Synthetic RNA Vectors Reducing CpG UpA Dinucleotides
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Solution Overview
Problem
Current RNA expression systems face challenges in enhancing protein expression due to the presence of CpG and UpA dinucleotides, which can activate immune responses and reduce expression levels, particularly in RNA-based systems where TLR9 recognition is not applicable.
Innovation Solution
Development of synthetic RNA expression vectors with reduced CpG and UpA dinucleotide frequencies, achieved through nucleotide modifications in specific regions of the vector, to enhance expression levels by minimizing immune activation and optimizing nucleotide composition.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If CpG and UpA dinucleotides are present in RNA expression vectors, then the sequence maintains natural composition and coding capacity, but immune responses are activated and expression levels are reduced
Solution Approach 1:
The patent applies parameter changes by systematically modifying the nucleotide composition of RNA expression vectors, specifically reducing the frequency of CpG and UpA dinucleotides to below natural background levels. This compositional parameter optimization resolves the contradiction by eliminating immune activation triggers while preserving coding capacity through synonymous mutations and sequence redesign.
Solution Approach 2:
The invention extracts and removes the harmful elements (CpG and UpA dinucleotides) from the RNA expression vector sequence. By identifying and eliminating these specific dinucleotide motifs through in silico design and synthetic construction, the patent separates the beneficial coding function from the harmful immune activation function.
2Productivity
If nucleotide composition is modified to reduce CpG and UpA frequencies, then expression levels increase and immune activation decreases, but sequence design complexity increases
Solution Approach 1:
The patent applies preliminary action by performing in silico sequence design and optimization before actual RNA vector construction. The desired nucleotide composition (reduced CpG and UpA frequencies) is predetermined and built into the sequence design phase, allowing systematic optimization of expression vectors before experimental validation and reducing trial-and-error complexity.
Solution Approach 2:
The invention uses copying by creating synthetic RNA sequences that replicate the desired nucleotide composition characteristics. Through in silico design, optimized sequences are generated and copied into synthetic vector constructs, allowing the propagation of beneficial compositional features across multiple vector designs without manual redesign.
Data Source
AI summary
The present invention relates to methods and compositions for enhancing expression from RNA expression vectores. The invention is based upon the observation that reducing the frequency of the dinucleotide CpG and UpA has a significant effect on expression from such vectores. Aspects of the invention include, amongst others, synthetic RNA vectores, virions, cells, methods of producing vaccines and methods of treatment or immunisation.