Gam Protein Fusion Base Editors Reduce Indel Formation
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Solution Overview
Problem
Current base editors, such as BE3, often produce undesired byproducts and have limitations in editing efficiency, product purity, and indel frequencies during the conversion of C:G base pairs to T:A base pairs, necessitating the development of improved technologies that minimize indel formation and enhance editing precision.
Innovation Solution
The integration of a Gam protein, which binds to double-stranded DNA breaks, into base editors like BE3 and BE4 to reduce indel formation and improve product purity, resulting in more efficient and precise C:G to T:A base editing, as seen in variants like BE3-Gam and BE4-Gam.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If traditional base editors (e.g., BE3) are used for C:G to T:A base editing, then base editing can be achieved without DSBs or HDR, but undesired byproducts and indels are formed reducing product purity
Solution Approach 1:
The patent introduces an intermediary protein (Gam, Ku70, or Ku80) that binds to double-stranded DNA breaks and prevents their degradation. This intermediary component blocks the harmful NHEJ pathway that would otherwise process DSBs into indels, thereby preventing indel formation without requiring HDR or increasing DSB formation. The intermediary protein acts as a mediator between the base editing process and the cellular DNA repair machinery.
Solution Approach 2:
The patent extracts and removes the harmful NHEJ pathway from the base editing process by using a catalytically impaired Cas9 protein that cannot generate DSBs. Instead, the system uses a single-strand break mechanism with a tethered cytidine deaminase that directly converts C:G to T:A base pairs without triggering the NHEJ pathway, thereby eliminating the source of indel formation.
2Manufacturing precision
If DSBs are introduced for genome editing, then HDR can occur for precise manipulation, but editing efficiency is limited due to competition with NHEJ and dependence on mitosis
Solution Approach 1:
The patent replaces the mechanical DSB-based editing system with a biochemical base editing system. Instead of using Cas9 to create DSBs and rely on cellular HDR machinery, the system uses a tethered cytidine deaminase enzyme that directly chemically converts C:G base pairs to T:A base pairs. This substitution eliminates the need for mitotic HDR and DSB-dependent processes, enabling editing in non-dividing cells and significantly improving editing efficiency.
3Object-affected harmful factors
If catalytically impaired Cas9 is used for base editing, then DSBs are avoided, but indel formation still occurs through NHEJ of DSBs
Solution Approach 1:
The patent introduces an intermediary protein (Gam, Ku70, or Ku80) that binds to double-stranded DNA breaks and prevents their degradation. This intermediary component blocks the harmful NHEJ pathway that would otherwise process DSBs into indels, thereby preventing indel formation without requiring HDR or increasing DSB formation. The intermediary protein acts as a mediator between the base editing process and the cellular DNA repair machinery.
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 new base editors, BE3-Gam and BE4-Gam, demonstrate enhanced editing efficiency, higher product purity, and reduced indel frequencies compared to previous generations, achieving greater precision in genome editing tasks.
Implementation Method 1
Cytidines within this window may be hydrolytically deaminated to uracils, resulting in G:U intermediates
Implementation Method 2
base editors fused to a protein that binds to the ends of double strand breaks, for example, the Gam protein of bacteriophage Mu
Implementation Method 3
Base excision repair (BER) is the cell's primary response to G:U mismatches and is initiated by excision of the uracil by uracil N-glycosylase (UNG)
Data Source
Figure 1A
Figure 1B~1C
Figure 2A
AI summary
Some aspects of this disclosure provide strategies, systems, reagents, methods, and kits that are useful for the targeted editing of nucleic acids, including editing a single site within the genome of a cell or subject, e.g., within the human genome. In some embodiments, fusion proteins comprise a Gam protein, a napDNAbp, and a cytidine deaminase. In some embodiments, the fusion proteins further comprise a UGI domain. In some embodiments, methods for targeted nucleic acid editing are provided. In some embodiments, reagents and kits for the generation of targeted nucleic acid editing proteins, e.g., fusion proteins of a Gam protein, a cytidine deaminase and nucleic acid editing proteins or domains, are provided.