Proven Intelligence Accelerating Next-Generation Therapies.

Executive Summary

Accurate quantification of full, partially full, and empty AAV capsids is a primary analytical challenge for gene therapy developers. The ratio of encapsidated to non-encapsidated vectors directly impacts product potency, dose determination, and the potential for immunogenic responses. Size-Exclusion Chromatography with Multi-Angle Light Scattering (SEC-MALS) provides a robust, first-principles method for characterizing these quality attributes, delivering precise data required for IND-enabling toxicology studies and CMC submissions.

The Challenge of Capsid Heterogeneity in AAV Production

During AAV vector production, the packaging of the single-stranded DNA genome into the viral capsid is an imperfect process. This results in a heterogeneous population of particles: fully packaged vectors, vectors containing partial or incorrect genomes, and empty capsids. An excess of empty capsids can contribute to unnecessary immune responses without providing therapeutic benefit, complicating the interpretation of preclinical data and potentially reducing clinical efficacy.

For gene therapy developers, achieving a consistent and high-purity AAV product is a prerequisite for a successful program. Quantifying this heterogeneity is not a simple task, requiring advanced analytical methods that can resolve these distinct populations with high precision.

SEC-MALS for Definitive Characterization

Size-Exclusion Chromatography (SEC) separates molecules based on their hydrodynamic radius, followed by a series of in-line detectors. The addition of a Multi-Angle Light Scattering (MALS) detector allows for the determination of the absolute molar mass of the particles eluting from the column.

Because a full AAV capsid containing a DNA genome has a significantly higher molar mass than an empty one, SEC-MALS can directly quantify the proportion of each species in a given sample. This approach provides a clear profile of the vector preparation.

Franklin Biolabs Vector Analytics Facilities

“We started collaborating with UPenn Vector core in 2023 and the AAV vector which they manufactured laid a foundation for development of a gene therapy candidate which will enter soon preclinical studies. The key people from UPenn Vector Core joined Franklin Biolabs and our partnership transitioned without interruption from UPenn Vecor Core to Franklin Biolabs Research Vector Division. Franklin Biolabs is integral to our AAV-vector based gene therapy candidate development, and we hope to continue the collaboration for years to come.”
— Biotech Partner

From Analytics to IND-Enabling Success

A well-characterized vector is the foundation of a successful therapeutic program. The ability to achieve desired biological outcomes, such as effective CNS delivery and mitigation of inflammation demonstrated in AAV gene therapy evaluations (PMID: 26447927), depends on the quality of the vector administered. By providing precise data on the empty/full capsid ratio, SEC-MALS analysis directly informs dose optimization for IND-enabling toxicology studies and minimizes clinical risk.

This analytical rigor is a component of our integrated approach, which has supported a 100% successful IND rate for programs initiated since 2019. While the Franklin Biolabs brand launched in 2024, our scientific lineage and proven platforms enable sponsors to move candidates toward IND within an 18-24 month timeline. Our work is conducted within a >100,000 sq ft facility designed for GxP-compliant analytical and preclinical services.