Zinc Finger Nuclease (ZFN)
CompoZr® Zinc Finger Nuclease Technology
Zinc finger nucleases (ZFNs) are a class of engineered DNA-binding proteins that facilitate genome editing by creating a double-stranded break in DNA at a user-specified location.
A double-stranded break is important for site-specific mutagenesis in that it stimulates the cell’s natural DNA-repair processes, namely homologous recombination and Non-Homologous End Joining (NHEJ).
Using well-established and robust protocols, these cellular processes can be harnessed to generate precisely targeted in vitro or in vivo genomic edits with targeted gene deletions (Knockouts), integrations, or modifications.
CompoZr ZFNs – Now More Affordable
Improvements in CompoZr ZFN design and manufacturing have acted to significantly increase the affordability of genome editing with CompoZr ZFN technology for the research community. All researchers now have access to this well characterized and highly published technology.
What Is ZFN Technology?
Zinc finger nucleases (ZFNs) are a class of engineered DNA-binding proteins that facilitate targeted editing of the genome by creating double-strand breaks in DNA at user-specified locations.
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Figure 1: Each Zinc Finger Nuclease (ZFN) consists of two functional domains: a.) A DNA-binding domain comprised of a chain of two-finger modules, each recognizing a unique hexamer (6 bp) sequence of DNA. Two-finger modules are stitched together to form a Zinc Finger Protein, each with specificity of ≥ 24 bp. b.) A DNA-cleaving domain comprised of the nuclease domain of Fok I. When the DNA-binding and DNA-cleaving domains are fused together, a highly-specific pair of 'genomic scissors' are created. - See more at: http://www.sigmaaldrich.com/life-science/zinc-finger-nuclease-technology/learning-center/what-is-zfn.html#sthash.Xi8JoIN9.dpuf
Double-strand breaks are important for site-specific mutagenesis in that they stimulate the cell's natural DNA-repair processes, namely homologous recombination and Non-Homologous End Joining (NHEJ). By implementing established, field proven methods, these processes are harnessed to generate precisely targeted genomic edits, resulting in cell lines with targeted gene deletions, integrations, or modifications. - See more at:
Benefits
• Rapid disruption of, or integration into, any genomic loci
• Mutations made are permanent and heritable
• Works in a variety of mammalian somatic cell types
• Edits induced through a single transfection experiment
• Knockout or knock-in cell lines in as little as two months
• Single or biallelic edits occur in 1–20% of clone population
• No antibiotic selection required for screening
Target Applications
• Functional Genomics/Target Validation
o Creation of gene knockouts in multiple cell lines
o Complete knockout of genes not amenable to RNAi
• Cell-based screening
o Creation of knock-in cell lines with promoters, fusion tags or reporters integrated into endogenous genes
• Cell Line Optimization
o Creation of cell lines that produce higher yields of proteins or antibodies
Figure 2: ZFN-mediated genome editing takes place in the nucleus when a ZFN pair targeting the user’s gene of interest is delivered into a parental cell line, either by transfection, electroporation or viral delivery.
How Do ZFNs Work?
Cell Line Engineering Made Simple
CompoZr™ ZFNs are used to create modified cell lines with targeted gene deletions, gene insertions, or gene corrections.
The CompoZr protocol for cell line modification starts with the delivery of a ZFN pair into a cell line of interest, and has been designed to be compatible with various standard methods of cellular delivery, including lipid-based transfection, electroporation and nucleofection™. Following delivery into the cell, ZFN-mediated editing will occur in as little as three days (see Figure 1), at which point the clonal pool is ready to be assayed for rate-of-mutation.
Using ZFNs to Create Modified Cell Lines
Figure 1: Cell line modification using ZFNs is simple and relies on standard processes such as transfection, dilution cloning, and genotyping.
Gauging ZFN Efficiency
In the absence of an exogenous repair template, ZFN-induced double-strand breaks are typically repaired by a non-perfect cellular repair mechanism called Non-Homologous End Joining (NHEJ). Due to the imperfect fidelity of NHEJ, a minority of double-strand breaks within a ZFN-treated cellular population will be misrepaired, leading to cells in which either random heterogeneous genetic insertions or deletions have been made at the site of the double-stand break. Sigma uses a mismatch sensitive enzyme to look for these imperfect repairs, thereby quantifying the effectiveness of a ZFN pair.
Quantifying ZFN Efficiency
Figure 2: A nucleotide mismatch assay is used to quantify the effectiveness of ZFNs. The mismatch assay consists of amplifying the target region from ZFN-treated genomic DNA via standard PCR. Resultant PCR products are denatured and allowed to re-anneal. A fraction of re-annealed products will contain bulges of DNA where heterogeneous mismatches occur. When a mismatch sensitive enzyme is added to the reaction, DNA digestion will occur at the site of the nucleotide mismatch. PCR pools are analyzed via PAGE. Sample pools 3–5 above contain cells that have been edited via ZFN-induced editing. The ratio of digested PCR products vs. wildtype PCR product is quantified by densitometry to determine rate of ZFN effectiveness.
CompoZr™ ZFNs for Targeted Knockout Animals
Enabling Unprecedented Research in Virtually Any Species Including Rats, Mice,
Rabbits, Zebrafish and More
Benefits
Recent Developments in Animals
ZFN Knockout Animal Creation via Microinjection
How to Order
CompoZr Zinc Finger Nuclease (ZFN) Technology is a novel system for rapid creation of targeted gene knockouts, genomic insertions or gene editing in eukaryotic systems. ZFNs are highly efficient pairs of custom nucleases designed and made by Sigma-Aldrich to target your gene or genomic sequence of interest. ZFNs (mRNA or plasmid formats) are delivered to cells by transfection methods or to embryos by microinjection. Upon cleavage of the target site, endogenous cellular processes are harnessed to produce targeted mutations that result in gene knockout.
Benefits:
• Unlimited Species Possibilities—
Animals with ES cell method limitations can now be targeted
• Rapid Animal Engineering—
Fastest method for creation of knockout rodents (2-3 months) and other higher eukaryotes
• Robust Mutation Rate—
Achieve up to a 10-15% mutation rate in founder animals
• Heritable Transmission—
Faithful germline transmission of targeted mutations
• Universal Tool—
Move quickly from cell line proof-of-concept studies into animals
Recent Developments in Animals
Recent work has shown that the ZFN-based gene knockout method is highly effective not only in cell lines, but also in embryos for the creation of animal models. Such developments enable targeted genetic engineering of organisms such as rats and zebrafish, where conventional methods of genetic manipulation have been unsuccessful. ZFN-based gene targeting has been proven to work in a wide variety of organisms including rats, mice, rabbits, zebrafish, Drosophila and C. elegans with testing in additional model systems underway.
CompoZr ZFN-based genetic engineering does not require the use of embryonic stem (ES) cells because ZFNs can be injected directly into early stage embryos (see illustration below). This allows targeted gene disruption in a wider spectrum of organisms (i.e. rats and zebrafish) and in much shorter timeframes. Knockout rats and mice can be created in as little as 2-3 months at high efficiencies (monoallelic 10-15%, biallelic 1%) compared to the ES cell method in mice that can take up to 12-18 months. ZFN methods result in efficient germline transmission of targeted genetic mutations without incorporation of foreign DNA sequences.
ZFN Knockout Animal Creation via Microinjection
Knockout model creation using Zinc Finger Nucleases starts with a fertilized single cell embryo (see illustration below). The ZFN, in mRNA form, is microinjected into the nucleus, cytoplasm, or yolk (e.g. zebrafish) where it locates the target sequence and creates a double strand break. ZFNs in plasmid form may also be injected into the nucleus. The double strand break stimulates the cellular process of non-homologous end joining and results in the mis-repair of the DNA sequence. The resulting mutation usually gives rise to a knockout genotype/phenotype. The embryos are then plated or implanted into the foster mother and allowed to divide and grow into whole organisms. At birth, the animals are screened for mutations and the founder animals are identified. Biallelic knockouts are achievable in the founder generation. However, monoallelic knockouts can also be interbred to produce biallelic knockout animals.
inquiry form. After discussion of the ZFN project details, you will be provided with pricing and relevant licensing details (if applicable). - See more at: http://www.sigmaaldrich.com/life-science/zinc-finger-nuclease-technology/learning-center/zfns-in-animals.html#sthash.wuOVSol8.dpufHow to Order CompoZr ZFNs (Product No. CSTZFN-1KT) are considered custom projects and are quoted through your local sales representative. You may start the process by completing online ZFN inquiry form. After discussion of the ZFN project details, you will be provided with pricing and relevant licensing details (if applicable). - See more at:
How to Order
CompoZr ZFNs (Product No. CSTZFN-1KT) are considered custom projects and are quoted through your local sales representative. You may start the process by completing online ZFN inquiry form. After discussion of the ZFN project details, you will be provided with pricing and relevant licensing details (if applicable). - See more at: http://www.sig