Literature DB >> 11497924

Histone core slips along DNA and prefers positioning at the chain end.

T Sakaue1, K Yoshikawa, S H Yoshimura, K Takeyasu.   

Abstract

We studied the stability and dynamics of a model of a nucleosome, the fundamental unit for the packing of long DNA in eukaryotes, using a Brownian dynamics simulation. For the proper folding of a stiff polymer on a core particle, moderate attractive interaction is shown to be essentially important, which explains the empirical experimental protocol for the reconstitution of nucleosomes. The effect of the chain end on the positioning of the core particle is examined and compared with the experimental data by atomic force microscopy measurement. It is also suggested that the core particle exhibits sliding motion along the chain as a manifestation of Brownian motion.

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Year:  2001        PMID: 11497924     DOI: 10.1103/PhysRevLett.87.078105

Source DB:  PubMed          Journal:  Phys Rev Lett        ISSN: 0031-9007            Impact factor:   9.161


  11 in total

1.  Evidence for DNA translocation by the ISWI chromatin-remodeling enzyme.

Authors:  Iestyn Whitehouse; Chris Stockdale; Andrew Flaus; Mark D Szczelkun; Tom Owen-Hughes
Journal:  Mol Cell Biol       Date:  2003-03       Impact factor: 4.272

2.  Dynamic properties of nucleosomes during thermal and ATP-driven mobilization.

Authors:  Andrew Flaus; Tom Owen-Hughes
Journal:  Mol Cell Biol       Date:  2003-11       Impact factor: 4.272

3.  Transcription of giant DNA complexed with cationic nanoparticles as a simple model of chromatin.

Authors:  Anatoly A Zinchenko; François Luckel; Kenichi Yoshikawa
Journal:  Biophys J       Date:  2006-12-01       Impact factor: 4.033

Review 4.  Nuclear architecture and chromatin dynamics revealed by atomic force microscopy in combination with biochemistry and cell biology.

Authors:  Yasuhiro Hirano; Hirohide Takahashi; Masahiro Kumeta; Kohji Hizume; Yuya Hirai; Shotaro Otsuka; Shige H Yoshimura; Kunio Takeyasu
Journal:  Pflugers Arch       Date:  2008-01-03       Impact factor: 3.657

5.  Electro-entropic excluded volume effects on DNA looping and relaxation in nanochannels.

Authors:  Yeng-Long Chen
Journal:  Biomicrofluidics       Date:  2013-10-22       Impact factor: 2.800

6.  Nucleosome positioning by genomic excluding-energy barriers.

Authors:  Pascale Milani; Guillaume Chevereau; Cédric Vaillant; Benjamin Audit; Zofia Haftek-Terreau; Monique Marilley; Philippe Bouvet; Françoise Argoul; Alain Arneodo
Journal:  Proc Natl Acad Sci U S A       Date:  2009-12-14       Impact factor: 11.205

7.  Ensembles of Breathing Nucleosomes: A Computational Study.

Authors:  Koen van Deelen; Helmut Schiessel; Lennart de Bruin
Journal:  Biophys J       Date:  2019-12-12       Impact factor: 4.033

8.  Human SWI/SNF drives sequence-directed repositioning of nucleosomes on C-myc promoter DNA minicircles.

Authors:  Hillel I Sims; Jacqueline M Lane; Natalia P Ulyanova; Gavin R Schnitzler
Journal:  Biochemistry       Date:  2007-09-18       Impact factor: 3.162

9.  Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization.

Authors:  Chris A Brackley; Stephen Taylor; Argyris Papantonis; Peter R Cook; Davide Marenduzzo
Journal:  Proc Natl Acad Sci U S A       Date:  2013-09-03       Impact factor: 11.205

10.  Predicting nucleosome positions on the DNA: combining intrinsic sequence preferences and remodeler activities.

Authors:  Vladimir B Teif; Karsten Rippe
Journal:  Nucleic Acids Res       Date:  2009-07-22       Impact factor: 16.971

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