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

Overview Specifications Data

AccuBase is also available in GMP.

Bundling GMP AccuBase with Synthego’s best-in-class GMP gRNAs offers an advanced, comprehensive solution to streamline your therapeutic development. Both products are manufactured under true GMP standards, ensuring the highest level of quality, safety, and consistency from development to clinical use. This combination enhances specificity, reduces off-target activity, and ensures scalability, providing a robust base editing solution for IND-enabling studies and clinical-scale applications. Check out GMP AccuBase.

Overview

Advantages of AccuBase for CRISPR-based therapeutics

Safer for therapeutic applications: By avoiding DNA cuts, it eliminates double-strand breaks (DSBs) and chromosomal translocations, significantly reducing genomic instability. Additionally, AccuBase demonstrates remarkably low off-target activity in both DNA and RNA, ensuring fewer unintended edits.
Greater genome editing control: AccuBase’s RNP format provides you with greater control over gene editing activity by delivering immediate functionality upon delivery. Unlike mRNA or plasmid systems, which can result in prolonged and unpredictable editing, AccuBase gives you predictable and efficient editing right from the start.
Superior multiplex gene editing: AccuBase excels in multiplex gene editing applications, delivering high on-target efficiency combined with low off-target rates. This precision is crucial for simultaneously editing multiple genes, reducing downstream complications and increasing efficiency for complex therapeutic development.
Easier path to commercialization: AccuBase offers a clear and secure path to commercialization through exclusive global IP rights held by Base Therapeutics, with comprehensive Freedom-to-Operate (FTO) assessments performed by Base Therapeutics confirming it is legally distinct from competing CRISPR and base editing technologies. This careful evaluation helps reduce uncertainties, allowing you to move forward with greater confidence in the development of your therapeutic innovations. Connect with our team to learn how AccuBase can support your therapeutic pipeline with a clear and efficient licensing strategy.
Approved for clinical trials: AccuBase has been validated as a proven technology in an IND-approved clinical program by Base Therapeutics. With demonstrated efficacy and reliability, AccuBase meets the rigorous demands of regulated environments and demonstrates its readiness to drive advanced therapeutic applications.
Efficient scalability from preclinical to clinical: AccuBase seamlessly scales from research use-only (RUO) to GMP-grade requirements, bridging the gap between preclinical development and clinical trial implementation. This scalability allows you to optimize your processes without compromising quality, ensuring that pipeline development remains efficient and cost-effective.

What are you waiting for? Switch to an engineered cytosine base editor today!

Overview of Synthego's Cytosine Base Editor

From RUO-to-GMP, Accubase, Synthego’s high fidelity engineered cytosine base editor (CBE) was purpose-built for high precision base editing in therapeutic applications. This engineered CBE contains a cytosine deaminase embedded within Cas9 nickase, that activates only when bound to the DNA target site, preventing unintended genome editing. Once bound to the DNA target site, Accubase exposes the deaminase enzyme enabling efficient and controlled conversion of cytosine (C) to thymine (T) within the 3-12 base editing window.

AccuBase CBE achieves high on-target editing in single and multiplexed applications with no detectable off-target editing or chromosomal translocations, offering an ideal solution for safe and effective base editing in cell and gene therapies. Where mRNA-delivered CBEs remain active in cells for longer increasing the chance of off-target editing, AccuBase is the only CBE supplied as a recombinant protein for transient expression. This allows scientists greater control over the duration and precision of editing, helping to minimize off-target risk potential and optimize outcomes in therapeutic genome engineering.

Using traditional cytosine base editors in cell and gene therapies presents key challenges. One major limitation is the use of mRNA delivery formats, which can result in prolonged protein expression within cells. This extended exposure increases the risk of off-target editing, leading to genotoxicity or unpredictable cellular behavior - unacceptable risks for cell and gene therapies. Furthermore, many current cytosine base editors exhibit off-target activity due to their continuous active state until they are eventually degraded in the cell. Therefore, finding a base editor that maintains high on-target precision without promiscuous off-target edits and translocation events has proven difficult - until AccuBase cytosine base editor.

AccuBase is also available in GMP. Bundling GMP AccuBase with Synthego’s best-in-class GMP gRNAs offers an advanced, comprehensive solution to streamline your therapeutic development. Both products are manufactured under true GMP standards, ensuring the highest level of quality, safety, and consistency from development to clinical use. This combination enhances specificity, reduces off-target activity, and ensures scalability, providing a robust base editing solution for IND-enabling studies and clinical-scale applications. Check out GMP AccuBase.

Understanding the editing window and designing AccuBase gRNAs

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.

Maximize your base editing success

We highly recommend using our AccuBase Cytosine Base Editor and gRNA User Guide to ensure a smooth and successful start to your CRISPR base editing experiments. We also provide a variety of protocols designed specifically for our CRISPR solutions, including nucleofection, electroporation, and lipofection, you can adapt for your AccuBase base editing experiments.

Product Number	R10ACCUBASE
Concentration	10 mg/ml
Intended Use	This product is intended for research use only
Shipping	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%

It is strongly encouraged that you work in an RNase-free and sterile environment when using AccuBase and its gRNA. Additionally, we strongly encourage you to use sterile filter pipette tips to decrease risk of introducing RNase or other contaminants into your samples.

AccuBase is engineered for therapeutics

Challenge: Traditional base editors rely on the fusion of the deaminase to either the C- or N-terminus of the editing complex. This configuration can lead to challenges in achieving optimal positioning and coordination of editing components, potentially affecting precision and efficiency. Additionally, such fusions can result in a continuously active deaminase enzyme, which may heighten the risk of off-target modifications and unintended genetic alterations. Delivery formats, including mRNA, may also introduce variability in expression levels and editing outcomes, presenting hurdles for consistent and reliable gene-editing performance. These factors can create additional complexity for researchers aiming to balance precision and scalability in therapeutic development.

Solution: AccuBase is engineered with an cytosine deaminase embedded within the Cas9 nickase that activates only when bound to the DNA target site. This integrated design minimizes off-target activity and enables controlled conversion of C-to-T within the editing window. Furthermore, delivering AccuBase in a ready-to-use protein format reduces the risk of off-targets due to its transient expression and are species-agnostic eliminating the need for tedious codon optimization. The protein format not only ensures robust and predictable activity but also simplifies delivery, offering faster onset of editing and greater control over dosage.

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

AccuBase RNP Excels in Single and Multiplex Gene Editing

Challenge: Many base editors struggle with low rates of on-target editing, even when maintaining high fidelity, reducing their usefulness in achieving precise modifications. Multiplex editing adds further complexity, with greater risks of off-target edits leading to unintended changes in the genome. Efficiency is another major hurdle; consistent and accurate edits across multiple targets are difficult to achieve. Additionally, methods relying on DSBs pose a significant risk of genomic instability, including chromosomal translocations, which can undermine safety in therapeutic applications.

Solution: AccuBase addresses these challenges by combining high efficiency with exceptional fidelity, ensuring precise on-target editing in both single and multiplex gene editing applications. By eliminating the need for DSBs, AccuBase significantly reduces the risk of genomic instability from chromosomal translocation or large deletions, thereby enhancing safety. Its high fidelity engineering minimizes off-target edits, providing greater accuracy and reliability. Furthermore, AccuBase delivers consistent gene editing efficiency across multiple gene targets, providing a dependable approach for addressing complex genetic modifications to advance both research and therapeutic development.

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.

Data

AccuBase Prevents Cell Death Following Multiplex Editing

Challenge: Multiplex gene editing presents unique challenges, including significant cell death that can occur during the editing process. This loss of cell viability reduces editing efficiency and impacts the success of experiments. High cell death rates create hurdles for researchers aiming to achieve reliable, scalable, and effective gene edits, particularly in complex applications requiring multiple simultaneous edits.

Solution: AccuBase overcomes this limitation by eliminating the need for double strand breaks in its editing process. This precision-focused approach significantly reduces the impact on cell health, maintaining high levels of cell viability even in multiplex editing applications. By preserving cell integrity, AccuBase allows researchers to achieve efficient and effective edits without compromising the viability of their samples, ultimately supporting more reliable and scalable outcomes.

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.

AccuBase Does Not Induce DSBs

Challenge: Traditional CRISPR gene editing relies on creating double strand breaks (DSBs) in DNA that result in changes to the genomic sequence. While effective, DSBs can lead to unintended consequences, such as insertions and deletions (indels) at off-target locations. These unintended disruptions can compromise gene function, result in genotoxic mutations, and introduce variability that hinders the precision and reliability required for sensitive applications.

Solution: AccuBase eliminates the need for DSBs due to its single base editing mechanism. This innovative approach directly modifies a single DNA base without cutting both strands, thereby avoiding the risk of indels or unintended gene edits. With AccuBase, researchers gain the power of precision editing, ensuring controlled and predictable outcomes while preserving the integrity of the surrounding genomic context. By prioritizing accuracy and minimizing collateral damage, AccuBase sets a new standard for safe and reliable gene editing.

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).

AccuBase Eliminates Single Nucleotide Variants from Gene Editing

Challenge: Single nucleotide variants (SNVs) introduced during gene editing can lead to unintended DNA changes with far-reaching consequences. These changes may result in harmful mutations, compromising the safety and effectiveness of therapeutic applications. The presence of SNVs poses significant challenges for achieving the precision and reliability required to develop safe and effective treatments.

Solution: AccuBase stands apart with its unparalleled precision, significantly reducing, even eliminating, off-target edits, including DNA SNVs. By maintaining strict specificity, AccuBase minimizes the risk of adverse safety events and ensures the integrity of your gene edits. This allows researchers to advance therapeutic development with greater confidence in their 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).

AccuBase Eliminates Translocations from Gene Editing

Challenge: Chromosomal translocations, where segments of DNA are rearranged between chromosomes, can be a problem when performing genomic modifications. These unintended events can disrupt genetic function, cause harmful effects, and pose significant safety risks, especially in therapeutic applications. The unpredictability of translocations creates challenges in ensuring the reliability and safety of gene editing outcomes.

Solution: AccuBase addresses this risk by eliminating chromosomal translocations during the editing process. Its precise, single base editing approach avoids creating DSBs, thereby avoiding large-scale genomic disruptions, significantly reducing the likelihood of translocations. This level of control provides researchers with greater confidence in the safety and integrity of their edits, making AccuBase a dependable choice for advancing therapeutic development.

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).

RESOURCES

Resource - Protocol

AccuBase™ protein and gRNA User Guide