Brownian dynamics simulation of DNA condensation

DNA condensation observed in vitro with the addition of polyvalent counteri ons is due to intermolecular attractive forces. We introduce a quantitative model of these forces in a Brownian dynamics simulation in addition to a s tandard mean-field Poisson-Boltzmann repulsion. The comparison of a theoret ical value of the effective diameter calculated from the second virial coef ficient in cylindrical geometry with some experimental results allows a qua ntitative evaluation of the one-parameter attractive potential. We show aft erward that with a sufficient concentration of divalent salt (typically sim ilar to 20 mM MgCl2), s supercoiled DNA adopts a collapsed form where oppos ing segments of interwound regions present zones of lateral contact. Howeve r, under the same conditions the same plasmid without torsional stress does not collapse. The condensed molecules present coexisting open and collapse d plectonemic regions. Furthermore, simulations show that circular DNA in 5 0% methanol solutions with 20 mM MgCl2 aggregates without the requirement o f torsional energy. This confirms known experimental results. Finally, a si mulated DNA molecule confined in a box of variable size also presents some local collapsed zones in 20 mM MgCl2, above a critical concentration of the DNA. Conformational entropy reduction obtained either by supercoiling or b y confinement seems thus to play a crucial role in all forms of condensatio n of DNA.