Targeted Nucleic Acid Editing for G-to-A and C-to-T Mutations

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Solution Overview

Problem

Current genome-editing technologies are inadequate for correcting G→A and C→T point mutations, which represent about 47% of known pathogenic SNPs, as they primarily focus on A→G and T→C mutations.

Innovation Solution

A method utilizing a Cpf1 nickase protein, a guide molecule with a direct repeat sequence, and an adenosine deaminase protein to specifically deaminate adenine at a target locus, forming a heteroduplex with an A-C mismatch to convert adenine to inosine, which pairs with cytosine and functions like guanine, thereby correcting G→A and C→T mutations.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Adaptability or versatility

If cytidine deaminase is used for targeted deamination, then A→G and T→C point mutations can be corrected, but G→A and C→T point mutations (47% of pathogenic SNPs) cannot be addressed

Engineering Contradiction:

Improveability to correct different types of point mutationsVSAvoidcoverage of pathogenic SNP correction

Core Design Contradiction:

Adaptability or versatilityVSReliability

Solution Approach 1:

The patent replaces the cytidine-specific deaminase with an adenosine deaminase that can process adenine bases, enabling the system to correct G→A and C→T mutations. This enzyme substitution expands the system's functionality from correcting only A→G/T→C mutations to correcting both A→G/T→C and G→A/C→T mutations, achieving multi-functional capability for comprehensive SNP correction

Inventive Principle:

Principle #6Universality (Multi-functionality)

2Manufacturing precision

If existing genome-editing technologies are used, then A→G and T→C mutations can be corrected, but the technologies are inadequate for G→A and C→T mutations

Engineering Contradiction:

Improveprecision of mutation correctionVSAvoidrange of correctable mutation types

Core Design Contradiction:

Manufacturing precisionVSAdaptability or versatility

Solution Approach 1:

The patent changes the enzymatic parameter by substituting cytidine deaminase with adenosine deaminase, which has different substrate specificity. This parameter change allows the system to recognize and process adenine bases instead of cytidine bases, thereby expanding the range of correctable mutations from A→G/T→C to include G→A/C→T mutations while maintaining correction precision

Inventive Principle:

Principle #35Parameter changes

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 effectively addresses G→A and C→T mutations, enabling targeted genome editing and potential therapeutic applications by restoring healthy genotypes and inactivating undesirable gene activities, thus treating diseases such as cancer, haemophilia, and Marfan syndrome.

Implementation Method 1

the adenosine deaminase protein or catalytic domain thereof deaminates the Adenine in the heteroduplex opposite to the non-pairing Cytosine

Methodology Applied

Scientific EffectDeamination: Hydrolysis

Data Source

PatentEP3625343B1Systems, methods, and compositions for targeted nucleic acid editing

Publication Date: 2025.09.10 THE BROAD INST INC

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AI summary

The invention provides for systems, methods, and compositions for targeting and editing nucleic acids. In particular, the invention provides non-naturally occurring or engineered DNA-targeting systems comprising a DNA-targeting Cpfl protein, at least one guide molecule, and at least one adenosine deaminase protein or catalytic domain thereof.