mRNA Folding Algorithms for Structure and Codon Optimization
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arXiv
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| Main Authors: | , , |
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| Format: | Preprint |
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2025
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| _version_ | 1866916661927346176 |
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| author | Ward, Max Richardson, Mary Metkar, Mihir |
| author_facet | Ward, Max Richardson, Mary Metkar, Mihir |
| contents | mRNA technology has revolutionized vaccine development, protein replacement therapies, and cancer immunotherapies, offering rapid production and precise control over sequence and efficacy. However, the inherent instability of mRNA poses significant challenges for drug storage and distribution, particularly in resource-limited regions. Co-optimizing RNA structure and codon choice has emerged as a promising strategy to enhance mRNA stability while preserving efficacy. Given the vast sequence and structure design space, specialized algorithms are essential to achieve these qualities. Recently, several effective algorithms have been developed to tackle this challenge that all use similar underlying principles. We call these specialized algorithms "mRNA folding" algorithms as they generalize classical RNA folding algorithms. A comprehensive analysis of their underlying principles, performance, and limitations is lacking. This review aims to provide an in-depth understanding of these algorithms, identify opportunities for improvement, and benchmark existing software implementations in terms of scalability, correctness, and feature support. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2503_19273 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | mRNA Folding Algorithms for Structure and Codon Optimization Ward, Max Richardson, Mary Metkar, Mihir Biomolecules Quantitative Methods mRNA technology has revolutionized vaccine development, protein replacement therapies, and cancer immunotherapies, offering rapid production and precise control over sequence and efficacy. However, the inherent instability of mRNA poses significant challenges for drug storage and distribution, particularly in resource-limited regions. Co-optimizing RNA structure and codon choice has emerged as a promising strategy to enhance mRNA stability while preserving efficacy. Given the vast sequence and structure design space, specialized algorithms are essential to achieve these qualities. Recently, several effective algorithms have been developed to tackle this challenge that all use similar underlying principles. We call these specialized algorithms "mRNA folding" algorithms as they generalize classical RNA folding algorithms. A comprehensive analysis of their underlying principles, performance, and limitations is lacking. This review aims to provide an in-depth understanding of these algorithms, identify opportunities for improvement, and benchmark existing software implementations in terms of scalability, correctness, and feature support. |
| title | mRNA Folding Algorithms for Structure and Codon Optimization |
| topic | Biomolecules Quantitative Methods |
| url | https://arxiv.org/abs/2503.19273 |