Book of Abstracts: Albany 2003
June 17-21 2003
Effect of Nucleic Acid Oligomer Length on Salt Ion Accumulation; NLPB Analysis at Experimental Salt Concentrations
Experimental and theoretical studies of effects of salt concentration ([salt]) on nucleic acid processes provide information on the difference in the number of salt ions thermodynamically associated with products and reactants. The thermodynamic degree of ion association per nucleic acid charge (n) (defined in terms of the salt-nucleic acid preferential interaction coefficient) is a combined effect of accumulation of counterions and exclusion of coions. We use nonlinear Poisson-Boltzmann (NLPB) equation to calculate thermodynamic degree of ion accumulation near nucleic acid oligomer as a function of oligomer length for single-stranded (ss) and double-stranded (ds) nucleic acids in [salt] range 0.15 M - 1M. Preaveraged structural model of a nucleic acid takes into account key parameters, axial charge separation, radial distance of closest approach of ion to oligomer axis, and number of oligomer phosphate charges. Investigated lengths for both ss and ds nucleic acids are between 2 and 70 phosphate charges. Combined with previous analyses at lower [salt] (1, 2) this analysis provides complete picture of salt- and length-dependence of ion accumulation by ss- or ds- nucleic acid oligomers between 1 mM and 1 M univalent salt.
Ion accumulation by a polyion strongly depends on axial charge density changing between two limits, n=1 (per charge of a highly charged polyion) and n=0 (per charge of a weakly charged polyion), and decreases with increase in [salt]. Oligomers exhibit less accumulation per charge than polyion of same axial charge density and radius. Obtained results provide explicit expression for decrease of n with decreasing number of oligomer charges. Even for an oligomer with high axial charge density ion accumulation per charge approaches zero as oligomer length is reduced.
Results in Table I show that at 0.01 M salt, individual n's differ for oligomer (n10 (ss) and n20 (ds)) and polymer (n∞ (ss) and n∞ (ds)) but Δn is coincidentally the same. At higher salt, 0.15 M - 1 M, Table I predicts 25-33% reduction in ion release in melting of 10 base pair two strand duplex (Δn20-2(10)) as compared to polymeric value (Δn∞). This prediction is consistent with empirical salt-dependences of duplex stability (ΔG037) and experimental melting temperature of DNA duplexes fewer than 17 base pair at the same [salt] range (3). Obtained results provide explicit length-dependence of non-specific salt effects on DNA processes and background for treating specific interactions of uni- and multivalent ions with DNA oligomers.
I. A. Shkel1