Conformational and thermodynamic properties of supercoiled DNA.

Work in the 1990s has substantially increased our understanding of supercoiling conformations and energetics. We now know many of the basic properties of supercoiled DNA as a result of the synergy between experimental and theoretical analyses. We conclude by summarizing the results. 1. All available data indicate a plectonemic structure for supercoiled DNA. First, three types of EM (conventional, cryo, and scanning force) show the plectonemic form. Second, the topology of the catenanes and knots generated from supercoiled DNA by the Int recombinase demands that the substrate supercoils are plectonemic, as does the topology of knotting by type-2 topoisomerases. Third, all the theoretical and computer analyses indicate that the superhelix has the interwound form. 2. The superhelix conformations are often branched, as observed using EM and Monte Carlo simulation. Moreover, branching is required to explain the distribution of knots and catenanes produced by Int or topoisomerases as well as the dependence of s and Rg on sigma. Branching frequency is very sensitive to sigma, DNA length, ionic conditions, DNA bends, and temperature. Despite the qualitative agreement, the quantitative differences between experimental and computational data point out the need for further studies of branching. 3. The results of Monte Carlo simulations, theoretical analyses, and cryo-EM show that the conformational and thermodynamic properties of supercoiled DNA depend strongly on ionic conditions. The reason for such a dependence is clear. Counterions shield DNA negative charges and decrease the repulsion of DNA segments in the tight interwound structure. The effective double-helix diameter increases from 3 to 15 nm as the salt concentration is reduced from 1.00 to 0.01 M. Experimental investigations of the dependence on ionic conditions of supercoiled DNA properties are just beginning. The following conclusions refer to conditions of moderate to high monovalent or divalent ion concentrations (> or = 0.1 M [Na+] or > or = 0.01 M [Mg2+], respectively). 1. Wr takes up about 3/4 of the delta Lk, and Wr/delta Tw is independent of sigma for DNA > or = 2.5 kb in length. A constant ratio is implied by the CD data, and Wr/delta Tw has been determined with conventional EM, cryo-EM, the Int topological method, and Monte Carlo simulation. 2. The average number of supercoils is (0.8 to 0.9) x delta Lk and is independent of DNA length. These results were obtained with EM, the Int topological method, and computer simulation.(ABSTRACT TRUNCATED AT 400 WORDS)