The current status of the ab initio calculations for the electronic states, stable structures and dynamics of DNA and associated molecular systems is reviewed. Using computational tools such as the fragment molecular orbital method, the (ab initio and classical) molecular dynamics method and the charge equilibration method, we are analyzing the mechanism of transcriptional regulation in which the molecular recognition between DNA and proteins plays a vital role. In addition, we are studying the electron transfer or transport properties of DNA which have recently attracted considerable attention in the context of radiation biology and nanotechnology applications. In these problems, the interfaces among DNA, proteins, ligand molecules, solvent, counter ions and electrodes are often essential for their relevant functions. The theoretical issues remaining to be elucidated are also addressed.