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DNA-binding protein
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=== 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''.
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