View source for Zinc finger

{{short description|Small structural protein motif found mostly in transcriptional proteins}}
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[[Image:Zinc finger rendered.png|thumb|300px|right|Cartoon representation of the Cys2His2 zinc finger motif, consisting of an [[alpha helix|α helix]] and an antiparallel [[Beta sheet|β sheet]]. The [[zinc]] ion (green) is coordinated by two [[histidine]] residues and two [[cysteine]] residues.]]
[[Image:Zinc finger DNA complex.png|thumb|300px|right|Cartoon representation of the protein [[Zif268]] (blue) containing three zinc fingers in complex with DNA (orange). The coordinating amino acid residues and zinc ions (green) are highlighted.]]

A '''zinc finger''' is a small [[protein]] [[structural motif]] that is characterized by the [[Coordination complex|coordination]] of one or more [[zinc]] [[ion]]s (Zn<sup>2+</sup>) which stabilizes the fold. It was originally coined to describe the finger-like appearance of a hypothesized structure from the [[African clawed frog]] (''Xenopus laevis'') [[GTF3A|transcription factor IIIA]]. However, it has been found to encompass a wide variety of differing protein structures in [[Eukaryote|eukaryotic]] cells.<ref name="novel">{{cite journal | vauthors = Klug A, Rhodes D | title = Zinc fingers: a novel protein fold for nucleic acid recognition | journal = Cold Spring Harbor Symposia on Quantitative Biology | volume = 52 | pages = 473–82 | year = 1987 | pmid = 3135979 | doi = 10.1101/sqb.1987.052.01.054 }}</ref> ''[[Xenopus laevis]]'' TFIIIA was originally demonstrated to contain zinc and require the metal for function in 1983, the first such reported zinc requirement for a gene regulatory protein<ref>{{cite journal | vauthors = Hanas JS, Hazuda DJ, Bogenhagen DF, Wu FY, Wu CW | title = Xenopus transcription factor A requires zinc for binding to the 5 S RNA gene | journal = The Journal of Biological Chemistry | volume = 258 | issue = 23 | pages = 14120–5 | date = December 1983 | doi = 10.1016/S0021-9258(17)43831-2 | pmid = 6196359 | doi-access = free }}</ref><ref name=":0">{{cite journal | vauthors = Berg JM | title = Zinc fingers and other metal-binding domains. Elements for interactions between macromolecules | journal = The Journal of Biological Chemistry | volume = 265 | issue = 12 | pages = 6513–6 | date = April 1990 | doi = 10.1016/S0021-9258(19)39172-0 | pmid = 2108957 | doi-access = free }}</ref> followed soon thereafter by the [[Krüppel]] factor in ''[[Drosophila]]''.<ref name="Bruno-et-al-2019">{{cite journal | vauthors = Bruno M, Mahgoub M, Macfarlan TS | title = The Arms Race Between KRAB-Zinc Finger Proteins and Endogenous Retroelements and Its Impact on Mammals | journal = Annual Review of Genetics | volume = 53 | issue = 1 | pages = 393–416 | date = December 2019 | pmid = 31518518 | doi = 10.1146/annurev-genet-112618-043717 | publisher = [[Annual Reviews (publisher)|Annual Reviews]] | s2cid = 202572327 }}</ref> It often appears as a [[metal-binding domain]] in multi-domain proteins.<ref name=":0" />

Proteins that contain zinc fingers ('''zinc finger proteins''') are classified into several different structural families. Unlike many other clearly defined [[supersecondary structure]]s such as [[Greek key (protein structure)|Greek keys]] or [[Beta hairpin|β hairpins]], there are a number of types of zinc fingers, each with a unique three-dimensional architecture. A particular zinc finger protein's class is determined by its three-dimensional structure, but it can also be recognized based on the primary structure of the protein or the identity of the [[ligands]] coordinating the zinc ion. In spite of the large variety of these proteins, however, the vast majority typically function as interaction modules that bind [[DNA]], [[RNA]], proteins, or other small, useful molecules, and variations in structure serve primarily to alter the binding specificity of a particular protein.

Since their original discovery and the elucidation of their structure, these interaction modules have proven ubiquitous in the biological world and may be found in 3% of the genes of the human genome.<ref name="pmid20192761"/>  In addition, zinc fingers have become extremely useful in various therapeutic and research capacities. Engineering zinc fingers to have an affinity for a specific sequence is an area of active research, and [[zinc finger nucleases]] and [[zinc finger transcription factors]] are two of the most important applications of this to be realized to date.

== History ==
Zinc fingers were first identified in a study of transcription in the [[African clawed frog]], ''Xenopus laevis'' in the laboratory of [[Aaron Klug]]. A study of the transcription of a particular RNA sequence revealed that the binding strength of a small [[transcription factor]] (transcription factor IIIA; TFIIIA) was due to the presence of zinc-coordinating finger-like structures.<ref name="pmid4040853">{{cite journal | vauthors = Miller J, McLachlan AD, Klug A | title = Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes | journal = The EMBO Journal | volume = 4 | issue = 6 | pages = 1609–14 | date = June 1985 | pmid = 4040853 | pmc = 554390 | doi =  10.1002/j.1460-2075.1985.tb03825.x}}</ref> Amino acid sequencing of TFIIIA revealed nine tandem sequences of 30 amino acids, including two invariant pairs of cysteine and histidine residues. [[Extended x-ray absorption fine structure]] confirmed the identity of the zinc ligands: two cysteines and two histidines.<ref name="pmid20192761">{{cite journal | vauthors = Klug A | title = The discovery of zinc fingers and their applications in gene regulation and genome manipulation | journal = Annual Review of Biochemistry | volume = 79 | pages = 213–31 | year = 2010 | pmid = 20192761 | doi = 10.1146/annurev-biochem-010909-095056 }}{{subscription required|via=Annual Reviews}}</ref> The DNA-binding loop formed by the coordination of these ligands by zinc were thought to resemble fingers, hence the name.<ref name="novel" /> This was followed soon thereafter by the discovery of the [[Krüppel]] factor in ''[[Drosophila]]'' by the Schuh team in 1986.<ref name="Bruno-et-al-2019" /> More recent work in the characterization of proteins in various organisms has revealed the importance of zinc ions in polypeptide stabilization.<ref name="pmid20448202">{{cite journal | vauthors = Miller Y, Ma B, Nussinov R | title = Zinc ions promote Alzheimer Abeta aggregation via population shift of polymorphic states | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 107 | issue = 21 | pages = 9490–5 | date = May 2010 | pmid = 20448202 | pmc = 2906839 | doi = 10.1073/pnas.0913114107 | bibcode = 2010PNAS..107.9490M | doi-access = free }}</ref><ref name="pmid12051939">{{cite journal | vauthors = Low LY, Hernández H, Robinson CV, O'Brien R, Grossmann JG, Ladbury JE, Luisi B | title = Metal-dependent folding and stability of nuclear hormone receptor DNA-binding domains | journal = Journal of Molecular Biology | volume = 319 | issue = 1 | pages = 87–106 | date = May 2002 | pmid = 12051939 | doi = 10.1016/S0022-2836(02)00236-X }}</ref>

The crystal structures of zinc finger-DNA complexes solved in 1991 and 1993 revealed the canonical pattern of interactions of zinc fingers with DNA.<ref name="Pavletich_Pabo_1991"/><ref>{{cite journal | vauthors = Fairall L, Schwabe JW, Chapman L, Finch JT, Rhodes D | title = The crystal structure of a two zinc-finger peptide reveals an extension to the rules for zinc-finger/DNA recognition | journal = Nature | volume = 366 | issue = 6454 | pages = 483–7 | date = December 1993 | pmid = 8247159 | doi = 10.1038/366483a0 | s2cid = 4371511 | bibcode = 1993Natur.366..483F }}</ref> The binding of zinc finger is found to be distinct from many other DNA-binding proteins that bind DNA through the 2-fold symmetry of the double helix, instead zinc fingers are linked linearly in tandem to bind nucleic acid sequences of varying lengths.<ref name="pmid20192761"/>  Zinc fingers often bind to a sequence of DNA known as the [[GC box]].<ref>{{cite journal | vauthors = Lundin M, Nehlin JO, Ronne H | title = Importance of a flanking AT-rich region in target site recognition by the GC box-binding zinc finger protein MIG1 | journal = Molecular and Cellular Biology | volume = 14 | issue = 3 | pages = 1979–85 | date = March 1994 | pmid = 8114729 | pmc = 358557 | doi = 10.1128/MCB.14.3.1979 }}</ref> The modular nature of the zinc finger motif allows for a large number of combinations of DNA and RNA sequences to be bound with high degree of affinity and specificity, and is therefore ideally suited for engineering protein that can be targeted to and bind specific DNA sequences. In 1994, it was shown that an artificially-constructed three-finger protein can block the expression of an oncogene in a mouse cell line. Zinc fingers fused to various other effector domains, some with therapeutic significance, have since been constructed.<ref name="pmid20192761"/>

Such was its importance that "the zinc-finger motif" was cited in the Scientific Background to the 2024 [[Nobel Prize in Chemistry]] (awarded to [[David Baker (biochemist)|David Baker]], [[Demis Hassabis]], and [[John M. Jumper]] for computational protein design and protein structure prediction). <ref>https://www.nobelprize.org/uploads/2024/10/advanced-chemistryprize2024.pdf</ref>

==Domain==
Zinc finger (Znf) [[protein domain|domains]] are relatively small [[protein motif]]s that contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains [[Molecular binding|bind]] zinc, but many do not, instead binding other metals such as iron, or no metal at all. For example, some family members form [[Salt bridge (protein and supramolecular)|salt bridge]]s to stabilise the finger-like [[protein folding|fold]]s. They were first identified as a DNA-binding motif in [[transcription factor]] TFIIIA from ''[[Xenopus]] laevis'' (African clawed frog), however they are now recognised to bind DNA, RNA, protein, and/or [[lipid]] [[substrate (biochemistry)|substrates]].<ref name="pmid10529348">{{cite journal | vauthors = Klug A | title = Zinc finger peptides for the regulation of gene expression | journal = Journal of Molecular Biology | volume = 293 | issue = 2 | pages = 215–8 | date = October 1999 | pmid = 10529348 | doi = 10.1006/jmbi.1999.3007 }}</ref><ref name="pmid15963892">{{cite journal | vauthors = Hall TM | title = Multiple modes of RNA recognition by zinc finger proteins | journal = Current Opinion in Structural Biology | volume = 15 | issue = 3 | pages = 367–73 | date = June 2005 | pmid = 15963892 | doi = 10.1016/j.sbi.2005.04.004 | url = https://zenodo.org/record/1259349 }}</ref><ref name="pmid15718139">{{cite journal | vauthors = Brown RS | title = Zinc finger proteins: getting a grip on RNA | journal = Current Opinion in Structural Biology | volume = 15 | issue = 1 | pages = 94–8 | date = February 2005 | pmid = 15718139 | doi = 10.1016/j.sbi.2005.01.006 }}</ref><ref name="pmid17210253">{{cite journal | vauthors = Gamsjaeger R, Liew CK, Loughlin FE, Crossley M, Mackay JP | title = Sticky fingers: zinc-fingers as protein-recognition motifs | journal = Trends in Biochemical Sciences | volume = 32 | issue = 2 | pages = 63–70 | date = February 2007 | pmid = 17210253 | doi = 10.1016/j.tibs.2006.12.007 }}</ref><ref name="pmid12665246">{{cite journal | vauthors = Matthews JM, Sunde M | title = Zinc fingers--folds for many occasions | journal = IUBMB Life | volume = 54 | issue = 6 | pages = 351–5 | date = December 2002 | pmid = 12665246 | doi = 10.1080/15216540216035 | s2cid = 22109146 | doi-access = free }}</ref> Their binding properties depend on the [[amino acid sequence]] of the finger domains and on the linker between fingers, as well as on the higher-order [[secondary structure|structure]]s and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. Znf motifs occur in several unrelated [[protein superfamilies]], varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g., some bind DNA, others protein), suggesting that Znf [[sequence motif|motif]]s are stable scaffolds that have [[evolution|evolved]] specialised functions. For example, Znf-containing proteins function in [[gene]] transcription, translation, mRNA trafficking, [[cytoskeleton]] organization, [[epithelial]] development, [[cell adhesion]], protein folding, [[chromatin]] remodeling, and zinc sensing, to name but a few.<ref name="pmid11179890">{{cite journal | vauthors = Laity JH, Lee BM, Wright PE | title = Zinc finger proteins: new insights into structural and functional diversity | journal = Current Opinion in Structural Biology | volume = 11 | issue = 1 | pages = 39–46 | date = February 2001 | pmid = 11179890 | doi = 10.1016/S0959-440X(00)00167-6 }}</ref> Zinc-binding motifs are stable structures, and they rarely undergo [[conformational change]]s upon binding their target.

== Classes ==
Initially, the term zinc finger was used solely to describe DNA-binding motif found in ''Xenopus laevis''; however, it is now used to refer to any number of structures related by their coordination of a zinc ion. In general, zinc fingers coordinate zinc ions with a combination of [[cysteine]] and [[histidine]] residues. Originally, the number and order of these residues was used to classify different types of zinc fingers ( e.g., Cys<sub>2</sub>His<sub>2</sub>, Cys<sub>4</sub>, and Cys<sub>6</sub>). More recently, a more systematic method has been used to classify zinc finger proteins instead. This method classifies zinc finger proteins into "fold groups" based on the overall shape of the protein backbone in the folded domain.  The most common "fold groups" of zinc fingers are the Cys<sub>2</sub>His<sub>2</sub>-like (the "classic zinc finger"), treble clef, and zinc ribbon.<ref name="pmid12527760">{{cite journal | vauthors = Krishna SS, Majumdar I, Grishin NV | title = Structural classification of zinc fingers: survey and summary | journal = Nucleic Acids Research | volume = 31 | issue = 2 | pages = 532–50 | date = January 2003 | pmid = 12527760 | pmc = 140525 | doi = 10.1093/nar/gkg161 }}</ref>

The following table<ref name="pmid12527760"/> shows the different structures and their key features:

{| class = "wikitable" style = "font-size:85%; margin-left:15px; width:60%"
! Fold Group !! Representative structure !! Ligand placement
|-
| Cys<sub>2</sub>His<sub>2</sub> || [[File:PDB 1zaa EBI.jpg|150px]]|| Two ligands from a knuckle and two more from the c terminus of a helix.
|-
| Gag knuckle || [[File:PDB 1ncp EBI.jpg|150px]] || Two ligands from a knuckle and two more from a short helix or loop.
|-
| Treble clef ||  || Two ligands from a knuckle and two more from the [[N-terminus]] of a helix.
|-
| Zinc ribbon || [[File:PDB 1pft EBI.jpg|150px]] || Two ligands each from two knuckles.
|-
| Zn<sub>2</sub>/Cys<sub>6</sub> || [[File:PDB 1d66 EBI.jpg|150px]] || Two ligands from the N terminus of a helix and two more from a loop.
|-
| TAZ2 domain like ||  || Two ligands from the termini of two helices.
|}
{{clear}}

=== Cys<sub>2</sub>His<sub>2</sub> <span class="anchor" id="C2H2"></span>===
{{Infobox protein family
| Symbol = zf-C2H2
| Name = Zinc finger, C2H2 type
| image = 
| width = 
| caption = 
| Pfam = PF00096
| Pfam_clan = CL0361
| ECOD = 386.1.1
| InterPro = IPR007087
| SMART = 
| PROSITE = PS00028
| MEROPS =
| SCOP = 
| TCDB = 
| OPM family = 
| OPM protein = 
}}

The Cys<sub>2</sub>His<sub>2</sub>-like fold group (C2H2) is by far the best-characterized class of zinc fingers, and is common in mammalian transcription factors. Such domains adopt a simple ββα fold and have the amino acid [[sequence motif]]:<ref name=Pabo2001/>

:X<sub>2</sub>-Cys-X<sub>2,4</sub>-Cys-X<sub>12</sub>-His-X<sub>3,4,5</sub>-His

This class of zinc fingers can have a variety of functions such as binding RNA and mediating protein-protein interactions, but is best known for its role in sequence-specific DNA-binding proteins such as [[Zif268]] (Egr1).  In such proteins, individual zinc finger domains typically occur as tandem repeats with two, three, or more fingers comprising the DNA-binding domain of the protein.  These tandem arrays can bind in the major groove of DNA and are typically spaced at 3-bp intervals.  The α-helix of each domain (often called the "recognition helix") can make sequence-specific contacts to DNA bases; residues from a single recognition helix can contact four or more bases to yield an overlapping pattern of contacts with adjacent zinc fingers.
{{clear}}

===Gag-knuckle===
{{Infobox protein family
| Symbol = zf-CCHC
| Name = Zinc knuckle
| image = 
| width = 
| caption = 
| Pfam = PF00098
| Pfam_clan = 
| InterPro = IPR001878
| SMART = SM00343
| PROSITE = PS50158
| MEROPS =
| SCOP = 
| TCDB = 
| OPM family = 
| OPM protein = 
}}

This fold group is defined by two short β-strands connected by a turn (zinc knuckle) followed by a short helix or loop and resembles the classical Cys<sub>2</sub>His<sub>2</sub> motif with a large portion of the helix and β-hairpin truncated.

The retroviral nucleocapsid (NC) protein from HIV and other related retroviruses are examples of proteins possessing these motifs. The gag-knuckle zinc finger in the HIV NC protein is the target of a class of drugs known as [[zinc finger inhibitor]]s.
{{clear}}

===Treble-clef===
The treble-clef motif consists of a β-hairpin at the N-terminus and an α-helix at the C-terminus that each contribute two ligands for zinc binding, although a loop and a second β-hairpin of varying length and conformation can be present between the N-terminal β-hairpin and the C-terminal α-helix.  These fingers are present in a diverse group of proteins that frequently do not share sequence or functional similarity with each other.  The best-characterized proteins containing treble-clef zinc fingers are the [[nuclear hormone receptor]]s.

===Zinc ribbon===
{{Infobox protein family
| Symbol = TF_Zn_Ribbon
| Name = TFIIB zinc-binding
| Pfam = PF08271
| Pfam_clan = CL0167 	
| ECOD = 375.1.1
| InterPro = IPR013137
| SMART = 
| PROSITE = PS51134
| MEROPS =
| SCOP = 
| TCDB = 
| OPM family = 
| OPM protein = 
}}

The zinc ribbon fold is characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites.
{{clear}}

=== Zn<sub>2</sub>/Cys<sub>6</sub> ===
{{Infobox protein family
| Symbol = Zn_clus
| Name = Fungal Zn(2)-Cys(6) binuclear cluster domain
| image = 
| width = 
| caption = 
| Pfam = PF00172
| Pfam_clan = 
| InterPro = IPR001138
| SMART = GAL4
| PROSITE = PS00463
| MEROPS =
| SCOP = 
| TCDB = 
| OPM family = 
| OPM protein = 
| CDD = cd00067
}}

The canonical members of this class contain a binuclear zinc cluster in which two zinc ions are bound by six [[cysteine]] residues. These zinc fingers can be found in several transcription factors including the yeast [[Gal4]] protein.

{{Infobox protein family
| Symbol = zf-C2HC
| Name = zf-C2HC
| image = PDB 1pxe EBI.jpg
| width = 
| caption = solution structure of a cchhc domain of neural zinc finger factor-1
| Pfam = PF01530
| Pfam_clan =  
| InterPro = IPR002515
| SMART = 
| PROSITE = 
| MEROPS = 
| SCOP = 
| TCDB = 
| OPM family = 
| OPM protein = 
| CAZy = 
| CDD = 
}}
{{Infobox protein family
| Symbol = zf-C2HC5
| Name = zf-C2HC5
| image = 
| width = 
| caption = 
| Pfam = PF06221
| Pfam_clan =  
| InterPro = IPR009349
| SMART = 
| PROSITE = 
| MEROPS = 
| SCOP = 
| TCDB = 
| OPM family = 
| OPM protein = 
| CAZy = 
| CDD = 
}}

=== Miscellaneous ===

The ''zinc finger antiviral protein'' ({{vanchor|ZAP}}) binds to the CpG site. It is used in mammals for antiviral defense.<ref name="Xia2020">Xuhua Xia: [https://academic.oup.com/mbe/article/doi/10.1093/molbev/msaa094/5819559 Extreme genomic CpG deficiency in SARS-CoV-2 and evasion of host antiviral defense]. In: Molecular Biologa and Evolution, Academic Press, April 14th, 2020, [[doi:10.1093/molbev/msaa094]]</ref><ref>[https://scitechdaily.com/evidence-of-stray-dogs-as-possible-origin-of-covid-19-pandemic/ Evidence of Stray Dogs as Possible Origin of COVID-19 Pandemic]. On: SciTechDaily, April 14th, 2020. Source: University of Ottawa</ref>

== Applications ==
Various [[protein engineering]] techniques can be used to alter the DNA-binding specificity of zinc fingers<ref name=Pabo2001>{{cite journal | vauthors = Pabo CO, Peisach E, Grant RA | title = Design and selection of novel Cys2His2 zinc finger proteins | journal = Annual Review of Biochemistry | volume = 70 | pages = 313–40 | year = 2001 | pmid = 11395410 | doi = 10.1146/annurev.biochem.70.1.313 }}</ref> and tandem repeats of such engineered zinc fingers can be used to target desired genomic DNA sequences.<ref name=Jamieson2003>{{cite journal | vauthors = Jamieson AC, Miller JC, Pabo CO | title = Drug discovery with engineered zinc-finger proteins | journal = Nature Reviews. Drug Discovery | volume = 2 | issue = 5 | pages = 361–8 | date = May 2003 | pmid = 12750739 | doi = 10.1038/nrd1087 | s2cid = 6417869 }}</ref>  Fusing a second protein domain such as a transcriptional activator or repressor to an array of engineered zinc fingers that bind near the promoter of a given gene can be used to alter the transcription of that gene.<ref name=Jamieson2003/> Fusions between engineered zinc finger arrays and protein domains that cleave or otherwise modify DNA can also be used to target those activities to desired genomic loci.<ref name=Jamieson2003/>  The most common applications for engineered zinc finger arrays include [[Zinc Finger Transcription Factor|zinc finger transcription factor]]s and [[zinc finger nuclease]]s, but other applications have also been described. Typical engineered zinc finger arrays have between 3 and 6 individual zinc finger motifs and bind target sites ranging from 9 basepairs to 18 basepairs in length.  Arrays with 6 zinc finger motifs are particularly attractive because they bind a target site that is long enough to have a good chance of being unique in a mammalian genome.<ref name="pmid9159105">{{cite journal | vauthors = Liu Q, Segal DJ, Ghiara JB, Barbas CF | title = Design of polydactyl zinc-finger proteins for unique addressing within complex genomes | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 94 | issue = 11 | pages = 5525–30 | date = May 1997 | pmid = 9159105 | pmc = 20811 | doi = 10.1073/pnas.94.11.5525 | bibcode = 1997PNAS...94.5525L | doi-access = free }}</ref>

=== Zinc finger nucleases ===
Engineered zinc finger arrays are often fused to a DNA cleavage domain (usually the cleavage domain of [[FokI]]) to generate [[zinc finger nucleases]].  Such zinc finger-FokI fusions have become useful reagents for manipulating genomes of many higher organisms including ''[[Drosophila melanogaster]]'', ''[[Caenorhabditis elegans]]'', [[tobacco]], [[maize|corn]],<ref name="Shukla_2009"/> [[zebrafish]],<ref name="pmid2849655">{{cite journal | vauthors = Reynolds IJ, Miller RJ | title = [3H]MK801 binding to the N-methyl-D-aspartate receptor reveals drug interactions with the zinc and magnesium binding sites | journal = The Journal of Pharmacology and Experimental Therapeutics | volume = 247 | issue = 3 | pages = 1025–31 | date = December 1988 | pmid = 2849655 }}</ref> various types of mammalian cells,<ref name="pmid18784746">{{cite journal | vauthors = Carroll D | title = Progress and prospects: zinc-finger nucleases as gene therapy agents | journal = Gene Therapy | volume = 15 | issue = 22 | pages = 1463–8 | date = November 2008 | pmid = 18784746 | pmc = 2747807 | doi = 10.1038/gt.2008.145 }}</ref> and [[rat]]s.<ref name="pmid19628861">{{cite journal | vauthors = Geurts AM, Cost GJ, Freyvert Y, Zeitler B, Miller JC, Choi VM, Jenkins SS, Wood A, Cui X, Meng X, Vincent A, Lam S, Michalkiewicz M, Schilling R, Foeckler J, Kalloway S, Weiler H, Ménoret S, Anegon I, Davis GD, Zhang L, Rebar EJ, Gregory PD, Urnov FD, Jacob HJ, Buelow R | title = Knockout rats via embryo microinjection of zinc-finger nucleases | journal = Science | volume = 325 | issue = 5939 | pages = 433 | date = July 2009 | pmid = 19628861 | pmc = 2831805 | doi = 10.1126/science.1172447 | bibcode = 2009Sci...325..433G }}</ref> Targeting a double-strand break to a desired genomic locus can be used to introduce frame-shift mutations into the coding sequence of a gene due to the error-prone nature of the non-homologous DNA repair pathway.  If a homologous DNA "donor sequence" is also used then the genomic locus can be converted to a defined sequence via the homology directed repair pathway.  An ongoing clinical trial is evaluating [[Zinc finger nucleases]] that disrupt the CCR5 gene in CD4<sup>+</sup> human T-cells as a [[Zinc finger nuclease treatment of HIV|potential treatment]] for [[HIV/AIDS]].<ref name="url_ClinicalTrials.gov">{{cite web | url = http://clinicaltrials.gov/ct2/show/NCT00842634 | title = Autologous T-Cells Genetically Modified at the CCR5 Gene by Zinc Finger Nucleases SB-728 for HIV | publisher = ClinicalTrials.gov | vauthors = Tebas P, Stein D | year = 2009 }}</ref>

=== Methods of engineering zinc finger arrays ===
The majority of engineered zinc finger arrays are based on the zinc finger domain of the murine transcription factor Zif268, although some groups have used zinc finger arrays based on the human transcription factor SP1.  Zif268 has three individual zinc finger motifs that collectively bind a 9 bp sequence with high affinity.<ref name="pmid2510170">{{cite journal | vauthors = Christy B, Nathans D | title = DNA binding site of the growth factor-inducible protein Zif268 | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 86 | issue = 22 | pages = 8737–41 | date = November 1989 | pmid = 2510170 | pmc = 298363 | doi = 10.1073/pnas.86.22.8737 | bibcode = 1989PNAS...86.8737C | doi-access = free }}</ref> The structure of this protein bound to DNA was solved in 1991<ref name="Pavletich_Pabo_1991">{{cite journal | vauthors = Pavletich NP, Pabo CO | title = Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A | journal = Science | volume = 252 | issue = 5007 | pages = 809–17 | date = May 1991 | pmid = 2028256 | doi = 10.1126/science.2028256 | bibcode = 1991Sci...252..809P | s2cid = 38000717 }}</ref> and stimulated a great deal of research into engineered zinc finger arrays.  In 1994 and 1995, a number of groups used [[phage display]] to alter the specificity of a single zinc finger of Zif268.<ref name="pmid8303274">{{cite journal | vauthors = Rebar EJ, Pabo CO | title = Zinc finger phage: affinity selection of fingers with new DNA-binding specificities | journal = Science | volume = 263 | issue = 5147 | pages = 671–3 | date = February 1994 | pmid = 8303274 | doi = 10.1126/science.8303274 | bibcode = 1994Sci...263..671R }}</ref><ref name="pmid8180194">{{cite journal | vauthors = Jamieson AC, Kim SH, Wells JA | title = In vitro selection of zinc fingers with altered DNA-binding specificity | journal = Biochemistry | volume = 33 | issue = 19 | pages = 5689–95 | date = May 1994 | pmid = 8180194 | doi = 10.1021/bi00185a004 }}</ref><ref name="pmid7972027">{{cite journal | vauthors = Choo Y, Klug A | title = Toward a code for the interactions of zinc fingers with DNA: selection of randomized fingers displayed on phage | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 91 | issue = 23 | pages = 11163–7 | date = November 1994 | pmid = 7972027 | pmc = 45187 | doi = 10.1073/pnas.91.23.11163 | bibcode = 1994PNAS...9111163C | doi-access = free }}</ref><ref name="pmid7831288">{{cite journal | vauthors = Wu H, Yang WP, Barbas CF | title = Building zinc fingers by selection: toward a therapeutic application | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 92 | issue = 2 | pages = 344–8 | date = January 1995 | pmid = 7831288 | pmc = 42736 | doi = 10.1073/pnas.92.2.344 | bibcode = 1995PNAS...92..344W | doi-access = free }}</ref> There are two main methods currently used to generate engineered zinc finger arrays, modular assembly, and a bacterial selection system, and there is some debate about which method is best suited for most applications.<ref name="pmid20111032">{{cite journal | vauthors = Kim JS, Lee HJ, Carroll D | title = Genome editing with modularly assembled zinc-finger nucleases | journal = Nature Methods | volume = 7 | issue = 2 | pages = 91; author reply 91–2 | date = February 2010 | pmid = 20111032 | pmc = 2987589 | doi = 10.1038/nmeth0210-91a }}</ref><ref name = "Joung_2010">{{cite journal | vauthors = Joung JK, Voytas DF, Cathomen T | title = Reply to "Genome editing with modularly assembled zinc-finger nucleases" | journal = Nat. Methods | volume = 7 | issue = 2 | pages = 91–2 | date = February 2010 | pmid = <!--none--> | doi = 10.1038/nmeth0210-91b | pmc = 2987589 }}</ref>

The most straightforward method to generate new zinc finger arrays is to combine smaller zinc finger "modules" of known specificity. The structure of the zinc finger protein Zif268 bound to DNA described by Pavletich and Pabo in their 1991 publication has been key to much of this work and describes the concept of obtaining fingers for each of the 64 possible base pair triplets and then mixing and matching these fingers to design proteins with any desired sequence specificity.<ref name="Pavletich_Pabo_1991"/>
The most common modular assembly process involves combining separate zinc fingers that can each recognize a 3-basepair DNA sequence to generate 3-finger, 4-, 5-, or 6-finger arrays that recognize target sites ranging from 9 basepairs to 18 basepairs in length.  Another method uses 2-finger modules to generate zinc finger arrays with up to six individual zinc fingers.<ref name="Shukla_2009">{{cite journal | vauthors = Shukla VK, Doyon Y, Miller JC, DeKelver RC, Moehle EA, Worden SE, Mitchell JC, Arnold NL, Gopalan S, Meng X, Choi VM, Rock JM, Wu YY, Katibah GE, Zhifang G, McCaskill D, Simpson MA, Blakeslee B, Greenwalt SA, Butler HJ, Hinkley SJ, Zhang L, Rebar EJ, Gregory PD, Urnov FD | title = Precise genome modification in the crop species Zea mays using zinc-finger nucleases | journal = Nature | volume = 459 | issue = 7245 | pages = 437–41 | date = May 2009 | pmid = 19404259 | doi = 10.1038/nature07992 | bibcode = 2009Natur.459..437S | s2cid = 4323298 }}</ref> The Barbas Laboratory of The Scripps Research Institute used [[phage display]] to develop and characterize zinc finger domains that recognize most DNA triplet sequences<ref name="pmid10077584">{{cite journal | vauthors = Segal DJ, Dreier B, Beerli RR, Barbas CF | title = Toward controlling gene expression at will: selection and design of zinc finger domains recognizing each of the 5'-GNN-3' DNA target sequences | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 96 | issue = 6 | pages = 2758–63 | date = March 1999 | pmid = 10077584 | pmc = 15842 | doi = 10.1073/pnas.96.6.2758 | bibcode = 1999PNAS...96.2758S | doi-access = free }}</ref><ref name="pmid16107335">{{cite journal | vauthors = Dreier B, Fuller RP, Segal DJ, Lund CV, Blancafort P, Huber A, Koksch B, Barbas CF | title = Development of zinc finger domains for recognition of the 5'-CNN-3' family DNA sequences and their use in the construction of artificial transcription factors | journal = The Journal of Biological Chemistry | volume = 280 | issue = 42 | pages = 35588–97 | date = October 2005 | pmid = 16107335 | doi = 10.1074/jbc.M506654200 | doi-access = free }}</ref><ref name="pmid11340073">{{cite journal | vauthors = Dreier B, Beerli RR, Segal DJ, Flippin JD, Barbas CF | title = Development of zinc finger domains for recognition of the 5'-ANN-3' family of DNA sequences and their use in the construction of artificial transcription factors | journal = The Journal of Biological Chemistry | volume = 276 | issue = 31 | pages = 29466–78 | date = August 2001 | pmid = 11340073 | doi = 10.1074/jbc.M102604200 | doi-access = free }}</ref> while another group isolated and characterized individual fingers from the human genome.<ref name="pmid12592413">{{cite journal | vauthors = Bae KH, Kwon YD, Shin HC, Hwang MS, Ryu EH, Park KS, Yang HY, Lee DK, Lee Y, Park J, Kwon HS, Kim HW, Yeh BI, Lee HW, Sohn SH, Yoon J, Seol W, Kim JS | title = Human zinc fingers as building blocks in the construction of artificial transcription factors | journal = Nature Biotechnology | volume = 21 | issue = 3 | pages = 275–80 | date = March 2003 | pmid = 12592413 | doi = 10.1038/nbt796 | s2cid = 29575555 }}</ref> A potential drawback with modular assembly in general is that specificities of individual zinc finger can overlap and can depend on the context of the surrounding zinc fingers and DNA. A recent study demonstrated that a high proportion of 3-finger zinc finger arrays generated by modular assembly fail to bind their intended target with sufficient affinity in a bacterial two-hybrid assay and fail to function as [[zinc finger nucleases]], but the success rate was somewhat higher when sites of the form GNNGNNGNN were targeted.<ref name="pmid18446154">{{cite journal | vauthors = Ramirez CL, Foley JE, Wright DA, Müller-Lerch F, Rahman SH, Cornu TI, Winfrey RJ, Sander JD, Fu F, Townsend JA, Cathomen T, Voytas DF, Joung JK | title = Unexpected failure rates for modular assembly of engineered zinc fingers | journal = Nature Methods | volume = 5 | issue = 5 | pages = 374–5 | date = May 2008 | pmid = 18446154 | doi = 10.1038/nmeth0508-374 | s2cid = 30677821 | pmc = 7880305 }}</ref>

A subsequent study used modular assembly to generate [[zinc finger nucleases]] with both 3-finger arrays and 4-finger arrays and observed a much higher success rate with 4-finger arrays.<ref name="pmid19470664">{{cite journal | vauthors = Kim HJ, Lee HJ, Kim H, Cho SW, Kim JS | title = Targeted genome editing in human cells with zinc finger nucleases constructed via modular assembly | journal = Genome Research | volume = 19 | issue = 7 | pages = 1279–88 | date = July 2009 | pmid = 19470664 | pmc = 2704428 | doi = 10.1101/gr.089417.108 }}</ref>  A variant of modular assembly that takes the context of neighboring fingers into account has also been reported and this method tends to yield proteins with improved performance relative to standard modular assembly.<ref name=Sander2011>{{cite journal | vauthors = Sander JD, Dahlborg EJ, Goodwin MJ, Cade L, Zhang F, Cifuentes D, Curtin SJ, Blackburn JS, Thibodeau-Beganny S, Qi Y, Pierick CJ, Hoffman E, Maeder ML, Khayter C, Reyon D, Dobbs D, Langenau DM, Stupar RM, Giraldez AJ, Voytas DF, Peterson RT, Yeh JR, Joung JK | title = Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA) | journal = Nature Methods | volume = 8 | issue = 1 | pages = 67–9 | date = January 2011 | pmid = 21151135 | pmc = 3018472 | doi = 10.1038/nmeth.1542 }}</ref>

Numerous selection methods have been used to generate zinc finger arrays capable of targeting desired sequences.  Initial selection efforts utilized [[phage display]] to select proteins that bound a given DNA target from a large pool of partially randomized zinc finger arrays.  This technique is difficult to use on more than a single zinc finger at a time, so a multi-step process that generated a completely optimized 3-finger array by adding and optimizing a single zinc finger at a time was developed.<ref name="pmid9005850">{{cite journal | vauthors = Greisman HA, Pabo CO | title = A general strategy for selecting high-affinity zinc finger proteins for diverse DNA target sites | journal = Science | volume = 275 | issue = 5300 | pages = 657–61 | date = January 1997 | pmid = 9005850 | doi = 10.1126/science.275.5300.657 | s2cid = 46237752 }}</ref> More recent efforts have utilized yeast one-hybrid systems, bacterial one-hybrid and two-hybrid systems, and mammalian cells.  A promising new method to select novel 3-finger zinc finger arrays utilizes a bacterial two-hybrid system and has been dubbed "OPEN" by its creators.<ref name="pmid18657511">{{cite journal | vauthors = Maeder ML, Thibodeau-Beganny S, Osiak A, Wright DA, Anthony RM, Eichtinger M, Jiang T, Foley JE, Winfrey RJ, Townsend JA, Unger-Wallace E, Sander JD, Müller-Lerch F, Fu F, Pearlberg J, Göbel C, Dassie JP, Pruett-Miller SM, Porteus MH, Sgroi DC, Iafrate AJ, Dobbs D, McCray PB, Cathomen T, Voytas DF, Joung JK | title = Rapid "open-source" engineering of customized zinc-finger nucleases for highly efficient gene modification | journal = Molecular Cell | volume = 31 | issue = 2 | pages = 294–301 | date = July 2008 | pmid = 18657511 | pmc = 2535758 | doi = 10.1016/j.molcel.2008.06.016 }}</ref>  This system combines pre-selected pools of individual zinc fingers that were each selected to bind a given triplet and then utilizes a second round of selection to obtain 3-finger arrays capable of binding a desired 9-bp sequence.  This system was developed by the Zinc Finger Consortium as an alternative to commercial sources of engineered zinc finger arrays. It is somewhat difficult to directly compare the binding properties of proteins generated with this method to proteins generated by modular assembly as the specificity profiles of proteins generated by the OPEN method have never been reported.

==Examples==
This entry represents the CysCysHisCys (C2HC) type zinc finger domain found in [[eukaryotes]]. [[Proteins]] containing these domains include:

*MYST family [[histone acetyltransferase]]s<ref name="pmid16339723">{{cite journal | vauthors = Smith AT, Tucker-Samaras SD, Fairlamb AH, Sullivan WJ | title = MYST family histone acetyltransferases in the protozoan parasite Toxoplasma gondii | journal = Eukaryotic Cell | volume = 4 | issue = 12 | pages = 2057–65 | date = December 2005 | pmid = 16339723 | pmc = 1317489 | doi = 10.1128/EC.4.12.2057-2065.2005 }}</ref><ref name="pmid11258702">{{cite journal | vauthors = Akhtar A, Becker PB | title = The histone H4 acetyltransferase MOF uses a C2HC zinc finger for substrate recognition | journal = EMBO Reports | volume = 2 | issue = 2 | pages = 113–8 | date = February 2001 | pmid = 11258702 | pmc = 1083818 | doi = 10.1093/embo-reports/kve022 }}</ref>
*[[Myelin]] [[transcription (genetics)|transcription]] factor [[MYT1|Myt1]]<ref name="pmid9373037">{{cite journal | vauthors = Kim JG, Armstrong RC, v Agoston D, Robinsky A, Wiese C, Nagle J, Hudson LD | title = Myelin transcription factor 1 (Myt1) of the oligodendrocyte lineage, along with a closely related CCHC zinc finger, is expressed in developing neurons in the mammalian central nervous system | journal = Journal of Neuroscience Research | volume = 50 | issue = 2 | pages = 272–90 | date = October 1997 | pmid = 9373037 | doi = 10.1002/(SICI)1097-4547(19971015)50:2<272::AID-JNR16>3.0.CO;2-A | s2cid = 37120295 | url = https://zenodo.org/record/1235486 }}</ref>
*Suppressor of tumourigenicity protein 18 (ST18)<ref name="pmid15489893">{{cite journal | vauthors = Jandrig B, Seitz S, Hinzmann B, Arnold W, Micheel B, Koelble K, Siebert R, Schwartz A, Ruecker K, Schlag PM, Scherneck S, Rosenthal A | title = ST18 is a breast cancer tumor suppressor gene at human chromosome 8q11.2 | journal = Oncogene | volume = 23 | issue = 57 | pages = 9295–302 | date = December 2004 | pmid = 15489893 | doi = 10.1038/sj.onc.1208131 | doi-access = free }}</ref>

== See also ==
{{Portal|Biology|Technology}}
{{div col}}
* [[B-box zinc finger]]
* [[DNA-binding protein]]
* [[FPG IleRS zinc finger]]
* [[Krüppel associated box]]
* [[RING finger domain]]
* [[Sequence motif]]
* [[Steroid hormone receptor]]
* [[Structural motif]]
* [[TAL effector]]
* [[Transcription Activator-Like Effector Nuclease]]
* [[Zinc finger inhibitor]]
* [[Zinc finger nuclease]]
* [[Zinc Finger Transcription Factor]]
{{div col end}}

== References ==
{{reflist|30em}}

== External links ==
*[http://planttfdb.cbi.pku.edu.cn/family.php?fam=C2H2 C2H2 family] {{Webarchive|url=https://web.archive.org/web/20160215092327/http://planttfdb.cbi.pku.edu.cn/family.php?fam=C2H2 |date=2016-02-15 }} at [http://planttfdb.cbi.pku.edu.cn PlantTFDB: Plant Transcription Factor Database] {{Webarchive|url=https://web.archive.org/web/20160422025922/http://planttfdb.cbi.pku.edu.cn/ |date=2016-04-22 }}
* {{ cite web | url= http://www.ebi.ac.uk/interpro/potm/2007_3/Page1.htm | title= Protein of the Month: Zinc Fingers|access-date= 2008-01-13 | author= McDowall J | publisher=  European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI) }}
* {{cite web | url= http://www.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb87_1.html | title= Molecule of the Month: Zinc Fingers | access-date= 2008-01-13 | vauthors = Goodsell DS | publisher= Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank (PDB) | archive-date= 2008-05-31 | archive-url= https://web.archive.org/web/20080531153036/http://www.rcsb.org/pdb/static.do?p=education_discussion%2Fmolecule_of_the_month%2Fpdb87_1.html | url-status= dead }}
* [https://translate.google.com/translate?client=tmpg&hl=en&u=http://bianconiglio06.blogspot.com/2008/11/la-doppia-elica-fra-le-dita-di-zinco.html&langpair=it|en The double helix between the zinc finger]
* [https://archive.today/20130113103307/http://www.zincfingertools.org/ Zinc Finger Tools design and information site]
* [http://znf.igb.illinois.edu/human/ Human KZNF Gene Catalog] {{Webarchive|url=https://web.archive.org/web/20120316175612/http://znf.igb.illinois.edu/human/ |date=2012-03-16 }}
* [http://www.expasy.org/cgi-bin/nicedoc.pl?PDOC00028 Zinc finger C2H2-type domain] {{Webarchive|url=https://web.archive.org/web/20200413060026/https://web.expasy.org/cgi-bin/unavailable.cgi?type=redirect&query=nicedoc.pl |date=2020-04-13 }} in [[PROSITE]]
* [http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=ZnF_C2H2 Entry for zinc finger class C2H2 in the SMART database]
* [http://www.zincfingers.org The Zinc Finger Consortium]
* [http://bindr.gdcb.iastate.edu/ZiFiT/ ZiFiT- Zinc Finger Design Tool]
* [http://www.addgene.org/zfc Zinc Finger Consortium Materials from Addgene]
* [http://zf.princeton.edu Predicting DNA-binding Specificities for C2H2 Zinc Finger Proteins]

{{Protein domains}}
{{Transcription factors|g2}}

{{DEFAULTSORT:Zinc Finger}}
[[Category:Protein domains]]
[[Category:Protein structural motifs]]
[[Category:Protein folds]]
[[Category:DNA-binding substances]]
[[Category:Zinc finger proteins]]
[[Category:Thiolates]]
[[Category:Protein superfamilies]]