Configurational transitions in Fourier series-represented DNA supercoils.
A new Fourier series representation of supercoiled DNA is employed in Langevin dynamics simulations to study large-scale configurational motions of intermediate-length chains. The polymer is modeled as an ideal elastic rod subject to long-range van der Waals' interactions. The van der Waals' term prevents the self-contact of distant chain segments and also mimics attractive forces thought to stabilize the association of closely spaced charged rods. The finite Fourier series-derived polymer formulation is an alternative to the piecewise B-spline curves used in past work to describe the motion of smoothly deformed supercoiled DNA in terms of a limited number of independent variables. This study focuses on two large-scale configurational events: the interconversion between circular and figure-8 forms at a relatively low level of supercoiling, and the transformation between branched and interwound structures at a higher superhelical density.
Liu
G
G
Department of Chemistry, Rutgers, the State University of New Jersey, New Brunswick 08903, USA.
Schlick
T
T
Olson
A J
AJ
Olson
W K
WK
D055592:Biophysical Phenomena; D001703:Biophysics; D003198:Computer Simulation; D004278:DNA, Superhelical / Q000737:chemistry*; D005583:Fourier Analysis; D066298:In Vitro Techniques; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D013816:Thermodynamics
D004278:DNA, Superhelical