Many therapeutic drugs bind to DNA as a mode of action. With a wide range of pharmaceutical applications, it is not surprising that many research efforts focus on understanding the fundamental principles behind small molecule-DNA interactions. In the present work, several biophysical techniques (isothermal titration calorimetry (ITC), UV-visible spectrophotometric titration and DNA thermal melting studies) were used to study the binding of a model pair of homologous naphthalene diimides (NDI) to DNA. Within the NDI series, the core intercalating component remains the same and each member differ only in the structure of the side chain that extend from either side of the intercalating core moiety. Preliminary binding affinity data obtained using spectrophotometry corroborated results obtained using ITC. Our results strongly suggest that substituent size plays a significant role during binding. Also studied, were several well known DNA binders; a common chemotherapeutic drug (daunomycin), a classical intercalator (ethidium), and a known minor-groove binder (hoechst33258). These provided an excellent means of evaluating our studies. The binding constant for daunomycin and ethidium were consistent with the published literature values under the conditions used in this study. The binding analysis for the minor-groove binder hoechst33258 exhibited strong heterogeneity showing an initial strong binding affinity at low drug/DNA ratios followed by a much weaker interaction at high drug/DNA ratio. This was consistent with an initial DNA minor-groove binding mode followed by intercalation. Future studies will involve other members of the NDI series to identify structural trends that could improve compound binding to DNA.