Conformational flexibility of junctions between contiguous B- and Z-DNAs in supercoiled plasmids

The junctions between contiguous right- and left-handed helical DNA segments in supercoiled plasmids are shown to exhibit both sequence- and superhelical-dependent conformational flexibility. The nonalternating (purine-pyrimidine) tetranucleotide d(G-A-T-C), which is imbedded within a (dC-dG) tract and exists as a junction at low-density values, may be adopting a left-handed helix under the influence of higher negative supercoiling. The effect of supercoiling on the transition from a right- to a left-handed state for (dC-dG)n inserts, where n = 16, 13, and 5, also was evaluated. Only moderate amounts of superhelicity (-0.03 to -0.075) are required for formation and stabilization of left-handed DNA even for the (dC-dG) region of 10 dC X dG base pairs. Finally, we demonstrate that junction formation within a BamHI restriction site causes a drastic inhibition (greater than 80%) of cleavage by this restriction endonuclease.