Salt-Nucleic Acid Interactions

Abstract

Coulombic interactions of salt ions with polymeric and oligomeric nucleic acids in solution have large and distinctive effects on ion distributions, on thermodynamic coefficients, and hence on equilibrium processes involving nucleic acids, such as their conformational transitions and binding interactions. In experimental or theoretical studies where an oligonucleotide is taken to represent the corresponding polynucleotide, the impact of coulombic end effects on molecular and thermodynamic properties must be taken into account. Observable consequences of coulombic interactions in nucleic acid solutions have been calculated by using models with varying degrees of detail and methods formulated at varying levels of rigor. From comparisons of experimental results with predictions of the prevalent theoretical approaches, this review concludes that the more rigorous methods have proved capable of accounting for thermodynamic (and some molecular) consequences of coulombic interactions with a minimal number of preaveraged parameters that represent the most important structural features of the nucleic acid solution.

Predicting Stability of DNA Duplexes in Solutions Containing Magnesium and Monovalent Cations

“…DNA duplexes formed from two complementary strands in Na + buffers do not show a significant dependence of ∆n on N bp (33). This may be due to the fact that the number of negative charges per molecule is halved upon strand separation and thereby masking the Coulombic end effects (11,61,62). Surprisingly, we observe the opposite end effects with magnesium ions (Figure 10).…”

“…Useful salt-correction equations for free energies, ∆G°, and entropies, ∆S°, of DNA hybridization can be developed from eq 16 if the following assumptions are made: (i) Duplex melting is a two-state process. (ii) Counterion effects are mostly entropic (31,61,66). (iii) Enthalpies and entropies of DNA melting reactions are temperature independent, i.e., ∆C p is zero.…”

Extracting water and ion distributions from solution x-ray scattering experiments

“…[1][2][3][4][5][6][7] Elucidating how ions and water molecules distribute themselves around the solutes can provide valuable insights into their function and can also provide experimental tests for theoretical predictions. [4][5][6][8][9][10] However, there are few experimental methods that directly probe the positions of ions and water molecules in the solution. Ion counting via dialysis can provide a quantitative measure of the ionic atmosphere around the solute, but it provides only a total (excess) number, and not any information the shape of the ion cloud.…”

Mg 2+ -dependent conformational change of RNA studied by fluorescence correlation and FRET on immobilized single molecules

“…Specific binding sites for magnesium ions (1) have been observed crystallographically in a number of systems, including tRNA (2), hammerhead ribozyme (3), the P4-P6 domain of the Tetrahymena thermophila group I intron (4), and a 5S ribosomal RNA domain (5). Metal ions can also stabilize the RNA structure nonspecifically by screening the negatively charged backbone (6). Furthermore, the role of counterions is critical to understanding protein-nucleic acid interactions (7).…”