Oligonucleotide Probe Sets for Sensitive Genomic Detection
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Solution Overview
Problem
Current oligonucleotide probes used in in situ hybridization are less sensitive due to their short length and limited label amount, making them less effective for detecting low-abundant genomic targets, and they often require longer times and higher probe concentrations.
Innovation Solution
A set of at least 100 different single-stranded oligonucleotide probes, each complementary to different regions of a genomic target sequence and labeled, is used for detection, allowing for faster, more sensitive, and cost-effective detection of genomic targets with reduced probe amounts and hybridization time.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If conventional oligonucleotide probes are used, then the detection method is simple, but the sensitivity is low and detection time is long
Solution Approach 1:
The patent combines multiple oligonucleotide probes (at least 100 different probes) into a single hybridization mixture that targets the same genomic locus. This merging of multiple probes working simultaneously increases the total binding capacity and detection sensitivity while reducing the time required compared to using individual probes sequentially.
Solution Approach 2:
The invention creates a composite probe system consisting of diverse oligonucleotide sequences with different affinities and specificities. This composite approach allows the probe mixture to overcome the limitations of individual short probes by collectively providing both high sensitivity and appropriate binding kinetics.
2Measurement precision
If longer probes are used to increase sensitivity, then the detection sensitivity improves, but the probe cost and complexity increase
Solution Approach 1:
Instead of using one long complex probe, the invention segments the target region and uses multiple shorter oligonucleotide probes (20-100 nucleotides) that collectively cover the target locus. Each probe is simple in design, but their combination achieves the sensitivity equivalent to or better than a single long probe while reducing individual probe complexity and cost.
3Productivity
If higher probe concentrations are used to speed up detection, then the detection speed increases, but the probe amount required increases
Solution Approach 1:
The patent merges the effects of multiple probes working in parallel at moderate concentrations. The cumulative binding effect of at least 100 different probes achieves high detection speed without requiring high concentrations of any single probe, thus reducing the total probe amount needed compared to conventional single-probe methods.
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 the detection of low-abundant genomic sequences with higher specificity and sensitivity, reducing the time and amount of probes needed compared to existing methods, while maintaining optimal binding efficiency.
Implementation Method 1
a set of oligonucleotide probes directed to a genomic target sequence of interest... incubating a set of oligonucleotide probes with a sample under conditions conducive to the binding of the set of oligonucleotide probes to the genomic target sequence
Data Source
AI summary
The present disclosure relates to a set of at least 100 single-stranded oligonucleotide probes directed against (or complementary to) portions of a genomic target sequence of interest. The present disclosure also relates to a method of detecting a genomic target sequence of interest using the set of oligonucleotide probes and a method of generating the set of oligonucleotide probes. Further, the present disclosure relates to a kit comprising the set of oligonucleotide probes and at least one further component.