The study explores the synthesis, structural analysis, and binding properties of eight analogs of 2-amino-1,8-naphthyridine dimers (ANPxys) targeting DNA and RNA. These dimers, derived from ANP77, are connected at varying positions to investigate how positional alterations influence molecular conformations and their interactions with nucleic acids. The primary focus lies on evaluating the effects of these structural variations on DNA and RNA binding through fluorescence quenching and thermal denaturation assays. Absorption and fluorescence measurements revealed distinct electronic states for ANPxys, with emission maxima between 389.5 and 398.5 nm. Conformational analysis indicated that most ANPxys adopt unstacked conformations in aqueous solutions, though some, like ANP47 and ANP67, showed higher probabilities of stacked conformations. Thermal denaturation studies demonstrated ANPxys bind and stabilize cytosine-rich DNA motifs with varying affinities, with ANP77 showing the strongest effects. RNA binding studies targeting U/CC motifs across 256 sequences revealed unique fluorescence quenching patterns for each ANPxy, reflecting sequence specificity. Hierarchical clustering grouped ANPxys into parallel-stacked and twisted-stacked clusters, correlating their conformations with binding preferences. This work highlights the critical role of connection positions in determining ANPxy binding specificity and conformational behavior. The findings provide a basis for designing small molecules with tunable structures and enhanced RNA-binding capabilities, paving the way for the development of RNA-targeted therapeutics.