PRODUCT

AccuBase™ Cytosine Base Editor

High-fidelity cytosine base editor

AccuBase™ is an engineered cytosine base editor designed for therapeutic applications. It enables precise single-base conversions from C to T, minimizing off-target activity and eliminating the risk of double-strand breaks. This makes it a safer and more reliable solution for advancing clinical and commercial applications in cell and gene therapy.

Engineered for high-efficiency and exceptional fidelity.
Eliminates double-strand breaks, reducing genomic instability.
Demonstrates remarkably low off-target activity for safer therapeutics.
Activates only when bound to the DNA target site, preventing unintended edits.

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AccuBase™ Cytosine Base Editor (100ug)

#R10ACCUBASE-Sm

Description Deliverables Specifications gRNA Design Data FAQ Resources

Description

Advantages of AccuBase for CRISPR-Based Therapeutics

AccuBase is Synthego’s engineered high-fidelity cytosine base editor (CBE) designed for safe and efficient genome editing in therapeutic applications. It is the only CBE supplied as a recombinant protein for transient expression. AccuBase enables transient, controlled editing, avoiding prolonged activity that can increase off-target effects common with mRNA-based CBEs. By embedding a cytosine deaminase within SpCas9 nickase, AccuBase precisely converts cytosine (C) to thymine (T) within a defined 3–12 nucleotide editing window, minimizing bystander edits and eliminating double-strand breaks or chromosomal translocations. Compatible with chemically modified guide RNAs and available in GMP-grade, AccuBase provides researchers and therapeutic developers with a scalable, clinically validated solution for both single and multiplex gene editing.

AccuBase RNP complex schematic. Depicted in the schematic is genomic DNA (light blue) and PAM sequence (pink). The guide RNA (gRNA) is composed of the target sequence (green) and scaffold (dark blue). The embedded cytosine deaminase (orange) performs precise C→T base conversion within the editing window.

Key Features

High-Fidelity Base Editing:
Minimal off-target activity in DNA and RNA; avoids chromosomal translocations and double-strand breaks.

Transient Recombinant Protein Delivery:
Immediate and controlled editing activity, reducing risks associated with prolonged expression from mRNA or plasmid systems.

Optimized for Multiplexing:
Efficient simultaneous editing of multiple genomic targets with high precision.

Scalable from RUO to Clinical:
Flexible formats allow smooth workflow from research to GMP-grade therapeutic production.

Enhanced Precision with Chemically Modified gRNAs:
Optimized guide RNAs increase stability, reliability, and editing efficiency.

Product Number	R10ACCUBASE
Concentration	10 mg/mL
Intended Use	This product is intended for research use only
Shipping Conditions	Cold Pack
Buffer Composition	30 mM Tris, 300 mM NaCl, 1 mM DTT, 0.1 mM EDTA, 50% Glycerol, pH 8.0
Source	E. coli
Purity	≥ 80.0%

Specifications

Specification	AccuBase Base Editor
Editor Type	Cytosine Base Editor (CBE)
Cas9 Backbone	SpCas9 Nickase
PAM Sequence (N = any nucleotide)	5′-NGG-3′
DNA Modification	C → T (G → A on opposite strand)
Editing Window*	~3–12 nucleotides upstream of PAM
gRNA Length	97 - 103 nt
Target Sequence Length	20 nt

* Editing window may vary based on target sequence and guide design.

Guide RNA

Designing your gRNA for AccuBase

AccuBase cytosine base editor contains an SpCas9 nickase, meaning its gRNA design process closely resembles that of traditional SpCas9 systems, with added considerations specific to cytosine base editing. Achieving high-efficiency editing with minimal bystander edits requires careful attention to the editing window and precise gRNA design.

Targeting the optimal editing window

For AccuBase systems, the editing window spans nucleotides 3 to 12 (with position 1 being furthest from the 5'-NGG-3' PAM). The target cytosine must ideally fall within this editing window to maximize active editing while reducing unintended modifications. When selecting binding sites:

Ensure PAM proximity: Choose a 5’-NGG-3’ PAM sequence that aligns the target cytosine centrally within the editing window.
Avoid boundary targets: Cytosine bases outside this editing range may have significantly reduced editing efficiency.
Evaluate bystander cytosines: If multiple cytosines fall within or near the editing window, prioritize designs that limit edits to irrelevant or non-critical regions to avoid unintentional consequences.

To demonstrate the editing window of AccuBase, the image below highlights positions where C-to-T base conversions could occur using our AccuBase positive control gRNA as examples.

Accurately targeting the optimal editing window is essential for maximizing the precision and efficiency of AccuBase cytosine base editor. Incorporating our standard SpCas9 chemical modifications* further enhance gRNA stability and reliability throughout the editing process. By combining precise targeting with these modifications, you can achieve consistent, reproducible results for your applications.

*2'-O-Methyl analog at the first 3 and last 3 bases and 3' phosphorothioate bonds between first 3 and last 2 bases

Designing your AccuBase guide RNA

Designing highly effective gRNAs is a crucial step in achieving precise and efficient base editing with AccuBase. To streamline this process, specialized base editing design tools are available to help you optimize target selection, minimize off-target effects, and position edits within the optimal window.

BE-Designer: Design optimal gRNAs for cytosine and adenine base editors
BE-Hive: Predict editing efficiency and off-target edits for base editors
DeepBaseEditor: Deep learning-based prediction of base editing outcomes
BE-DICT: Predict off-target deamination sites specific to base editors
CHOPCHOP: Design optimal gRNA and flexible platform to upload information specific to your base editor

We encourage you to design multiple Accubase gRNAs to fully evaluate the best gRNA for your therapeutic development. Each of these resources ensure your design aligns with AccuBase’s performance capabilities, setting your experiments up for success.

Data

AccuBase is Engineered for Therapeutics

Traditional cytosine base editors often rely on terminal deaminase fusions that can compromise spatial control and leave the deaminase constitutively active, increasing the risk of off-target edits. In addition, delivery formats,like mRNA, may introduce variability in expression levels, making it difficult to achieve consistent and predictable editing outcomes required for therapeutic development.

AccuBase is engineered with a cytosine deaminase embedded within a Cas9 nickase, activating only upon binding to the intended DNA target. This design enables controlled C-to-T conversion within a defined editing window while minimizing unintended activity. Supplied as a ready-to-use protein, AccuBase offers transient, tightly controlled editing without the need for codon optimization, supporting predictable performance, simplified dosing, and reduced off-target risk across therapeutic workflows.

Depiction of traditional base editors (right) compared to AccuBase cytosine base editor (left).

RNP Enables Precise Single and Multiplex Gene Editing

Many base editors face trade-offs between fidelity and efficiency, particularly in multiplex workflows where maintaining consistent on-target editing across multiple loci is difficult. Approaches that rely on double-strand breaks (DSBs) further increase the risk of genomic instability, including large deletions and chromosomal translocations—key safety concerns in therapeutic development.

AccuBase delivers high-efficiency, high-fidelity base editing in both single and multiplex applications without introducing DSBs. By enabling precise C-to-T conversions while minimizing off-target activity, AccuBase supports consistent editing across multiple gene targets with reduced risk of unintended genomic alterations. This combination of accuracy, efficiency, and DSB-free editing makes AccuBase a reliable solution for complex genome engineering in research and therapeutic workflows.

Editing Strategy	Gene Target	Knockout Efficiency
Single Editing	TRAC	95.4%
PDCD1	93.1%
B2M	81.0%
Dual Editing	TRAC & PDCD1	88.9%
PDCD1 & B2M	80.1%
Triple Editing	TRAC & PDCD1 & B2M	80.0%

In human primary T cells, AccuBase protein and gRNAs (listed above) were delivered to cells via electroporation. Single-site, dual-site, and triple-site editing were performed in parallel. The listed data represent the average knockout efficiency from three independent experiments.

Preserves Cell Viability in Multiplex Editing

Multiplex gene editing can place significant stress on cells, often leading to reduced viability and limiting downstream analysis or scalability. Approaches that rely on double-strand breaks further exacerbate this issue, increasing cellular damage during simultaneous edits.

AccuBase maintains high cell viability in multiplex workflows by enabling precise base editing without introducing double-strand breaks. This DSB-free mechanism minimizes cellular stress while supporting efficient, accurate edits across multiple targets. By preserving cell health, AccuBase enables more reliable outcomes and improves the feasibility of complex genome engineering in both research and therapeutic applications.

In human primary T cells, two or three genes were edited simultaneously using either AccuBase protein or Cas9 protein. RNP complexes were delivered into the cells via electroporation, and the cell expansion fold was calculated at various time points. Data and error bars represent the mean ± s.d. (n = 3 independent biological replicates). Electroporation was carried out independently by two laboratory personnel.

Enables DSB Free Genome Editing

Conventional CRISPR approaches rely on double-strand DNA breaks (DSBs) to introduce genetic changes, which can lead to unintended insertions, deletions, and genotoxic effects at both on- and off-target sites. These outcomes introduce variability and limit the level of control required for sensitive research and therapeutic applications.

AccuBase performs single-base editing without creating DSBs, directly converting cytosine to thymine while preserving genomic integrity. By avoiding strand breaks, AccuBase minimizes the risk of indels and unintended gene disruption, delivering precise, predictable edits with reduced collateral damage. This DSB-free mechanism supports safer, more controlled genome editing across both single and multiplex workflows.

AccuBase does not induce DSBs. In human primary T cells, the PDCD1, TRAC, and B2M genes were edited using either AccuBase protein or Cas9 protein. The editing components, including the respective proteins and sgRNAs, were delivered into the cells via electroporation. Indel formation at the target sites was assessed three days post-transfection. While AccuBase predominantly does not induce indels, Cas9 primarily mediates gene editing through indel generation. Data and error bars represent the mean ± s.d. (n = 3 independent biological replicates).

Minimizes Unintended Single-Nucleotide Variants

Unintended single-nucleotide variants (SNVs) introduced during genome editing can compromise edit fidelity and raise safety concerns in therapeutic applications. Even low-frequency SNVs may have downstream biological consequences, making precision and control critical for clinical development.

AccuBase is engineered for highly specific cytosine base editing with minimal off-target activity, significantly reducing the occurrence of unintended DNA SNVs. By tightly controlling deaminase activity and limiting editing to the intended target site, AccuBase helps preserve genomic integrity and supports safer, more predictable gene-editing outcomes. This level of precision enables researchers to advance therapeutic programs with greater confidence in both accuracy and safety.

AccuBase Eliminates Single-Nucleotide Variants from Gene Editing. The bar graph shows the total numbers of single-nucleotide variants (SNVs) detected by GOTI (Genome-Wide Off-Target Analysis by Two-Cell Embryo Injection). The AccuBase base editing technology significantly reduces sgRNA-independent off-target effects. Data and error bars represent the mean ± s.d. (n = 3 independent biological replicates).

Eliminates Chromosomal Translocations

Chromosomal translocations are a known safety concern in genome editing, often arising from double-strand breaks (DSBs) that trigger error-prone DNA repair pathways. These large-scale genomic rearrangements can disrupt gene function and pose significant risks in therapeutic applications, making their mitigation critical for clinical development.

AccuBase is designed to avoid DSBs entirely, using a single-base editing mechanism that directly converts cytosine to thymine without cutting both DNA strands. By eliminating DSB-driven repair processes, AccuBase significantly reduces the risk of chromosomal translocations, helping preserve genomic integrity and improve the safety profile of edited cells. This controlled editing approach enables more predictable outcomes and supports the development of safer cell and gene therapies.

AccuBase Eliminates Translocations from Gene Editing. In human primary T cells, the PDCD1, B2M, and TRAC genes were simultaneously edited using either AccuBase protein or Cas9 protein. Translocation frequencies were quantified using droplet digital PCR (ddPCR). Data and error bars represent the mean ± s.d. (n = 3 independent biological replicates).

FAQ

Answers to Commonly Asked AccuBase Questions

If you have additional questions please connect with a member of our team.

What does AccuBase do differently than standard CRISPR-Cas9 nucleases?

AccuBase is a cytosine base editor that performs precise single-base conversions (C → T) instead of generating double-strand breaks (DSBs). This allows you to introduce point mutations, disrupt splice sites, or create stop codons with minimal risk of large insertions/deletions, translocations, or chromosomal instability. Because it avoids DSBs, AccuBase also enables safer multiplex editing, making it ideal for experiments requiring multiple simultaneous base changes.

In what formats is AccuBase supplied and what are the benefits for delivery, control, and therapeutic development?

AccuBase is supplied as a recombinant protein (i.e., ready-to-use base editor), delivered in RNP format with gRNA.

This format gives you immediate, transient editing activity. The enzyme acts, does the base conversion, and is degraded, which reduces prolonged exposure, and thereby reduces off-target risk. It also offers better control over dosage, timing, and editing activity versus plasmid or mRNA‑based systems.

Can AccuBase scale from research to GMP/clinical-grade workflows?

Yes. AccuBase is offered in both research-grade (RUO) and GMP-grade formats.

Where can I find a complete workflow for base editing experiments with AccuBase?

Our webinar, Getting Started with Base Editing, covers gRNA design, delivery, editing, and analysis, providing a step-by-step guide for efficient experiments.

RESOURCES