Double-Stranded Neoantigen DNA Pools Without Error-Prone Ligation
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Solution Overview
Problem
Current methods are limited in producing long DNA molecules encoding tumor-specific antigens or infectious disease epitopes, and they introduce errors due to multiple ligation steps, restricting the number of personalized vaccine components and immunological response efficacy.
Innovation Solution
A synthetic DNA molecule design with segments for transcription and translation, including a promoter, MHC addressing, and poly A tail, allowing chemical synthesis and assembly into a pool of DNA molecules without ligation, enabling high immunological response through diverse tumor neoantigens or infectious agent epitopes.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Length of moving object
If multiple ligation steps are used to assemble DNA fragments, then the length of DNA molecules can be extended, but errors are introduced and manufacturing precision deteriorates
Solution Approach 1:
The patent extracts and eliminates the ligation step from the DNA assembly process. Instead of using traditional ligation-based assembly methods that introduce errors, the invention uses a ligation-independent assembly approach where DNA fragments are designed with overlapping homology regions that enable direct recombination without enzymatic ligation, thereby removing the source of assembly errors while still achieving long DNA molecule construction
Solution Approach 2:
The patent replaces the mechanical/enzymatic ligation system with a homology-based recombination system. DNA fragments are assembled through their overlapping homologous sequences rather than through ligase enzyme action, substituting a error-prone biochemical mechanism with a more precise homology-directed repair mechanism that maintains manufacturing precision while achieving the desired DNA length
2Adaptability or versatility
If the number of DNA fragments is increased to enhance immunological response, then vaccine efficacy is improved, but device complexity and process difficulty increase
Solution Approach 1:
The patent divides the vaccine design into modular DNA fragments, each encoding a specific neoantigen or epitope. These standardized fragments with uniform homology regions can be independently designed, synthesized, and then assembled into pools of varying sizes and compositions. This segmentation allows flexible adjustment of pool complexity to match immunological requirements without proportionally increasing assembly difficulty
Solution Approach 2:
The patent creates universal DNA fragment structures with standardized homology regions that can be reused across multiple different neoantigen sequences. This universal design allows the same assembly methodology to handle any number of different fragments, making the process scalable and reducing the complexity increase that would normally accompany higher fragment counts
Data Source
AI summary
A synthetic DNA molecule comprising one segment encoding a tumor neoantigen or an epitope from an infectious agent under the control of a promoter for the transcription into a corresponding RNA molecule and a segment for the translation of the said translated RNA molecule into a peptide.