Editing DNA-binding protein (section)

== 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>