· The most recent class of base editors utilize DddAtox, a deaminase domain that can act upon double-stranded DNA. Here the authors target DddAtox fragments and a FokI-based nickase to the human
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· Metrics. The human genome encodes some 350 Krüppel-associated box (KRAB) domain-containing zinc-finger proteins (KZFPs), the products of a rapidly evolving gene family that has been traced
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:Zinc [email protected]We find that each available zinc finger structure can be placed into one of eight fold groups that we define based on the structural properties in the vicinity of the zinc-binding site.
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The design of functional proteins is one of the most challenging areas of protein research. We have constructed zinc finger peptides with metal-dependent hydrolytic abilities by mutating the zinc ligands in classical zinc fingers, without the need to add a Fok I or other DNA cleavage domain.I or other DNA cleavage domain.
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Zinc finger proteins are one of the most abundant families of proteins and present a wide range of structures and functions. The structural zinc ion provides the correct conformation to specifically recognize DNA, RNA and protein sequences. Zinc fingers have essential functions in transcription, protein degr
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· Currently, 30 types of ZNFs are approved by The HUGO Gene Nomenclature Committee, 9 and ZNF classification is based on the zinc-finger domain structure. A complete list of ZNF types with a
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:Zinc Finger SequenceZinc Finger Motif Dna BindingZinc Finger DomainZinc fingers (ZnFs) are small (∼20–100-residue) domains that coordinate one or more zinc ions, usually through cysteine and histidine sidechains, to stabilize their fold. The term
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· Abstract The ability to perform molecular-level computation in mammalian cells has the potential to enable a new wave of sophisticated cell-based therapies and diagnostics. To this end, we developed a Boolean logic framework utilizing artificial Cys 2 –His 2 zinc finger transcription factors (ZF-TFs) as computing elements. . Artificial ZFs
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Engineered zinc-finger (ZF) protein-based repression of transcription may represent a novel approach for treating gain-of-function mutations, although proof-of-concept of this use is still lacking. Here, we generated a series of transcriptional repressors to silence human rhodopsin (hRHO), the gene most abundantly expressed in retinal photoreceptors.
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Zinc-finger nucleases (ZFNs) have developed into a major playmaker in the genome engineering field and have been employed to trigger the targeted editing of genomes at over 50 gene loci in 11 model organisms, including fruitfly, zebrafish and rat, with allelic frequencies reaching the double digit percentage range.
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· We find that each available zinc finger structure can be placed into one of eight fold groups that we define based on the structural properties in the vicinity of the zinc‐binding site. Three of these fold groups comprise the majority of zinc fingers, namely, C2H2‐like finger, treble clef finger and the zinc ribbon.
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Zinc finger nuclease (ZFN) technology can mediate targeted genome modification to produce transgenic animals in a high-efficient and biological-safe way. Modular assembly is a rapid, convenient and open-source method for the synthesis of ZFNs. However, this biotechnology is hampered by multistep con
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:Cell Death DiscoveryZinc Finger Proteins Gene ExpressionHaving created a lexicon of zinc finger domains and a means of connecting them to achieve genome-wide levels of specificity, an ever-growing number of zinc finger-based
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· Due to zinc finger identified functions in several diseases, they have been increasingly recognized as drug targets. The replacement of the Zn (II) by another metal ion in zinc finger has been one
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· DOI: 10.1038/nbt796 Corpus ID: 29575555 Human zinc fingers as building blocks in the construction of artificial transcription factors @article{Bae2003HumanZF, title={Human zinc fingers as building blocks in the construction of artificial transcription factors}, author={Kwang-Hee Bae and Young
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· Full sequence design protein FSD-1 is a designed protein based on the motif of zinc finger protein. In this work, its folding mechanism and thermal stability are investigated using the replica exchange molecular dynamics model with the water molecules being treated explicitly. The results show that
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· A tunable zinc finger-based framework for Boolean logic computation in mammalian cells Jason J. Lohmueller 1,2, Thomas Z. Armel 1 and Pamela A. Silver 1,2, * 1 Department of Systems Biology and 2
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Having created a lexicon of zinc finger domains and a means of connecting them to achieve genome-wide levels of specificity, an ever-growing number of zinc finger-based applications became possible. The inherent modularity of our customization strategy also allowed us to develop the first web server, Zinc Finger Tools, for automated zinc finger
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· Zinc. Zinc finger (ZF) domains, that represent the majority of the DNA-binding motifs in eukaryotes, are involved in several processes ranging from RNA packaging to transcriptional activation, regulation of apoptosis, protein folding and assembly, and lipid binding. While their amino acid composition vari.
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· Customized zinc-finger nucleases (ZFNs) have developed into a promising technology to precisely alter mammalian genomes for biomedical research, biotechnology, or human gene therapy. In the context of synthetic biology, the targeted integration of a transgene or
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Zinc finger proteins are one of the most abundant families of proteins and present a wide range of structures and functions. The structural zinc ion provides the correct conformation to specifically recognize DNA, RNA
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· and biotechnology. Here, we present a base editing platform, termed zinc finger deaminases (ZFDs), composed of custom As anticipated from our plasmid-based assays described above, two ZFD
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Zinc Finger Folds and Functions, Table 1 Fold classes of zinc finger. Full size table. A large proportion of ZnFs use pairs of short bidentate zinc-coordinating motifs (e.g., C-X 2–4 -C) separated by intervening sequences or loops, the sequences and structures of which vary according to the class of ZnF. These motifs usually take the form of
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Here we use protein-DNA structures to predict binding specificity and consider the possibility of predicting position weight matrices (PWM) for an entire protein family based on the structures of just a few family members. A particular focus is the sensitivity of prediction accuracy to the docking geometry of the structure used.
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:Zinc FingerPublish Year:2015 · Zinc finger (ZF) domains, that represent the majority of the DNA-binding motifs in eukaryotes, are involved in several processes ranging from RNA packaging to
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· This ZFN-based technology to generate targeted knockouts in this aquatic animal opens the door to an array of new biological models of human disease and genetic testing. The ability to manipulate the genome is critical to develop and test hypotheses based on genetics. Knockdown strategies focused on RNAi and/or morpholinos are
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· Metrics. The human genome encodes some 350 Krüppel-associated box (KRAB) domain-containing zinc-finger proteins (KZFPs), the products of a rapidly evolving gene family that has been traced back
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Zinc-finger nuclease. 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 specific desired DNA sequences and this enables zinc-finger nucleases to target unique sequences within complex genomes.
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· The zinc-finger-based ATFs specifically recognize targeting sites in chromosomes and effectively up- and downregulate expression of their target genes not only in vitro, but also in vivo. In this review, after briefly introducing Cys(2)His(2)-type ZFPs, I will review the studies of endogenous human gene regulation by zinc-finger-based ATFs
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· Zinc finger design is facilitated with a deep-learning model. Cys2His2 zinc finger (ZF) domains engineered to bind specific target sequences in the genome provide an effective strategy for
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