Among the many types of DNA binding domains, C2H2 zinc finger proteins (ZFPs) have proven to be the most malleable for creating custom DNA-binding proteins. In Engineered Zinc Finger Proteins: Methods and Prools, expert researchers from some of the most active laboratories in this field present detailed methods, guidance, and perspectives.
A C2H2-type zinc finger protein, SGR5, is involved in early events of gravitropism in Arabidopsis inflorescence stems. Plant J. 47, 619–628 (2006). CAS PubMed Article Google Scholar
A zinc finger is a small, functional, independently folded domain that coordinates one or more zinc ions to stabilize its structure through cysteine and/or histidine residues. Zinc fingers are structurally diverse and exhibit a wide range of functions, from DNA- or RNA-binding to protein-protein interactions and membrane association. 1.
Using zinc fingers, a scientist could create tissues for testing by combining individual cells. Scientists can produce the different cell types of a particular tissue or organ using induced pluripotent stem cells (iPSCs). These stem cells, produced from human tissue cells, can produce any other cell type. The different cell types would then get ...
Abstract Zinc fingers are small, compact protein subunits, folding around chelated zinc ions. Functionally, these motifs carry out a wide variety of tasks within cells by providing stable structural scaffolds and driving critical binding interactions, especially among proteins, DNA, and RNA. The motifs are particularly important in gene regulation, where many proteins employ them to bind DNA ...
Abstract. Zinc fingers are small protein domains in which zinc plays a structural role contributing to the stability of the domain. Zinc fingers are structurally diverse and are present among proteins that perform a broad range of functions in various cellular processes, such as replication and repair, transcription and translation, metabolism and signaling, cell proliferation and apoptosis.
One zinc "finger" binding domain recognizes and binds to a three nucleotide sequence, one can thus increase the binding specificity of a ZFN by adding more zinc fingers. The DNA cleaving-domain (Fok 1 nuclease) can then be used to create a double-stranded break in DNA at the desired point (Fig. 1).
Each zinc finger domain is 30 amino acids long and forms a ββα configuration, where individual amino acids in the α-helix interact with three successive nucleotide bases in the major groove of DNA (Figure 3.1(a)). 39,41 Arrays of several engineered zinc finger domains can be generated using a highly conserved linker sequence to connect the ...
Zinc-finger (ZF) plasmids, in the pCMV-SPORT6 backbone, consisted of a ZF DNA-binding domain and hemagglutinin (HA) epitope tag, connected to a StaPL module via a DEMEEC/S or EDVVCC/H cleavage ...
Zinc-finger nucleases (ZFNs) have emerged as powerful tools for delivering a targeted genomic double-strand break (DSB) to either stimulate local homologous recombination with investigator-provided donor DNA or induce gene mutations at the site of cleavage in the absence of a donor by nonhomologous end joining both in plant cells and in mammalian cells, including human cells.
Designer Zinc Finger Proteins: Tools for Creating Artificial DNA-Binding Functional Proteins. Accounts of Chemical Research 2006, 39 (1), 45-52. DOI: 10.1021/ar050158u. Akira Onoda,, Nozomi Arai,, Naoto Shimazu,, Hitoshi Yamamoto, and, Takeshi Yamamura. Calcium Ion Responsive DNA Binding in a Zinc Finger Fusion Protein. ...
Zinc finger antiviral protein (ZAP) protects cells from infection by diverse RNA viruses through its ability to specifically detect and deplete viral RNAs that have a greater frequency of CG dinucleotides than host messenger RNAs. We solved an X-ray crystal structure of the domain of ZAP that recognizes RNA and found that a crucial component of RNA recognition by ZAP is a pocket on the …
– Zinc-finger proteins can be engineered to create many unique proteins relatively easily – Zinc-finger proteins can be fused with dimerization domains to increase cooperativity – A cellular logic technology of only zinc-finger proteins should hopefully be easier to characterize
Evolutionary success of natural zinc finger proteins, however, evinces that nature created specific evolutionary traits and strategies, such as modularity and rank-specific recognition to cope with binding complexity that are critical for creating clinical viable tools …
The zinc finger motif was discovered in 1985 by Miller, McLachlan, and Klug in a protein responsible for controlling gene expression – the Xenopus transcription factor IIIA (TFIIIA). Originally, nine novel consecutive repeats were found, each ~30 amino acids in length. Since every repeat had a conserved pair of cysteines and histidines at defined positions, Klug proposed that these residues ...
Zinc finger transcription factors do not have the typical, deep binding pockets often found in enzymes. DNA appears to bind to zinc finger transcription factors by forming interactions primarily with surface atoms. Using a homology model of VEZF1 and an active lead compound, M1012, potential binding sites on the VEZF1/DNA binding surface will ...
Sangamo has licensed the use of zinc fingers to Dow Agrosciences for creating new crop plants, and has reserved medical uses for itself. It has four Phase 2 …
Zinc-finger nucleases (ZFNs) are artificial restriction enzymes generated by fusing a zinc finger DNA-binding domain to a DNA-cleavage domain. Zinc finger domains can be engineered to target desired DNA sequences and this enables zinc-finger nucleases to target unique sequences within complex genomes. By taking advantage of endogenous DNA repair machinery, these reagents can be used to ...
Engineered zinc finger nucleases (ZFN) are rapidly gaining popularity as a means to enhance the rate and specificity of DNA modifications in plant an ... Zinc finger nucleases to create custom-designed modifications in the swine (Sus scrofa) genome,, Journal of Animal Science, Volume 90, Issue 4, April 2012, Pages 1111–1117, https://doi ...
Zinc fingers take their name from the structure illustrated in Figure 21.3, in which a small group of conserved amino acids binds a zinc ion, and forms a relatively independent domain in the protein. Two types of DNA-binding proteins have structures of this type: the classic "zinc finger" proteins; and the steroid receptors.
The zinc finger proteins, which typically contain many fingers linked in tandem fashion, are some of the most studied DNA-binding proteins. The zinc finger protein's tandem arrangement and its the ability to recognize a wide variety of DNA sequences make it an attractive framework to design novel DNA-binding peptides/proteins.
Zinc finger domains provide a powerful scaffold for creating custom DNA-binding proteins that recognize specific DNA sequences. We previously demonstrated sequence-enabled reassembly of TEM-1 β-lactamase (SEER-LAC), a system consisting of two inactive fragments of β-lactamase each linked to engineered zinc finger proteins (ZFPs).
We have incorporated a bicyclic beta-turn mimetic (BTD; beta-turn dipeptide) into a zinc finger, creating a zinc finger with an artificial beta-turn. The designed peptide chelates zinc and has the same fold as the unmodified native zinc finger (finger 3 of the human YY1 protein). A combination of 1H NMR and structure calculations reveals that ...
Creating zinc finger nucleases to manipulate the genome in a site-specific manner using a modular-assembly approach. Porteus M. Homologous recombination is the most precise way to manipulate the genome. It has been used extensively in bacteria, yeast, murine embryonic stem cells, and a few other specialized cell lines, but it has not been ...
This was applied commercially by our MRC spin-off company Gendaq for up to 2×4 5 =2048 binding sites to create a large archive of zinc finger peptides that recognize a vast number of nine DNA base pair sequences. This archive was later acquired by Sangamo Biosciences, and used in their zinc finger constructs.
In these proteins, termed zinc fingers, a short chain of 20-30 amino acids is enough to create a solid, stable structure. Zinc fingers are so useful that they are found in thousands of our proteins, and are common in all plants and animals.
Zinc-finger nucleases (ZFNs) have emerged as powerful tools for delivering a targeted genomic double-strand break (DSB) to either stimulate local homologous recombination with investigator-provided donor DNA or induce gene mutations at the site of cleavage in the absence of a donor by nonhomologous end joining both in plant cells and in mammalian cells, including human cells.
The Drosophila earmuff (erm) gene encodes a zinc finger transcription factor homologous to forebrain embryonic zinc finger proteins (Fezf) [1, 2] and therefore is a member of the Erm/FezF gene family [].Erm expression starts in early embryos with an anterior expression pattern resembling an earmuff [].In later embryonic stages expression is restricted to the brain, and brain …
Zinc-finger nucleases (ZFNs) are targetable DNA cleavage reagents that have been adopted as gene-targeting tools. ZFN-induced double-strand breaks are subject to cellular DNA repair processes that lead to both targeted mutagenesis and targeted gene replacement at remarkably high frequencies. This article briefly reviews the history of ZFN development and summarizes applications …
Zinc-finger recognition depends only on a match to DNA sequence, and mechanisms of DNA repair, both homologous recombination and nonhomologous end joining, are shared by essentially all species. As noted above, methods for effective delivery of ZFNs and donor DNA will differ among applications, and biological variations in the availability of ...
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