Protein-DNA interaction

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The lambda repressor is linked to the DNA sequence of the lambda operator.

A protein-DNA interaction refers to the binding of a protein to DNA . This controls various processes of DNA replication , gene expression and epigenetics .

properties

Proteins that interact with DNA are called DNA-binding proteins , e.g. B. proteins of DNA biosynthesis , transcription factors , DNA-modifying enzymes or proteins of DNA repair . Most of the time, it binds to the major groove of B-DNA . The interactions can be divided into sequence-specific and sequence-independent protein-DNA interactions. The DNA-binding proteins, the sequence specificity of which are specifically changed in the course of a protein design , include z. B. the zinc finger nucleases or the transcription activator-like effector nucleases (TALEN).

Interactions defined in the same way are e.g. B. protein-lipid interactions , protein-RNA interactions, and protein-protein interactions .

Verification procedure

Various methods can be used for characterization ( DNA sequence , DNA-binding proteins ). These include ligand binding tests to determine affinity , such as the filter binding test and the electrophoretic mobility shift assay , electron microscopy , ChIP , ChIP-on-Chip , ChIP-Seq , DNase footprinting assay , surface plasmon resonance spectroscopy , yeast One-Hybrid-System (Y1H), the Bacterial-One-Hybrid-System (B1H) and the DamID . The South Western blot allows using specific labeled DNA the detection of DNA-binding proteins previously by SDS-PAGE were separated. In addition, structure elucidation can be carried out by X-ray structure analysis or by NMR spectroscopy .

Individual evidence

  1. ^ CA Bewley, AM Gronenborn, GM Clore: Minor groove-binding architectural proteins: structure, function, and DNA recognition . In: Annu. Rev. Biophys. Biomol. Struct . 27, 1998, pp. 105-131. doi : 10.1146 / annurev.biophys.27.1.105 . PMID 9646864 .
  2. ↑ KJ Clark, DF Voytas, SC Ekker: A TALE of two nucleases: gene targeting for the masses? . In: Zebrafish . 8, No. 3, September 2011, pp. 147-149. doi : 10.1089 / zeb.2011.9993 . PMID 21929364 .
  3. ↑ YH Cai, H. Huang: Advances in the study of protein-DNA interaction. In: Amino acids. Volume 43, Number 3, September 2012, pp. 1141-1146, doi : 10.1007 / s00726-012-1377-9 . PMID 22842750 .
  4. ↑ Arthur. D. Riggs, Suzanne Bourgeois, Ronald F. Newby, Melvin Cohn DNA binding of the lac repressor. In: Journal of Molecular Biology Volume 34, Number 6, 1968, 365-368, doi : 10.1016 / 0022-2836 (68) 90261-1 , PMID 4938552
  5. ↑ C. Brack: DNA electron microscopy. In: CRC critical reviews in biochemistry. Volume 10, Number 2, 1981, pp. 113-169, PMID 6163590 (Review).
  6. ↑ T. Sahr, C. Buchrieser: Co-immunoprecipitation: protein-RNA and protein-DNA interaction. In: Methods in molecular biology (Clifton, NJ). Volume 954, 2013, pp. 583-593, doi : 10.1007 / 978-1-62703-161-5_36 , PMID 23150422 .
  7. ↑ B. Deplancke, A. Mukhopadhyay, W. Ao, AM Elewa, CA Grove, NJ Martinez, R. Sequerra, L. Doucette strain, JS Reece-Hoyes, IA Hope, HA Tissenbaum, SE Mango, AJ Walhout: A gene-centered C. elegans protein-DNA interaction network. In: Cell. Volume 125, Number 6, June 2006, pp. 1193-1205, doi : 10.1016 / j.cell.2006.04.038 , PMID 16777607 .