MOLECULAR-DYNAMICS STUDY OF THE EFFECT OF ION CONCENTRATION ON THE B-DNA, Z-DNA AND DNA-DAUNOMYCIN COMPLEX

Molecular Dynamics simulations were used to study the internal mobility of B-DNA double helix, Z-DNA double helix, and B-DNA complex with daunomycin, an anthracycline antibiotic, as a function of sodium ion concentration. The simulations were carried out during 100 ps by using Amber force field in DISCOVER force field libraries. The helix form of DNA was preserved throughout the simulations. The results show that the mobility of B-DNA increases as the sodium ion concentration increases, but that of Z-DNA decreases. The motions of the B-DNA complex with daunomycin are smaller than those of B-DNA without daunomycin. The presence of daunomycin stabilizes B-DNA double helix. The transition from Z-DNA complex to B-DNA complex with daunomycin was investigated.