The physics of chromatin

Journal of Physics Condensed Matter

Volumn 15, Issue 19, 2003, Pages

  Schiessel, Helmut ^a  

^a MAX PLANCK INSTITUTE FOR POLYMER RESEARCH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMISTRY; CRYSTAL STRUCTURE; DNA SEQUENCES; ENZYMES; GRAPH THEORY; IONIC STRENGTH; MATHEMATICAL MODELS; MOLECULAR STRUCTURE; NUMERICAL ANALYSIS; POLYELECTROLYTES; PROTEINS; X RAY CRYSTALLOGRAPHY;

CHROMATIN; DNA FOLDING; NUCLEOSOME;

MOLECULAR BIOLOGY;

EID: 0037604739     PISSN: 09538984     EISSN: None     Source Type: Journal    
DOI: 10.1088/0953-8984/15/19/203     Document Type: Review

References (216)

1. Alberts B, Bray D, Lewis J, Raff M, Roberts K and Watson J D 1994 Molecular Biology of the Cell 3rd edn (New York: Garland)
2. Bloomfield V A 1996 Curr. Opin. Struct. Biol. 6 334
3. Olson N H, Gingery M, Eisterling F A and Baker T S 2001 Virology 279 385
4. Cerritelli M E, Cheng N, Rosenberg A H, McPherson C E, Booy F P and Steven A C 1997 Cell 91 271
5. Kindt J, Tzlil S, Ben-Shaul A and Gelbart W M 2001 Proc. Natl Acad. Sci. USA 98 13671
6. Kornberg R D 1974 Science 184 868
7. Kornberg R D and Lorch Y 1999 Cell 98 285
8. Khrapunov S N, Dragan A I, Sivolob A V and Zagariya A M 1997 Biochim. Biophys. Acta 1351 213
9. Raspaud E I, Chaparon I, Leforestier A and Livolant F 1999 Biophys. J. 77 1547
10. Luger K, Mäder A W, Richmond R K, Sargent D F and Richmond T J 1997 Nature 389 251
11. Davey C A, Sargent D F, Luger K, Maeder A W and Richmond T J 2002 J. Mol. Biol. 319 1097
12. Thoma F, Koller Th and Klug A 1979 J. Cell. Biol. 83 403
13. Widom J 1986 J. Mol. Biol. 190 411
14. van Holde K E 1989 Chromatin (New York: Springer)
15. Widom J 1989 Annu. Rev. Biophys. Chem. 18 365
16. van Holde K and Zlatanova J 1995 J. Biol. Chem. 93 8373
17. van Holde K and Zlatanova J 1996 Proc. Natl Acad. Sci. USA 93 10548
18. Finch J T and Klug A 1976 Proc. Natl Acad. Sci. USA 73 1897
19. Widom J and Klug A 1985 Cell 43 207
20. Woodcock C L, Grigoryev S A, Horowitz R A and Whitaker N 1993 Proc. Natl Acad. Sci. USA 90 9021
21. Horowitz R A, Agard D A, Sedat J W and Woodcock C L 1994 J. Cell Biol. 131 1365
22. Leuba S H, Yang G, Robert C, Samori B, van Holde K, Zlatanova J and Bustamante C 1994 Proc. Natl Acad. Sci. USA 91 11621
23. Bednar J, Horowitz R A, Grigoryev S A, Carruthers L M, Hansen J C, Koster A J and Woodcock C L 1998 Proc. Natl Acad. Sci. USA 95 14173
24. Schiessel H, Gelbart W M and Bruinsma R 2001 Biophys. J. 80 1940
25. Workman J L and Kingston R E 1998 Annu. Rev. Biochem. 67 545
26. Widom J 1998 Annu. Rev. Biophys. Struct. 27 285
27. Polach K J and Widom J 1995 J. Mol. Biol. 254 130
28. Polach K J and Widom J 1996 J. Mol. Biol. 258 800
29. Pennings S, Meerseman G and Bradbury E M 1991 J. Mol. Biol. 220 101
30. Meersseman G, Pennings S and Bradbury E M 1992 EMBO J. 11 2951
31. Pennings S. Meerseman G and Bradbury E M 1994 Proc. Natl Acad. Sci. 91 10275
32. Varga-Weisz P D and Becker P B 1998 Curr. Opin. Cell Biol. 10 346
33. Guschin D and Wolffe A P 1999 Curr. Biol. 9 R742
34. Peterson C L 2000 FEBS Lett. 476 68
35. Flaus A and Owen-Hughes T 2001 Curr. Opin. Genet. Dev. 11 148
36. Studitsky V M, Clark D J and Felsenfeld G 1994 Cell 76 371
37. Studitsky V M, Clark D J and Felsenfeld G 1995 Cell 83 19
38. Felsenfeld G, Boyes J, Chung J, Clark D and Studitsky V 1996 Proc. Natl Acad. Sci. USA 93 9384
39. Studitsky V M, Kassavetis G A, Geiduschek E P and Felsenfeld G 1997 Science 278 1960
40. Felsenfeld G, Clark D and Studitsky V M 2000 Biophys. Chem. 86 231
41. Luger K and Richmond T J 1998 Curr. Opin. Genet. Dev. 8 140
42. Grosberg A Yu, Nguyen T T and Shklovskii B I 2002 Rev. Mod. Phys. 74 329
43. Park S Y, Bruinsma R F and Gelbart W M 1999 Europhys. Lett. 46 454
44. Mateescu E M, Jeppesen C and Pincus P 1999 Europhys. Lett. 46 493
45. Gurovitch E and Sens P 1999 Phys. Rev. Lett. 82 339
46. Netz R R and Joanny J-F 1999 Macromolecules 32 9026
47. Kunze K-K and Netz R R 2000 Phys. Rev. Lett. 85 4389
48. Nguyen T T and Shklovskii B I 2001 Physica A 293 324
49. Nguyen T T and Shklovskii B I 2001 J. Chem. Phys. 114 5905
50. Nguyen T T and Shklovskii B I 2001 J. Chem. Phys. 115 7298
51. Schiessel H, Bruinsma R F and Gelbart W M 2001 J. Chem. Phys. 115 7245
52. Nguyen T T, Grosberg A Yu and Shklovskii B I 2001 Electrostatic Effects in Soft Matter and Biophysics ed C Holm, P Kékicheff and R Podgornik (Dordrecht: Kluwer) p 469
53. Gelbart W M 2001 Electrostatic Effects in Soft Matter and Biophysics ed C Holm, P Kékicheff and R Podgornik (Dordrecht: Kluwer) p 53
54. Kunze K-K and Netz R R 2002 Phys. Rev. E 66 011918
55. Schiessel H 2003 Macromolecules at press
56. Odijk T 1980 Macromolecules 13 1542
57. Pincus P A, Sandroff C J and Witten T A 1984 J. Physique 45 725
58. von Goeler F and Muthukumar M 1994 J. Chem. Phys. 100 7796
59. Wallin T and Linse P 1996 Langmuir 12 305
60. Wallin T and Linse P 1996 J. Phys. Chem. 100 17873
61. Wallin T and Linse P 1997 J. Phys. Chem. B 101 5506
62. Wallin T and Linse P 1998 J. Chem. Phys. 109 5089
63. Haronska P, Vilgis T A, Grottenmüller R and Schmidt M 1998 Macromol. Theory Simul. 7 241
64. Jonsson M and Linse P 2001 J. Chem. Phys. 115 3406
65. Chodanowski P and Stoll S 2001 Macromolecules 34 2320
66. Sakaue T, Yoshikawa K, Yoshimura S H and Takeyasu K 2001 Phys. Rev. Lett. 87 078105
67. Messina R, Holm C and Kremer K 2002 Phys. Rev. E 65 041805
68. Messina R, Holm C and Kremer K 2002 J. Chem. Phys. 117 2947
69. Jonsson M and Linse P 2001 J. Chem. Phys. 115 10975
70. Akinchina A and Linse P 2002 Macromolecules 35 5183
71. Dzubiella J, Moreira A G and Pincus P A 2003 Macromolecules 36 1741
72. Yager T D, McMurray C T and van Holde K E 1989 Biochemistry 28 2271
73. Marky N L and Manning G S 1991 Biopolymers 31 1543
74. Schiessel H, Rudnick J, Bruinsma R F and Gelbart W M 2000 Europhys. Lett. 51 237
75. Schiessel H, Widom J, Bruinsma R F and Gelbart W M 2001 Phys. Rev. Lett. 86 4414
76. Schiessel H, Widom J, Bruinsma R F and Gelbart W M 2002 Phys. Rev. Lett. 88 129902
77. Kulić I and Schiessel H 2003 Biophys. J. at press
78. Kulić I and Schiessel H 2003 Phys. Rev. Lett. submitted
79. de Gennes P G 1971 J. Chem. Phys. 55 572
80. de Gennes P-G 1979 Scaling Concepts in Polymer Physics (Ithaca, NY: Cornell University Press)
81. Doi M and Edwards S F 1986 The Theory of Polymer Dynamics (Oxford: Clarendon)
82. Cui Y and Bustamante C 2000 Proc. Natl Acad. Sci. USA 97 127
83. Bennink M L, Leuba S H, Leno G H, Zlatanova J, de Grooth B G and Greve J 2001 Nat. Struct. Biol. 8 606
84. Brower-Toland B D, Smith C L, Yeh R C, Lis J T, Peterson C L and Wang M D 2002 Proc. Natl Acad. Sci. USA 99 1960
85. Ben-Haim E, Lesne A and Victor J-M 2001 Phys. Rev. E 64 0519219
86. Victor J-M, Ben-Haim E and Lesne A 2002 Phys. Rev. E 66 060901(R)
87. Katritch V, Bustamante C and Olson W K 2000 J. Mol. Biol. 295 29
88. Wedemann G and Langowski J 2002 Biophys. J. 82 2847
89. Mangenot S, Leforestier A, Vachette P, Durand D and Livolant F 2002 Biophys. J. 82 345
90. Mangenot S, Raspaud E, Tribet C, Belloni L and Livolant F 2002 Eur. Phys. J. E 7 221
91. Marko J F and Siggia E D 1997 Biophys. J. 73 2
92. Schiessel H 2002 Europhys. Lett. 58 140
93. Houchmandzadeh B, Marko J F, Chatenay D and Libchaber A 1997 J. Cell. Biol. 139 1
94. Poirier M G, Eroglu S, Chatenay D and Marko J F 2000 Mol. Biol. Cell 11 269
95. Poirier M G, Nemani A, Gupta P, Eroglu S and Marko J F 2001 Phys. Rev. Lett. 86 360
96. Poirier M G, Monhait T and Marko J F 2002 J. Cell. Biochem. 85 422
97. Marko J F and Siggia E D 1997 Mol. Biol. Cell 8 2217
98. Arents G, Burlingame R W, Wang B-C, Love W E and Moudrianakis E N 1991 Proc. Natl Acad. Sci. USA 88 10148
99. Anderson J D and Widom J 2000 J. Mol. Biol. 296 979
100. Hagerman P J 1988 Annu. Rev. Biophys. Biophys. Chem. 17 265
101. Harries R A and Hearst J E 1966 J. Chem. Phys. 44 2595
102. Strauss J K and Maher L J 1994 Science 266 1829
103. Braunlin W H, Strick T J and Record M T 1982 Biopolymers 21 1301
104. Mascotti D P and Lohmann T M 1990 Proc. Natl Acad. Sci. USA 87 3142
105. Rädler J O, Koltover I, Salditt T and Safinya C R 1999 Science 275 810
106. Koltover L, Salditt T and Safinya C R 1999 Biophys. J. 77 915
107. Record M T, Anderson C F and Lohmann T M 1978 Q. Rev. Biophys. 11 103
108. Bruinsma R 1998 Eur. Phys. J. B 4 75
109. Harries D, May S, Gelbart W M and Ben-Shaul A 1998 Biophys. J. 75 159
110. Sens P and Joanny J-F 2000 Phys. Rev. Lett. 84 4862
111. Oosawa F 1971 Polyelectrolytes (New York: Dekker)
112. Manning G S 1978 Q. Rev. Biophys. 11 179
113. Rouzina I and Bloomfield V A 1996 J. Phys. Chem. 100 4292
114. Alexander S, Chaikin P M, Grant P, Morales G J, Pincus P and Hone D 1984 J. Chem. Phys. 80 5776
115. Golestanian R 1999 Phys. Rev. Lett. 83 2473
116. Sens P 1999 Phys. Rev. Lett. 83 2474
117. Netz R R and Joanny J-F 1999 Macromolecules 32 9013
118. Schiessel J and Aranda-Espinoza H 2001 Eur. Phys. J. E 5 499
119. Nguyen T T, Grosberg A Yu and Shklovskii B I 2000 J. Chem. Phys. 113 1110
120. Ganachaud F, Elaïssari A, Pichot F, Laayoun A and Cros P 1997 Langmuir 13 701
121. Sukhorukov G B, Donath E, Davis S, Lichtenfeld H, Caruso F, Popov Vi I and Möhwald H 1998 Polym. Adv. Technol. 9 759
122. Kabanov A V, Sergeyev V G, Pyshkina O A, Zinchenko A A, Zezin A B, Joosten J G H, Brackman J and Yoshikawa K 2000 Macromolecules 33 9587
123. McQuigg D W, Kaplan J I and Dubin P L 1992 J. Phys. Chem. 96 1973 and references therein
124. Frank-Kamentskii M D 1997 Phys. Rep. 288 13
125. Schlick T 1995 Curr. Opin. Struct. Biol. 5 245
126. Love A E 1944 A Treatise of the Mathematical Theory of Elasticity 4th edn (New York: Dover) ch 18 and 19
127. Nizette M and Goriely A 1999 J. Math. Phys. 40 2830
128. Benham C J 1977 Proc. Natl Acad. Sci. USA 74 2397
129. Benham C J 1979 Biopolymers 18 609
130. Le Bret M 1979 Biopolymers 18 1709
131. Le Bret M 1984 Biopolymers 23 1835
132. Shi Y M and Hearst J E 1994 J. Chem. Phys. 101 5186
133. Fain B and Rudnick J 1997 Phys. Rev. E 55 7364
134. Swigdon D, Coleman B D and Tobias I 1998 Biophys. J. 74 2515
135. Fain B and Rudnick J 1999 Phys. Rev. E 60 7239
136. Coleman B D, Swigdon D and Tobias I 2000 Phys. Rev. E 61 747
137. Zandi R and Rudnick J 2001 Phys. Rev. E 64 051918
138. Yamakawa H and Stockmayer W 1972 J. Chem. Phys. 57 2843
139. Beard P 1978 Cell 15 955
140. Spadafora C, Oudet P and Chambon P 1979 Eur. J. Biochem. 100 225
141. Watkins J F and Smerdon M J 1985 Biochemistry 24 7279
142. Simpson R T and Stafford D W 1983 Proc. Natl Acad. Sci. USA 50 51
143. Wu H-M and Crothers D M 1984 Nature 308 509
144. Loomans D, Schiessel H and Blumen A 1997 J. Chem. Phys. 107 2636
145. Schiessel H, Sokolov I M and Blumen A 1997 Phys. Rev. E 56 R2390
146. Schwinefus J J and Bloomfield V A 2000 Biopolymers 54 572
147. Ura K, Nightingale K and Wolffe A P 1996 EMBO J. 15 4959
148. Ura K, Kurumizaka H, Dimitrov S, Almouzni G and Wolffe A P 1997 EMBO J. 16 2096
149. Flaus A, Luger K, Tan S and Richmond T J 1996 Proc. Natl Acad. Sci. USA 93 1370
150. Flaus A and Richmond T J 1998 J. Mol. Biol. 275 427
151. Hamiche A, Kang J-G, Dennis C, Xiao H and Wu C 2001 Proc. Natl Acad. Sci. USA 98 14316
152. van Holde K E and Yager T D 1985 Structure and Function of the Genetic Apparatus (NATO ASI series A) vol 98, ed C Nicolini and P O P Ts'o p 35
153. Sukhishvili S A, Chen Y, Müller J D, Gratton E, Schweizer K S and Granick S 2000 Nature 406 146
154. Sukhishvili S A, Chen Y, Müller J D, Gratton E, Schweizer K S and Granick S 2002 Macromolecules 35 1776
155. Abramowitz M and Stegun I 1972 Handbook of Mathematical Functions (New York: Dover)
156. Bouchaud J P and Georges A 1990 Phys. Rep. 195 127
157. Klafter J, Shlesinger M F and Zumofen G 1993 Chem. Phys. 177 821
158. Sokolov I M, Mai J and Blumen A 1997 Phys. Rev. Lett. 79 857
159. Mandelbrot B B 1982 The Fractal Geometry of Nature (San Francisco, CA: Freeman)
160. de Cloizeaux J and Jannick G 1990 Polymers in Solution (Oxford: Clarendon)
161. Frenkel J and Kontorova T 1938 Zh. Eksp. Teor. Fiz. 8 1340
162. Frenkel J and Kontorova T 1939 J. Physique (Moscow) 1 137
163. Floria L M and Mazo J J 1996 Adv. Phys. 45 505
164. Braun O M, Dauxois T, Paliy M V and Peyrard M 1997 Phys. Rev. Lett. 78 1295
165. Strunz T and Elmer F-J 1998 Phys. Rev. E 58 1601
166. Pietronero L, Schneider W R and Strässler S 1981 Phys. Rev. B 24 2187
167. Aubry S 1983 J. Phys. 44 147
168. Watanabe S, van der Zant H S J, Strogatz S H and Orlando T P 1996 Physica D 97 429
169. Uhler W and Schilling R 1988 Phys. Rev. B 37 5787
170. Schiessel H, Oshanin G, Cazabat A M and Moreau M 2002 Phys. Rev. E 66 056130
171. Marko J F 1998 Phys. Rev. E 57 2134
172. Marko J F 1997 Europhys. Lett. 38 183
173. Kamien R D, Lubensky T V, Nelson P and O'Hern C S 1997 Europhys. Lett. 38 237
174. Levinthal C and Crane H 1956 Proc. Natl Acad. Sci. USA 42 456
175. Nelson P Proc. Natl Acad. Sci. USA 96 14342
176. van Kampen N G 1992 Stochastic Processes in Physics and Chemistry (Amsterdam: North-Holland)
177. Mattei S, Sampaolese B, De Santis P and Savino M 2002 Biophys. Chem. 97 173
178. Anselmi C, Bocchinfuso G, De Santis P, Savino M and Scipioni A 2000 Biophys. J. 79 601
179. Lorch Y, Zhang M and Kornberg R D 1999 Cell 96 389
180. Bazett-Jones D P, Côté J, Landel C C, Peterson C L and Workman J L 1999 Mol. Cell. Biol. 19 1470
181. Längst G and Becker P B 2001 Mol. Cell 8 1085
182. Rees A R, Keller R W, Vesenka J P, Yang G and Bustamante C 1993 Science 260 1646
183. Schulz A, Mucke N, Langowski J and Rippe K 1998 J. Mol. Biol. 283 821
184. Rivetti C, Guthold M and Bustamante C 1999 EMBO J. 18 4464
185. Kulić I 2002 private communication
186. Woodcock C L and Dimitrov S 2001 Curr. Opin. Genet. Dev. 11 130
187. Zlatanova J, Leuba S H and van Holde K 1998 Biophys. J. 74 2554
188. Maret G 1976 PhD thesis Konstanz University
189. Maret G, v. Schickfus M, Mayer A and Dransfeld K 1975 Phys. Rev. Lett. 35 397
190. Maret G and Weill G 1983 Biopolymers 22 2727
191. Martino J A, Katritch V and Olson W K 1999 Struct. Fold. Des. 7 1009
192. Widom J 1992 Proc. Natl Acad. Sci. USA 89 1095
193. Plewa J S and Witten T A 2000 J. Chem. Phys. 112 10042
194. Stryer L 1995 Biochemistry 4th edn (New York: Freeman) p 420
195. Mergell B, Schiessel H and Everaers R in preparation
196. Daban J-R 2000 Biochemistry 39 3861
197. Janninck G, Duplantier B and Sikorav J L 1996 Biophys. J. 71 451
198. Cluzel P, Lebrun A, Heller C, Lavery R, Viovy J L, Chatenay D and Caron F 1996 Science 271 792
199. Smith S B, Cui Y and Bustamante C 1996 Science 271 795
200. Mergell B, Ejtehadi M J and Everaers R 2002 Phys. Rev. E 66 011903
201. Nyrkova I A, Semenov A N, Joanny J-F and Khokhlov A R 1996 J. Physique II 6 1411
202. Livolant F and Leforestier A 2000 Biophys. J. 78 2716
203. Fraden S and Kamien R D 2000 Biophys. J. 78 2189
204. Ehrlich L, Münkel C, Chirico G and Langowski J 1997 Cabios 13 271
205. Beard D A and Schlick T 2001 Structure 9 105
206. Münkel C and Langowski J 1998 Phys. Rev. E 57 5888
207. Ladoux B, Quivy J-P, Doyle P, du Roure O, Almouzni G and Viovy J-L 2000 Proc. Natl Acad. Sci. USA 97 14251
208. Bennink M L, Pope L H, Leuba S H, de Grooth B G and Greve J 2001 Single Mol. 2 91
209. Rief M, Gautel M, Oesterhelt F, Fernandez J and Gaub H 1997 Science 276 1109
210. Oberhauser A, Hansma P, Carrion-Vazquez M and Fernandez J 2001 Proc. Natl Acad. Sci. USA 98 468
211. Kulić I and Schiessel H Preprint
212. Barrat J-L and Joanny J-F 1996 Adv. Chem. Phys. 94 1
213. Tóth K, Brun N and Langowski J 2001 Biochemistry 40 6921
214. Grunstein M 1997 Nature 389 349
215. Hansen J C, Tse C and Wolffe A P 1998 Biochemistry 37 17637
216. Strahl B D and Allis D 2000 Nature 403 41