Genome Editing Service

Saccharomyces cerevisiae Base Editing

Precise, markerless single-base substitutions in yeast using CRISPR nickase-mediated deaminase technology.

Custom guide RNA design for each target locus
Nickase-deaminase fusion construct assembly
Sanger-verified edited strain delivered

Service Overview

Our base editing service enables targeted point mutations in Saccharomyces cerevisiae without double-strand breaks or donor templates, streamlining metabolic engineering and functional genomics applications.

C→T or A→G conversions at user-defined loci
Markerless editing – no selection scars retained
Streamlined workflow from design to verified clone

Custom Designs

Sanger QC

Verified Strain

Approach

Precise Base Editing in Baker's Yeast

Leveraging a CRISPR nickase fused to a cytidine or adenosine deaminase, we achieve targeted single-base transitions with high accuracy and minimal off-target effects.

Guide Design & Construct Assembly

We analyze your target region and design a high-specificity guide RNA. The nickase-deaminase fusion and guide expression cassette are cloned into a yeast vector for transformation.

Guide RNA designed for optimal targeting
Nickase-deaminase fusion (CBE or ABE) assembled
Plasmid construct verified by sequencing

Transformation, Screening & Delivery

The construct is transformed into S. cerevisiae via chemical methods. After selection, colonies are screened by PCR and Sanger sequencing to confirm the intended base change. A purified, verified clone is archived and delivered.

LiAc/SS carrier DNA/PEG transformation
Colony PCR and Sanger sequencing of target locus
Single-colony purified and cryopreserved

Gene-Specific Guide RNA Design

Custom guide RNAs are designed to minimize off-target binding and evaluate on-target efficiency, using proprietary algorithms.

Base Editing Plasmid Construction

We assemble a plasmid encoding the nickase-deaminase fusion and the guide RNA expression cassette, tailored to your strain.

Sanger Verification

Every edited clone is verified by Sanger sequencing spanning the target site to confirm the intended single-base change and absence of unwanted mutations.

Deliverables

What You Receive

Each project delivers a verified edited S. cerevisiae strain along with project documentation of the editing process and QC results.

Standard Deliverables

Verified edited Saccharomyces cerevisiae strain (≥1 purified single-colony isolate)
Base editing plasmid construct (nickase-deaminase + guide RNA)
Guide RNA sequences and design report
Sanger sequencing chromatogram of the target locus

QC Documentation

Sequencing confirmation of intended base change
Quality control report (genotype verification, purity check)
Strain purification and cryopreservation records

Service Scope

Project Parameters

Each project is customized to your target gene and strain. Typical parameters are described below; final scope is defined in the statement of work.

Parameter	Typical project scope
Host Strain	Any S. cerevisiae strain supplied by client or our standard laboratory strain (e.g., BY4741).
Editing Type	Single C→T (cytidine base editor) or A→G (adenine base editor) substitution.
Guide RNA Design	Scoped per project after consultation
Construct	Nickase-deaminase fusion expression plasmid with guide RNA cassette, assembled in-house.
Transformation Method	LiAc/SS carrier DNA/PEG chemical transformation.
Selection	Auxotrophic or drug marker if required; markerless editing available (no selection scar).
Screening Depth	Typically 4–8 colonies per target screened by colony PCR and Sanger sequencing.
Clone Purification	Single-colony isolation and re-streaking for purity.
Cryopreservation	Archived glycerol stock of verified edited strain.

Workflow

How It Works

A structured five-step process from target selection to delivery of your verified base-edited yeast strain.

Guide RNA Design

We analyze your target genomic region and design a guide RNA with high specificity. The guide sequence is optimized to minimize off-target binding and evaluate on-target editing efficiency.

Construct Assembly

A base editing plasmid is assembled by cloning the nickase-deaminase fusion (CBE or ABE) and guide RNA expression cassette into a yeast vector. The construct is verified by restriction digestion and sequencing.

Yeast Transformation

The plasmid is introduced into S. cerevisiae using a standard lithium acetate/single-stranded carrier DNA/PEG protocol. Transformants are plated on selective medium and incubated until colonies appear.

Screening & Verification

Individual colonies are picked, the target genomic region is PCR-amplified, and Sanger sequencing is performed to confirm the intended base change. Editing efficiency is recorded per project.

Strain Purification & Delivery

A verified single colony is re-streaked for purity, archived as a glycerol stock, and shipped along with the base editing plasmid, sequencing data, and a detailed QC report.

Applications

Where Base Editing Adds Value

Targeted single-base changes in S. cerevisiae enable precise functional studies and metabolic pathway optimization.

Pathway Optimization

Introduce point mutations in rate-limiting enzymes or regulatory proteins to evaluate flux toward desired metabolites.

Precise single-base change in target gene
No marker scar retained
Verified clone delivered for further testing

Gene Function Studies

Generate allelic series or test specific missense mutations to dissect protein function and cellular pathways.

Targeted substitution without DSB
High editing efficiency in S. cerevisiae
Sanger-verified mutant strains

Structure-Function Analysis

Create point mutations to probe active sites, binding interfaces, or stability determinants in yeast-expressed proteins.

Single amino acid change as designed
Markerless editing for seamless expression
Purified clone available for expression studies

FAQ

Frequently Asked Questions

Common questions about service scope, QC, and technical considerations for base editing in S. cerevisiae.

We offer both cytidine base editing (C→T) and adenine base editing (A→G). These conversions are achieved by fusing a nickase Cas9 with a cytidine deaminase or adenosine deaminase, respectively. The target must be within a suitable PAM-proximal window, typically positions 4–8 of the protospacer. Our design team evaluates each target and selects the appropriate editor.
Editing efficiency is determined by Sanger sequencing of individual colonies after transformation. We typically screen 4–8 colonies per target and report the proportion that carry the intended base change. Efficiency varies with target locus, guide RNA design, and strain background; please consult our team for typical expectations.
QC includes Sanger sequencing of the target region from the purified clone to confirm the intended base change and absence of unwanted indels. The editing plasmid is sequenced at construction. A final QC report documents the base change, chromatogram, strain purity, and cryopreservation details.
Base editing can edit multiple genome copies, but efficiency may be lower for polyploid strains due to the need to edit all alleles. We recommend discussing your specific strain ploidy with our project managers to design an appropriate screening strategy. Markerless editing is still feasible when multiple alleles contain the target sequence.

Scientific Literature

References

Pan Y, Xia S, Dong C, et al. Random Base Editing for Genome Evolution in Saccharomyces cerevisiae. ACS synthetic biology. 2021;10(10):2440-2446. View on PubMed
Yin S, Jarosz DF, Ting AY. Towards CRISPR-based editing of the mitochondrial genome in yeast. Proceedings of the National Academy of Sciences of the United States of America. 2026;123(3):e2505894123. View on PubMed
Kuroda K, Ueda M. CRISPR Nickase-Mediated Base Editing in Yeast. Methods in molecular biology (Clifton, N.J.). 2021;2196:27-37. View on PubMed

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