Modeling of DNA compaction by polycations

In this work we study polycations as efficient compacting agents of a medium size polyanion by means of Monte Carlo simulations. The systems are characterized in terms of a conformational analysis in which shape, overall dimensions, structure factors, radial distribution functions, and the degree of accumulation of the compaction agent near the polyanion are taken into consideration. Results show that the degree of compaction depends on the size of the positive chains and their number. The role of electrostatic interactions is paramount in the compaction process, and an increase in the number of molecules of the compacting agent or in the number of charges of each molecule leads to collapse, which may be followed by some unfolding in situations of overcharging. Compaction is associated with polycations promoting bridging between different sites in the polyanion. When the total charge of the polycations is significantly lower than that of the polyanion, interaction produces only a small degree of intrachain segregation in the latter, allowing for significant translational motion of the compacting agent along the longer chain. However, complete charge neutralization is not mandatory to achieve compact forms. (C) 2003 American Institute of Physics.