mRNASyner: An Integrative Framework for Full-Length mRNA Sequence Optimization via Multimodule Synergistic Design

Messenger RNA (mRNA) technology holds great promise in biomedicine; however, its therapeutic efficacy relies heavily on translation efficiency and the in vivo stability of mRNA sequences, both of which are governed by dynamic interactions between the coding and noncoding regions. Existing optimization approaches typically focus on individual sequence components and lack the capacity for global, synergistic optimization. Moreover, their performance is often limited when processing long sequences or supporting iterative sequence refinement. To overcome these challenges, we propose a unified and interpretable in silico framework for full-length mRNA sequence design, integrating CDS optimization, UTR generation, and degradation modeling. In silico case studies based on respiratory syncytial virus (RSV) vaccine design demonstrated that mRNASyner achieved a favorable balance between translational accessibility and structural stability. mRNASyner thus enables the design of full-length mRNA sequences, supports long-sequence optimization, and offers a novel solution for the development of personalized mRNA therapeutics.