CRISPR Lateral Flow Diagnostics with ML Guide Design
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Current nucleic acid detection methods face challenges in achieving high sensitivity and specificity while being cost-effective and portable, with existing CRISPR-based diagnostics limited by the lack of predictive guide design tools for optimal assay design.
Innovation Solution
Development of a lateral flow device using CRISPR effector systems with machine learning-driven guide RNA design for multiplexed nucleic acid detection, enabling rapid and sensitive detection of multiple targets in a one-pot reaction with a portable lateral flow readout.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If qPCR approaches are used for nucleic acid detection, then sensitivity is improved, but device complexity and cost increase due to complex instrumentation requirements
Solution Approach 1:
The patent replaces complex mechanical/qPCR instrumentation with a CRISPR-based biochemical system that uses Cas13a enzyme and guide RNA to detect nucleic acids through collateral RNA cleavage activity, enabling sensitive detection without sophisticated instruments
Solution Approach 2:
The patent introduces an intermediary CRISPR-Cas13a system that bridges the gap between simple lateral flow devices and sensitive molecular detection, using guide RNA-programmed Cas13a enzymes to specifically recognize and amplify target signals through collateral cleavage of reporter RNA
2Device complexity
If isothermal nucleic acid amplification with portable platforms is used, then device complexity is reduced for point-of-care settings, but detection sensitivity decreases
Solution Approach 1:
The patent merges isothermal amplification (RPA) with CRISPR-Cas13a detection in a single integrated system, combining the portability benefits of isothermal methods with the high sensitivity of CRISPR-based detection to achieve both goals simultaneously
Solution Approach 2:
The patent optimizes reaction parameters including temperature control at 37°C for both RPA and Cas13a activity, pH conditions, and component concentrations to maximize sensitivity while maintaining portability and simplicity of the detection platform
3Adaptability or versatility
If multiplexed detection of multiple targets is implemented, then adaptability improves, but device complexity increases due to multiple CRISPR systems required
Solution Approach 1:
The patent creates a universal CRISPR-detect platform where a single Cas13a enzyme can detect multiple different targets by simply changing the guide RNA sequence, enabling multiplexed detection without requiring multiple different CRISPR systems
Solution Approach 2:
The patent segments the detection function into modular components: a universal Cas13a enzyme and interchangeable guide RNAs, allowing different guide RNAs to be used with the same enzyme to detect different targets, simplifying the overall system architecture
4Ease of operation
If predictive guide design tools are developed, then ease of operation improves for assay design, but device complexity increases due to machine learning integration
Solution Approach 1:
The patent implements self-service through automated machine learning tools that predict optimal guide RNA sequences based on target sequence input, allowing users to design assays without deep expertise in CRISPR guide selection, with the algorithm automatically optimizing guide performance
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 solution enables rapid, sensitive, and cost-effective detection of nucleic acids with single-nucleotide specificity, facilitating robust and portable assays in various settings, including clinical and field applications, by optimizing CRISPR guide RNA design and utilizing CRISPR effector proteins like Cas13 and Cas12 for collateral activity-based detection.
Implementation Method 1
The ability to rapidly detect nucleic acids with high sensitivity and single-base specificity... CRISPR enzymes called SHERLOCK... which combines pre-amplification with the RNA-guided RNase CRISPR-Cas13 and DNase CRISPR-Cas12 for sensing of nucleic acids
Implementation Method 2
Nucleic acid detection with SHERLOCK relies on the collateral activity of Cas13 and Cas12, which unleashes promiscuous cleavage of reporters upon target detection
Implementation Method 3
each guide sequence configured to bind one or more target molecules
Implementation Method 4
lateral flow device comprising a substrate... enabling rapid and sensitive detection of multiple targets in a one-pot reaction with a portable lateral flow readout
Data Source
AI summary
Systems and methods for rapid diagnostics related to the use of CRISPR effector systems and optimized guide sequences, including multiplex lateral flow diagnostic devices and methods of use, are provided.