Optical tweezers stretching of chromatin

Journal of Muscle Research and Cell Motility

Volumn 23, Issue 5-6, 2002, Pages 397-407

  Pope, Lisa H ^a   Bennink, Martin L ^a   Greve, Jan ^a  

^a UNIVERSITY OF TWENTE   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

CHROMATIN STRUCTURE; DISSOCIATION CONSTANT; DNA HISTONE INTERACTION; DNA REPLICATION; DNA TEMPLATE; ENERGY TRANSFER; MOLECULAR DYNAMICS; NUCLEOSOME; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN PROCESSING; REVIEW; TRANSCRIPTION REGULATION;

ANIMALS; CHROMATIN; ELASTICITY; HUMANS; KINETICS; LASERS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; NUCLEOSOMES; OPTICS;

EID: 0038246252     PISSN: 01424319     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1023450204528     Document Type: Review

References (63)

1. Baumann CG, Smith SB, Bloomfield VA and Bustamante C (1997) Ionic effects on the elasticity of single DNA molecules. Proc Natl Acad Sci USA 94: 6185-6190.
2. Bednar J, Horowitz RA, Dubochet J and Woodcock CL (1995) Chromatin conformation and salt-induced compaction: three-dimensional structural information from cryoelectron microscopy. J Cell Biol 131: 1365-1376.
3. Bednar J, Horowitz RA, Grigoryev SA, Carruthers LM, Hansen JC, Koster AJ and Woodcock CL (1998) Nucleosomes, linker DNA, and linker histone form a unique structural motif that directs the higher order folding and compaction of chromatin. Proc Natl Acad Sci USA 95(24): 14,173-14,178.
4. Bennink ML, Leuba SH, Leno GH, Zlatanova J, de Grooth BG and Greve J (2001a) Unfolding individual nucleosomes by stretching single chromatin fibers with optical tweezers. Nature Str Biol 8: 606-610.
5. Bennink ML, Pope LH, Leuba SH, de Grooth BG and Greve J (2001b) Single chromatin fibre assembly using optical tweezers. Single Mol 2: 91-97.
6. Brower-Toland BD, Smith CL, Yeh RC, Lis JT, Peterson CL and Wang MD (2002) Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA. Proc Natl Acad Sci USA 99: 1960-1965.
7. Bustamante C, Marko JF, Siggia ED and Smith SB (1994) Entropic elasticity of λ-phage DNA. Science 265: 1599-1600.
8. Bustamante C, Zuccheri G, Leuba SH, Yang G and Samori B (1997) Visualization and analysis of chromatin by scanning force microscopy. Methods: Comp Methods Enzymol 12: 73-83.
9. Cluzel P, Lebrun A, Heller C, Lavery R, Viovy J-L, Chatenay D and Caron F (1996) DNA: an extensible molecule. Science 271: 792-794.
10. Cui Y and Bustamante C (2000) Pulling a single chromatin fiber reveals the forces that maintain its higher-order structure. Proc Natl Acad Sci USA 97: 127-132.
11. Daban JR and Cantor CR (1982) Role of histone pairs H2A, H2B and H3, H4 in the self-assembly of nucleosome core particles. J Mol Biol 156: 771-789.
12. Dobosy JR and Selker EU (2001) Emerging connections between DNA methylation and histone acetylation. Cell Mol Life Sci 58: 721-727.
13. Evans E (1998) Energy landscapes of biomolecular adhesion and receptor anchoring at interfaces explored with dynamic force spectrocopy. Faraday discuss 111: 1-16.
14. Evans E (2001) Probing the relation between force - lifetime - and chemistry in single molecular bonds. Annu Rev Biophys Biomol Str 30: 105-128.
15. Evans E and Ritchie K (1997) Dynamic strength of molecular adhesion bonds. Biophys J 72: 1541-1555.
16. Evans E and Ritchie K (1999) Strength of a weak bond connecting flexible polymer chains. Biophys J 76: 2439-2447.
17. Finch JT and Klug A (1976) Solenoidal model for superstructure in chromatin. Proc Natl Acad Sci USA 73: 1897-1901.
18. Furrer P, Bednar J, Dubochet J, Hamiche A and Prunell A (1995) DNA at the entry-exit of the nucleosome observed by cryoelectron microscopy. J Struct Biol 114: 177-183.
19. Harada Y, Ohara O, Takatsuki A, Itoh H, Shimamoto N and Kinosita K (2001) Direct observation of DNA rotation during transcription by Escherichia coli RNA polymerase. Nature 409: 113-115.
20. Havas K, Flaus A, Phelan M, Kingston R, Wade PA, Lilley DMJ and Owen-Hughes T (2000) Generation of superhelical torsion by ATP-dependent chromatin remodelling activities. Cell 103: 1133-1142.
21. Horowitz RA, Agard DA, Sedat JW and Woodcock CL (1994) The three-dimensional architecture of chromatin in situ: electron tomography reveals fibers composed of a continuously variable zig-zag nucleosomal ribbon. J Cell Biol 125: 1-10.
22. Horowitz RA, Koster AJ, Walz J and Woodcock CL (1997) Automated electron microscope tomography of frozen-hydrated chromatin: the irregular three-dimensional zigzag architecture persists in compact, isolated fibers. J Struct Biol 120: 353-362.
23. Houchmandzadeh B, Marko JF, Chatenay D and Libchaber A (1997) Elasticity and structure of eukaryote chromosomes studied by micromanipulation and micropipette aspiration. J Cell Biol 139: 1-12.
24. Hsieh J and Fire A (2000) Recognition and silencing of repeated DNA. Annu Rev Genet 34: 187-204.
25. Katritch V, Bustamante C and Olson WK (2000) Pulling chromatin fibers: computer simulations of direct physical micromanipulations. J Mol Biol 295: 29-40.
26. Kornberg RD and Lorch Y (1999) Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell 98: 285-294.
27. Ladoux B, Quivy J-P, Doyle P, du Roure O, Almouzni G and Viovy J-L (2000) Fast kinetics of chromatin assembly revealed by single-molecule videomicroscopy and scanning force microscopy. Proc Natl Acad Sci USA 97: 14,251-14,256.
28. Laskey RA, Mills AD and Morris NR (1977) Assembly of SV40 chromatin in a cell-free system from Xenopus eggs. Cell 10: 237-243.
29. Léger JF, Romano G, Sarkar A, Robert J, Bourdieu L, Chatenay D and Marko JF (1999) Structural transitions of a twisted and stretched DNA molecule. Phys Rev Lett 83: 1066-1069.
30. Leuba SH, Bustamante C, van Holde K and Zlatanova J (1998b) Contributions of linker histories and histone H3 to chromatin structure: scanning force microscopy studies on trypsinized fibers. Biophys J 74: 2823-2829.
31. Leuba SH, Bustamante C, Zlatanova J and van Holde K (1998a) Linker histone talis and N-tails of historic H3 are redundant: scanning force microscopy studies of reconstituted fibers. Biophys J 74: 2830-2839.
32. Leuba SH, Yang G, Robert C, Samori B, van Holde K, Zlatanova J and Bustamante C (1994) Three-dimesional structure of extended chromatin fibers as revealed by tapping-mode scanning force microscopy. Proc Natl Acad Sci USA 91: 11,621-11,625.
33. Leuba SH, Zlatanova J, Karymov MA, Bash R, Liu Y-Z, Lohr D, Harrington RE and Lindsay SM (2000) The mechanical properties of single chromatin fibres under tension. Single Mol 1: 185-192.
34. Liu LF and Wang JC (1987) Supercoiling of the DNA template during transcription. Proc Natl Acad Sci USA 84: 7024-7027.
35. Luger K, Meader AW, Richmond RK, Sargent DF and Richmond TJ (1997) X-ray structure of the nucleosome core particle at 2.8 Å resolution. Nature 389: 251-259.
36. Luger K and Richmond TJ (1998) DNA binding within the nucleosome core. Curr Op Str Biol 8: 33-40.
37. Marko JF and Siggia ED (1995) Stretching DNA. Macromolecules 28: 8759-8770.
38. Marko JF and Siggia ED (1997) Driving proteins off DNA using applied tension. Biophys J 73: 2173-2178.
39. Marszalek PE, Lu H, Li H, Carrion-Vazquez M, Oberhauser AF, Schulten K and Fernandez JM (1999) Mechanical unfolding intermediates in titin modules. Nature 402: 100-103.
40. Merkel R, Nassoy P, Leung A, Ritchie K and Evans E (1999) Energy landscapes of receptor-ligand bonds explored with dynamic force spectroscopy. Nature 397: 50-53.
41. Poirier M, Eroglu S, Chatenay D and Marko JF (2000) Reversible and irreversible unfolding of mitotic newt chromosomes by applied force. Mol Biol Cell 11: 269-276.
42. Poirier MG, Nemani A, Gupta P, Eroglu S and Marko JF (2001) Probing chromosome structure with dynamic force relaxation. Phys Rev Lett 86: 360-363.
43. Polach KJ, Lowary PT and Widom J (2000) Effects of core histone tail domains on the equilibrium constants for dynamic DNA site accessibilty in nucleosomes. J Mol Biol 298: 211-223.
44. Polach KJ and Widom J (1995) Mechanism of protein access to specific DNA sequences in chromatin: a dynamic equilibrium model for gene regulation. J Mol Biol 254: 130-149.
45. Pope LH, Bennink ML, Arends MP and Greve J (2002) Optical tweezers for force-induced rupture of chromatin. Biophys J 82: 2476.
46. Pope LH, Davies MC, Laughton CA, Roberts CJ, Tendler SJB and Williams PM (2001) Force-induced melting of a short DNA double helix. Eur Biophys J 30: 53-62.
47. Ramsperger U and Stahl H (1995) Unwinding of chromatin by the SV40 large T-antigen DNA helicase. EMBO J 14: 3215-3225.
48. Sarkar A and Marko JF (2001) Removal of DNA-bound proteins by DNA twisting. Phys Rev E 64: 1-9.
49. Smith SB, Cui Y and Bustamante C (1996) Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules. Science 271: 795-799.
50. Stein A (1979) DNA folding by histories: the kinetics of chromatin core particle reassembly and the interaction of nucleosomes with histones. J Mol Biol 130: 103-134.
51. Strick T, Allemand J-F, Croquette V and Bensimon D (2000) Twisting and stretching single DNA molecules. Prog Biophys Mol Biol 74: 115-140.
52. Strunz T, Oroszlan K, Schäfer R and Guntherödt H (1999) Dynamic force spectroscopy of single DNA molecules. Proc Natl Acad Sci USA 96: 11,277-11,282.
53. Van Holde KE (1989) In: Rich A (ed.) Chromatin, pp. 111-148, Springer-Verlag, New York.
54. Van Holde K and Zlatanova J (1999) The nucleosome core particle: does it have structural and physiologic relevance? BioEssays 21: 776-780.
55. Wang M, Schnitzer MJ, Yin H, Landick R, Gelles J and Block SM (1998) Force and velocity measured for single molecules of RNA polymerase. Science 282: 902-907.
56. Wang MD, Yin H, Landick R, Gelles J and Block SM (1997) Stretching DNA with optical tweezers. Biophys J 72: 1335-1346.
57. Widom J (1998) Structure, dynamics, and function of chromatin in vitro. Ann Rev Biophys Biomol Struct 27: 285-327.
58. Widom J and Klug A (1985) Structure of the 300 Å chromatin filament: X-ray diffraction from oriented samples. Cell 43: 207-213.
59. Williams MC, Rouzina I and Bloomfield VA (2002) Thermodynamics of DNA interactions from single molecule stretching experiments. Acc Chem Res 35: 159-166.
60. Workman JL and Kingston RE (1998) Alteration of nucleosome structure as a mechanism of transcriptional regulation. Annu Rev Biochem 67: 545-579.
61. Yin H, Wang MD, Svoboda K, Landick R, Block SM and Gelles J (1995) Transcription against an applied force. Science 270: 1653-1657.
62. Zlatanova J, Leuba SH and van Holde K (1998) Chromatin fiber structure: morphology, molecular determinants, structural transitions. Biophys J 74: 2554-2566.
63. Zlatanova J, Leuba SH, Yang G, Bustamante C and van Holde K (1994) Linker DNA accessibility in chromatin fibers of different conformations: a reevaluation. Proc Natl Acad Sci USA 91: 5277-5280.