Figure 3: Comparison of electrophoretic mobility and radius of gyration values.

(a) Left, distance each topoisomer migrated during polyacrylamide gel electrophoresis, measured from the well to the centre of the band (Fig. 1 a), relative to the migration of the linearized 336 bp minicircle. Data shown are the mean values from three separate gels run under identical conditions. Middle, average radius of gyration values obtained from cryo-ET density maps for each topoisomer (n=23, 78, 40, 60, 47, 56 and 159 for topoisomers ΔLk=−3, −2, −1, 0, 1, 2 and 3, respectively). Right, radius of gyration (averaged over time) in continuum solvent MD simulations for each topoisomer. Error bars for each of the three graphs represent s.d. values. (b) Comparison of cryo-ET data and the equivalent conformations as observed in MD simulations. Examples from negatively supercoiled (ΔLk=−2) and positively supercoiled (ΔLk=+1) topoisomers are shown. MD simulation data are depicted as double-stranded DNA backbone traces.