Automated Nucleic Acid Workflows for Codon-Optimized Protein Production
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Solution Overview
Problem
Current in vitro protein synthesis methods, whether based on RNA or DNA templates, face inefficiencies in workflow performance and yield of nucleic acid and protein molecules, particularly due to differences in codon usage and stability of mRNA in prokaryotic and eukaryotic systems, and the need for improved automation in nucleic acid molecule design and protein production.
Innovation Solution
The development of compositions and methods for designing nucleic acid molecules with optimized codon usage for specific organisms, using automated processes to generate mRNA and proteins, and the use of mechanical devices for workflow automation, including reagent management and protein detection/purification.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If standard translation systems use RNA as a template, then protein synthesis can be performed, but workflow efficiency and yield are limited
Solution Approach 1:
The patent combines transcription and translation into a single coupled reaction system, eliminating the need for separate purification steps between RNA synthesis and protein translation. This merging of two previously separate processes into one integrated workflow directly improves productivity while reducing time loss.
Solution Approach 2:
The patent performs preliminary optimization of codon usage in the DNA template design stage to match the preferences of the expression system. By pre-optimizing the nucleic acid sequence before the actual protein synthesis, the system achieves higher translation efficiency and yield without requiring additional time-consuming adjustments later.
2Reliability
If coupled transcription/translation systems use DNA templates, then protein synthesis is achieved, but mRNA stability and translation efficiency vary due to codon usage differences between prokaryotic and eukaryotic systems
Solution Approach 1:
The patent applies local optimization to the nucleic acid sequence by specifically optimizing codon usage in the coding regions while maintaining other functional elements. This localized adjustment of codon frequency and composition in specific regions of the DNA template improves mRNA stability and translation efficiency without altering the overall structure or function of the gene.
Solution Approach 2:
The patent changes the codon usage parameters of the nucleic acid sequence to match the preferences of the target expression system. By adjusting parameters such as codon frequency, GC content, and codon pair bias in the DNA template, the system achieves more stable mRNA and higher protein yield across different prokaryotic and eukaryotic expression platforms.
3Productivity
If manual processes are used for nucleic acid design and protein production, then flexibility is maintained, but automation and workflow efficiency are reduced
Solution Approach 1:
The patent employs a universal automated platform that can handle multiple tasks including DNA design, synthesis, transcription, translation, and protein purification through a single integrated system. This multi-functional automation platform improves workflow efficiency across the entire protein production pipeline while managing complexity through standardized protocols and reagents.
Data Source
AI summary
The present disclosure generally relates to devices, compositions and methods for designing and producing nucleic acid molecules and the production of encoded proteins using these nucleic acid molecules. In some aspect, the disclosure relates to automation for the in vitro generation of coding DNA molecules, the in vitro transcription of these DNA molecules to generate protein coding RNA molecules, and the in vitro translation of these protein coding RNA molecules to produce proteins.