Polypyridyl based ruthenium(II) complexes, [Ru(bpy)2(furphen)](PF6)2 (1) and [Ru(bpy)2(imiphen)](PF6)2 (2) {furphen: 2-(furan-2-yl)-1H-imidazo[4,5-f][1,10]phenanthroline and imiphen: 2-(1H-imidazol-2-yl)-1H-imidazo[4,5-f][1,10]phenanthroline} were synthesized and characterized by ESI-MS, NMR, UV-Visible and fluorescence spectroscopic techniques. The interaction of Ru(II) complexes with calf-thymus DNA (CT DNA) as well as oligonucleotides containing mismatches and abasic sites was studied along with unmodified control DNA. Based on absorption titration studies, binding constants (Kb) for the interaction of complexes 1 and 2 with DNA were found to be 6.7 ± 0.2 × 10(3) and 4.9 ± 0.2 × 10(4) M(-1), respectively. Hydrodynamic studies revealed weak interactions between the two complexes and CT-DNA. Luminescence studies revealed that both the complexes exhibit a five-fold increase in emission upon addition of CT-DNA. The integrated emission intensity of complexes 1 and 2 with CC mismatch oligonucleotides was 1.5 and 1.2 fold higher than that of control GC match oligonucleotides, respectively. Both the complexes did not show any specificity towards abasic or other mismatch sites except for CC mismatch. The results from this study provide an insight into the requirements of ligand shape in recognising DNA mutations such as mismatch and selectivity between DNA mismatches.