA polymerase core enzyme on substrate superhelicity is interpreted in terms of a model in which the rate‐limiting step in the initiation event is the formation of a complex between the enzyme and a single‐stranded region. Related experimental results are shown to be qualitatively consistent with the suggestion that sufficiently supercoiled DNA contains locally melted regions.