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Demonstration of the DNA Fiber Assay for Investigating DNA Damage and Repair Dynamics Induced by Nanoparticles
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Crowding by anionic nanoparticles causes DNA double-strand instability and compaction.

Anatoly Zinchenko1, Kanta Tsumoto, Shizuaki Murata

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Anionic nanoparticles compact DNA from a coil to a globule, decreasing its melting temperature. This DNA structural transition occurs with negatively charged silica nanoparticles of varying sizes.

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Area of Science:

  • Biophysics
  • Materials Science
  • Nanotechnology

Background:

  • DNA structural transitions are well-documented with cationic polymers and neutral polymers.
  • Limited knowledge exists regarding DNA interactions with like-charge species.

Purpose of the Study:

  • Investigate DNA structural changes induced by anionic nanoparticles.
  • Explore the effect of nanoparticle size on DNA conformation and stability.

Main Methods:

  • Single-molecule DNA fluorescent microscopy to monitor DNA conformational dynamics.
  • Spectroscopic methods to analyze changes in DNA secondary structure.

Main Results:

  • Anionic silica nanoparticles induced DNA compaction from a coil to a globule.
  • DNA melting temperature decreased upon nanoparticle interaction.
  • DNA formed toroidal condensates (20-30 nm diameters).
  • Smaller nanoparticles initiated compaction at lower concentrations.

Conclusions:

  • Anionic nanoparticles can induce significant DNA structural transitions.
  • Nanoparticle size influences the concentration required for DNA collapse.
  • The exclusion volume for DNA collapse is consistent across nanoparticle types.