title: Single-chain compaction of long duplex DNA by cationic nanoparticles: modes of interaction and comparison with chromatin.
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.
authors: Department of Physics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan. zinchenko@ urban.env.nagoya-u.ac.jp
authors: Anatoly A
authors: AA
authors: Zinchenko
authors: Takahiro
authors: T
authors: Sakaue
authors: Sumiko
authors: S
authors: Araki
authors: Kenichi
authors: K
authors: Yoshikawa
authors: Damien
authors: D
authors: Baigl
mesh_terms: D002412:Cations / Q000737:chemistry*; D002843:Chromatin / Q000737:chemistry* / Q000648:ultrastructure*; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000648:ultrastructure*; D046529:Microscopy, Electron, Transmission; D008856:Microscopy, Fluorescence; D053758:Nanoparticles / Q000737:chemistry* / Q000648:ultrastructure*; D009690:Nucleic Acid Conformation; D010316:Particle Size
chemical_list: D002412:Cations; D002843:Chromatin; D004247:DNA