Optimization & Comparative Analysis Of Host Cell DNA/RNA Quantification And Plasmid Supercoiled Percentage: Cost-Effective Agarose Gel Electrophoresis vs High Sensitivity qPCR And IEC-HPLC

By Delicia Henriques, PhD; Murali Jujjavarapu, Ryan Rubino, Aneri Maniar, Eric Gliniak, Aparna Nandakumar, Minqi Jiang, Philemon Asfeha

Ensuring plasmid purity and structural integrity is critical for safe and effective biopharmaceutical production. Traditional methods like qPCR and IEC-HPLC deliver high sensitivity but can be costly and time-intensive, limiting their use for routine screening. Recent advancements demonstrate that agarose gel electrophoresis (AGE), when optimized with refined loading and imaging parameters, can serve as a practical alternative for host cell DNA/RNA detection and plasmid supercoil percentage analysis.

Comparative studies show AGE achieves results within ±2% of HPLC measurements for supercoiled plasmid content, while reducing processing time from two days to just two hours. AGE also provides semi-quantitative capabilities for host nucleic acid detection, meeting specifications for initial screening at a fraction of the cost. These findings highlight a valuable trade-off between sensitivity and affordability, enabling resource-conscious facilities to maintain compliance without sacrificing quality.

Explore how this approach can streamline plasmid quality control and support GMP readiness while optimizing operational efficiency.