The investigation of changes in arrangement of water molecules and salt ions around the DNA molecule in melting process: A Molecular Dynamics Simulation Study

We have performed molecular dynamics simulation on B-DNA duplex (CGCGAATTGCGC) at different temperatures. The DNA was immerged in a salt-water medium with 1 M NaCl concentration. At each temperature the radial distribution function is calculated for different atoms of DNA molecule. Almost for all atoms of the DNA by double helix single-stranded transition, the water molecules release from DNA duplex and cations ions are close to single-stranded DNA, but this behavior does not seen in melting temperature, clearly. Therefore release of water molecules and approaching of cations to DNA by increasing temperature does not affect in sharpness of transition curve. The most of the water molecules and cations are around the negatively charged phosphate oxygen atoms. The number of water molecules released form first shell hydration upon melting in minor groove is higher than major groove and intrusion of cations into minor groove after melting is higher than major groove. Imino-proton exchange rates are dependent to type of bases and influence on the hydration of protons.