mRNA optimiser

mRNA optimiser optimizes mRNA secondary structure by adjusting minimum free energy (MFE) to improve protein synthesis while preserving the encoded polypeptide sequence.

Key Features:

• MFE modulation: Adjusts minimum free energy (MFE) upward or downward to strengthen or weaken mRNA secondary structure.
• Hairpin approximation: Uses an approach that approximates hairpin formation to achieve significant changes in structural strength, including reported increases in MFE up to 40%.
• Synonymous sequence preservation: Alters nucleotide sequence without changing the encoded amino acid sequence to maintain protein identity.
• Time-efficient processing: Implements a time-efficient computational process for structure optimization.
• Algorithmic independence: Operates without relying on existing algorithms that predict RNA secondary structures or generate sequences for predefined structures.
• Multi-objective optimization: Supports joint optimization of MFE with other gene expression metrics such as codon adaptation index (CAI).
• Genome-scale optimization: Enables optimization of secondary structures at a genomic level to enhance gene expression efficiency.
• Translation-focused rationale: Targets secondary-structure features that can impede ribosome initiation and progression to improve protein yield.

Scientific Applications:

• Gene expression enhancement: Improves protein synthesis by optimizing mRNA secondary structure to reduce structural impediments to translation.
• Multi-objective gene design: Enables combined optimization of MFE and codon adaptation index (CAI) for engineered genes.
• Genome-wide structural optimization: Applies secondary-structure optimization across genomes to increase expression efficiency in diverse biological systems.

Methodology:

Approximates hairpin formation and modifies nucleotide sequence via synonymous changes to alter MFE while preserving the amino acid sequence; implements a time-efficient computational process and explicitly does not use existing RNA secondary-structure prediction or sequence-generation algorithms.