Quantifying chromatin-associated interactions: The HI-FI system

Methods in Enzymology

Volumn 512, Issue , 2012, Pages 243-274

  Winkler, Duane D ^a   Luger, Karolin ^a   Hieb, Aaron R ^a  

^a Department of Environmental and Radiological Health Sciences   (United States)

Author keywords

Affinity; Chromatin; Fluorescence; FRET; H2B H2A; H3 H4; Interaction; Nucleosome; Quantitative; Stoichiometry

Indexed keywords

3 [(3 CHOLAMIDOPROPYL)DIMETHYLAMMONIO] 1 PROPANESULFONIC ACID; ALTERNATIVE COMPLEMENT PATHWAY C3 C5 CONVERTASE; CYSTEINE; DETERGENT; DNA; DODECYL SULFATE SODIUM; ETHIDIUM BROMIDE; FACTOR A; FLUORESCENT DYE; GUANIDINE; HISTONE H2A; HISTONE H2B; HISTONE H3; HISTONE H4; IODOACETAMIDE; MALEIMIDE; MUTANT PROTEIN; OCTYL GLUCOSIDE; POLYACRYLAMIDE GEL; PROTEIN VARIANT; RECOMBINANT PROTEIN; SILICATE; TRITON X 114;

ARTICLE; BINDING AFFINITY; BINDING ASSAY; BINDING COMPETITION; BLEACHING; CHROMATIN; CHROMATIN ASSEMBLY AND DISASSEMBLY; CHROMATIN STRUCTURE; COMPLEX FORMATION; CRITICAL MICELLE CONCENTRATION; DATA ANALYSIS; DIALYSIS; DISSOCIATION CONSTANT; DNA BINDING; DNA CONFORMATION; DNA MICROARRAY; DNA PROTEIN COMPLEX; FLUORESCENCE ANALYSIS; FLUORESCENCE IMAGING; FLUORESCENCE RESONANCE ENERGY TRANSFER; FLUOROMETER; FREEZE DRYING; GEL PERMEATION CHROMATOGRAPHY; GENE MUTATION; HI FI SYSTEM; HIGH THROUGHPUT SEQUENCING; HUMAN; IN VITRO STUDY; MOLECULAR INTERACTION; MOLECULAR RECOGNITION; MOLECULAR WEIGHT; NONHUMAN; NUCLEOSOME; PH; PHOTOCHEMICAL QUENCHING; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN DENATURATION; PROTEIN PROCESSING; PROTEIN PROTEIN INTERACTION; PROTEIN REFOLDING; QUALITY CONTROL; QUANTUM YIELD; REACTION ANALYSIS; REACTION OPTIMIZATION; REPRODUCIBILITY; ROOM TEMPERATURE; SACCHAROMYCES CEREVISIAE; SENSITIVITY ANALYSIS; STOICHIOMETRY; THERMODYNAMICS; XENOPUS LAEVIS;

EID: 84865310327     PISSN: 00766879     EISSN: 15577988     Source Type: Book Series    
DOI: 10.1016/B978-0-12-391940-3.00011-1     Document Type: Chapter

References (30)

1. B.J. Anderson, C. Larkin, K. Guja, and J.F. Schildbach Using fluorophore-labeled oligonucleotides to measure affinities of protein-DNA interactions Methods in Enzymology 450 2008 253 272
2. A.J. Andrews, G. Downing, K. Brown, Y.J. Park, and K. Luger A thermodynamic model for Nap1-histone interactions The Journal of Biological Chemistry 283 2008 32412 32418
3. A.J. Andrews, and K. Luger A coupled equilibrium approach to study nucleosome thermodynamics Methods in Enzymology 488 2011 265 285
4. A.J. Andrews, and K. Luger Nucleosome structure(s) and stability: Variations on a theme Annual Review of Biophysics 40 2011 99 117
5. V. Bohm, A.R. Hieb, A.J. Andrews, A. Gansen, A. Rocker, and K. Toth Nucleosome accessibility governed by the dimer/tetramer interface Nucleic Acids Research 39 2011 3093 3102
6. E.I. Campos, and D. Reinberg Histones: Annotating chromatin Annual Review of Genetics 43 2009 559 599
7. C. Das, J.K. Tyler, and M.E. Churchill The histone shuffle: Histone chaperones in an energetic dance Trends in Biochemical Sciences 35 2010 476 489
8. P.N. Dyer, R.S. Edayathumangalam, C.L. White, Y. Bao, S. Chakravarthy, and U.M. Muthurajan Reconstitution of nucleosome core particles from recombinant histones and DNA Methods in Enzymology 375 2004 23 44
9. C.M. English, M.W. Adkins, J.J. Carson, M.E. Churchill, and J.K. Tyler Structural basis for the histone chaperone activity of Asf1 Cell 127 2006 495 508
10. C. Flors DNA and chromatin imaging with super-resolution fluorescence microscopy based on single-molecule localization Biopolymers 95 2011 290 297
11. R.M. Garavito, and S. Ferguson-Miller Detergents as tools in membrane biochemistry Journal of Biological Chemistry 276 2001 32403 32406
12. A.R. Hieb, S. D'Arcy, M.A. Kramer, A.E. White, and K. Luger Fluorescence strategies for high-throughput quantification of protein interactions Nucleic Acids Research 40 2012 e33
13. A.R. Hieb, W.A. Halsey, M.D. Betterton, T.T. Perkins, J.F. Kugel, and J.A. Goodrich TFIIA changes the conformation of the DNA in TBP/TATA complexes and increases their kinetic stability Journal of Molecular Biology 372 2007 619 632
14. A.P. Jamakhandi, P. Kuzmic, D.E. Sanders, and G.P. Miller Global analysis of protein-protein interactions reveals multiple CYP2E1-reductase complexes Biochemistry 46 2007 10192 10201
15. S.N. Khrapunov, A.I. Dragan, A.V. Sivolob, and A.M. Zagariya Mechanisms of stabilizing nucleosome structure. Study of dissociation of histone octamer from DNA Biochimica et Biophysica Acta 1351 1997 213 222
16. N.K. Lee, A.N. Kapanidis, Y. Wang, X. Michalet, J. Mukhopadhyay, and R.H. Ebright Accurate FRET measurements within single diffusing biomolecules using alternating-laser excitation Biophysical Journal 88 2005 2939 2953
17. D. Linke Detergents: An overview Methods in Enzymology 463 2009 603 617
18. X. Lu, J.M. Klonoski, M.G. Resch, and J.C. Hansen In vitro chromatin self-association and its relevance to genome architecture Biochemical Cell Biology 84 2006 411 417
19. K. Luger, A.W. Mader, R.K. Richmond, D.F. Sargent, and T.J. Richmond Crystal structure of the nucleosome core particle at 2.8 angstrom resolution Nature 389 1997 251 260
20. K. Luger, T.J. Rechsteiner, and T.J. Richmond Expression and purification of recombinant histones and nucleosome reconstitution Methods in Molecular Biology 119 1999 1 16
21. Y.J. Park, P.N. Dyer, D.J. Tremethick, and K. Luger A new fluorescence resonance energy transfer approach demonstrates that the histone variant H2AZ stabilizes the histone octamer within the nucleosome Journal of Biological Chemistry 279 2004 24274 24282
22. M. Ransom, B.K. Dennehey, and J.K. Tyler Chaperoning histones during DNA replication and repair Cell 140 2010 183 195
23. C.A. Royer, and S.F. Scarlata Fluorescence approaches to quantifying biomolecular interactions Methods in Enzymology 450 2008 79 106
24. M. Schaferling, and S. Nagl Forster resonance energy transfer methods for quantification of protein-protein interactions on microarrays Methods in Molecular Biology 723 2011 303 320
25. J.O. Thomas The higher order structure of chromatin and histone H1 Journal of Cell Science. Supplement 1 1984 1 20
26. K. Toth, N. Brun, and J. Langowski Chromatin compaction at the mononucleosome level Biochemistry 45 2006 1591 1598
27. H. Wang, E. Nakata, and I. Hamachi Recent progress in strategies for the creation of protein-based fluorescent biosensors Chembiochem: A European journal of chemical biology 10 2009 2560 2577
28. D.D. Winkler, U.M. Muthurajan, A.R. Hieb, and K. Luger Histone chaperone FACT coordinates nucleosome interaction through multiple synergistic binding events Journal of Biological Chemistry 286 2011 41883 41892
29. J.L. Workman Nucleosome displacement in transcription Genes & Development 20 2006 2009 2017
30. H. Xin, S. Takahata, M. Blanksma, L. McCullough, D.J. Stillman, and T. Formosa yFACT induces global accessibility of nucleosomal DNA without H2A-H2B displacement Molecular Cell 35 2009 365 376