Mechanical deformability of DNA, both on global (flexible-rod) and local (base-pair step) level is of fundamental importance in many biological processes, such as protein binding or DNA packing in the nucleus. We show that all-atom molecular dynamics simulations with explicit inclusion of solvent and ions are a useful tool not only for investigating DNA deformability, but also for elucidating spatial and temporal correlations of DNA movements on mesoscopic level or the effects of modified bases. Methodological issues, such as the force-field dependence, were studied as well.