Kinetic study of DNA condensation by cationic peptides used in nonviral gene therapy: Analogy of DNA condensation to protein folding

Synthetic nonviral vector systems are attractive because of their apparent simplicity of preparation and use. However, there are many barriers to success at the moment, including the formulation of uniform and reproducible particles of transfection competent, condensed nucleic acids such as plasmid DNA (pDNA). For this reason, we have been studying the kinetics of cationic peptide-mediated pDNA condensation and the reverse process following peptide dissociation by stopped-flow techniques under conditions commonly used to prepare synthetic nonviral vector systems. We observe that the process of pDNA condensation and the reverse process of pDNA expansion appear to be equivalent to protein folding and unfolding, respectively. We also observe chaotic behavior at low peptide/pDNA ratios that becomes more uniform at higher ratios suggesting that with suboptimal ratios, pDNA is condensing in a multitude of conformations, each representing different stages of hydrophobic collapse in the search for the thermodynamically most stable (i.e., the fully condensed pDNA molecule). At higher ratios, peptide/pDNA complexes formed appear to be increasingly irreversible consistent with the formation of kinetically and/or thermodynamically stable, condensed pDNA molecules. Such stable states could create problems for the successful transcription of pDNA post delivery to cells.