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Base pair compositional variability influences DNA structural stability and tunes hydration thermodynamics and

Brataraj Ghosh1, Sarbajit Layek1, Dhananjay Bhattacharyya2

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DNA hydration and deformability are key to biological processes. This study reveals how DNA sequence and structure influence water dynamics and thermodynamics, impacting gene expression and packaging.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Structural Biology

Background:

  • DNA deformability and differential hydration significantly impact biological functions like genetic material packaging and gene expression.
  • The precise relationship between DNA structure, hydration, and dynamics remains incompletely understood.

Purpose of the Study:

  • To investigate the dynamic and thermodynamic responses of local DNA hydration across various base pair sequences.
  • To elucidate how DNA sequence, conformation, and groove dimensions influence hydration characteristics.

Main Methods:

  • In silico sampling and in-house analyses were employed to study DNA conformational propensities and hydration.
  • Calculations of excess (pair) entropy and application of the Rosenfeld approximation were used to assess hydration and water molecule diffusivity.

Main Results:

  • The transition from A-form to B-form DNA involves lengthwise structural deformation.
  • Intermittent CG base pairs in AT sequences dynamically affect the surrounding hydration layer.
  • A-conformations exhibit higher hydration water content compared to B-conformations.
  • Water molecule diffusivity is lowest in the minor groove of the canonical B-conformation.

Conclusions:

  • DNA structure, base pair composition, and conformation collectively influence local hydration.
  • These hydration characteristics are critical determinants for various biological processes involving DNA.