Interactions between manganese ions and the DNA molecules were studied by means of UV and IR spectroscopy, as well as electronic and vibrational circular dichroism. It was shown that the process of manganese ion binding can be subdivided into three stages depending on the content of manganese ions. At the first stage, when the content of manganese ions is low, the interaction of the metal ions with DNA phosphates occurs, causing partial screening of their negative charge and stabilization of the double helix. This stage ends when the manganese-to-phosphate ratio reaches 1 ([Mn]/[P] < 1). At the second stage, at 1 < [Mn]/[P] < 6, synchronous binding to phosphate groups and nitrogen bases of DNA is observed. At this stage, one manganese ion can be simultaneously coordinated to the oxygen of the phosphate group and to the neighboring nitrogen base of DNA. At a higher [Mn]/[P] ratio, the destabilization of the double-helix begins and partial breakage of the hydrogen bonds in the base pairs occurs.