THE INFLUENCE OF SALT ON THE STRUCTURE AND ENERGETICS OF SUPERCOILED DNA

We present a detailed computational study of the influence of salt on the configurations, energies, and dynamics of supercoiled DNA. A poten tial function that includes both elastic and electrostatic energy comp onents is employed. Specifically, the electrostatic term, with salt-de pendent coefficients, is modeled after Stigter's pioneering work on th e effective diameter of DNA as a function of salt concentration. Becau se an effective charge per unit length is used, the electrostatic form ulation does not require explicit modeling of phosphates and can be us ed to study long DNAs at any desired resolution of charge. With explic it consideration of the electrostatic energy, an elastic bending const ant corresponding to the nonelectrostatic part of the bending contribu tion to the persistence length is used. We show, for a series of salt concentrations ranging from 0.005 to 1.0 M sodium, how configurations and energies of supercoiled DNA (1000 and 3000 base pairs) change dram atically with the stimulated salt environment. At high salt, the DNA a dopts highly compact and bent interwound states, with the bending ener gy dominating over the other components, and the electrostatic energy playing a minor role in comparison to the bending and twisting terms. At low salt, the DNA supercoils are much more open and loosely interwo und, and the electrostatic components are dominant. Over the range of three decades of salt examined, the electrostatic energy changes by a factor of 10. The buckling transition between the circle and figure-8 is highly sensitive to salt concentration: this transition is delayed as salt concentration decreases, with a particularly sharp increase be low 0.1 M. For example, for a bending-to-twisting force constant ratio of AIC = 1.5, the linking number difference (Delta Lk) corresponding to equal energies for the circle and figure-8 increases from 2.1 to 3. 25 as salt decreases from 1.0 to 0.005 M. We also present in detail a family of three-lobed supercoiled DNA configurations that are predicte d by elasticity theory to be stable at low Delta Lk. To our knowledge, such three-dimensional structures have not been previously presented in connection with DNA supercoiling. These branched forms have a highe r bending energy than the corresponding interwound configurations at t he same Delta Lk but, especially at low salt, this bending energy diff erence is relatively small in comparison with the total energy, which is dominated by the electrostatic contributions. Significantly, the el ectrostatic energies of the three-lobed and (straight) interwound form s are comparable at each salt environment. We show how the three-lobed configurations change slowly with Delta Lk, resulting in branched int erwound forms at higher salt. In longer chains, the branched forms are highly interwound, with bent arms. At low salt, the branched supercoi ls are asymmetric, with a longer interwound stem and two shorter arms. From molecular dynamics simulations we observe differences in the mot ions of the DNA as a function of salt. At high salt, the supercoiled c hain is quite compact but fairly rigid, whereas at low salt the DNA is loosely coiled but more dynamic. Especially notable at low salt are t he large-scale opening and closing of the chain as a whole and the rap id ''slithering'' of individual residues past one another. Toroidal fo rms are not detected under these conditions. However, the overall feat ures of the open, loose supercoils found at low salt are more similar to those of toroidal than interwound configurations. Indeed, simulated x-ray scattering profiles reveal the same trends observed experimenta lly and are consistent with a change from closed to open forms as salt is decreased. Like the minimization studies, the dynamics reveal a cr itical point near 0.1 M associated with the collapse of loose to tight supercoils. Near this physiological concentration, enhanced flexibili ty of the DNA is noted. The collective observations suggest a potentia l regulatory role for salt on supercoiled DNA function, not only for c losed circular DNA, but also for linear DNA with small looped regions.