A comparative analysis was conducted on DNA interaction with two new manganese complexes (mononuclear complex with one 1,10-phenanthroline, binuclear complex with six 1,10-phenanthroline ligands), as well as with free 1,10-phenanthroline and Mn2+ ions in solutions with different NaCl concentrations. The results showed that manganese in the mononuclear complex coordinates to N7 of guanine in the major groove of DNA. This binding facilitates the penetration of 1,10-phenanthroline into the same groove, where it subsequently intercalates between DNA bases. In contrast, the binuclear manganese complex binds externally through electrostatic interactions at the periphery of the double helix. Such binding screens the negative charges of DNA and promotes intra- and intermolecular DNA — DNA contacts through the association of hydrophobic phenanthroline ligands. Intercalation of 1,10-phenanthroline is unfavourable for the binuclear manganese complex. DNA conformational changes upon its binding with Mn2+ ions and free 1,10-phenanthroline show both similarities and significant differences compared with those caused by the manganese complexes. Computer modelling revealed that free 1,10-phenanthroline preferentially binds within the minor groove of DNA, exhibiting specificity for A−T base pairs. However, it can also localize near the major groove, particularly adjacent to G−C base pairs.