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Nina Kasyanenko1, Bolorkhuu Khansetsen1, Andrey Baryshev1

  • 1Department of Physics, Saint-Petersburg State University, 199034 Saint Petersburg, Russia.

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|January 10, 2026
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Changes in DNA conformation due to pH shifts affect its persistent length and volume. These alterations, driven by base protonation/deprotonation, impact DNA stability and hydrogen bonds without initially disrupting base stacking.

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Physical Chemistry

Background:

  • The native conformation of DNA is crucial for its biological functions.
  • Understanding DNA's response to environmental factors like pH is essential for molecular studies.

Purpose of the Study:

  • To investigate alterations in DNA's native conformation induced by pH changes in alkaline and acidic ranges.
  • To elucidate the relationship between pH-induced charge changes on DNA bases and macromolecular properties.

Main Methods:

  • Low gradient viscometry
  • Flow birefringence
  • Spectrophotometry (absorption spectra)

Main Results:

  • Protonation and deprotonation of nitrogen bases alter DNA's persistent length.
  • Changes in persistent length primarily dictate the DNA coil's volume changes.
  • Additional charges on DNA bases are not shielded by counterions, affecting pK values with ionic strength.
  • Hydrogen bonds weaken with base charging, but stacking interactions remain intact initially.

Conclusions:

  • DNA's persistent length and coil volume are sensitive to pH-induced base modifications.
  • The stability of the DNA double helix is linked to its equilibrium rigidity.
  • Initial pH-induced changes affect hydrogen bonds before significantly impacting base stacking interactions.