The effect of ionic conditions on the conformations of supercoiled DNA. II. Equilibrium catenation

Abstract

We studied the equilibrium formation of DNA catenanes to assess the conformational properties of supercoiled DNA as a function of ionic conditions and supercoiling density. Catenanes were formed by cyclizing linear DNA with long cohesive ends in the presence of supercoiled molecules. The efficiency of the catenation depends on the distance between opposing segments of DNA in the interwound superhelix. The fraction of cyclizing molecules that becomes topologically Linked with the supercoiled DNA is the product of the concentration of the supercoiled DNA and a proportionality constant, B, that depends on conformations of supercoiled DNA. In parallel with these experimental studies, we calculated the values of B using Monte Carlo simulations of the equilibrium distribution of DNA conformations. There were no adjustable parameters in the calculations because all three parameters of the DNA model, bending and torsional elasticity of DNA and DNA effective diameter, specifying intersegment interactions, were known from independent studies. We found very good agreement between measured and simulated values of B for all the ionic conditions and DNA superhelix densities studied; the discrepancy was less than a factor of 2 over the 200-fold variation in B. The value of B decreases nearly exponentially with increasing superhelicity, this dependence being especially strong at low salt concentration. The dependence of B on the concentration of NaCl, MgCl2, and spermidine can be described with good accuracy in terms of changes of the DNA effective diameter. We found no indication of superhelix collapse under any ionic conditions studied. We discuss, in light of these results, the biological importance of the effect of DNA supercoiling on the unlinking of the products of DNA replication.