Isothermal SARS-CoV-2 Detection via Toehold Switches

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Solution Overview

Problem

Current diagnostic technologies for COVID-19, such as PCR-based assays, require significant infrastructure, trained personnel, and are costly, making them inefficient for rapid and widespread detection of SARS-CoV-2.

Innovation Solution

Development of a rapid, highly sensitive assay using isothermal amplification reactions and riboregulators like toehold switches and SNIPRs that can detect SARS-CoV-2 RNA without sophisticated equipment, allowing for colorimetric or fluorometric readouts and operation at room temperature, enabling easy deployment and low-cost testing.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Measurement precision

If PCR-based assays are used for SARS-CoV-2 detection, then high sensitivity and specificity are achieved, but substantial infrastructure investment, trained personnel, and high cost are required

Engineering Contradiction:

Improvedetection sensitivityVSAvoidinfrastructure requirements

Core Design Contradiction:

Measurement precisionVSDevice complexity

Solution Approach 1:

The patent replaces the complex thermal cycling mechanical system of PCR with an isothermal amplification system that operates at a constant temperature (37°C), eliminating the need for sophisticated thermal cyclers and complex temperature control infrastructure while maintaining detection sensitivity

Inventive Principle:

Principle #28Mechanics substitution (Replace mechanical system)

Solution Approach 2:

The invention employs disposable paper-based microfluidic devices that integrate the entire amplification and detection process in a single-use format, eliminating the need for reusable expensive equipment, complex infrastructure, and extensive personnel training while achieving high detection sensitivity

Inventive Principle:

Principle #27Cheap short-living objects (Disposable)

2Measurement precision

If PCR-based assays are used for SARS-CoV-2 detection, then high sensitivity and specificity are achieved, but high cost and long time for results are incurred

Engineering Contradiction:

Improvedetection sensitivityVSAvoidtime to results

Core Design Contradiction:

Measurement precisionVSLoss of time

Solution Approach 1:

The patent replaces time-consuming thermal cycling with isothermal amplification that proceeds continuously at 37°C, dramatically reducing the time required to achieve sufficient amplification for detection while maintaining high sensitivity, enabling same-day results

Inventive Principle:

Principle #28Mechanics substitution (Replace mechanical system)

Solution Approach 2:

The isothermal amplification system operates continuously without the repeated heating and cooling cycles of PCR, maintaining constant productive action throughout the reaction period, thereby reducing total assay time while preserving detection sensitivity

Inventive Principle:

Principle #20Continuity of useful action

3Measurement precision

If sophisticated laboratory equipment is used for SARS-CoV-2 detection, then high sensitivity is achieved, but high cost and complex infrastructure are required

Engineering Contradiction:

Improvedetection sensitivityVSAvoiddeployment simplicity

Core Design Contradiction:

Measurement precisionVSEase of manufacture

Solution Approach 1:

The patent employs disposable paper-based microfluidic devices that are inexpensive to manufacture and use, eliminating the need for expensive reusable equipment while achieving high detection sensitivity, thereby simplifying deployment to resource-limited settings

Inventive Principle:

Principle #27Cheap short-living objects (Disposable)

Solution Approach 2:

The paper-based device integrates multiple functions (sample processing, isothermal amplification, and detection) into a single universal platform that operates at constant temperature, simplifying deployment infrastructure requirements while maintaining high detection sensitivity across different settings

Inventive Principle:

Principle #6Universality (Multi-functionality)

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 assay provides same-day results, reduces the burden on healthcare systems, and offers improved specificity and sensitivity compared to antibody-based tests, with the potential for at-home use and rapid adaptation to new viral strains.

Implementation Method 1

amplifying the released viral RNA obtained from a biological sample of a subject, wherein amplifying comprises isothermal amplification

Methodology Applied

Scientific EffectIsothermal amplification:

Implementation Method 2

contacting the amplified nucleic acid to a toehold switch-based sensor, wherein the toehold switch-based sensor encodes at least a portion of a reporter protein and comprises one or more single-stranded toehold sequence domains that are complementary to a target SARS-CoV-2 nucleic acid

Methodology Applied

Scientific EffectNucleic acid hybridization:

Data Source

PatentUS11952637B2Rapid low-cost detection of SARS-CoV-2 using isothermal amplification and sensing methods

Publication Date: 2024.04.09 THE ARIZONA BOARD OF REGENTS ON BEHALF OF THE UNIV OF ARIZONA

AI summary

Provided herein are methods and compositions for rapid, highly sensitive detection of SARS-CoV-2 in biological samples. In particular, provided herein is a rapid, low-cost method for detecting SARS-CoV-2 that provides reliable, visible test results and does not require PCR reagents, elaborate biosafety precautions, or sophisticated laboratory equipment.