Oligonucleotide Probe for Cis-Trans SNP Configuration Detection
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Solution Overview
Problem
Current methods for determining whether two single nucleotide polymorphisms (SNPs) are in the cis or trans configuration are complex and costly, hindering the development of effective therapeutic strategies for cancer treatment resistance, particularly for EGFR tyrosine kinase inhibitors.
Innovation Solution
An oligonucleotide probe with a reporter region, an anchor region, and a linker region is designed to detect the presence of SNPs, utilizing a fluorescent dye for sensitive and accurate determination of SNP configuration by measuring fluorescence intensity, allowing for the differentiation between cis and trans configurations using a single probe.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If next generation sequencer or digital PCR is used to determine cis-trans configuration of SNPs, then measurement precision is improved, but device complexity and cost increase
Solution Approach 1:
The probe is segmented into three functional regions: a reporter region (10-20 nucleotides) containing a fluorescent dye for detecting the first SNP, an anchor region (15-30 nucleotides) for detecting the second SNP, and a linker region (5-15 nucleotides) connecting them. This segmentation allows the single probe to simultaneously detect both SNPs and determine their cis-trans configuration through hybridization patterns, replacing complex next-generation sequencing systems.
Solution Approach 2:
The oligonucleotide probe performs multiple functions: it detects the presence/absence of the first SNP through the reporter region, detects the presence/absence of the second SNP through the anchor region, and determines the cis-trans configuration between the two SNPs. This multi-functionality eliminates the need for separate detection systems and reduces overall device complexity while maintaining measurement precision.
2Measurement precision
If next generation sequencer or digital PCR is used to determine cis-trans configuration of SNPs, then measurement precision is improved, but manufacturing cost increases
Solution Approach 1:
The probe is segmented into three functional regions: a reporter region (10-20 nucleotides) containing a fluorescent dye for detecting the first SNP, an anchor region (15-30 nucleotides) for detecting the second SNP, and a linker region (5-15 nucleotides) connecting them. This segmentation allows the single probe to simultaneously detect both SNPs and determine their cis-trans configuration through hybridization patterns, replacing complex next-generation sequencing systems.
Solution Approach 2:
The oligonucleotide probe is a simple, inexpensive, disposable reagent that can be synthesized using standard oligonucleotide synthesis methods. Each probe contains a fluorescent dye that quenches upon hybridization, providing a readout signal. This disposable probe approach eliminates the need for expensive, complex next-generation sequencing instruments and reduces manufacturing costs significantly while maintaining the ability to accurately determine SNP configurations.
3Device complexity
If a single oligonucleotide probe is designed to detect both SNPs and determine configuration, then device complexity is reduced, but measurement precision may be compromised
Solution Approach 1:
Different regions of the probe have specialized functions optimized for their specific roles: the reporter region (10-20 nucleotides) is designed with a fluorescent dye for sensitive detection of the first SNP through quenching effects, the anchor region (15-30 nucleotides) is designed for stable hybridization to detect the second SNP, and the linker region (5-15 nucleotides) provides appropriate spacing and flexibility. This local optimization of each region's properties ensures that the single probe maintains high measurement precision for SNP configuration determination.
Solution Approach 2:
The probe design adds a spatial dimension to SNP detection by using the physical arrangement and spacing of the reporter and anchor regions. The linker region length (5-15 nucleotides) creates appropriate spatial separation that allows the probe to distinguish between cis and trans configurations based on hybridization patterns. This spatial dimensionality enables accurate configuration determination while using a single probe instead of multiple separate assays.
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 enables simple and cost-effective detection of SNP configurations, facilitating the selection of appropriate therapeutic measures to overcome resistance to EGFR tyrosine kinase inhibitors in cancer treatment.
Implementation Method 1
the reporter region comprises an oligonucleotide consisting of a sequence perfectly matching with the first target sequence, and a fluorescent dye that quenches when the first target sequence and the reporter region hybridize
Implementation Method 2
the reporter region comprises an oligonucleotide consisting of a sequence perfectly matching with the first target sequence... the anchor region comprises an oligonucleotide consisting of a sequence perfectly matching with the second target sequence
Data Source
AI summary
A probe comprising a reporter region for detecting a first single nucleotide polymorphism, an anchor region for detecting a second single nucleotide polymorphism, and a linker region is disclosed. The reporter region comprises an oligonucleotide consisting of a sequence perfectly matching with the first target sequence, and a fluorescent dye that quenches when hybridized to the first target sequence where the first single nucleotide polymorphism is present. The anchor region comprises an oligonucleotide consisting of a sequence perfectly matching with a second target sequence where the second single nucleotide polymorphism is present. A length of the oligonucleotide of the reporter region is shorter than a length of the oligonucleotide of the anchor region.