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Unraveling the DNA Packaging Mystery: Histones, Nucleosome Positioning, and DNA Bending

Explore the intricate DNA packaging into nucleosomes, histone-DNA interactions, and bending flexibility. Learn how DNA sequence influences histone binding and nucleosome structure. Delve into the energy landscape matrix method and the structure of DNA within nucleosomes.

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Unraveling the DNA Packaging Mystery: Histones, Nucleosome Positioning, and DNA Bending

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  1. Nucleosome Positioning Histones and DNA Bending

  2. DNA packaging • 3 X 109 base pairs in human genome • ~1 m if unraveled • Compacted into nucleus • 100 mm in diamter

  3. Histones

  4. 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.gifhttp://www2.kenyon.edu/Depts/BioEllipse/courses/biol114/Chap01/chrom1.gif

  9. 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

  10. DNA as a Rod

  11. Bend Twist

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

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

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

  15. Base Pairing

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

  17. Base Stacking Richmond & Davey 2003

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

  19. 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

  20. 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

  21. Energy Landscape

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

  23. 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. 1986191:659-75

  24. 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

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

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

  27. 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?

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