Engineered Cell Peptide Tag Quantification
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Solution Overview
Problem
Current measurement technologies for engineered biological systems are inadequate for quick, precise, and high-throughput identification and quantification of DNA, RNA, and protein species, hindering the design and testing of engineered organisms due to their complexity and requirement for expensive equipment and specialized expertise.
Innovation Solution
The development of engineered cells with predefined synthetic oligonucleotides encoding unique peptide tags for proteins, allowing for quantification by mass spectrometry, and the use of computer-aided design tools to optimize the genome for simplified analysis, including mutations to remove difficult-to-sequence regions and background cleavage sites.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If conventional measurement technologies are used for genome, transcriptome and proteome analysis, then measurement precision can be maintained, but the analysis process becomes very time-consuming and requires expensive equipment and specialized expertise
Solution Approach 1:
The patent segments the genome into regions with specific properties (e.g., regions with unique peptide tags, regions without background cleavage sites) that can be analyzed more efficiently. By dividing the complex biological system into manageable segments with optimized characteristics, the overall analysis time is reduced while maintaining measurement precision through targeted analysis of each segment.
Solution Approach 2:
The patent performs preliminary actions by engineering the genome in advance to include features that facilitate faster analysis, such as removing difficult-to-sequence regions and background cleavage sites before analysis begins. This preparatory modification of the biological system allows subsequent measurements to be completed more quickly without compromising precision.
2Measurement precision
If conventional measurement technologies are used for genome, transcriptome and proteome analysis, then measurement accuracy can be maintained, but the complexity of the analysis process increases due to requirement for expensive equipment and specialized expertise
Solution Approach 1:
The patent extracts and removes problematic elements from the genome that complicate analysis, such as difficult-to-sequence regions and background cleavage sites. By taking out these interfering components beforehand, the remaining genome can be analyzed with simpler, less expensive equipment and fewer specialized techniques, reducing overall system complexity while maintaining accuracy.
Solution Approach 2:
The patent applies local quality by creating regions with specific optimized properties at particular locations in the genome. Different regions are engineered with different characteristics (e.g., unique peptide tags in some regions, removed cleavage sites in others) to facilitate targeted analysis with appropriate methods, reducing the need for complex universal analysis systems.
3Productivity
If the genome is engineered with additional features for quantification, then productivity of the design-build-test loop is improved, but the device complexity of the engineered cell increases
Solution Approach 1:
The patent performs preliminary action by pre-engineering the genome with quantification-friendly features such as unique peptide tags and removed background sites before the design-build-test cycle begins. This advance preparation enables rapid measurement and characterization during testing, significantly improving productivity of the overall loop despite the additional genetic engineering steps required upfront.
Solution Approach 2:
The patent introduces intermediary elements (unique peptide tags, simplified regions) that act as mediators between the complex biological system and the measurement apparatus. These intermediaries facilitate easier and faster quantification by providing clear, distinguishable signals that can be measured with simpler methods, improving productivity while the complexity is confined to well-defined genetic elements.
Applied Scientific Principles
This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.
Function Achieved in This Case
Enables rapid characterization and localization of failures in engineered organisms, facilitating the development of computer-aided design tools and accelerating the design-build-test loop for the engineering of biological systems.
Implementation Method 1
The quantitatively measurable value can be measurable by mass spectrometry
Implementation Method 2
the unique peptide tags are separable from one another by chromatography, capillary electrophoresis or combinations thereof
Implementation Method 3
the unique peptide tags are separable from one another by chromatography, capillary electrophoresis or combinations thereof
Data Source
AI summary
Systems, methods, libraries, kits, and computer software tools are provided for designing and producing engineered cells. Such engineered cells can be used for cell state quantification, such as genome, transcriptome and/or proteome quantification. In one aspect, an engineered cell having a plurality of artificially designed oligonucleotides introduced into the genome of the cell is provided. The oligonucleotides are each located in proximity of a gene of interest encoding a protein of interest, and are different from one another. The oligonucleotides can each encode a unique peptide tag for each protein of interest, wherein each peptide tag has a unique quantitatively measurable value such as mass-to-charge ratio which can be quantified by a mass spectrometer. The engineered cell is capable of expressing a plurality of proteins of interest each fused to its corresponding unique peptide tag, wherein each peptide tag is capable of being released therefrom.