The advent of gene therapy and polynucleotide-based vaccines has resul
ted in the use of plasmid DNA as a drug substance. Although biological
ly (cell or animal) based assays must currently be employed to establi
sh the identity and potency of such drugs, we argue that in the future
, a combination of microchip-based mutation detection devices combined
with an array of chromatographic, electrophoretic, hydrodynamic, and
spectroscopic methods can be employed to rigorously establish these pr
operties. We review a variety of such methods in this context and also
consider the issue of the chemical stability of plasmids. Extensive c
omparison is made to protein-based pharmaceuticals with the unique imp
ortance of polynucleotide sequence emphasized in comparison to protein
tertiary structure.