Base Editor Fusion Protein with Chromatin-Modulating Peptides

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Solution Overview

Problem

Current base editors, such as AncBE4max and ABEmax, face challenges with low editing efficiency and high frequencies of undesired random base insertion and deletion, limiting their clinical application and precision in genome editing.

Innovation Solution

Incorporating chromatin-modulating peptides (CMPs) into fusion proteins based on the CRISPR/Cas9 system, specifically using deadCas9 instead of nickaseCas9, to enhance base editing efficiency and reduce random indel occurrences, while maintaining or improving target specificity.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Productivity

If conventional base editors (AncBE4max, ABEmax) are used, then base editing capability is achieved, but editing efficiency is low and random indel frequency is high

Engineering Contradiction:
Improvebase editing efficiencyVSAvoidrandom indel frequency
Core Design Contradiction:
ProductivityVSReliability

Solution Approach 1:

The patent creates a composite base editor by fusing chromatin-modulating peptides (CMPs) with the base editor protein structure. This composite structure combines the DNA editing capability of the base editor with the chromatin accessibility enhancement of CMPs, thereby improving both editing efficiency and reducing random indels through enhanced target site accessibility

Inventive Principle:
Principle #40Composite materials

Solution Approach 2:

The patent modifies the base editor structure by incorporating CMPs that alter the physical and chemical parameters of the editor-chromatin interaction. This structural parameter change enables the base editor to access condensed chromatin regions more effectively, improving editing efficiency while maintaining precision

Inventive Principle:
Principle #35Parameter changes

2Reliability

If deadCas9 is used instead of nickaseCas9, then random indel frequency is reduced, but editing efficiency may be affected

Engineering Contradiction:
Improverandom indel frequencyVSAvoidbase editing efficiency
Core Design Contradiction:
ReliabilityVSProductivity

Solution Approach 1:

The CMP acts as an intermediary that bridges the gap between deadCas9 and the chromatin structure. By facilitating chromatin relaxation and DNA accessibility, the CMP compensates for the reduced cleavage activity of deadCas9, maintaining editing efficiency while eliminating random indels associated with nickaseCas9

Inventive Principle:
Principle #24Intermediary (Mediator)

3Productivity

If chromatin-modulating peptides are added to base editors, then chromatin accessibility is improved, but device complexity increases

Engineering Contradiction:
Improvechromatin accessibilityVSAvoidfusion protein complexity
Core Design Contradiction:
ProductivityVSDevice complexity

Solution Approach 1:

The patent segments the base editor into distinct functional domains, with CMPs as separate modular units that can be independently optimized and combined. This segmentation allows for systematic design and optimization of the fusion protein while maintaining clear functional boundaries between the chromatin-modulating and DNA-editing components

Inventive Principle:
Principle #1Segmentation

Data Source

PatentUS20230365992A1Novel enhanced base editing or revising fusion protein and use thereof
Publication Date: 2023.11.16 KOREA UNIV RES & BUSINESS FOUND
  • US20230365992A1 patent drawing
  • US20230365992A1 patent drawing
  • US20230365992A1 patent drawing

AI summary

The present invention relates to a fusion protein developed by adding configurational elements, such as chromatin-modulating peptides, etc., and modifying the arrangement thereof, on the basis of conventional developed base editors. The fusion protein of the present invention can be provided as a novel base editor which exhibits base editing efficiency due to the inclusion of CMP and is free of the occurrence of undesired random base insertion and deletion due to the employment of deadCas9 and as such, can be expected to find advantageous applications in the field of genetic engineering for various purposes, such as exquisite gene therapy, construction and research of transgenic animal models, etc.