Monte Carlo description of oligoelectrolyte properties of DNA oligomers: range of the end effect and the approach of molecular and thermodynamic properties to the polyelectrolyte limits.

Applications of the grand canonical Monte Carlo method demonstrate the importance of end effects on fundamental molecular and thermodynamic properties of oligoelectrolyte solutions. Simulations are carried out for a series of solutions containing double-helical DNA oligomers of varying numbers of phosphate charges N (8 less than or equal to N less than or equal to 100) and univalent electrolyte at fixed activity (a +/- = 1.76 mmol/dm3). These results are used to evaluate as follows: C+N(a), the local concentration of cations at various axial positions along the oligomer surface; C+N(a), the axial average of these concentrations; TN, the preferential interaction coefficient expressed per oligomer charge, which is directly related to the fractional thermodynamic extent of association of counterions. A sufficiently long oligomer (N greater than or equal to 48 under the conditions simulated) is characterized by an interior region over which C+N(a) is uniform and equal to C+ infinity (a), the polyion limit. This interior region is flanked by two symmetric terminal regions, in which C+N(a) varies linearly with axial position from the end of the oligomer to a distance approximately 18 monomer units (approximately 3.1 nm) from that end. For long oligomers, the characteristics of the terminal regions [length and axial profile of C+N(a)] do not vary with N and, by inference, also pertain to the polyion under the same conditions. Both C+N(a) and TN approach their polyelectrolyte limits as linear functions of 1/N. These linear dependences can be attributed to the increasing predominance of the contribution due to the polyion-like interior of the oligomer as N increases.