The effect of ionic conditions on the conformations of supercoiled DNA. I. Sedimentation analysis.
We studied the conformations of supercoiled DNA as a function of superhelicity and ionic conditions by determining its sedimentation coefficient both experimentally and by calculation. To cancel out unknown parameters from both calculations and experiments, we determined the ratio of the sedimentation coefficient, s, to that of open circular DNA, s(oc). Calculations of the sedimentation coefficient were based on direct solution of the Burgers-Oseen problem for an equilibrium set of DNA conformations generated for each condition by the Metropolis Monte Carlo procedure. There were no adjustable parameters in the Monte Carlo simulations because all three parameters of the DNA model used, bending and torsional elasticity of DNA and DNA effective diameter specifying electrostatic interactions, were known from independent data. The good agreement between measured and calculated values of s/s(oc) allowed us to interpret the sedimentation results in terms of DNA conformations, with particular emphasis on the marked effect of ionic conditions. As NaCl concentration decreases, s/s(oc) increases because the superhelix becomes less regular and more compact. In the presence of just 10 mM MgCl(2), supercoiled DNA adopts essentially the same set of conformations as in moderate to high concentrations of NaCl. Our simulations showed that s is a strong function of the superhelix branching frequency. At near physiological ionic conditions, there are about four branches in the 7 kb DNA molecule used in this work. We found no indication of superhelix collapse in any ionic conditions even remotely approaching physiological ones. For all ionic conditions studied, we conclude that the electrostatic interaction of DNA segments specified by the DNA effective diameter is the primary determinant of supercoiled DNA conformations.
Rybenkov
V V
VV
Department of Molecular and Cell Biology, University of California at Berkeley, 94720, USA.
Vologodskii
A V
AV
Cozzarelli
N R
NR
D002499:Centrifugation, Density Gradient; D055598:Chemical Phenomena; D002627:Chemistry, Physical; D003198:Computer Simulation; D004278:DNA, Superhelical / Q000737:chemistry*; D015636:Magnesium Chloride / Q000494:pharmacology*; D008958:Models, Molecular; D009010:Monte Carlo Method; D009690:Nucleic Acid Conformation; D010316:Particle Size; D010957:Plasmids; D012965:Sodium Chloride / Q000494:pharmacology*; D013095:Spermidine / Q000494:pharmacology
D004278:DNA, Superhelical; D015636:Magnesium Chloride; D012965:Sodium Chloride; D013095:Spermidine