Figure 7.

Non-equivalent stacking between adjacent DNA duplexes in the crystal pseudo-filament creates two different minor grooves. Only the DBD of SimR is shown. At the right-hand end of the central DNA duplex the base stacking allows the DNA phosphate backbone to transit smoothly (dotted lines) between adjacent duplexes, creating a relatively normal minor groove. At the left-hand end of the central DNA duplex the base stacking causes the phosphate backbone to veer away to avoid a steric clash (dotted lines), producing an abnormal minor groove. Adjacent DNA duplexes are shown in contrasting colours.