A fluorescence resonance energy transfer-based probe to monitor nucleosome structure

Analytical Biochemistry

Volumn 341, Issue 1, 2005, Pages 165-172

  Lovullo, D ^a,b   Daniel, D ^a   Yodh, J ^b   Lohr, D ^a   Woodbury, N W ^a  

^a ARIZONA STATE UNIVERSITY   (United States)

^b MIDWESTERN UNIVERSITY   (United States)

Author keywords

Chromatin; FRET; Nucleosome; Single molecule spectroscopy

Indexed keywords

DNA SEQUENCES; DYNAMICS; ENERGY TRANSFER; TRANSCRIPTION;

CHROMATIN; COMPOSITIONAL CHANGES; FLUORESCENCE RESONANCE ENERGY TRANSFER; FRET; NUCLEOSOMES; SINGLE MOLECULE LEVEL; SINGLE MOLECULE SPECTROSCOPY; SINGLE-MOLECULE DYNAMICS;

FORSTER RESONANCE ENERGY TRANSFER;

DNA;

ACCURACY; ARTICLE; CELL STRUCTURE; CONFORMATION; FLUORESCENCE RESONANCE ENERGY TRANSFER; MOLECULAR PROBE; NUCLEOSOME; PRIORITY JOURNAL; SIGNAL TRANSDUCTION; THERMODYNAMICS;

EUKARYOTA;

EID: 18144366598     PISSN: 00032697     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ab.2005.03.022     Document Type: Article

References (53)

1. W. Fischle, Y. Wang, and C.D. Allis Histone and chromatin cross-talk Curr. Opin. Cell Biol. 15 2003 172 183
2. R.E. Kingston, and G.J. Narlikar ATP-dependent remodeling and acetylation as regulators of chromatin fluidity Genes Dev. 13 1999 2339 2352
3. A.P. Wolffe, and J.J. Hayes Chromatin disruption and modification Nucleic Acids Res. 27 1999 711 720
4. P. Cheung, C.D. Allis, and P. Sassone-Corsi Signaling to chromatin through histone modifications Cell 103 2000 263 271
5. S.L. Berger Histone modifications in transcriptional regulation Curr. Opin. Genet. Dev. 12 2002 142 148
6. G.J. Narlikar, H.Y. Fan, and R.E. Kingston Cooperation between complexes that regulate chromatin structure and transcription Cell 108 2002 475 487
7. C.L. Peterson, and J.L. Workman Promoter targeting and chromatin remodeling by the SWI/SNF complex Curr. Opin. Genet. Dev. 10 2000 187 192
8. P.B. Becker, and W. Horz ATP-dependent nucleosome remodeling Annu. Rev. Biochem. 71 2002 247 273
9. M. Iizuka, and M.M. Smith Functional consequences of histone modifications Curr. Opin. Genet. Dev. 13 2003 154 160
10. J.A. Martens, and F. Winston Recent advances in understanding chromatin remodeling by Swi/Snf complexes Curr. Opin. Genet. Dev. 13 2003 136 142
11. A. Flaus, and T. Owen-Hughes Mechanisms for ATP-dependent chromatin remodelling: farewell to the tuna-can octamer? Curr. Opin. Genet. Dev. 14 2004 165 173
12. T. Ha Single-molecule fluorescence spectroscopy of enzyme conformational dynamics and cleavage mechanism Proc. Natl. Acad. Sci. USA 96 1999 893 898
13. S. Weiss Measuring conformational dynamics of biomolecules by single molecule fluorescence spectroscopy Nat. Struct. Biol. 7 2000 724 729
14. R. Rigler, and W. Wiegrabe Highlight: fluorescence correlation spectroscopy Biol. Chem. 382 2001 353 354
15. W.E. Moerner Single-molecule optical spectroscopy of autofluorescent proteins J. Chem. Phys. 117 2002 10925 10937
16. W.E. Moerner A dozen years of single-molecule spectroscopy in physics, chemistry, and biophysics J. Phys. Chem. B 106 2002 910 927
17. X. Michalet, and S. Weiss Single-molecule spectroscopy and microscopy Compt. Rend. Phys. 3 2002 619 644
18. T.A. Laurence, and S. Weiss How to detect weak pairs Science 299 2003 667 668
19. S. Chu Biology and polymer physics at the single-molecule level Phil. Trans. R. Soc. London Ser. a-Math. Phys. Engin. Sci. 361 2003 689 698
20. B. Schuler, E.A. Lipman, and W.A. Eaton Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy Nature 419 2002 743 747
21. H. Sosa, E.J. Peterman, W.E. Moerner, and L.S. Goldstein ADP-induced rocking of the kinesin motor domain revealed by single-molecule fluorescence polarization microscopy Nat. Struct. Biol. 8 2001 540 544
22. S.A. McKinney, A.C. Declais, D.M. Lilley, and T. Ha Structural dynamics of individual Holliday junctions Nat. Struct. Biol. 10 2003 93 97
23. X. Zhuang Correlating structural dynamics and function in single ribozyme molecules Science 296 2002 1473 1476
24. N. Shimamoto One-dimensional diffusion of proteins along DNA. Its biological and chemical significance revealed by single-molecule measurements J. Biol. Chem. 274 1999 15293 15296
25. T. Ha Initiation and re-initiation of DNA unwinding by the Escherichia coli Rep helicase Nature 419 2002 638 641
26. B. Ladoux Fast kinetics of chromatin assembly revealed by single-molecule videomicroscopy and scanning force microscopy Proc. Natl. Acad. Sci. USA 97 2000 14251 14256
27. H. Wang Using atomic force microscopy to study nucleosome remodeling on individual nucleosomal arrays in situ Biophys. J. 87 2004 1964 1971
28. K. Toth, N. Brun, and J. Langowski Trajectory of nucleosomal linker DNA studied by fluorescence resonance energy transfer Biochemistry 40 2001 6921 6928
29. 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 J. Biol. Chem. 279 2004 24274 24282
30. H. Eshaghpour, A.E. Dieterich, C.R. Cantor, and D.M. Crothers Singlet-singlet energy transfer studies of the internal organization of nucleosomes Biochemistry 19 1980 1797 1805
31. G. Li, and J. Widom Nucleosomes facilitate their own invasion Nat. Struct. Mol. Biol. 11 2004 763 769
32. A.E. Dieterich, R. Axel, and C.R. Cantor Salt-induced structural changes of nucleosome core particles J. Mol. Biol. 129 1979 587 602
33. A.E. Dieterich, and C.R. Cantor Kinetics of nucleosome unfolding at low ionic strength Biopolymers 20 1981 111 127
34. J.R. Daban, and C.R. Cantor Structural and kinetic study of the self-assembly of nucleosome core particles J. Mol. Biol. 156 1982 749 769
35. P. Diaz, and J.R. Daban Nucleosome core particle self-assembly kinetics and stability at physiological ionic strength Biochemistry 25 1986 7736 7744
36. D.G. Chung, and P.N. Lewis Internal architecture of the core nucleosome: fluorescence energy transfer studies at methionine-84 of histone H4 Biochemistry 25 1986 5036 5042
37. C. Thiriet, and J.J. Hayes A novel labeling technique reveals a function for histone H2A/H2B dimer tail domains in chromatin assembly in vivo Genes Dev. 15 2001 2048 2053
38. R.T. Simpson, and D.W. Stafford Structural features of a phased nucleosome core particle Proc. Natl. Acad. Sci. USA 80 1983 51 55
39. Z. Katiliene, E. Katilius, and N.W. Woodbury Single molecule detection of DNA looping by NgoMIV restriction endonuclease Biophys. J. 84 2003 4053 4061
40. R.T. Simpson, F. Thoma, and J.M. Brubaker Chromatin reconstituted from tandemly repeated cloned DNA fragments and core histones: a model system for study of higher order structure Cell 42 1985 799 808
41. R.B. Mujumdar, L.A. Ernst, S.R. Mujumdar, C.J. Lewis, and A.S. Waggoner Cyanine dye labeling reagents: sulfoindocyanine succinimidyl esters Bioconjug. Chem. 4 1993 105 111
42. R.C. Bash, J. Yodh, Y. Lyubchenko, N. Woodbury, and D. Lohr Population analysis of subsaturated 172-12 nucleosomal arrays by atomic force microscopy detects nonrandom behavior that is favored by histone acetylation and short repeat length J. Biol. Chem. 276 2001 48362 48370
43. K. Luger, T.J. Rechsteiner, and T.J. Richmond Preparation of nucleosome core particle from recombinant histones Methods Enzymol. 304 1999 3 19
44. S. Pennings Nucleoprotein gel assays for nucleosome positioning and mobility Methods Enzymol. 304 1999 298 312
45. S.Y. Huang, and W.T. Garrard Electrophoretic analyses of nucleosomes and other protein-DNA complexes Methods Enzymol. 170 1989 116 142
46. T.E. Shrader, and D.M. Crothers Effects of DNA sequence and histone-histone interactions on nucleosome placement J. Mol. Biol. 216 1990 69 84
47. J. Widom Role of DNA sequence in nucleosome stability and dynamics Q. Rev. Biophys. 34 2001 269 324
48. J. Babendure Development of a fluorescent probe for the study of nucleosome assembly and dynamics Anal. Biochem. 317 2003 1 11
49. K.E. Van Holde Chromatin 1988 Springer-Verlag Berlin
50. G.J. Czarnota, and F.P. Ottensmeyer Structural states of the nucleosomes J. Biol. Chem. 271 1996 3677 3683
51. F. Dong, and K.E. van Holde Nucleosome positioning is determined by the (H3-H4)2 tetramer Proc. Natl. Acad. Sci. USA 88 1991 10596 10600
52. J.J. Hayes, D.J. Clark, and A.P. Wolffe Histone contributions to the structure of DNA in the nucleosome Proc. Natl. Acad. Sci. USA 88 1991 6829 6833
53. 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 Å resolution Nature 389 1997 251 260