哈佛分子生物学讲义--《分子生物学基础》.ppt

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 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 *免疫学信息网 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 Enol A 99.99% 0.01% Base Tautomerization 5 Base Adenine Guanine Thymine Cytosine Nucleoside Deoxy adenosine Deoxy guanosine Deoxy thymidine Deoxy cytidine Nucleotide d A mono, di-, tri phosphate d G mono, di-, tri phosphate d T mono, di-, tri phosphate d C mono, di-, tri phosphate 6 1’ 9 Rotation About the N-Glycosidic Bond N3 A,B DNA Z DNA G only 7 A Phosphodiester Backbone 8 Pitch 34 ? Ri