A series of binuclear ruthenium(II)-polypyridyl complexes of the type [Ru(2) (N-N)(4) (BPIMBp)](4+) , in which N-N is 2,2'-bipyridine (bpy; 1), 1,10-phenanthroline (phen; 2), dipyrido[3,2-d:2',3-f] quinoxaline (dpq; 3), dipyrido[3,2-a:2',3'-c] phenanzine (dppz; 4), and 1,4'-bis[(2-pyridin-2-yl)-1H-imidazol-1-yl)methyl]-1,1'-biphenyl (BPIMBp) is a bridging ligand, have been synthesized and characterized. These complexes are charged (4+) cations and flexible due to the -CH(2) group of the bridging ligand and possess terminal ligands with variable intercalative abilities. The interaction of complexes 1-4 with calf thymus DNA (CT-DNA) was explored by using UV/Vis absorption spectroscopy, steady-state emission, emission quenching with K(4) [Fe(CN)(6) ], ethidium bromide displacement assay, Hoechst displacement assay, and viscosity measurements and revealed a groove-binding mode for all the complexes through a spacer and an intercalative mode for complexes 3 and 4. A decrease in the viscosity of DNA revealed bending and coiling of DNA, an initial step toward aggregation. Interestingly, a distinctive honeycomb-like ordered assembly of the DNA-complex species was visualized by fluorescence microscopy in the solution state. The use of SEM and AFM confirmed the disordered self-organization of the DNA-complex adduct on evaporation of the solvent. The small orderly nanosized DNA aggregates were confirmed by means of circular dichroism, dynamic light scattering (DLS), and TEM. These complexes are moderately cytotoxic against three different cell lines, namely, MCF-7, HeLa, and HL-60.