MFT scientists and Skolkovo together with foreign colleagues modeled the aqueous solutions of potassium and sodium, which repeat the medium around DNA. The results of the study published in Journal of Chemical Theory and Computation will help better take into account the behavior of nucleic acids inside the cell for the development of drugs. Briefly about scientific work is reported in a press release on the SDUNUKI website.rf.
Many artificial solutions with DNA contain a different ratio of sodium and potassium, while in the kernel of the living cell, potassium concentration significantly exceeds sodium concentration. This difference can significantly affect the results of experiments that cannot be transferred to live systems. Potassium and sodium are necessary to stabilize the structure of DNA threads, which otherwise will be disconnected due to the fact that they carry a large negative charge. In addition, ions are needed for the functioning of DNA and RNA.
In a new study, the team of scientists has created a simulation of the behavior of the DNA molecule in solutions with various combinations of models of water and ion molecules. In each case, the dependences of the sodium and potassium ions concentration were determined from the distance to the DNA axis, and the results were compared with experimental data. It turned out that the OPC model (Optimal Point Charge) was most preferable because it demonstrated the optimal degree of potassium binding and sodium with DNA.