Editing DNA-binding protein

{{short description|Proteins that bind with DNA, such as transcription factors, polymerases, nucleases and histones}}
[[Image:Cro protein complex with DNA.png|thumb|[[Cro repressor family|Cro]] protein complex with DNA]]
[[Image:Nucleosome1.png|thumb|Interaction of DNA (orange) with [[histone]]s (blue). These proteins' basic amino acids bind to the acidic phosphate groups on DNA.]]

[[Image:Lambda repressor 1LMB.png|thumb|right|185px|The [[Lambda phage|lambda]] [[repressor]] [[helix-turn-helix]] transcription factor bound to its DNA target<ref>Created from [http://www.rcsb.org/pdb/explore/explore.do?structureId=1LMB PDB 1LMB]</ref>]]
[[Image:EcoRV 1RVA.png|thumb|The [[restriction enzyme]] [[EcoRV]] (green) in a complex with its substrate DNA<ref>Created from [http://www.rcsb.org/pdb/explore/explore.do?structureId=1RVA PDB 1RVA]</ref>]]
'''DNA-binding proteins''' are [[protein]]s that have [[DNA-binding domain]]s and thus have a specific or general affinity for [[DNA#Base pairing|single- or double-stranded DNA]].<ref>{{cite book |author=Travers, A. A. |title=DNA-protein interactions |publisher=Springer |location=London |year=1993 |isbn=978-0-412-25990-6 }}</ref><ref>{{cite journal |vauthors=Pabo CO, Sauer RT |title=Protein-DNA recognition |journal=Annu. Rev. Biochem. |volume=53 |issue= 1|pages=293–321 |year=1984 |pmid=6236744 |doi=10.1146/annurev.bi.53.070184.001453 }}</ref><ref>{{cite journal |doi= 10.1038/scientificamerican1283-94 |author= Dickerson R.E. |title=The DNA helix and how it is read |journal=Sci Am |year= 1983 |volume=249 |issue= 6 |pages=94–111|bibcode=1983SciAm.249f..94D }}</ref> Sequence-specific DNA-binding proteins generally interact with the [[major groove]] of [[B-DNA]], because it exposes more [[functional group]]s that identify a [[base pair]].<ref>{{cite journal |vauthors=Zimmer C, Wähnert U |title=Nonintercalating DNA-binding ligands: specificity of the interaction and their use as tools in biophysical, biochemical and biological investigations of the genetic material |journal=Prog. Biophys. Mol. Biol. |volume=47 |issue=1 |pages=31–112 |year=1986 |pmid=2422697 |doi= 10.1016/0079-6107(86)90005-2 |doi-access=free }}</ref><ref>{{cite journal |author=Dervan PB |title=Design of sequence-specific DNA-binding molecules |journal=Science |volume=232 |issue=4749 |pages=464–71 |date=April 1986 |pmid=2421408 |doi= 10.1126/science.2421408|bibcode=1986Sci...232..464D }}</ref>

==Examples==
DNA-binding [[protein]]s include [[transcription factor]]s which [[Gene modulation|modulate]] the process of transcription, various [[polymerase]]s, [[nuclease]]s which cleave DNA molecules, and [[histone]]s which are involved in [[chromosome]] packaging and transcription in the [[cell nucleus]]. DNA-binding proteins can incorporate such domains as the [[zinc finger]], the [[helix-turn-helix]], and the [[leucine zipper]] (among many others) that facilitate binding to nucleic acid. There are also more unusual examples such as [[TAL effector|transcription activator like effectors]].

==Non-specific DNA-protein interactions==
Structural proteins that bind DNA are well-understood examples of non-specific DNA-protein interactions. Within chromosomes, DNA is held in complexes with structural proteins. These proteins organize the DNA into a compact structure called [[chromatin]]. In [[eukaryote]]s, this structure involves DNA binding to a complex of small basic proteins called [[histone]]s. In [[prokaryote]]s, multiple types of proteins are involved.<ref>{{cite journal |vauthors=Sandman K, Pereira S, Reeve J |title=Diversity of prokaryotic chromosomal proteins and the origin of the nucleosome |journal=Cell Mol Life Sci |volume=54 |issue=12 |pages=1350–64 |year=1998 |pmid=9893710 |doi=10.1007/s000180050259|s2cid=21101836 |pmc=11147202 }}</ref><ref>{{cite journal |author=Dame RT |title=The role of nucleoid-associated proteins in the organization and compaction of bacterial chromatin |journal=Mol. Microbiol. |volume=56 |issue=4 |pages=858–70 |year=2005 |pmid=15853876 |doi=10.1111/j.1365-2958.2005.04598.x|doi-access= }}</ref> The histones form a disk-shaped complex called a [[nucleosome]], which contains two complete turns of double-stranded DNA wrapped around its surface. These non-specific interactions are formed through basic residues in the histones making [[ionic bond]]s to the acidic sugar-phosphate backbone of the DNA, and are therefore largely independent of the base sequence.<ref>{{cite journal |vauthors=Luger K, Mäder A, Richmond R, Sargent D, Richmond T |title=Crystal structure of the nucleosome core particle at 2.8 A resolution |journal=Nature |volume=389 |issue=6648 |pages=251–60 |year=1997 |pmid=9305837 |doi= 10.1038/38444|bibcode=1997Natur.389..251L |s2cid=4328827 }}</ref> [[Chemical]] modifications of these basic [[amino acid]] residues include [[methylation]], [[phosphorylation]] and [[acetylation]].<ref>{{cite journal |vauthors=Jenuwein T, Allis C |title=Translating the histone code |journal=Science |volume=293 |issue=5532 |pages=1074–80 |year=2001 |pmid=11498575 |doi=10.1126/science.1063127|citeseerx=10.1.1.453.900 |s2cid=1883924 }}</ref> These chemical changes alter the strength of the interaction between the DNA and the histones, making the DNA more or less accessible to [[transcription factor]]s and changing the rate of transcription.<ref>{{cite book |author=Ito T |title=Protein Complexes that Modify Chromatin |chapter=Nucleosome Assembly and Remodeling |journal=Curr Top Microbiol Immunol |volume=274 |pages=1–22 |pmid=12596902 |year=2003 |doi=10.1007/978-3-642-55747-7_1|series=Current Topics in Microbiology and Immunology |isbn=978-3-642-62909-9 }}</ref> Other non-specific DNA-binding proteins in chromatin include the high-mobility group (HMG) proteins, which bind to bent or distorted DNA.<ref>{{cite journal |author=Thomas J |title=HMG1 and 2: architectural DNA-binding proteins |journal=Biochem Soc Trans |volume=29 |issue=Pt 4 |pages=395–401 |year=2001 |pmid=11497996 |doi=10.1042/BST0290395}}</ref> Biophysical studies show that these architectural HMG proteins bind, bend and loop DNA to perform its biological functions.<ref>{{Cite journal |doi = 10.1093/nar/gku635|pmid = 25063301|pmc = 4132745|title = DNA bridging and looping by HMO1 provides a mechanism for stabilizing nucleosome-free chromatin|journal = Nucleic Acids Research|volume = 42|issue = 14|pages = 8996–9004|year = 2014|last1 = Murugesapillai|first1 = Divakaran|last2 = McCauley|first2 = Micah J.|last3 = Huo|first3 = Ran|last4 = Nelson Holte|first4 = Molly H.|last5 = Stepanyants|first5 = Armen|last6 = Maher|first6 = L. James|last7 = Israeloff|first7 = Nathan E.|last8 = Williams|first8 = Mark C.}}</ref><ref>{{Cite journal | doi=10.1007/s12551-016-0236-4| pmid=28303166|title = Single-molecule studies of high-mobility group B architectural DNA bending proteins| journal=Biophysical Reviews| volume=9| issue=1| pages=17–40|year = 2017|last1 = Murugesapillai|first1 = Divakaran| last2=McCauley| first2=Micah J.| last3=Maher| first3=L. James| last4=Williams| first4=Mark C.| pmc=5331113}}</ref> These proteins are important in bending arrays of nucleosomes and arranging them into the larger structures that form chromosomes.<ref>{{cite journal |vauthors=Grosschedl R, Giese K, Pagel J |title=HMG domain proteins: architectural elements in the assembly of nucleoprotein structures |journal=Trends Genet |volume=10 |issue=3 |pages=94–100 |year=1994 |pmid=8178371 |doi=10.1016/0168-9525(94)90232-1}}</ref> Recently FK506 binding protein 25 (FBP25) was also shown to non-specifically bind to DNA which helps in DNA repair.<ref>{{Cite journal |last1=Prakash |first1=Ajit |last2=Shin |first2=Joon |last3=Rajan |first3=Sreekanth |last4=Yoon |first4=Ho Sup |date=2016-04-07 |title=Structural basis of nucleic acid recognition by FK506-binding protein 25 (FKBP25), a nuclear immunophilin |url=https://doi.org/10.1093/nar/gkw001 |journal=Nucleic Acids Research |volume=44 |issue=6 |pages=2909–2925 |doi=10.1093/nar/gkw001 |pmid=26762975 |pmc=4824100 |issn=0305-1048}}</ref>

==Proteins that specifically bind single-stranded DNA==
{{Further|Single-stranded binding protein}}
A distinct group of DNA-binding proteins are the DNA-binding proteins that specifically bind single-stranded DNA. In humans, [[replication protein A]] is the best-understood member of this family and is used in processes where the double helix is separated, including DNA replication, recombination and DNA repair.<ref>{{cite journal |vauthors=Iftode C, Daniely Y, Borowiec J |title=Replication protein A (RPA): the eukaryotic SSB |journal=Crit Rev Biochem Mol Biol |volume=34 |issue=3 |pages=141–80 |year=1999 |pmid=10473346 |doi=10.1080/10409239991209255}}</ref> These binding proteins seem to stabilize single-stranded DNA and protect it from forming [[stem-loop]]s or being degraded by [[nuclease]]s.

==Binding to specific DNA sequences==
[[File:Transcription factors DNA binding sites.svg|thumb|right|DNA contacts of different types of DNA-binding domains from transcription factors]]
In contrast, other proteins have evolved to bind to specific DNA sequences. The most intensively studied of these are the various [[transcription factor]]s, which are proteins that regulate transcription. Each transcription factor binds to one specific set of DNA sequences and activates or inhibits the transcription of genes that have these sequences near their promoters. The transcription factors do this in two ways. Firstly, they can bind the RNA polymerase responsible for transcription, either directly or through other mediator proteins; this locates the polymerase at the promoter and allows it to begin transcription.<ref>{{cite journal |vauthors=Myers L, Kornberg R |title=Mediator of transcriptional regulation |journal=Annu Rev Biochem |volume=69 |issue=1 |pages=729–49 |year=2000 |pmid=10966474 |doi= 10.1146/annurev.biochem.69.1.729}}</ref> Alternatively, transcription factors can bind [[enzyme]]s that modify the histones at the promoter. This alters the accessibility of the DNA template to the polymerase.<ref>{{cite journal |vauthors=Spiegelman B, Heinrich R |title=Biological control throughs regulated transcriptional coactivators |journal=Cell |volume=119 |issue=2 |pages=157–67 |year=2004 |pmid=15479634 |doi=10.1016/j.cell.2004.09.037|s2cid=14668705 |doi-access=free }}</ref>

These DNA targets can occur throughout an organism's genome. Thus, changes in the activity of one type of transcription factor can affect thousands of genes.<ref>{{cite journal |vauthors=Li Z, Van Calcar S, Qu C, Cavenee W, Zhang M, Ren B |title=A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells |journal=Proc Natl Acad Sci USA |volume=100 |issue=14 |pages=8164–9 |year=2003 |pmid=12808131 |doi= 10.1073/pnas.1332764100 |pmc=166200|bibcode=2003PNAS..100.8164L |doi-access=free }}</ref> Thus, these proteins are often the targets of the [[signal transduction]] processes that control responses to environmental changes or [[cellular differentiation]] and development. The specificity of these transcription factors' interactions with DNA come from the proteins making multiple contacts to the edges of the DNA bases, allowing them to ''read'' the DNA sequence. Most of these base-interactions are made in the major groove, where the bases are most accessible.<ref>{{cite journal |vauthors=Pabo C, Sauer R |title=Protein-DNA recognition |journal=Annu Rev Biochem |volume=53 |issue=1 |pages=293–321 |year=1984 |pmid=6236744 |doi= 10.1146/annurev.bi.53.070184.001453}}</ref> Mathematical descriptions of protein-DNA binding taking into account sequence-specificity, and competitive and cooperative binding of proteins of different types are usually performed with the help of the [[lattice model (biophysics)|lattice models]].<ref>{{cite journal |author=Teif V.B. |author2=Rippe K. |title=Statistical-mechanical lattice models for protein-DNA binding in chromatin. |journal=Journal of Physics: Condensed Matter|year=2010|arxiv=1004.5514|doi=10.1088/0953-8984/22/41/414105 |pmid=21386588 |volume=22 |issue=41 |pages=414105|bibcode=2010JPCM...22O4105T|s2cid=103345 }}</ref> Computational methods to identify the DNA binding sequence specificity have been proposed to make a good use of the abundant sequence data in the post-genomic era.<ref>{{cite journal | vauthors = Wong KC, Chan TM, Peng C, Li Y, Zhang Z | year = 2013 | title = DNA Motif Elucidation using belief propagation | url= | journal = Nucleic Acids Research | volume =  41| issue = 16| page =  e153| doi = 10.1093/nar/gkt574 | pmid = 23814189 | pmc = 3763557 }}</ref> In addition, progress has happened on  structure-based prediction of binding specificity across protein families using deep learning.<ref>{{Cite journal |last1=Mitra |first1=Raktim |last2=Li |first2=Jinsen |last3=Sagendorf |first3=Jared M. |last4=Jiang |first4=Yibei |last5=Cohen |first5=Ari S. |last6=Chiu |first6=Tsu-Pei |last7=Glasscock |first7=Cameron J. |last8=Rohs |first8=Remo |date=2024-08-05 |title=Geometric deep learning of protein–DNA binding specificity |journal=Nature Methods |volume=21 |issue=9 |pages=1674–1683 |language=en |doi=10.1038/s41592-024-02372-w |issn=1548-7091|doi-access=free |pmid=39103447 |pmc=11399107 }}</ref>  

== Protein–DNA interactions ==
Protein–DNA interactions occur when a [[protein]] binds a molecule of [[DNA]], often to regulate the [[Function (biology)|biological function]] of DNA, usually the [[Gene expression|expression]] of a [[gene]]. Among the proteins that bind to DNA are [[transcription factors]] that activate or repress gene expression by binding to DNA motifs and [[histones]] that form part of the structure of DNA and bind to it less specifically. Also proteins that [[DNA repair|repair DNA]] such as [[uracil-DNA glycosylase]] interact closely with it.

In general, proteins bind to DNA in the [[major groove]]; however, there are exceptions.<ref name="pmid9646864">{{cite journal|vauthors=Bewley CA, Gronenborn AM, Clore GM|year=1998|title=Minor groove-binding architectural proteins: structure, function, and DNA recognition|journal=Annu Rev Biophys Biomol Struct|volume=27|pages=105–31|doi=10.1146/annurev.biophys.27.1.105|pmid=9646864 |pmc= 4781445}}</ref> Protein–DNA interaction are of mainly two types, either specific interaction, or non-specific interaction. Recent single-molecule experiments showed that DNA binding proteins undergo of rapid rebinding in order to bind in correct orientation for recognizing the target site.<ref name = explore>{{Cite journal|last1=Ganji|first1=Mahipal|last2=Docter |first2=Margreet|last3=Le Grice|first3=Stuart F. J.|last4=Abbondanzieri|first4=Elio A.|date=2016-09-30|title=DNA binding proteins explore multiple local configurations during docking via rapid rebinding|journal=Nucleic Acids Research|volume=44|issue=17|pages=8376–8384|doi=10.1093/nar/gkw666|issn=0305-1048|pmc=5041478|pmid=27471033}}</ref>

=== Design ===
Designing DNA-binding proteins that have a specified DNA-binding site has been an important goal for biotechnology. [[Zinc finger]] proteins have been designed to bind to specific DNA sequences and this is the basis of [[zinc finger nucleases]]. Recently [[Tal effector nuclease|transcription activator-like effector nucleases]] (TALENs) have been created which are based on natural [[protein]]s secreted by ''[[Xanthomonas]]'' bacteria via their [[Type three secretion system|type III secretion system]] when they infect various [[plant]] species.<ref name="pmid21929364">{{cite journal|vauthors=Clark KJ, Voytas DF, Ekker SC|date=September 2011|title=A TALE of two nucleases: gene targeting for the masses?|journal=Zebrafish|volume=8|issue=3|pages=147–9|doi=10.1089/zeb.2011.9993|pmc=3174730|pmid=21929364}}</ref>

=== Detection methods ===
There are many ''in vitro'' and ''in vivo'' techniques which are useful in detecting DNA-Protein Interactions. The following lists some methods currently in use:<ref name="pmid22842750">{{cite journal|vauthors=Cai YH, Huang H|date=July 2012|title=Advances in the study of protein–DNA interaction|journal=Amino Acids|volume=43|issue=3|pages=1141–6|doi=10.1007/s00726-012-1377-9|pmid=22842750|s2cid=310256}}</ref> [[Electrophoretic mobility shift assay]] (EMSA) is a widespread qualitative technique to study protein–DNA interactions of known DNA binding proteins.<ref>{{cite journal |vauthors=Fried M, Crothers DM|title=Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis |journal=Nucleic Acids Res |date=1981 |volume=9 |issue=23 |pages=6505–6525 |doi=10.1093/nar/9.23.6505 |pmid=6275366|pmc=327619 }}</ref><ref>{{cite journal |vauthors=Garner MM, Revzin A  |title=A gel electrophoresis method for quantifying the binding of proteins to specific DNA regions: application to components of the Escherichia coli lactose operon regulatory system |journal=Nucleic Acids Res. |date=1981 |volume=9 |issue=13 |pages=3047–3060 |doi=10.1093/nar/9.13.3047 |pmid=6269071|pmc=327330 }}</ref> [[DNA-Protein-Interaction - Enzyme-Linked ImmunoSorbant Assay (DPI-ELISA)]] allows the qualitative and quantitative analysis of DNA-binding preferences of known proteins ''in vitro''.<ref>{{cite journal |vauthors=Brand LH, Kirchler T, Hummel S, Chaban C, Wanke D |title=DPI-ELISA: a fast and versatile method to specify the binding of plant transcription factors to DNA in vitro. |journal=Plant Methods |date=2010 |volume=25 |issue=6 |page=25 |doi=10.1186/1746-4811-6-25 |pmid=21108821|pmc=3003642 |doi-access=free }}</ref><ref>{{cite book |vauthors=Fischer SM, Böser A, Hirsch JP, Wanke D |title=Plant Synthetic Promoters |chapter=Quantitative Analysis of Protein–DNA Interaction by qDPI-ELISA |series=Methods Mol. Biol. |date=2016 |volume=1482 |issue=1482 |pages=49–66 |doi=10.1007/978-1-4939-6396-6_4 |pmid=27557760|isbn=978-1-4939-6394-2 }}</ref> This technique allows the analysis of protein complexes that bind to DNA (DPI-Recruitment-ELISA) or is suited for automated screening of several nucleotide probes due to its standard ELISA plate formate.<ref>{{cite journal |vauthors=Hecker A, Brand LH, Peter S, Simoncello N, Kilian J, Harter K, Gaudin V, Wanke D |title=The Arabidopsis GAGA-Binding Factor BASIC PENTACYSTEINE6 Recruits the POLYCOMB-REPRESSIVE COMPLEX1 Component LIKE HETEROCHROMATIN PROTEIN1 to GAGA DNA Motifs. |journal=Plant Physiol. |date=2015 |volume=163 |issue=3 |pages=1013–1024 |doi=10.1104/pp.15.00409 |pmid=26025051|pmc=4741334 |doi-access=free }}</ref><ref>{{cite journal |vauthors=Brand LH, Henneges C, Schüssler A, Kolukisaoglu HÜ, Koch G, Wallmeroth N, Hecker A, Thurow K, Zell A, Harter K, Wanke D |title=Screening for protein-DNA interactions by automatable DNA-protein interaction ELISA |journal=PLOS ONE |date=2013 |volume=8 |issue=10 |pages=e75177 |doi=10.1371/journal.pone.0075177 |pmid=24146751|pmc=3795721 |doi-access=free |bibcode=2013PLoSO...875177B }}</ref> [[DNase footprinting assay]] can be used to identify the specific sites of binding of a protein to DNA at basepair resolution.<ref>{{cite journal |vauthors=Galas DJ, Schmitz A |title=DNAse footprinting: a simple method for the detection of protein-DNA binding specificity |journal=Nucleic Acids Res. |date=1978 |volume=5 |issue=9 |pages=3157–3170 |doi=10.1093/nar/5.9.3157 |pmid=212715|pmc=342238 }}</ref> [[Chromatin immunoprecipitation]] is used to identify the ''in vivo'' DNA target regions of a known transcription factor. This technique when combined with high throughput sequencing is known as [[ChIP-Seq]] and when combined with [[Microarrays|microarray]]s it is known as [[ChIP-chip]]. [[Two-hybrid screening#One-hybrid|Yeast one-hybrid System]] (Y1H) is used to identify which protein binds to a particular DNA fragment. [[Bacterial one-hybrid system]] (B1H) is used to identify which protein binds to a particular DNA fragment. Structure determination using [[X-ray crystallography]] has been used to give a highly detailed atomic view of protein–DNA interactions.
Besides these methods, other techniques such as SELEX, PBM (protein binding microarrays), DNA microarray screens, DamID, FAIRE or more recently DAP-seq are used in the laboratory to investigate DNA-protein interaction ''in vivo'' and ''in vitro''.

=== Manipulating the interactions ===
The protein–DNA interactions can be modulated using stimuli like ionic strength of the buffer, macromolecular crowding,<ref name="explore" /> temperature, pH and electric field. This can lead to reversible dissociation/association of the protein–DNA complex.<ref>{{cite journal | vauthors = Hianik T, Wang J | year = 2009 | title = Electrochemical Aptasensors – Recent Achievements and Perspectives | journal = Electroanalysis | volume = 21 | issue = 11| pages = 1223–1235 | doi = 10.1002/elan.200904566 }}</ref><ref>{{cite journal | vauthors = Gosai A | display-authors = etal | year = 2016 | title = Electrical Stimulus Controlled Binding/Unbinding of Human Thrombin-Aptamer Complex | pmc = 5118750 | journal = Sci. Rep. | volume = 6 | page = 37449 | doi = 10.1038/srep37449 | pmid = 27874042 | bibcode = 2016NatSR...637449G }}</ref>

== See also ==
* [[bZIP domain]]
* [[ChIP-exo]]
* [[Comparison of nucleic acid simulation software]]
* [[DNA-binding domain]]
* [[Helix-loop-helix]]
* [[Helix-turn-helix]]
* [[HMG-box]]
* [[Leucine zipper]]
* [[Lexitropsin]] (a semi-synthetic DNA-binding ligand)   
* [[Deoxyribonucleoprotein]]   
* [[Protein–DNA interaction site predictor|Protein–DNA interaction site prediction software]]
* [[RNA-binding protein]]   
* [[Single-strand binding protein]]
* [[Zinc finger]]

== References ==
{{Reflist|2}}

== External links ==
* [https://generegulation.org/protein-dna-binding/ Protein-DNA binding: data, tools & models (annotated list, constantly updated)]
* [https://web.archive.org/web/20100307211109/http://www.biomolecular-modeling.com/Abalone/index.html Abalone] tool for modeling DNA-ligand interactions.
* [http://transcriptionfactor.org/ DBD database of predicted transcription factors] Uses a curated set of DNA-binding domains to predict transcription factors in all completely sequenced genomes
* {{MeshName|DNA-Binding+Proteins}}

{{DNA-binding proteins}}
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[[Category:DNA-binding proteins]]
[[Category:Molecular genetics]]
[[Category:DNA replication]]
[[Category:Transcription factors]]
[[Category:Biophysics]]