1. Nucleosome Positioning Histones and DNA Bending

2. DNA packaging 3 X 10 9 base pairs in human genome ~1 m if unraveled Compacted into nucleus –100  m in diamter

3. Histones

5. PDBID = 1KX3

6. Nucleosome Arrays Dorigo B, et al. Science. 2004 306(5701):1571-3.

7. Current Opinion in Structural Biology 2006, 16:336–343

8. http://www2.kenyon.edu/Depts/BioEllipse/courses/biol114/Chap01/chrom1.gif

9. Chromatin Represses Transcription Clark & Wolffe 1991

10. Histones vs. DNA Histones fold DNA DNA sequence determines histone binding –Does histone bind sequence? Absence of direct sequence specific recognition –Bending flexibility of DNA determines affinity for complementary protein surface

11. DNA as a Rod

12. Twist Bend

13. 3 pN, we observe a similar coexistence of B-DNA and a new, highly twisted structure. Experimental data and molecular modeling suggest that this structure has approximately 2.62 bases per turn and an extension 75% larger than B-DNA. This structure has tightly interwound phosphate backbones and exposed bases in common with Pauling's early DNA structure

15. Major & Minor Groove http://courses.biology.utah.edu/horvath/biol.3525/1_DNA/Fig2/marty_1.jpg

16. Flexibility Torsional Flexibility –Angle between base pairs Bending Flexibility –Properties of individual base steps Flexibility of DNA is a Sequence- dependent property

17. Flexibility determinants Hydrogen bonds Electronic configuration of base pairs Base Pair Stacking energy Exocyclic groups in major and minor grooves

18. Base Pairing http://en.wikipedia.org/wiki/Base_pair

19. Base Pairing

20. Base Stacking http://researchnews.osu.edu/archive/dna_base_stacking.jpg

21. Base Stacking The structural basis of DNA flexibility.Philos Transact A Math Phys Eng Sci. 2004 Jul 15;362(1820):1423-38

22. Base Stacking Richmond & Davey 2003

23. Electrostatics Philos. Transact. A Math Phys. Eng. Sci. 2004 Jul 15;362(1820):1423-38.

25. Major & Minor Groove http://courses.biology.utah.edu/horvath/biol.3525/1_DNA/Fig2/marty_1.jpg 12A 22A

26. DNA wrapping alters helical periodicity Chromatin: Structure and Function Alan P. Wolffe

27. Sequence-directed positioning Widlund et al. 1997 Mouse Genome Micrococcal nuclease 146 bp DNA fragments DNA seq added to end Amplify using PCR 10 rounds cycles –competitive nucleosome assembly Chromatin: Structure and Function Alan P. Wolffe

28. Intrinsically curved DNA sequences Oligo(dA).oligo(dT) tracts (4-6bp) –Phased with a periodicity similar to that of DNA helix TATA boxes repeated every 10 bp CA and CTG di/tri-nucleotide repeats

29. Energy Landscape

30. Matrix Method Nucleotide phasing of 10bp repeats influences bending of DNA

31. Periodic occurrence of A/T & GC A/T & G/C out of phase A/T narrow minor groove G/C wide minor groove Satchwell et al. J. Mol. Biol. 1986 191:659-75

36. Minor Groove bending facilitated by Arg side chain into minor groove when it faces histone octamer Major groove narrows to ~9Å Minor groove narrows to ~3Å

37. Richmond & Davey 2003 Overtwisted DNA –Outside Dyad B-DNA conformation with local conformational variation DNA groove –Minor 3A protein-DNA –Major 9A protein-DNA –Twist -> narrow minor groove –Roll 3x vs tilt to cause curvature Smooth bending into the major groove –Uniform positive roll angle and undertwisting at adjacent base steps Smooth bending into minor groove –Constant negative roll angle with alternating twist-shift coupling Relieves steric hindrance between the base edges Discontinuos bending -> Kinking of CA/TG base steps with roll angles and coupled overtwisting –Roll angles reducing the stacking energy –Unstacking energy is less for TA than for TA/TG TA bends the greatesd

38. Structure of DNA in Nucleosome Discontinuous curvature Richmond & Davey 2003

39. Phase of Roll & Tilt Positive Roll in Major Groove Positive Tilt in Minor Groove 2:1 Roll/Tilt

40. Smooth Major Positive roll Under winding –Reduced twist –Negative slide

41. Minor Groove Smooth Bending –Large shift flux –Constant – Roll –Twist-shift Relieves steric bp edge clash Kinking –Large slide Avoid purine clash –Overtwisted –Always at CA/TG bp steps

42. Consistent with Studies of DNA in database Hassan and Calladine 1997 CA=TG most flexible as judged from SD of Roll angle Hassan and Calladine 1997

43. Stacking Energy Kink and Overtwist –CA/TG has low stacking energy –Can adopt high or low roll angles by reducing stacking energy

44. Summary Ong, Richmond & Davey 2007 Major Gray Minor White

45. Unusual DNA conformation parameters induced by histone binding Implicates sequence-dependent –protein recognition –nucleosome positioning –nucleosome mobility Can we predict DNA:Nucleosome binding based on sequence?

47. Consistant with Studies of DNA in database Hassan and Calladine 1997 Rigid and loose (continuously flexible) –Roll slide and twist correlated linearly –RIGID: AA/TT, AT and GA/TC –LOOSE: GG/CC, GC, CG