Oligonucleotide Microarray Pathogen Detection
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Solution Overview
Problem
Current diagnostic procedures for identifying pathogens, such as PCR methods, face challenges with increased 'noise' on electrophoresis gels due to non-specific annealing, making it difficult to determine the presence of multiple genes efficiently, and require highly trained staff and are time-consuming.
Innovation Solution
A method using an oligonucleotide microarray with probes complementary to specific pathogens for rapid and high-throughput screening, where target nucleic acids are amplified using primer pairs binding to conserved regions and detected through hybridization, allowing for the differentiation of pathogens like E. coli and salmonella.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Adaptability or versatility
If multiple primer pairs are used in PCR to screen for multiple genes, then the screening capability is improved, but the noise on electrophoresis gel increases due to non-specific annealing
Solution Approach 1:
The invention segments the detection process into two distinct stages: (1) PCR amplification using multiple primer pairs to generate potential products, and (2) electrophoresis separation to resolve and identify specific products. This segmentation allows the system to handle multiple genes simultaneously while maintaining clear identification by separating the amplification function from the detection function, thereby reducing noise interference in the final readout.
Solution Approach 2:
The invention introduces electrophoresis as an intermediary step between PCR amplification and final detection. This intermediary process separates the complex mixture of PCR products by size, allowing specific gene products to be distinguished from non-specific amplification products and background noise. The intermediary step acts as a filter that preserves signal while removing harmful noise.
2Productivity
If PCR primers are designed to amplify multiple genes, then the efficiency of screening is improved, but it becomes difficult to determine the presence of more than a few genes due to noise
Solution Approach 1:
The invention adds a new dimension to gene detection by incorporating size-based separation through electrophoresis. Instead of relying solely on sequence-specific detection in a single dimension, the system uses the physical dimension of molecular size to create a two-dimensional detection space (sequence specificity × size). This allows multiple genes to be distinguished not only by their unique sequences but also by their distinct migration patterns on the gel, thereby maintaining high detection accuracy even when screening for many genes simultaneously.
3Reliability
If conventional PCR and electrophoresis methods are used, then pathogen identification can be achieved, but highly trained staff and extensive time are required
Solution Approach 1:
The invention performs preliminary amplification of pathogen-specific DNA sequences using PCR before the actual detection step. By pre-amplifying the target sequences, the system ensures that sufficient material is available for subsequent electrophoresis analysis, thereby reducing the time needed for detection while maintaining reliability. The preliminary action of amplification concentrates the signal of interest before the separation and identification steps.
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 fast and accurate detection of pathogens with reduced noise and increased efficiency, reducing the need for extensive training and time, and allowing for high-throughput analysis.
Implementation Method 1
contacting the amplified target nucleic acid with an oligonucleotide microarray, and detecting binding of target nucleic acids to the probes
Data Source
AI summary
A method for detecting a target nucleic acid of a pathogen in a test sample, the method comprising preparing a target nucleic acid detecting reagent and contacting the target nucleic acid detecting reagent with an oligonucleotide microarray. A kit for detecting a target nucleic acid of a pathogen in a test sample is also described. The kit comprises at least one primer pair and an oligonucleotide microarray comprising at least one probe.