Scientists from MIPT and Skolkovo have created an exact model of an aqueous solution around DNA and sodium, which replicate the environment around the DNA. The research findings, published in the Journal of Chemical Theory and Computation, will help better account for the behavior of nucleic acids inside the cell for drug development. Briefly about the scientific work is reported in a press release on the website Godnauki.rf.
Many artificial solutions with DNA contain a different ratio of sodium and potassium, while the concentration of potassium in the nucleus of a living cell significantly exceeds the concentration of sodium. This difference can significantly affect the accuracy of experiments, the results of which cannot be transferred to living systems. Potassium and sodium are needed to stabilize the structure of DNA strands, which would otherwise separate due to the fact that they carry a large negative charge. In addition, ions are essential for DNA and RNA to function.
In the new study, a team of scientists has created a simulation of the behavior of a DNA molecule in solutions with different combinations of models of water and ion molecules. In each case, the dependences of the concentration of sodium and potassium ions on the distance to the DNA axis were determined, and the results were compared with experimental data. It turned out that the optimal point charge (OPC) model was the most preferable because it demonstrated the optimal degree of binding of potassium and sodium to DNA.