CD Biosynsis offers cutting-edge Phaeodactylum tricornutum Base Editing Services, providing a high-precision, DNA-double-strand-break-free (DSB-free) method for single-nucleotide substitutions. While traditional CRISPR-Cas9 is powerful for creating knockouts via random indels, Base Editing (BE) allows for the direct chemical conversion of one base pair to another (e.g., C:G to T:A or A:T to G:C) at specific genomic coordinates. This technology is uniquely suited for the model diatom Phaeodactylum tricornutum, enabling the precise engineering of photosynthetic protein domains, the introduction of herbicide resistance mutations, and the fine-tuning of metabolic enzymes without the genomic toxicity or unpredictable rearrangements often associated with chromosomal breaks.
Our base editing platform addresses the specific genetic requirements of marine diatoms, characterized by their diploid genomes and distinct regulatory landscapes. By utilizing catalytically impaired Cas9 (nCas9) fused to specialized deaminase enzymes, we can achieve high-efficiency nucleotide conversion within a narrow "editing window." This capability is revolutionary for diatom synthetic biology, as it facilitates "scarless" point mutations that were previously difficult to achieve due to the low efficiency of Homology-Directed Repair (HDR) in microalgae. Whether you are performing functional proteomics on the light-harvesting complex or optimizing the catalytic efficiency of lipid-producing enzymes, our base editing services provide the precision required for sophisticated algal design.
Get a QuoteBase editing in Phaeodactylum tricornutum allows for the introduction of specific amino acid changes without altering the surrounding genomic context. This is achieved by targeting a deaminase to a specific DNA site via a guide RNA (gRNA). Once at the target, the deaminase converts the target base (C or A) into a different base, which the cell's replication or repair machinery then fixes into a permanent mutation. This approach is vital for engineering diatom strains with enhanced industrial properties, such as improved tolerance to high light or specialized nutrient utilization.
Our services are powered by codon-optimized base editors specifically designed for the nuclear environment of P. tricornutum. We account for the diatom's specific transcriptional signals and nuclear localization requirements to ensure that the base editing machinery is expressed at effective levels. By minimizing "bystander" editing—unwanted mutations in adjacent bases—we deliver strains with unprecedented genetic fidelity. This precision enables the systematic study of protein motifs and the rational design of metabolic pathways, moving algal biotechnology from random optimization to predictive engineering.
We provide a range of base editing tools tailored to different types of nucleotide conversions and research objectives in Phaeodactylum.
Mechanism
Utilizes a cytidine deaminase (e.g., APOBEC) to convert Cytosine to Uracil, which is read as Thymine during DNA replication, resulting in a C to T transition.
iSTOP Technology
Enables the induction of premature stop codons (TAG, TAA, TGA) at specific positions, providing a clean method for gene inactivation without indels.
Mechanism
Utilizes an adenosine deaminase (e.g., TadA) to convert Adenine to Inosine, which is read as Guanine, resulting in an A to G transition.
Residue Swapping
Ideal for altering specific amino acid residues in enzymes involved in EPA or fucoxanthin synthesis to modify substrate specificity or activity.
Herbicide Resistance
Introduction of precise mutations in genes like ALS or psbA to confer resistance to specific inhibitors, serving as clean selectable markers.
Promoter Engineering
Editing TATA boxes or transcription factor binding sites to modulate the strength of endogenous promoters without large-scale genomic disruption.
Our rigorous workflow ensures high-purity monoclonal strains with full genomic verification of the target edit.
1. Window Design & Codon Optimization
2. Tool Assembly & Transformation
3. Clonal Isolation & NGS Screening
4. Phenotypic Verification
Identification of the target nucleotide within the optimal editing window (typically positions 4-8 relative to the PAM). Design of gRNAs and codon optimization of the base editor for the Phaeodactylum nuclear genome.
Construction of diatom-specific episomal vectors or preparation of RNP complexes. Delivery via optimized biolistic bombardment (gene gun) or bacterial conjugation.
Analysis of protein function, growth kinetics, and metabolic output. Verification that the single-base change has resulted in the desired physiological shift. Delivery of cryopreserved strains and comprehensive data reports.
DSB-Free Integrity
By avoiding double-strand breaks, base editing preserves the overall integrity of the diatom genome and prevents p53-mediated stress responses.
Biallelic Efficiency
Our platform is optimized to achieve simultaneous editing of both alleles in the diploid Phaeodactylum host, ensuring immediate phenotypic expression.
Episomal Vector Reversal
Use of episomal delivery allows for the curing of the base editing machinery after the mutation is fixed, resulting in "scarless" modified strains.
High-Throughput Verification
We utilize NGS to precisely characterize the editing outcome, ensuring zero off-targets and quantifying any bystander edits in the window.
Technical insights for your Phaeodactylum base editing project.
Contact Us1. What is the typical "editing window" for diatoms?
For standard base editors, the activity window is usually a 5-nucleotide stretch (typically positions 4 to 8) within the gRNA sequence. We design gRNAs to place your target base precisely within this zone.
2. How do you handle "bystander" bases in the window?
If multiple target bases (e.g., multiple Cs) exist in the window, we use evolved deaminases with narrower windows or specialized gRNA designs to isolate the specific base intended for conversion.
3. Can base editing be used to create gene knockouts?
Yes, by using Cytidine Base Editors (CBE) to convert a sense codon into a premature stop codon (iSTOP), we can achieve gene inactivation without the indels associated with standard CRISPR-Cas9.
4. Is the base edit permanent and stable?
Absolutely. Once the chemical conversion is fixed by the cell's replication or DNA repair machinery, the mutation is as stable as any natural genomic sequence across generations.
5. Do you offer base editing in the chloroplast genome?
Yes, we offer specialized organelle-targeted base editing services utilizing DdCBE or chloroplast-localized base editors to modify photosynthetic complexes directly.
6. How do you confirm biallelic editing in diploid Phaeodactylum?
We utilize targeted deep sequencing (NGS). By analyzing the read counts, we can definitively distinguish between monoallelic (approx. 50%) and biallelic (approx. 100%) editing events.
7. Is codon optimization necessary for the base editor protein?
Yes. Diatoms have unique codon usage and nuclear localization requirements. We utilize base editors fully optimized for P. tricornutum to ensure maximal nuclear expression.
8. What is the typical turnaround time for a project?
A standard base editing project from design to verified monoclonal strain delivery typically takes 14 to 20 weeks.
CRISPR-Cas9 technology represents a transformative advancement in gene editing techniques. The main function of the system is to precisely cut DNA sequences by combining guide RNA (gRNA) with the Cas9 protein. This technology became a mainstream genome editing tool quickly after its 2012 introduction because of its efficient, simple and low-cost nature.
The CRISPR gene editing system with its Cas9 version stands as a vital instrument for current biological research. CRISPR technology enables gene knockout (KO) through permanent gene expression blockage achieved by sequence disruption. Various scientific domains including disease modeling and drug screening employ this technology to study gene functions. CRISPR KO technology demonstrates high efficiency and precision but requires confirmation and verification post-implementation because unsatisfactory editing may produce off-target effects or incomplete gene knockouts which impact experimental result reliability. For precise and efficient Gene Editing Services - CD Biosynsis, Biosynsis offers comprehensive solutions tailored to your research needs.
The CRISPR-Cas9 knockout cell line was developed using CRISPR/Cas9 gene editing to allow scientists to remove genes accurately for research on gene function and disease models and pharmaceutical discovery. Genetic research considers this technology essential due to its high efficiency together with simple operation and broad usability.
If your question is not addressed through these resources, you can fill out the online form below and we will answer your question as soon as possible.
CD Biosynsis is a leading customer-focused biotechnology company dedicated to providing high-quality products, comprehensive service packages, and tailored solutions to support and facilitate the applications of synthetic biology in a wide range of areas.