Solvent effects on the conformation of DNA dodecamer segment: A simulation study

Different solvent temperatures with five kinds of counterions are used to investigate solvent effects on the DNA microscopic structure. The dodecamer d (CGCGAATTCGCG) DNA segment is merged into the solvents and its conformation transition is studied with the molecular dynamics simulations in detail. For the simple point charge model of water molecule with Na+ counterions, as temperature increases from 200 K to 343 K, the duplex DNA changes from stiff B form to a state between A form and B form, which we define as mixed (A-B) structure, with a double helix unwinding. To study the counterions effects, other four alkali cations, Li+, K+, Rb+, or Cs+ ions, are substituted for Na+ ions at 298 K and 343 K, respectively. For the cases of Li+, Rb+, and Cs+ ions, the duplex DNA becomes more flexible with sugar configuration changing form C2'-endo to C1'-endo type and the width and depth of minor groove at CpG and GpC steps moving towards A values, as the mass of the counterions decreasing. For the case of K+ ions, DNA-K+ interaction widens the width of minor and major grooves at ApA steps and TpT steps, respectively. It seems that the light ions (Li+ or Na+) prefer to interact with the free phosphate oxygen atoms while the heavier ions (Rb+ and Cs+) strongly interact with the base pairs. (C) 2011 American Institute of Physics. [doi: 10.1063/1.3610549]