Validated chromatographic method for mcDNA quantification in complex samples

Minicircle DNA (mcDNA) is a non-viral vector known for its superior therapeutic potential and safety, making it a promising biopharmaceutical platform for gene therapy, DNA vaccination, and molecular biology applications. However, its structural similarity to parental plasmid (PP), the presence of isoforms (e.g., open circular mcDNA and supercoiled mcDNA), and host-derived impurities pose significant challenges for accurate detection and quantification, which are key steps for effective quality control. This work reports, for the first time, the development and validation of an anion-exchange chromatographic method for quantifying p53-mcDNA using a customized TSKgel® DNA-NPR column. Chromatographic parameters, including pH, elution gradient, gradient time, and flow rate, were optimized. Real samples from complex Escherichia coli lysates containing p53-mcDNA, p53-PP, miniplasmid (mP), and RNA were used, demonstrating applicability for process monitoring. The method demonstrated consistent linearity (R² = 0.9994) over the 10-100 µg/mL range for total DNA, with accuracy meeting FDA guidelines. The method was validated in terms of selectivity, linearity, accuracy, precision, and sensitivity over the concentration range of 10-100 µg/mL, with the lower limit of quantification (LLOQ) and detection (LOD) established at 10 µg/mL and 1 µg/mL, respectively. Intra- and inter-day precision studies confirmed reproducibility, with coefficients of variation below 6%. Overall, the chromatographic method here developed and proposed effectively separates p53-mcDNA from its parental plasmid and may support process monitoring during upstream and downstream operations.