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Drug binding disrupts chiral water structures in the DNA first hydration shell.

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Chiral SFG spectroscopy reveals how netropsin drug binding displaces strongly hydrogen-bonded water from DNA minor grooves. This finding advances understanding of DNA hydration and drug development targeting DNA.

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Area of Science:

  • Biophysics
  • Chemical Physics
  • Molecular Biology

Background:

  • Understanding DNA hydration is crucial for DNA biology and drug development.
  • Probing *in situ* DNA hydration changes during molecular interactions is challenging.

Purpose of the Study:

  • To investigate changes in DNA hydration structures upon drug binding using chiral-selective vibrational sum frequency generation spectroscopy (chiral SFG).
  • To elucidate the role of water in the site-specific binding of netropsin to DNA.

Main Methods:

  • Combined experimental and computational approach utilizing chiral SFG spectroscopy.
  • Analysis of spectral changes to detect water displacement and differentiate hydrogen-bonding states.

Main Results:

  • Chiral SFG successfully detected water displacement from the DNA minor groove upon netropsin binding.
  • The technique distinguished between weakly and strongly hydrogen-bonded water molecules.
  • Netropsin preferentially displaced strongly hydrogen-bonded water associated with thymine carbonyl groups.

Conclusions:

  • Chiral SFG offers mechanistic insights into DNA hydration dynamics during drug interactions.
  • Water molecules play a significant role in modulating the site-specificity of drug binding to DNA.
  • The findings hold promise for advancing DNA-targeted drug development.