Valence and structure relationships in oligonucleotides

There are many models that can be used to estimate the degree of shielding and predict the valence of a nucleic acid. Here, Counter-ion Condensation theory and Grand Canonical Monte Carlo simulations are compared with an experimental approach. Membrane-Confined Electrophoresis was used to measure the effective valence of several nucleic acid oligomers. The Debye-Huckel-Henry equation was then utilized to calculate the valence of these oligomers. The valence was determined to be -17.86 (+/- 1.03) for a 20 base-pair double-stranded DNA oligomer in 93 mM KCl and 10 mM Tris HCl, pH 8. This experimental value agrees well with rigorous Grand Canonical Monte Carlo simulations. The increase in charge density from a single-stranded to double stranded to quad stranded DNA oligomer and its effect on valence was also explored. The results indicate that as charge density increases, the portion of exposed charge decreases. From this data, we were able to determine an upper limit on the valence to surface area ratio for biological molecules. Finally, the valence of a ribosomal RNA fragment was measured in buffers of varying magnesium concentration. The data show a trend of decreasing valence with increasing magnesium concentration