Biomaterial Database

Construction and Evaluation of Zinc Finger Nucleases. 2017

Hiroshi Ochiai, and Takashi Yamamoto

PRESTO, JST, Higashi-Hiroshima, 739-8530, Japan. ochiai@hiroshima-u.ac.jp.

Zinc-finger nucleases (ZFNs) are programmable nucleases that have opened the door to the genome editing era. The construction of ZFNs recognizing a target sequence of interest is laborious, and has not been widely used recently. However, key ZFN patents are expiring over the next 2-4 years, enabling a wide range of deployments for clinical and industrial applications. This article introduces a ZFN construction protocol that uses bacterial one-hybrid (B1H) selection and single-stranded annealing (SSA) assay.

UI	MeSH Term	Description	Entries
D004277	DNA, Single-Stranded	A single chain of deoxyribonucleotides that occurs in some bacteria and viruses. It usually exists as a covalently closed circle.	Single-Stranded DNA,DNA, Single Stranded,Single Stranded DNA
D000072669	Gene Editing	Genetic engineering or molecular biology techniques that involve DNA REPAIR mechanisms for incorporating site-specific modifications into a cell's genome.	Base Editing,Genome Editing,Editing, Base,Editing, Gene,Editing, Genome
D000075804	Zinc Finger Nucleases	Genetically engineered nucleases that cleave DNA at a defined distance from specific DNA sequences recognized by ZINC FINGER DNA-BINDING DOMAINS. They are composed of a DNA cleaving domain adapted from DNA endonucleases fused to a zinc finger DNA-binding domain.	Zinc Finger Nuclease,Zinc-Finger Nuclease,Zinc-Finger Nucleases,Finger Nuclease, Zinc,Finger Nucleases, Zinc,Nuclease, Zinc Finger,Nuclease, Zinc-Finger,Nucleases, Zinc Finger,Nucleases, Zinc-Finger
D001419	Bacteria	One of the three domains of life (the others being Eukarya and ARCHAEA), also called Eubacteria. They are unicellular prokaryotic microorganisms which generally possess rigid cell walls, multiply by cell division, and exhibit three principal forms: round or coccal, rodlike or bacillary, and spiral or spirochetal. Bacteria can be classified by their response to OXYGEN: aerobic, anaerobic, or facultatively anaerobic; by the mode by which they obtain their energy: chemotrophy (via chemical reaction) or PHOTOTROPHY (via light reaction); for chemotrophs by their source of chemical energy: CHEMOLITHOTROPHY (from inorganic compounds) or chemoorganotrophy (from organic compounds); and by their source for CARBON; NITROGEN; etc.; HETEROTROPHY (from organic sources) or AUTOTROPHY (from CARBON DIOXIDE). They can also be classified by whether or not they stain (based on the structure of their CELL WALLS) with CRYSTAL VIOLET dye: gram-negative or gram-positive.	Eubacteria
D015202	Protein Engineering	Procedures by which protein structure and function are changed or created in vitro by altering existing or synthesizing new structural genes that direct the synthesis of proteins with sought-after properties. Such procedures may include the design of MOLECULAR MODELS of proteins using COMPUTER GRAPHICS or other molecular modeling techniques; site-specific mutagenesis (MUTAGENESIS, SITE-SPECIFIC) of existing genes; and DIRECTED MOLECULAR EVOLUTION techniques to create new genes.	Genetic Engineering of Proteins,Genetic Engineering, Protein,Proteins, Genetic Engineering,Engineering, Protein,Engineering, Protein Genetic,Protein Genetic Engineering
D016335	Zinc Fingers	Motifs in DNA- and RNA-binding proteins whose amino acids are folded into a single structural unit around a zinc atom. In the classic zinc finger, one zinc atom is bound to two cysteines and two histidines. In between the cysteines and histidines are 12 residues which form a DNA binding fingertip. By variations in the composition of the sequences in the fingertip and the number and spacing of tandem repeats of the motif, zinc fingers can form a large number of different sequence specific binding sites.	Zinc Finger DNA-Binding Domains,Zinc Finger Motifs,Finger, Zinc,Fingers, Zinc,Motif, Zinc Finger,Motifs, Zinc Finger,Zinc Finger,Zinc Finger DNA Binding Domains,Zinc Finger Motif
D053903	DNA Breaks, Double-Stranded	Interruptions in the sugar-phosphate backbone of DNA, across both strands adjacently.	Double-Stranded DNA Breaks,Double-Strand DNA Breaks,Double-Stranded DNA Break,Break, Double-Strand DNA,Break, Double-Stranded DNA,Breaks, Double-Strand DNA,Breaks, Double-Stranded DNA,DNA Break, Double-Strand,DNA Break, Double-Stranded,DNA Breaks, Double Stranded,DNA Breaks, Double-Strand,Double Strand DNA Breaks,Double Stranded DNA Break,Double Stranded DNA Breaks,Double-Strand DNA Break
D020798	Two-Hybrid System Techniques	Screening techniques first developed in yeast to identify genes encoding interacting proteins. Variations are used to evaluate interplay between proteins and other molecules. Two-hybrid techniques refer to analysis for protein-protein interactions, one-hybrid for DNA-protein interactions, three-hybrid interactions for RNA-protein interactions or ligand-based interactions. Reverse n-hybrid techniques refer to analysis for mutations or other small molecules that dissociate known interactions.	One-Hybrid System Techniques,Reverse One-Hybrid System Techniques,Reverse Two-Hybrid System Techniques,Three-Hybrid System Techniques,Yeast Two-Hybrid Assay,Yeast Two-Hybrid System Techniques,One-Hybrid System Technics,Reverse Three-Hybrid System Techniques,Three-Hybrid System Technics,Tri-Hybrid System Techniques,Two-Hybrid Assay,Two-Hybrid Method,Two-Hybrid System Technics,Yeast One-Hybrid System Techniques,Yeast Three-Hybrid Assay,Yeast Three-Hybrid System,Yeast Three-Hybrid System Techniques,Yeast Two-Hybrid System,n-Hybrid System Techniques,Assay, Two-Hybrid,Assay, Yeast Three-Hybrid,Assay, Yeast Two-Hybrid,Assays, Two-Hybrid,Assays, Yeast Three-Hybrid,Assays, Yeast Two-Hybrid,Method, Two-Hybrid,Methods, Two-Hybrid,One Hybrid System Technics,One Hybrid System Techniques,One-Hybrid System Technic,One-Hybrid System Technique,Reverse One Hybrid System Techniques,Reverse Three Hybrid System Techniques,Reverse Two Hybrid System Techniques,System Technique, n-Hybrid,System Techniques, n-Hybrid,System, Yeast Three-Hybrid,System, Yeast Two-Hybrid,Systems, Yeast Three-Hybrid,Systems, Yeast Two-Hybrid,Technic, One-Hybrid System,Technic, Three-Hybrid System,Technic, Two-Hybrid System,Technics, One-Hybrid System,Technics, Three-Hybrid System,Technics, Two-Hybrid System,Technique, One-Hybrid System,Technique, Three-Hybrid System,Technique, Tri-Hybrid System,Technique, Two-Hybrid System,Technique, n-Hybrid System,Techniques, One-Hybrid System,Techniques, Three-Hybrid System,Techniques, Tri-Hybrid System,Techniques, Two-Hybrid System,Techniques, n-Hybrid System,Three Hybrid System Technics,Three Hybrid System Techniques,Three-Hybrid Assay, Yeast,Three-Hybrid Assays, Yeast,Three-Hybrid System Technic,Three-Hybrid System Technique,Three-Hybrid System, Yeast,Three-Hybrid Systems, Yeast,Tri Hybrid System Techniques,Tri-Hybrid System Technique,Two Hybrid Assay,Two Hybrid Method,Two Hybrid System Technics,Two Hybrid System Techniques,Two-Hybrid Assay, Yeast,Two-Hybrid Assays,Two-Hybrid Assays, Yeast,Two-Hybrid Methods,Two-Hybrid System Technic,Two-Hybrid System Technique,Two-Hybrid System, Yeast,Two-Hybrid Systems, Yeast,Yeast One Hybrid System Techniques,Yeast Three Hybrid Assay,Yeast Three Hybrid System,Yeast Three Hybrid System Techniques,Yeast Three-Hybrid Assays,Yeast Three-Hybrid Systems,Yeast Two Hybrid Assay,Yeast Two Hybrid System,Yeast Two Hybrid System Techniques,Yeast Two-Hybrid Assays,Yeast Two-Hybrid Systems,n Hybrid System Techniques,n-Hybrid System Technique