Urea-enhanced gel electrophoresis of nicked and gapped DNA. (
a) Nicked DNA molecule undergoes stacked-unstacked transition governed by stacking parameter

. Stacked state is close to intact molecule; unstacked state is approximated by a molecule with a gap. (
b) DNA molecules with solitary nicks and gaps in forward (F) or reverse (R) strand were obtained by enzymatic digestion. Nicking enzymes and their recognition sites are shown in one color; cleavage sites are indicated by arrowheads. In KL/F and KL/R fragments nick is positioned within KL/K′L′ dinucleotide stack. Fragments with 2 nt-long gaps, G2/F and G2/R, are the result of sequential digestion by two nicking enzymes as shown. (
c) Effect of temperature of PAGE on the separation of intact (I), nicked (N) and gapped (G) DNA fragments. Nicked stacks are shown at the top of each lane; arrowheads point to the location of the nick. Gapped and nicked fragments resolved in one lane have lesions in the same strand. PAGE was conducted in the presence of 2.3 M urea at temperatures indicated to the left of each panel.