Literature DB >> 21792745

Salt-modulated structure of polyelectrolyte-macroion complex fibers.

Hoda Boroudjerdi1, Ali Naji, Roland R Netz.   

Abstract

The structure and stability of strongly charged complex fibers, formed by complexation of a single long semi-flexible polyelectrolyte chain and many oppositely charged spherical macroions, are investigated numerically at the ground-state level using a chain-sphere cell model. The model takes into account chain elasticity as well as electrostatic interactions between charged spheres and chain segments. Using a numerical optimization method based on a periodically repeated unit cell, we obtain fiber configurations that minimize the total energy. The optimal fiber configurations exhibit a variety of helical structures for the arrangement of macroions including zig-zag, solenoidal and beads-on-a-string patterns. These structures result from the competition between attraction between spheres and the polyelectrolyte chain (which favors chain wrapping around the spheres), chain bending rigidity and electrostatic repulsion between chain segments (which favor unwrapping of the chain), and the interactions between neighboring sphere-chain complexes which can be attractive or repulsive depending on the system parameters such as salt concentration, macroion charge and chain length per macroion (linker size). At about physiological salt concentration, dense zig-zag patterns are found to be energetically most stable when parameters appropriate for the DNA-histone system in the chromatin fiber are adopted. In fact, the predicted fiber diameter in this regime is found to be around 30 nanometers, which roughly agrees with the thickness observed in in vitro experiments on chromatin. We also find a macroion (histone) density of 5-6 per 11nm which agrees with results from the zig-zag or cross-linker models of chromatin. Since our study deals primarily with a generic chain-sphere model, these findings suggest that structures similar to those found for chromatin should also be observable for polyelectrolyte-macroion complexes formed in solutions of DNA and synthetic nano-colloids of opposite charge. In the ensemble where the mean linear density of spheres on the chain is fixed, the present model predicts a phase separation at intermediate salt concentrations into a densely packed complex phase and a dilute phase.

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Year:  2011        PMID: 21792745     DOI: 10.1140/epje/i2011-11072-1

Source DB:  PubMed          Journal:  Eur Phys J E Soft Matter        ISSN: 1292-8941            Impact factor:   1.890


  54 in total

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2.  Histone depletion facilitates chromatin loops on the kilobasepair scale.

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3.  A physical model for the condensation and decondensation of eukaryotic chromosomes.

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4.  EM measurements define the dimensions of the "30-nm" chromatin fiber: evidence for a compact, interdigitated structure.

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Journal:  Proc Natl Acad Sci U S A       Date:  2006-04-14       Impact factor: 11.205

5.  Two-angle model and phase diagram for chromatin.

Authors:  Philipp M Diesinger; Dieter W Heermann
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2006-09-08

6.  Stochastic model for nucleosome sliding under an external force.

Authors:  L Mollazadeh-Beidokhti; J Deseigne; D Lacoste; F Mohammad-Rafiee; H Schiessel
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2009-03-30

7.  An absolute method for the determination of the persistence length of native DNA from electron micrographs.

Authors:  C Frontali; E Dore; A Ferrauto; E Gratton; A Bettini; M R Pozzan; E Valdevit
Journal:  Biopolymers       Date:  1979-06       Impact factor: 2.505

8.  Transcription. The omnipotent nucleosome.

Authors:  K van Holde
Journal:  Nature       Date:  1993-03-11       Impact factor: 49.962

9.  Structure of chromatin and the linking number of DNA.

Authors:  A Worcel; S Strogatz; D Riley
Journal:  Proc Natl Acad Sci U S A       Date:  1981-03       Impact factor: 11.205

10.  Polymer chain models of DNA and chromatin.

Authors:  J Langowski
Journal:  Eur Phys J E Soft Matter       Date:  2006-03-20       Impact factor: 1.890

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  4 in total

1.  Structure-driven homology pairing of chromatin fibers: the role of electrostatics and protein-induced bridging.

Authors:  A G Cherstvy; V B Teif
Journal:  J Biol Phys       Date:  2013-01-17       Impact factor: 1.365

2.  Elasticity of DNA and the effect of dendrimer binding.

Authors:  Santosh Mogurampelly; Bidisha Nandy; Roland R Netz; Prabal K Maiti
Journal:  Eur Phys J E Soft Matter       Date:  2013-06-28       Impact factor: 1.890

3.  Global analysis of the ground-state wrapping conformation of a charged polymer on an oppositely charged nano-sphere.

Authors:  Hoda Boroudjerdi; Ali Naji; A Naji; R Netz
Journal:  Eur Phys J E Soft Matter       Date:  2014-03-31       Impact factor: 1.890

Review 4.  Revisiting higher-order and large-scale chromatin organization.

Authors:  Qian Bian; Andrew S Belmont
Journal:  Curr Opin Cell Biol       Date:  2012-03-27       Impact factor: 8.382

  4 in total

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