Synthetic Gene Optimization via Sequence Context Modeling
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Genes cloned from one organism often fail to express or express poorly when introduced into a different organism, due to sequence-specific issues such as message termination, RNA destabilization, and regulatory effects that vary across organisms or contexts, necessitating optimization methods that account for these factors.
Innovation Solution
A method for making synthetic genes by identifying stable and disallowed sequences, developing a statistical model based on the target expression system's genome or transcriptome, and modifying the candidate gene sequence to optimize expression without removing stable sequences, thereby enhancing gene expression by mimicking the target system's sequence context.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Adaptability or versatility
If a gene is cloned from one organism and expressed in another organism, then the gene can be studied or produced in a different system, but the gene often fails to express or expresses poorly due to sequence-specific issues
Solution Approach 1:
The patent applies parameter changes by modifying the nucleic acid sequence parameters of the candidate gene to match the target organism's genomic characteristics. This includes adjusting codon usage frequency, GC content, and other sequence parameters that are specific to the target organism, thereby improving expression reliability while maintaining cross-organism applicability
Solution Approach 2:
The patent applies local quality by making specific localized modifications to the gene sequence at critical positions rather than complete redesign. This includes modifying specific codons, removing specific regulatory sequences, or adjusting specific regions that are known to cause poor expression, while preserving other functional regions
2Productivity
If sequences are removed to improve gene expression, then expression can be enhanced by removing harmful sequences, but essential stable sequences may be lost
Solution Approach 1:
The patent applies the taking out principle by identifying and removing specific harmful sequences (disallowed sequences) from the candidate gene while preserving stable sequences. The method extracts only the problematic elements that cause poor expression, such as termination sequences or degradation signals, while leaving intact essential regulatory elements and stable sequence regions
Solution Approach 2:
The patent converts harmful sequence elements into beneficial ones by strategically placing stable sequences at positions where they provide regulatory benefits. For example, stable sequences that normally might cause termination or degradation are repositioned or modified to function as beneficial regulatory elements that enhance expression, transforming potential harm into advantage
3Productivity
If the gene sequence is optimized to match the target system, then expression can be significantly improved, but the original sequence characteristics are altered
Solution Approach 1:
The patent applies partial action by making only the necessary minimal modifications to achieve optimal expression, rather than completely redesigning the sequence. This includes making partial codon optimizations, removing only specific harmful sequences, and adjusting only the critical regulatory regions, thereby improving expression while preserving the maximum amount of original sequence composition
Data Source
AI summary
Methods for making a synthetic gene are provided. The methods find use in optimizing a candidate gene nucleic acid sequence for expression in a selected target expression system. The method identifies stable or retained sequences in the candidate gene nucleic acid sequence, identifies disallowed sequences, develops a statistical model based on a whole genome, a partial genome, or transcriptome sequences of the target expression system, generates an optimized candidate gene nucleic acid sequence for use in the target expression system, and makes a synthetic gene comprising the optimized candidate gene nucleic acid sequence. The method allows for optimization of the candidate gene nucleic acid sequence without removing certain stable or retained sequences. Rather, the activity of these sites is positionally modulated or inactivated through upstream and downstream modifications of codons and/or sequence patterns.