Studies on the hydration of B-,Z-DNA and vitamin C molecule

Abstract

Part A A theoretical study on the hydration of B-and Z-DNA double helices has been carried out using empirical potential energy functions. The interaction energy between water and the model compounds has been computed considering only the first hydration shell. The results show the number of binding water molecules to be thirtysix and twenty-five in B- and Z-DNA, respectively. The water molecules in the first hydration shell of B-DNA are very well ordered along the phosphate groups of the backbone whereas those of Z-DNA are more disordered than in B-DNA and are more strongly bound. the water molecules near the first hydration shell of Z-DNA are thought to move more freely than those of B-DNA. Part B Monte Carlo simulations have been performed on the pure liquid water and the dilute aqueous solution of Vitamin C molecule at 298 K, 273 K and 253 K. The simulations were carried out by using optimized intermolecular potential function and TIP4P water model. In each case, the following properties are calculated, such as distribution of several water ring structures and free energy of the solution. The results show that the free energy of water around Vitamin c molecule is lower than pure water at same temperature and shift to lower value as the temperature decrease. And also, the hydrogen bond linkage of water molecules show several kind of cyclic form. The concentration of six membered ring is more dominant than other cyclic form and increased as the tmeperature decreases from 298 K to 253 K, respectively. In the solution of Vitamin C, the concentration of six membered ring is more increased than pure liquid water at same temperature. Part C The Molecular Dynamics (MD) simulations are used to study the internal mobility of B- and Z-DNA double helix, and B-DNA complex with daunomycin, an anthracycline antibiotic, according to the increase of the sodium ion concentration. The simulations were carried out during 100 ps by using Amber force field in DISCOVER force fiel...