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Mapping Absolute DNA Density in Cell Nuclei using Single-molecule Localization Microscopy
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Solvent effects on charge spatial extent in DNA and implications for transfer.

Yves A Mantz1, Francesco Luigi Gervasio, Teodoro Laino

  • 1Computational Science, Department of Chemistry and Applied Biosciences, ETH Zurich, US I Campus, Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland. ymantz@phys.chem.ethz.ch

Physical Review Letters
|October 13, 2007
PubMed
Summary

Water plays a crucial role in DNA charge transport. Simulations reveal that water restructuring around adenine bases can lead to charge localization, impacting DNA

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Area of Science:

  • Computational chemistry
  • Molecular dynamics
  • Biophysics

Background:

  • Long-range charge transport in DNA is a fundamental process with implications for DNA damage and repair.
  • The precise role of the surrounding water solvent in mediating this transport remains incompletely understood.

Purpose of the Study:

  • To elucidate the role of explicit water in facilitating long-range charge transport through DNA.
  • To investigate the microscopic conditions that govern charge localization in DNA.

Main Methods:

  • State-of-the-art self-interaction corrected density-functional quantum mechanics/molecular mechanics (SIC-QM/MM) simulations.
  • Simulations performed on ionized adenine:thymine bridge models in explicit water at finite temperatures.

Main Results:

  • Charge is partially delocalized across random solvent configurations.
  • Charge localization on distinct adenine bases is observed and linked to solvation shell restructuring.

Conclusions:

  • Explicit water is demonstrated to be critical in the mechanism of long-range DNA charge transport.
  • The study reveals specific microscopic conditions that promote charge localization within DNA.