Nucleosome dynamics between tension-induced states

Biophysical Journal

Volumn 102, Issue 10, 2012, Pages 2235-2240

  Mollazadeh Beidokhti, Laleh ^a   Mohammad Rafiee, Farshid ^a   Schiessel, Helmut ^b  

^a INSTITUTE FOR ADVANCED STUDIES IN BASIC SCIENCES IASBS   (Iran)

^b UNIVERSITEIT LEIDEN   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ARTICLE; BINDING SITE; BIOLOGICAL MODEL; CHEMISTRY; CONFORMATION; MECHANICAL STRESS; METABOLISM; NUCLEOSOME; THERMODYNAMICS; TIME;

BINDING SITES; DNA; MODELS, BIOLOGICAL; NUCLEIC ACID CONFORMATION; NUCLEOSOMES; STRESS, MECHANICAL; THERMODYNAMICS; TIME FACTORS;

EID: 84861138987     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2012.04.012     Document Type: Article

References (23)

1. H. Schiessel The physics of chromatin J. Phys. Condens. Matter 15 2003 R699 R774
2. K. Luger, and A.W. Mäder T.J. Richmond Crystal structure of the nucleosome core particle at 2.8 A resolution Nature 389 1997 251 260 (Pubitemid 27406632)
3. T.J. Richmond, and C.A. Davey The structure of DNA in the nucleosome core Nature 423 2003 145 150 (Pubitemid 36569532)
4. P. Prinsen, and H. Schiessel Nucleosome stability and accessibility of its DNA to proteins Biochimie 92 2010 1722 1728
5. K.J. Polach, and J. Widom Mechanism of protein access to specific DNA sequences in chromatin: a dynamic equilibrium model for gene regulation J. Mol. Biol. 254 1995 130 149
6. C. Hodges, and L. Bintu C. Bustamante Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase II Science 325 2009 626 628
7. J.J.F.A. van Vugt, and M. de Jager C. Logie Multiple aspects of ATP-dependent nucleosome translocation by RSC and Mi-2 are directed by the underlying DNA sequence PLoS ONE 4 2009 e6345
8. C. Bustamante, Z. Bryant, and S.B. Smith Ten years of tension: single-molecule DNA mechanics Nature 421 2003 423 427 (Pubitemid 36157948)
9. Y. Cui, and C. Bustamante Pulling a single chromatin fiber reveals the forces that maintain its higher-order structure Proc. Natl. Acad. Sci. USA 97 2000 127 132 (Pubitemid 30055795)
10. M.L. Bennink, and S.H. Leuba J. Greve Unfolding individual nucleosomes by stretching single chromatin fibers with optical tweezers Nat. Struct. Biol. 8 2001 606 610 (Pubitemid 32613009)
11. B.D. Brower-Toland, and C.L. Smith M.D. Wang Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA Proc. Natl. Acad. Sci. USA 99 2002 1960 1965 (Pubitemid 34168997)
12. G.J. Gemmen, and R. Sim D.E. Smith Forced unraveling of nucleosomes assembled on heterogeneous DNA using core histones, NAP-1, and ACF J. Mol. Biol. 351 2005 89 99 (Pubitemid 40967057)
13. S. Mihardja, and A.J. Spakowitz C. Bustamante Effect of force on mononucleosomal dynamics Proc. Natl. Acad. Sci. USA 103 2006 15871 15876 (Pubitemid 44657559)
14. M. Kruithof, and J. van Noort Hidden Markov analysis of nucleosome unwrapping under force Biophys. J. 96 2009 3708 3715
15. M.A. Hall, and A. Shundrovsky M.D. Wang High-resolution dynamic mapping of histone-DNA interactions in a nucleosome Nat. Struct. Mol. Biol. 16 2009 124 129
16. I.M. Kulić, and H. Schiessel DNA spools under tension Phys. Rev. Lett. 92 2004 228101
17. B. Sudhanshu, and S. Mihardja A.J. Spakowitz Tension-dependent structural deformation alters single-molecule transition kinetics Proc. Natl. Acad. Sci. USA 108 2011 1885 1890
18. T. Wocjan, K. Klenin, and J. Langowski Brownian dynamics simulation of DNA unrolling from the nucleosome J. Phys. Chem. B 113 2009 2639 2646
19. C. Bustamante, and S.B. Smith D. Smith Single-molecule studies of DNA mechanics Curr. Opin. Struct. Biol. 10 2000 279 285 (Pubitemid 30333096)
20. A.B. Kolomeisky, and M.E. Fisher Periodic sequential kinetic models with jumping, branching and deaths Physica A 279 2000 1 20
21. P. Hänggi, P. Talkner, and M. Borkovec Reaction-rate theory: fifty years after Kramers Rev. Mod. Phys. 62 1990 251 342
22. D.T. Gillespie A general method for numerically simulating the stochastic time evolution of coupled chemical reactions J. Comput. Phys. 22 1976 403 434
23. M.M. Tirado, and J.G. de la Torre Rotational dynamics of rigid, symmetric top macromolecules. Application to circular cylinders J. Chem. Phys. 73 1980 1986 1993