Single-chain compaction of long duplex DNA by cationic nanoparticles: Modes of interaction and comparison with chromatin

Anatoly A. Zinchenko, Takahiro Sakaue, Sumiko Araki, Kenichi Yoshikawa, Damien Baigl

Research output: Contribution to journalArticle

75 Citations (Scopus)

Abstract

The compaction of long duplex DNA by cationic nanoparticles (NP) used as a primary model of histone core particles has been investigated. We have systematically studied the effect of salt concentration, particle size, and particle charge by means of single-molecule observations-fluorescence microscopy (FM) and transmission electron microscopy (TEM)-and molecular dynamics (MD) simulations. We have found that the large-scale DNA compaction is progressive and proceeds through the formation of beads-on-a-string structures of various morphologies. The DNA adsorbed amount per particle depends weakly on NP concentration but increases significantly with an increase in particle size and is optimal at an intermediate salt concentration. Three different complexation mechanisms have been identified depending on the correlation between DNA and NPs in terms of geometry, chain rigidity, and electrostatic interactions: free DNA adsorption onto NP surface, DNA wrapping around NP, and NP collection on DNA chain.

Original languageEnglish
Pages (from-to)3019-3031
Number of pages13
JournalJournal of Physical Chemistry B
Volume111
Issue number11
DOIs
Publication statusPublished - Mar 22 2007

Fingerprint

chromatin
Nanoparticles
Chromatin
Compaction
DNA
deoxyribonucleic acid
nanoparticles
interactions
Particle Size
Salts
Particle size
salts
Fluorescence microscopy
Molecular Dynamics Simulation
Coulomb interactions
Complexation
Static Electricity
Transmission Electron Microscopy
Fluorescence Microscopy
rigidity

All Science Journal Classification (ASJC) codes

  • Physical and Theoretical Chemistry
  • Surfaces, Coatings and Films
  • Materials Chemistry

Cite this

Single-chain compaction of long duplex DNA by cationic nanoparticles : Modes of interaction and comparison with chromatin. / Zinchenko, Anatoly A.; Sakaue, Takahiro; Araki, Sumiko; Yoshikawa, Kenichi; Baigl, Damien.

In: Journal of Physical Chemistry B, Vol. 111, No. 11, 22.03.2007, p. 3019-3031.

Research output: Contribution to journalArticle

Zinchenko, Anatoly A. ; Sakaue, Takahiro ; Araki, Sumiko ; Yoshikawa, Kenichi ; Baigl, Damien. / Single-chain compaction of long duplex DNA by cationic nanoparticles : Modes of interaction and comparison with chromatin. In: Journal of Physical Chemistry B. 2007 ; Vol. 111, No. 11. pp. 3019-3031.
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