The three-dimensional spatial arrangements of double helical DNA deformed along various supercoiled trajectories will be generated by direct computer modeling and Monte Carlo simulations and then analyzed at the detailed molecular level. The extent to which the regular linear duplex can be forced to bend and twist will then be monitored by semiempirical potential energy calculations. Bond lengths, valence angles, and torsion angles will be kept within normally prescribed limits, and steric and electrostatic interactions of nonbonded atoms and groups will be estimated with standard functions. Of particular interest will be the effects of base sequence on overall conformation and the long-range effects associated with close contacts of sequentially distant chain residues. Long-range ionic effects will be included to access the stabilities of various three-dimensional forms (e.g., toroidal, interwound, circular, etc.). The relative contributions of bending and twisting to the total energy will be computed directly and compared with elastic models of supercoiling. The ability of the potential energy functions to account for macroscopic properties of the supercoils will be tested using established statistical mechanical procedures. The major objective of the work is to understand and visualize the structure and properties of supercoiled DNA. The immediate goal is to describe average chain structure and properties in terms of realistic molecular models. The studies may clarify the role of the primary base sequence and the polyelectrolyte sugar-phosphate backbone on the folding of the chain. A more long-range goal is to uncover structural details of supercoil-induced transitions of DNA, including the possible formation of Z-DNA, cruciforms, and local melted regions.
Showing the most recent 10 out of 66 publications
