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Local dynamics coupled to hydration water determines DNA-sequence-dependent deformability.

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DNA flexibility depends on base pair step dynamics and hydration. Simulating DNA dynamics reveals sequence-specific movements influencing water interactions and DNA deformability above a transition temperature.

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Area of Science:

  • Biophysics
  • Computational Biology
  • Structural Biology

Background:

  • DNA deformability and dynamics are crucial for biological functions.
  • Hydration water plays a significant role in DNA structural transitions.
  • Understanding sequence-dependent DNA dynamics is key to predicting its behavior.

Purpose of the Study:

  • To investigate the sequence-dependent dynamics of hydrated DNA dodecamers.
  • To correlate DNA base pair step dynamics with hydration water interactions.
  • To elucidate the relationship between DNA deformability and local dynamics.

Main Methods:

  • Molecular dynamics (MD) simulations were performed on two DNA dodecamers with differing flexibility.
  • Quasielastic neutron scattering (QENS) experiments were used to probe DNA dynamics.
  • Analysis focused on dynamics above the observed dynamical transition temperature (200-240 K).

Main Results:

  • Both rigid (AATT) and flexible (TTAA) DNA dodecamers showed a dynamical transition around 200-240 K.
  • The AATT sequence exhibited smaller fluctuation amplitude and longer relaxation times compared to TTAA.
  • Sequence-dependent DNA base pair step dynamics were observed above the transition temperature and correlated with hydrogen bond breaking with water.

Conclusions:

  • DNA deformability is intrinsically linked to the local dynamics of base pair steps.
  • These DNA dynamics are coupled to the behavior of hydration water in the minor groove.
  • The AT base pair step is kinetically more stable than the TA step, influencing overall DNA flexibility.