Derivatives of amine, azepane, pyrrolidine, and piperazines are important structural moieties found in many biologically active molecules whose chemical structures can also be designed as drug. Also the presence of nitrogen in these compounds enables the quaternization and ionic structure which is required for water solubility. Phthalocyanines appended with this kind of nitrogen-containing compounds have the ability to dissolve in water and can be used in photodynamic therapy as anticancer agents. In our previous work, 2-(azepane-1-yl)ethanol, 2,4,6-tris(N,N-dimethylaminomethyl)phenol, and 1-methylpyrrolidin-2-ylmethanol were attached with silicon phthalocyanines (Pcs) and mainly photodynamic therapy was experimented rather than their interactions with DNA. In this work, compounds 2-(azepane-1-yl)ethanol, 2,4,6-tris(N,N-dimethylaminomethyl)-phenol, and 1-methylpyrrolidin-2-ylmethanol free from phthalocyanines and 4-(2-hydroxyethyl)-1-piperazinepropanesulfonic acid were treated with calf-thymus DNA to test whether these nitrogen-containing compounds have more effects on binding mechanisms with DNA except making phthalocyanines water soluble. The results indicated that compounds 2-(azepane-1-yl)-ethanol, 4-(2-hydroxyethyl)-1-piperazinepropanesulfonic acid, and 1-methylpyrrolidin-2-ylmethanol bind to minor grooves of DNA while compound 2,4,6-tris(N,N-dimethylaminomethyl)phenol exhibited intercalative properties. The active sites of these compounds were guanine-cytosine which is important for cancer treatment. All binding processes were entropy driven and hydrogen bonds were strong according to calculated lengths of bonds. Compared to phthalocyanine-attached forms, they have direct and dominant effects on binding with DNA in Pc free forms.