3D Lattice Microarray for Multiplex Pathogen Detection
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Solution Overview
Problem
Current methods for pathogen identification in plant, agriculture, and food/water materials are inefficient due to high costs, time-consuming processes, inaccuracies, and limitations in detecting multiple pathogens simultaneously, especially in the presence of inhibitory substances like blood and plant constituents.
Innovation Solution
A 3-dimensional lattice microarray system is developed using a plastic substrate with oligodeoxythymidine linkers and nucleic acid probes, where the probes are crosslinked to form a lattice structure on the substrate, allowing for simultaneous detection of multiple pathogens without the need for pre-analysis DNA extraction, using a solvent mixture with a high boiling point water-miscible liquid to concentrate the probes and maintain accurate spacing for hybridization.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If standard culture and susceptibility tests are used for pathogen identification, then reliability of pathogen detection is improved, but loss of time and productivity deteriorate due to substantial investment of time and effort
Solution Approach 1:
The patent applies preliminary action by pre-immobilizing specific nucleic acid probes onto the microarray substrate before actual pathogen detection. These probes are prepared in advance and positioned at specific locations, allowing rapid detection when sample is applied without requiring time-consuming culture steps during the actual testing phase
Solution Approach 2:
The patent replaces the mechanical/culture-based detection system with a molecular biology approach using nucleic acid hybridization. Instead of cultivating microorganisms and observing colony growth (mechanical/biological process), the system uses DNA/RNA probe hybridization with fluorescent detection, dramatically reducing testing time while maintaining reliability
2Measurement precision
If DNA extraction is performed prior to PCR analysis, then measurement precision of pathogen detection is improved, but loss of time and device complexity worsen due to time-consuming and costly extraction step
Solution Approach 1:
The patent applies the taking out principle by selectively capturing only the necessary nucleic acid sequences through probe hybridization, bypassing the need for complete DNA extraction and purification. The probes specifically bind to target pathogen nucleic acids directly in the sample, extracting only the relevant information needed for identification
Solution Approach 2:
The microarray system provides multi-functionality by using a single platform to perform both detection and identification of multiple pathogens simultaneously. The same hybridization process serves to capture, concentrate, and identify target sequences, eliminating the need for separate extraction and analysis steps
3Ease of operation
If Colony PCR is used to eliminate pre-analysis extraction step, then ease of operation is improved, but measurement precision deteriorates due to interference from specimen constituents
Solution Approach 1:
The patent introduces nucleic acid probes as intermediaries between the sample and detection system. These probes specifically bind to target pathogen sequences, acting as mediators that selectively capture the signal of interest while excluding interference from non-target specimen constituents. The probes serve as a filtering mechanism that enhances precision without requiring complex sample preparation
4Measurement precision
If qPCR is used for single pathogen analysis, then measurement precision is improved, but productivity deteriorates when multiple pathogens need to be analyzed concurrently requiring parallel tests
Solution Approach 1:
The patent applies segmentation by dividing the detection task into multiple specific probe-target interactions occurring simultaneously on a single microarray platform. Each probe is segmented to recognize a specific pathogen or genetic marker, allowing parallel detection of multiple pathogens through spatially resolved hybridization events that are read out in a single experiment
Solution Approach 2:
The patent merges multiple detection capabilities into a single integrated microarray system. Multiple probes targeting different pathogens are immobilized on the same substrate, allowing simultaneous analysis of multiple pathogens in one sample application, combining the precision of specific detection with the productivity of multiplexing
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 method reduces processing steps, minimizes chemical use, and provides faster, accurate, and specific detection of pathogens, overcoming the limitations of existing techniques by enabling the analysis of multiple samples with improved reliability and specificity.
Implementation Method 1
using a solvent mixture with a high boiling point water-miscible liquid to concentrate the probes
Implementation Method 2
where the probes are crosslinked to form a lattice structure on the substrate
Data Source
AI summary
Provided herein is a method for manufacturing a microarray system, for example, 3-dimensional lattice microarray system, for DNA sequence detection and analysis. A solid support, such as a plastic substrate, is contacted with a formulation containing a plurality of nucleic acid probes, a plurality of bifunctional polymer linkers, such as oligothymidine linkers, and a solvent mixture of water and a water-miscible liquid. The bifunctional polymer linkers are attached to the solid support and the water is evaporated. Then the nucleic acid probes are attached to the bifunctional polymer linker.