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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=
2、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 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” Conformation
3、s,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:/,
6、A,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 Max
8、imizes 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:
9、P-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 Drew Major Conclusion: DNA structure can depend on sequence In predi
10、ctable, 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,(Transcript
11、ion),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,
