Figure 4

Knot distribution of cosmid DNA. (a) P4 viral particles containing P4cos-5 were purified by equilibrium density centrifugation. Extracted DNA was then electrophoresed in a 0.8% agarose gel equilibrated with TBE. The first dimension (top to bottom) was at 0.8 V/cm for 40 h at room temperature. The second dimension (left to right) was done in the same buffer at 3.4 V/cm for 4 h at room temperature. The gel blot was probed for P4cos-5. Positions of linear molecules (L), unknotted circles (C), individual knot populations containing three to eight crossings (3–8), and the tail of more complex knots (K) are indicated. (b) The electrophoresis velocity at low voltage (first gel dimension) is projected to estimate the complexity of the knot distribution. The histogram plots relative amounts of knot populations of increasing complexity by considering a linear relation between their gel velocity and their crossing number. The position and ideal configuration of the achiral knot of four crossings (4₁) is indicated.