The efficiency of nonviral vectors for gene delivery may be enhanced by understanding the key barriers that limit the translocation of the therapeutic DNA into the nucleus. One such barrier is the instability of DNA in the cytoplasm. In this work, we have developed a method to dual-label plasmid DNA to be utilized as a tool to elucidate DNA instability during its trafficking in the intracellular microenvironment. Plasmid DNA containing rhodamine and maleimide groups linked using peptide nucleic acid (PNA) linkers was utilized for conjugation. Covalent conjugation of the maleimide group with a second fluorophore, fluorescein, did not alter the electrophoretic mobility or the structural integrity of the DNA, as confirmed by gel electrophoresis. The intact DNA was visualized as a single color (yellow) due to the close proximity of the green and red fluorophores. DNA degradation was simulated using restriction endonucleases (BamH1 and PflMI) to cut the DNA at two or more sites resulting in color separation. Confocal time-lapse imaging was utilized to follow DNA stability upon incubation of Lipofectamine2000/dual-labeled DNA complexes in CHO-K1 cells. Yellow fluorescent voxels were seen in the cell cytoplasm indicating the presence of intact DNA. Red and green fluorescent voxels were also seen in a few cells, suggesting separation of the fluorophores and probable DNA degradation. The methodology developed in this report provides a new tracking tool for investigators to explore DNA degradation at the molecular level inside single cell.