Nanopore Detection of Small Molecules via Competition Assays
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Solution Overview
Problem
Current methods for detecting small molecules lack cost-effectiveness, specificity, sensitivity, and accuracy, often requiring specialized equipment and trained personnel, and are not suitable for portable devices, especially for small molecules that do not significantly alter electrical signals when passing through nanopores.
Innovation Solution
A competition assay using a nanopore device with a surrogate molecule and a fusion molecule, where the surrogate molecule competes with the target molecule for binding, inducing changes in electrical signals detectable by a sensor, allowing for the detection and quantification of small molecules without the need for complex equipment or trained personnel.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If small molecules are detected directly through nanopores, then the device remains simple and portable, but the detection sensitivity and accuracy are insufficient because small molecules do not significantly alter electrical signals
Solution Approach 1:
The patent introduces surrogate molecules as intermediaries that bind to small target molecules and possess detectable properties. These surrogate molecules act as mediators between the undetectable small molecules and the nanopore sensor, enabling indirect detection through competition assays where the surrogate's binding competes with the target molecule for the binding site.
Solution Approach 2:
The patent changes the detection parameter from direct electrical signal alteration by small molecules to measurement of binding competition effects. By monitoring changes in binding equilibrium and using surrogate molecules with distinct detectable properties, the system achieves sensitivity for small molecules that would otherwise be undetectable.
2Measurement precision
If complex analytical methods like mass spectrometry are used, then measurement precision improves, but device complexity and cost increase significantly
Solution Approach 1:
The surrogate molecules serve as intermediaries that bridge the gap between simple nanopore devices and complex analytical requirements. By using detectable surrogate molecules in competition assays, the system achieves quantification accuracy comparable to complex methods while maintaining device simplicity.
Solution Approach 2:
The patent transforms the detection approach from direct physical/chemical analysis requiring complex equipment to measurement of binding competition effects. This parameter change enables accurate quantification using simple electrical measurements of binding events rather than requiring mass spectrometry or chromatography.
3Productivity
If dye binding assays are used for high throughput detection, then productivity increases, but measurement precision decreases due to non-specific binding and false positives
Solution Approach 1:
The surrogate molecules act as specific intermediaries that maintain the throughput advantage of automated assays while eliminating non-specificity problems. The competition-based detection using specific surrogate molecules provides both high throughput and high specificity, as the surrogates can be designed to bind only to their target small molecules.
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
The method provides high specificity and sensitivity for detecting small molecules, achieving confidence levels of over 90% in detecting target molecules and allowing for accurate quantification, even for molecules that do not significantly alter electrical signals, on a low-cost, portable device.
Implementation Method 1
Target molecules of a sufficient size (>20 kDa) when passed through a solid-state nanopore cause a change in the current impedance, translocation time, or other measurable parameter
Implementation Method 2
said fusion molecule comprising a polymer scaffold binding domain adapted to bind said polymer scaffold to form a scaffold/fusion molecule complex
Implementation Method 3
performing a competition assay by combining said surrogate molecule and said fusion molecule with said sample, wherein said target molecule competes with said surrogate molecule for binding to said target molecule binding domain
Implementation Method 4
applying a voltage across said nanopore, wherein said first volume comprises said polymer scaffold, said fusion molecule, said surrogate molecule, and said sample suspected of comprising said target molecule
Data Source
AI summary
Disclosed herein are methods and compositions for detection of target small molecules in a mixed sample by performing a competition assay between the target and a surrogate and subsequently detecting the complex types in a nanopore device.