Circular RNA (circRNA) vaccines have attracted increasing attention due to their stable closed-loop structures and persistent protein expression ability. During the synthesis process, nicked circRNAs with similar molecular weights to those of circRNAs are generated. Analytical techniques based on differences in molecular weight, such as capillary electrophoresis, struggle to distinguish between circRNAs and nicked circRNAs. The characteristic degradation products of circRNAs and their biological activities remain unclear. Therefore, developing methods to identify target circRNAs and non-target components and investigating degradation patterns will be beneficial to gaining an in-depth understanding of the properties and quality control of circRNAs vaccines. The reversed-phase HPLC (RP-HPLC) method was established for identification of target circRNAs, product-related substances, and impurities. Subsequently, we investigated the degradation patterns of circRNAs under thermal acceleration conditions and performed biological analysis of degradation products and linear precursors. Here, RP-HPLC method effectively identified circRNAs and nicked circRNAs. With thermal acceleration, circRNAs exhibited a “circular→nicked circRNAs→degradation products” degradation pattern. Biological analysis revealed that the immunogenicity of degradation products significantly decreased, whereas linear precursors did not possess immunogenicity. Thus, our established RP-HPLC method can be used for purity analysis of circRNA vaccines, which contributes to the quality control of circRNA vaccines and promoting the development of circRNA technology.

Background: Self-amplifying mRNA (saRNA) holds promising application prospects. However, due to the inclusion of a replicase sequence, its extended length leads to premature termination during in vitro transcription (IVT), resulting in poor product integrity. This study aims to optimize the IVT process for saRNA vaccines to enhance integrity, thereby addressing the key challenge in saRNA vaccine manufacturing. Method: Guided by the Quality by Design (QbD) framework, Design of Experiment (DoE) methodology was employed to design diverse combinations of process parameters for IVT reactions. Predictive models were established to identify critical process parameters (CPPs) influencing integrity and yield. An optimized parameter set and process design space, meeting predefined yield and integrity standards, were developed. The impact of integrity on the immunogenicity of saRNA vaccines was further investigated. Results: Mg²⁺ concentration exerted the most pronounced effect on saRNA integrity. Under optimized IVT conditions, integrity exceeded 85%. Mathematical modeling simulations defined the IVT design space, meeting the preset criteria of ≥80% integrity and ≥600 μg/100 μL yield while accommodating longer saRNA constructs. Notably, murine model data revealed that higher saRNA integrity significantly enhanced antigen-specific antibody and T-cell responses. Conclusion: This study successfully established a multivariate IVT design space fulfilling preset integrity and yield criteria, providing critical data references for the industrialization and quality specification development of saRNA vaccines.