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DNA-binding proteins A transcription factor that interacts with a n upstream or response element has 2 domains:

DNA-binding proteins A transcription factor that interacts with a n upstream or response element has 2 domains:. a DNA - binding domain specifically recognises the target sequence; a n activation domain contacts a basal transcription factor (e. g. TFIID, TFIIA or TFIIB).

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DNA-binding proteins A transcription factor that interacts with a n upstream or response element has 2 domains:

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  1. DNA-binding proteins A transcription factor that interacts with an upstream or response element has 2 domains: a DNA-binding domain specifically recognises the target sequence; an activation domain contacts a basal transcription factor (e. g. TFIID, TFIIA or TFIIB). There are 4 main types: Helix-turn-helix Zinc fingers Leucine zippers Helix-loop-helix

  2. Helix-turn-helix motifs are typically found in prokaryotic DNA-binding proteins. The recognition helix binds within the major groove. AA side chains extending outwards interact with the edges of specific base pairs.

  3. His Cys Zn2+ Cys His Zinc fingers A small group of conserved AAs co-ordinates a Zn2+ ion to form a finger. The finger contains -sheet and -helical structure. The -helix makes sequence-specific contact with DNA. The TFIIIA and Sp1 proteins have zinc finger domains.

  4. Leucine Zipperproteins have stretches in which LEU occurs every7 residues. The leucines are located on one face of an helix. Interactions between the leucines results in dimerisation. This orientates 2 basic domains. DNA-binding domains The cAMP RE binding protein has a leucine zipper.

  5. HLH HLH Basic Basic Helix-loop-helix domains Hydrophobic interactions between HLH domains dimerise the protein and orientate the basic regions. Two basic domains are required for interaction with DNA

  6. Gene expression and demethylation. In animal cell DNA, cytosines within CG dinucleotides are usually methylated. The 5’ ends of some genes contain CG-rich islands that are 1 -2 kb in length. Undermethylation of these regions allows the transcription. The absence of methyl groups relaxes chromatin packaging.

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