Protein-DNA interaction 1

Protein-DNA interaction

The lambda repressor protein interacting with the lambda operatorDNA.

Protein–DNA interactions are when a protein binds amolecule of DNA, often to regulate the biologicalfunction of DNA, usually the expression of a gene.Among the proteins that bind to DNA are transcriptionfactors that activate or repress gene expression bybinding to DNA motifs and histones that form part ofthe structure of DNA and bind to it less specifically.Also proteins that repair DNA such as uracil-DNAglycosylase interact closely with it.

In general, proteins bind to DNA in the major groove,however there are exceptions.[1] Protein-DNAinteraction are of mainly two types, either specificinteraction, or non-specific interaction.

Design

Designing DNA-binding proteins that have a specifiedDNA-binding site has been an important goal forbiotechnology. Zinc finger proteins have been designedto bind to specific DNA sequences and this is the basisof zinc finger nucleases. Recently transcriptionactivator-like effector nucleases (TALENs) have beencreated which are based on natural proteins secreted byXanthomonas bacteria via their type III secretionsystem when they infect various plant species.[2]

Detection methodsThere are many in vitro and in vivo techniques which are useful in detecting DNA-Protein Interactions. Thefollowing lists some methods currently in use:[3]

• Electrophoretic mobility shift assay is a widespread technique to identify protein-DNA interactions.• DNase footprinting assay can be used to identify the specific site of binding of a protein to DNA.• Chromatin immunoprecipitation is used to identify the sequence of the DNA fragments which bind to a known

transcription factor. This technique when combined with high throughput sequencing is known as ChIP-Seq andwhen combined with microarrays it is known as ChIP-chip.

• 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.

Protein-DNA interaction 2

References[1] Bewley CA, Gronenborn AM, Clore GM (1998). "Minor groove-binding architectural proteins: structure, function, and DNA recognition".

Annu Rev Biophys Biomol Struct 27: 105–31. doi:10.1146/annurev.biophys.27.1.105. PMID 9646864.[2] Clark KJ, Voytas DF, Ekker SC (September 2011). "A TALE of two nucleases: gene targeting for the masses?". Zebrafish 8 (3): 147–9.

doi:10.1089/zeb.2011.9993. PMID 21929364.[3] Cai YH, Huang H (July 2012). "Advances in the study of protein-DNA interaction". Amino Acids. doi:10.1007/s00726-012-1377-9.

PMID 22842750.

Article Sources and Contributors 3

Article Sources and ContributorsProtein-DNA interaction  Source: http://en.wikipedia.org/w/index.php?oldid=505279951  Contributors: Alexbateman, Miguel Andrade, NPrice, VAR121, 5 anonymous edits

Image Sources, Licenses and ContributorsFile:Lambda repressor 1LMB.png  Source: http://en.wikipedia.org/w/index.php?title=File:Lambda_repressor_1LMB.png  License: GNU Free Documentation License  Contributors: Originaluploader was Zephyris at en.wikipedia

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