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BIOINFORMATIK I ÜBUNG 3

BIOINFORMATIK I ÜBUNG 3. HUBERT HACKL icbi.at/ bioinf. Regulation of transcription. TF classification by DNA-binding. A. Zinc fingers. B. Helix-turn-helix. C. Leucine zipper. D. Helix-loop-helix. Transcription factor dimerization. Leucine zippers. homo dimerization.

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BIOINFORMATIK I ÜBUNG 3

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  1. BIOINFORMATIK I ÜBUNG 3 HUBERT HACKL icbi.at/bioinf

  2. Regulation of transcription

  3. TF classification by DNA-binding A. Zinc fingers B. Helix-turn-helix C. Leucine zipper D. Helix-loop-helix

  4. Transcription factor dimerization Leucine zippers • homo dimerization • hetero dimerization

  5. Protein 3D-structure • PDB • JMol • Cn3D • POLYVIEW-3D • Proteopedia PDB identificationcode Example: PPARg::RXRa+Rosi, 9-cis RA, NCOA2 (3dzy)

  6. TF classification by function

  7. Recombinant DNA technology • Protein synthesis • In vitro expression • Libraries • Gene transfer in animalsandplants

  8. Recombinant DNA technology • Polymerases • Nucleases

  9. Recombinant DNA technology • restrictionenzymes

  10. Recombinant DNA technology • Ligases

  11. Cloning

  12. Cloning vector (pBR322) • Plasmid • Ampicillinresistance • Tetracyclineresistance • Polylinker • Origin ofreplication (ori)

  13. Selection by antibiotics

  14. Selection by X-gal

  15. Exercise 3 • 1. CLONING EXPERIMENT • Starting from a cloning sequence and find out which cloning vector (name, accnr, length) was used (e.g. using the tool VecScreen) • Where is the insert in the given sequence located (position from-to, length) • Identify the insert (name, accnr, organism, length, amino acid sequence, function) • Determine the restriction enzyme (6bp cutter) used for incorporating the insert (name, sequence) • Are there homolog proteins in humans (name, accnr, description, conserved domains) • 2. PROTEIN 3D-STRUCTURE • Show 3D protein structure of a homolog human protein (including DNA binding) (from 1.5) and give PDB identification code for this structure

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