斯坦福大学分子生物学讲义之DNA要点.ppt

Announcements Assigned Papers: download from website: /bcmp200/ Sign-up sheets A very useful number:660 Note to self:Discuss forces that affect helix formation Question: is all B-DNA structurally identical? DNA Topology* *Johannes’ Favorite Subject(Students’ least favorite subject) For a good treatment of topos, see the book: “DNA replication” Arthur Kornberg and Tania Baker Pyrimidine-Purine Steps Have Little Base Stacking Step Definition: Going along one strand of DNA in 5’to 3’ direction Four Possibles: P-Y, P-P, Y-P, Y-Y 5’ 3’ 3’ 5’ C G A T 19A Purine-Pyrimidine Steps Have Extensive Base Stacking 5’ 3’ 3’ C A T G 5’ 19B For further reading on effects of sequence on structure, “Understanding DNA-The Molecule and How it Works” By Calladine and Drew Major Conclusion: DNA structure can depend on sequence In predictable, yet complicated ways. Therefore, DNA binding proteins can recognize structure, And they can be designed to bind to highly flexible DNA. DNA Unwinding Causes Topological Problems (Transcription) Unwound Parental Duplex Over- Wound region 20 More Topological Problems 21 Properties of Topoisomerases 22 Strand Passage Model for Topo I Unwound Complex Cleavage Complex Covalent Tyrosine-5’P Strand Passage Re- ligation L=2 L=3 23 Topo I Reactions 24 Model for Topo II Mechanism 25 * Facts (“vocabulary”) Concepts Quantitation Techniques In vivo DNA binding pattern of the Polycomb Txn Factor What are the genes to which it binds? How does it affect these genes? 3. What determines where it Binds?? 1 Nitrogenous base Sugar Phosphate 1A 2. Structure of dCTP 3. Base Tautomerism Chargaff rules - A=T, G=C helical 10 layer Lines Between Cross Patterns (10 Residues Per turn) Evidence for the Double Helix 1. Fiber Diffraction data: -Helical geometry -3.4 A o spacing (1Ao = 10-10 m) -34 A o pitch NIH (not in handout) ?-2’-deoxyribose 2 Sugar “Pucker” Conformations A DNA B DNA 3 Pyrimidines Purines 4 G (Keto) G (Eno