Rate of B to Z structural transition of supercoiled DNA

The forward rate of the B to Z transition induced by negative supercoiling of plasmid DNA containing an alternating C-G sequence has been examined using the binding of Z -DNA specific antibodies to follow the transition. DNA samples of a plasmid containing a d(pCpG) 16 · d(pCpG) 16 insert were supercoiled to different extents and appropriate amounts of ethidium were bound to the DNAs to relax them and to keep the alternating C-G sequence in the right-hand helical form. Following the rapid removal of ethidium by passage through a column of cation exchange resin, the DNA becomes negatively supercoiled, which induces the flipping of the helical hand of the C-G insert. The rate of the transition is strongly dependent on the degree of supercoiling. The transition is complete in less than 50 seconds for a DNA with a specific linking difference (superhelical density) σ of −0.09. For the same DNA, the half-time of the transition is about two minutes at σ = −0.07 and about a factor of 10 slower at σ = −0.05.