1、免疫学信息网 http:/,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?,免疫学信息网 http:/,1,Nitrogenous base,Sugar,Phosphate,免疫学信息网 http:/,1A,2. Structure of dCTP,3. Base Tautomerism,Chargaff rules - A=T
2、, 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 spacing (1A = 10-10 m) -34 A pitch,免疫学信息网 http:/,NIH (not in handout),免疫学信息网 http:/,-2-deoxyribose,2,免疫学信息网 http:/,Sugar “Pucker” Conformations
3、,A DNA,B DNA,3,免疫学信息网 http:/,Pyrimidines,Purines,4,免疫学信息网 http:/,G (Keto) G (Enol) A,99.99% 0.01%,Base Tautomerization,5,免疫学信息网 http:/,Base Adenine Guanine Thymine Cytosine,Nucleoside (Deoxy)adenosine (Deoxy)guanosine (Deoxy)thymidine (Deoxy)cytidine,Nucleotide (d)A (mono, di-, tri) phosphate (d)G (
4、mono, di-, tri) phosphate (d)T (mono, di-, tri) phosphate (d)C (mono, di-, tri) phosphate,6,1,9,免疫学信息网 http:/,A very useful number: 660,免疫学信息网 http:/,Rotation About the N-Glycosidic Bond,N3,A,B DNA,Z DNA (G only),7,A,免疫学信息网 http:/,Phosphodiester Backbone,8,免疫学信息网 http:/,Pitch 34 ,Rise 3.4 ,Width 20
5、,Major Groove,Minor Groove,9,10.4 bp/turn,B-DNA: A right Handed double helix Why?,免疫学信息网 http:/,Twist 36,9,免疫学信息网 http:/,8.5 ,11.7 ,7.5 ,5.7 ,Major Groove,Minor Groove,10,免疫学信息网 http:/,11,免疫学信息网 http:/,Note to self: Discuss forces that affect helix formation,免疫学信息网 http:/,C-G,T-A,NIH,免疫学信息网 http:/,A
6、,B,Z,12,免疫学信息网 http:/,Base Displacement Determines Groove Depth,dx = +3-4 ,Z DNA,Major,Minor,13,免疫学信息网 http:/,A,B,Z,Mi,Ma,Ma,Mi,Mi,Ma,12,免疫学信息网 http:/,A,B,Z,Z-DNA Phosphate Backbone is Kinked,14,免疫学信息网 http:/,15,免疫学信息网 http:/,Question: is all B-DNA structurally identical?,Implications of structural
7、variation,Implications of flexibility,免疫学信息网 http:/,Degrees of freedom: 7 Torsion angles and sugar conformation,5,3,(Rigid),16,免疫学信息网 http:/,Structural Variation Defined by Bases,17,normal,frequent,never,Never (except in intercalation),Common,Common,免疫学信息网 http:/,5,3,3,3,3,5,5,5,Propeller Twist Maxi
8、mizes Base Stacking,NIH,免疫学信息网 http:/,Propeller Twist,Buckle,18,Textbook,Real Life,免疫学信息网 http:/,19,Naturally Occurring Variations in Roll, Slide, Twist,免疫学信息网 http:/,Pyrimidine-Purine Steps Have Little Base Stacking Step Definition: Going along one strand of DNA in 5to 3 direction Four Possibles: P
9、-Y, P-P, Y-P, Y-Y,19A,免疫学信息网 http:/,Purine-Pyrimidine Steps Have Extensive Base Stacking,19B,免疫学信息网 http:/,For further reading on effects of sequence on structure, “Understanding DNA-The Molecule and How it Works” By Calladine and DrewMajor Conclusion: DNA structure can depend on sequence In predict
10、able, yet complicated ways.Therefore, DNA binding proteins can recognize structure, And they can be designed to bind to highly flexible DNA.,免疫学信息网 http:/,DNA Topology* *Johannes Favorite Subject (Students least favorite subject),免疫学信息网 http:/,DNA Unwinding Causes Topological Problems,(Transcription
11、),Unwound Parental Duplex,Over- Wound region,20,免疫学信息网 http:/,More Topological Problems,21,免疫学信息网 http:/,Properties of Topoisomerases,22,免疫学信息网 http:/,Strand Passage Model for Topo I,Unwound Complex,Cleavage Complex,Covalent Tyrosine-5P,Strand Passage,Re- ligation,L=2,L=3,23,免疫学信息网 http:/,Topo I Reactions,24,免疫学信息网 http:/,Model for Topo II Mechanism,25,免疫学信息网 http:/,Topo II Reactions,26,免疫学信息网 http:/,For a good treatment of topos, see the book: “DNA replication” Arthur Kornberg and Tania Baker,
