UGE Detection System for Stacked Transgene Identification
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Solution Overview
Problem
Current methods for detecting genetically modified organisms (GMOs) are inefficient and costly due to the need for multiple assays for each transgenic event, especially when dealing with stacked transgenes, and lack the ability to distinguish between different GMOs and their combinations.
Innovation Solution
A system using unique exogenous genetic elements (UGEs) that can be detected with a single pair of oligonucleotide primers, allowing for the identification of multiple transgenic events in a single assay without requiring information about the integration site, utilizing universal primers and specific probes for fluorescence-based PCR assays.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If multiple assays are used for each transgenic event, then detection specificity is improved, but device complexity and analysis time increase
Solution Approach 1:
The patent employs universal primer pairs that can amplify unique exogenous genetic elements (UGEs) from multiple different transgenic events simultaneously. These universal primers bind to conserved flanking sequences surrounding UGEs, enabling a single assay system to detect diverse transgenic constructs without requiring event-specific primer sets for each GMO type.
Solution Approach 2:
The patent segments the detection target into unique exogenous genetic elements (UGEs) that are flanked by universal primer binding sites. By isolating the UGEs as distinct amplifiable units with standardized flanking regions, the system can differentiate between multiple transgenic events through the UGE sequences while using the same universal primers for all events.
2Measurement precision
If multiple assays are used for each transgenic event, then detection precision is improved, but loss of time increases
Solution Approach 1:
The patent merges the detection of multiple transgenic events into a single simultaneous PCR assay. By designing universal primers that work across different GMO types and using UGEs as distinctive targets, the system combines what would traditionally require multiple separate assays into one unified testing process, reducing time while maintaining precision through UGE-specific probe detection.
3Ease of operation
If generic genetic elements are used for detection, then ease of operation is improved, but measurement precision deteriorates
Solution Approach 1:
The patent applies local quality by using universal primers that bind to conserved flanking sequences (providing operational simplicity) while simultaneously employing UGE-specific probes that provide event-specific discrimination (providing measurement precision). The universal primers handle the ease of operation aspect, while the UGE probes ensure accurate identification of specific GMO types.
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
This approach provides unprecedented specificity and generalizability in detecting transgenic events, reducing the number of required assays and enabling the identification of stacked transgenes with high sensitivity and accuracy.
Implementation Method 1
contacting the DNA with a pair of oligonucleotide primers that specifically hybridize to the 5' and 3' polynucleotides
Implementation Method 2
amplifying an amplicon comprising the 5' polynucleotide, the UGE, and the 3' polynucleotide
Implementation Method 3
detecting the UGE using a specific probe (e.g., in a fluorescence-based PCR assay, such as a hydrolysis probe assay)
Data Source
AI summary
This disclosure concerns a system and method for detecting heterologous DNA in plant materials.