Precision Genome Editing Services

E. coli Base Editing

Introduce targeted single-base substitutions in Escherichia coli without double-strand breaks using a programmable deaminase system.

C→T and A→G base conversions
Plasmid-based delivery with selection
Sequence-verified clonal isolates

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Targeted Base Editing in E. coli

Our service provides a complete workflow from guide design to delivery of confirmed edited clones for research applications.

Custom guide RNA design and synthesis
Editor plasmid construction and QC
Colony isolation and Sanger verification

Plasmid-based

Deaminase fusion

Clonal purity

Approach

Precise Base Editing Capability

Our service introduces specific point mutations in the E. coli genome using a programmable deaminase system without inducing double-strand breaks.

Guide RNA Design

We computationally design multiple guide RNAs targeting your region of interest, evaluating on-target efficiency and off-target potential to select optimal candidates.

Bioinformatic target selection
In silico off-target prediction
Multiple guide candidate evaluation

Editor Plasmid Construction

Plasmid vectors encoding Cas nickase–deaminase fusions and guide expression cassettes are assembled and fully sequence-verified before transformation.

Custom cloning into standard backbones
Full-plasmid sequencing confirmation
Ready for E. coli transformation

C→T and A→G Editing

Each project uses a specific deaminase enzyme (cytidine or adenine) to achieve the desired base transition within a defined editing window.

Plasmid-Based System

Base editing machinery is delivered on a single plasmid with antibiotic selection, enabling straightforward transformation and screening.

Clonal Isolation

Individual colonies are picked, propagated, and verified by Sanger sequencing to support homogenous edited populations.

Deliverables

What You Receive

Each project concludes with a handoff package of verified biological materials and project documentation.

Biological Materials

Purified, sequence-verified edited E. coli clones
Plasmid constructs (editor and guide RNA)
Glycerol stocks of all delivered clones
Sanger sequencing chromatograms and alignment files

Documentation & Support

Detailed methods summary with editing efficiency
Sequence confirmation data package
Project report including guide design rationale
Named scientific contact at project start; milestone review calls.

Service Scope

Customizable Parameters

Project details are defined during the design phase to match your specific target and application needs.

Parameter	Typical project scope
Editing Type	C→T or A→G base substitution; other substitutions on a case-by-case basis
Target Region Size	Scoped per project after consultation
Guide RNA Count	Scoped per project after consultation
Number of Clones	Delivery of up to 5 confirmed edited clones (customizable during design)
Strain Compatibility	Common E. coli lab strains (e.g., MG1655, BW25113); other strains scoped per project
Off-Target Analysis	In silico prediction included; targeted amplicon sequencing of top predicted sites optional
Quality Control	Sanger sequencing of target region for every delivered clone; chromatogram and alignment provided

Workflow

How It Works

A streamlined five-step process from target design to clone delivery.

Target Design

We analyze your target sequence, design multiple guide RNAs, and select optimal candidates based on in silico off-target evaluation and editing window placement.

Editor Construction

Plasmid vectors encoding the Cas nickase-deaminase fusion and guide expression cassette are assembled using standard cloning or synthesis and confirmed by full-plasmid sequencing.

Transformation

The validated editor plasmid is transformed into the specified E. coli host strain; transformants are selected on antibiotic-containing.

Colony Screening

Individual colonies are isolated, cultured, and genomic DNA is extracted for PCR amplification of the target region.

Clone Verification

Sanger sequencing is performed on each clone; editing efficiency is assessed, and confirmed edited clones are purified and archived.

Applications

Where Base Editing Adds Value

Enabling precise point mutations for a range of research and engineering goals.

Gene Function Studies

Introduce missense or nonsense mutations in coding sequences to study gene function without the risk of double-strand break-induced lethality.

Single-amino-acid changes
Essential gene interrogation
Phenotypic characterization

Metabolic Engineering

Precisely alter enzyme active sites or regulatory regions to redirect metabolic flux and evaluate product yields.

Fine-tuning of rate-limiting steps
Introduction of feedback-resistant variants
Multiplex editing when scoped

Synthetic Biology

Generate promoter or ribosome-binding site mutations to modulate gene expression levels predictably.

Promoter engineering
RBS modification
Reporter system optimization

FAQ

Frequently Asked Questions

Common questions about our E. coli base editing service.

Editing efficiency depends on target sequence context and the protospacer adjacent motif (PAM) requirements of the Cas variant used. We evaluate multiple guide designs to identify the best-accessible site within your region of interest and will inform you if constraints limit editability.
The service currently supports C→T (cytosine deamination) and A→G (adenine deamination) conversions, each enabled by a specific deaminase enzyme. Transversions or other substitutions are not directly accessible but may be achieved by multiplex approaches on a custom basis.
In silico off-target prediction is performed for each guide RNA to identify potential mismatched sites. If needed, targeted amplicon sequencing of the top predicted off-target loci can be included to assess unintended edits within the project scope.
Each delivered clone is isolated from a single colony, and the edited region is confirmed by Sanger sequencing. A sequencing alignment file, chromatograms, and a summary of editing efficiency are provided. Additional QC such as off-target amplicon sequencing can be included as part of the project scope.

Scientific Literature

References

Li Q, Sun B, Chen J, et al. A modified pCas/pTargetF system for CRISPR-Cas9-assisted genome editing in Escherichia coli. Acta biochimica et biophysica Sinica. 2021;53(5):620-627. View on PubMed
Cho SI, Lee S, Mok YG, et al. Targeted A-to-G base editing in human mitochondrial DNA with programmable deaminases. Cell. 2022;185(10):1764-1776.e12. View on PubMed

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