The tracking of plasmid DNA (pDNA) movement within cells requires the attachment of labels to the DNA in a manner such that: (a) the pDNA remains intact during the labeling process and (b) the labels remain stably attached to the DNA. Keeping these two criteria in mind, we have recently developed a series of alkylating reagents that facilitate the one-step, covalent attachment of compounds directly onto nucleic acids in a nondestructive manner. Using these DNA-alkylating reagents, we have attached a wide range of both fluorescent and nonfluorescent reporter molecules onto pDNAs. We now show that even with the covalent attachment of various marker compounds, the pDNA remains expression competent. The ability to create labeled, expression-competent DNA allows for the simultaneous tracking of both pDNA location and reporter gene expression within living or fixed cells.