1. 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??

2. Nitrogenous base
Sugar
Phosphate 1

3. 1A Evidence for the Double Helix helical 1. Fiber Diffraction data:
-Helical geometry
-3.4 A º spacing (1Aº = m)
-34 A º pitch
helical
10 layer
Lines
Between
Cross
Patterns
(10
Residues
Per turn)
2. Structure of dCTP
3. Base Tautomerism
Chargaff rules
- A=T, G=C 1A

4. NIH
(not in handout)

5. -2’-deoxyribose 2

6. Sugar “Pucker” Conformations
A DNA
B DNA 3

7. Pyrimidines
Purines 4

8. Base Tautomerization
G (Keto) G (Enol) A
99.99% % 5

9. 6 9 1’ 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
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10. A very useful number: 660
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11. 7 Rotation About the N-Glycosidic Bond A A,B DNA Z DNA (G only) N3
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12. 8
Phosphodiester
Backbone
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13. 9 B-DNA: A right Handed double helix Why? Minor Groove Major Groove
Rise
3.4 Å
Minor
Groove
B-DNA: A right
Handed double helix
Why?
Major
Groove
Pitch
34 Å
10.4 bp/turn 9
Width 20 Å
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14. Twist 36° 9
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15. 10 Major Groove Minor Groove 8.5 Å 11.7 Å 7.5 Å 5.7 Å
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16. 11
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17. Note to self: Discuss forces that affect helix formation
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18. C-G
T-A
NIH
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19. A B Z
Pitch
Base Inclination
Handedness 12
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20. 13 Base Displacement Determines Groove Depth A DNA B DNA Z DNA
dx = -4 Å
A DNA
Major
Minor
dx = 0.8 Å
B DNA
Major
Minor
Z DNA
Major
Minor
dx = +3-4 Å 13
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21. A B Z Mi Ma Ma Mi Mi Ma 12
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22. Z-DNA Phosphate Backbone is Kinked14
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23. 15
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24. Question: is all B-DNA structurally identical?
Implications of structural variation
Implications of flexibility
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25. 16 5’ 3’ Degrees of freedom: 7 Torsion angles and sugar conformation
(Rigid) 5’ 3’ 16
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26. (except in intercalation)
Structural Variation Defined by Bases
normal
frequent
never
Never
(except in intercalation)
Common
Common 17
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27. NIH Propeller Twist Maximizes Base Stacking 5’ 3’ 5’ 3’ 3’ 5’ 3’ 5’
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28. Buckle
Propeller
Twist 18
Textbook
Real Life
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29. 19 Naturally Occurring Variations in Roll, Slide, Twist
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30. 19A Pyrimidine-Purine Steps Have Little Base Stacking 3’ 5’ C G A T
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’ C G A T
19A
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31. 19B Purine-Pyrimidine Steps Have Extensive Base Stacking 3’ 5’ A G C T
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32. 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.
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33. DNA Topology* *Johannes’ Favorite Subject (Students’ least favorite subject)
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34. 20 DNA Unwinding Causes Topological Problems Unwound Parental Duplex
(Transcription)
Over-
Wound
region 20
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35. More Topological Problems21
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36. Properties of Topoisomerases22
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37. 23 Strand Passage Model for Topo I L=2 L=3 Covalent Tyrosine-5’P
Re-
ligation
Unwound
Complex
Cleavage
Complex
L=2
L=3 23
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38. Topo I
Reactions 24
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39. Model for Topo II Mechanism25
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40. Topo II
Reactions 26
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41. For a good treatment of topos, see the book: “DNA replication”
Arthur Kornberg and Tania Baker
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