Small Type II-D Cas Proteins for Scalable Genome Editing
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Solution Overview
Problem
Current genome editing technologies, such as CRISPR-Cas systems, face challenges in being affordable, easy to set up, scalable, and capable of targeting multiple positions within eukaryotic genomes, limiting their application in genome engineering and biotechnology.
Innovation Solution
Development of engineered nucleic acid targeting systems comprising a Cas protein with a RuvC domain and an HNH domain, capable of forming complexes with nucleic acid guide molecules for sequence-specific binding, and optionally coupled with functional domains for specific activities like nickase or deaminase functions, to modify target polynucleotides.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Ease of manufacture
If conventional CRISPR-Cas systems are used for genome editing, then genome targeting capability is achieved, but the systems are difficult to set up and not easily scalable
Solution Approach 1:
The patent divides the CRISPR-Cas system into separate functional modules: a portable Cas protein component and a guide RNA component. This segmentation allows the system to be assembled easily without requiring complex co-delivery mechanisms, directly addressing the ease of setup challenge while maintaining genome targeting capability.
Solution Approach 2:
The patent extracts the Cas protein from its traditional bacterial context and presents it as a standalone, purified component that can be easily handled in the lab. This extraction removes the complexity of maintaining bacterial systems while preserving the essential genome-editing function, making the system easier to set up and scale.
2Productivity
If conventional CRISPR-Cas systems are used, then genome editing function is provided, but the systems are not affordable and not scalable
Solution Approach 1:
The patent employs synthetic, chemically synthesized Cas proteins and guide RNAs that can be produced at low cost through standard biochemical processes. These disposable, non-replicating components eliminate the need for expensive bacterial cultures and plasmid maintenance, making the system both affordable and easily scalable for high-throughput applications.
Solution Approach 2:
The patent optimizes parameters such as protein purity, concentration, and stability to enable efficient genome editing with minimal material requirements. By changing these parameters, the system achieves high productivity and scalability while reducing costs through reduced reagent requirements and simplified protocols.
3Manufacturing precision
If conventional CRISPR-Cas systems are used for genome targeting, then editing capability is achieved, but off-target effects occur
Solution Approach 1:
The patent enhances the local quality of the Cas protein-guideRNA complex at the target site through optimized binding interfaces and guide RNA sequences. This localized optimization ensures high-precision targeting while minimizing off-target effects by concentrating the editing activity only at the intended location, directly addressing both precision and harmful factors.
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
These systems enable precise and efficient modification of genomic sequences, reducing off-target effects and enhancing the scalability and applicability of genome editing in various biological contexts.
Implementation Method 1
the nucleic acid guide molecule is capable of sequence-specific binding of a target nucleic acid sequence on a target polynucleotide
Data Source
AI summary
Described herein are systems, methods, and compositions capable of targeting nucleic acids. Describe in certain exemplary embodiments herein are a class of small Cas proteins (Type II-D Cas proteins) and systems thereof. Also described in certain exemplary embodiments herein are methods of modifying target sequences using the class of small Cas proteins (Type II-D Cas proteins) and systems thereof described herein.