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Changes in Microenvironment Modulate the B- to A-DNA Transition.

Hong Zhang1, Haohao Fu1, Xueguang Shao1,2,3

  • 1Research Center for Analytical Sciences, College of Chemistry , Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition , Tianjin 300071 , China.

Journal of Chemical Information and Modeling
|February 16, 2019
PubMed
Summary
This summary is machine-generated.

Ethanol concentration influences DNA structure, causing a shift from B-DNA to A-DNA. Cation movement and reduced water mobility in the DNA microenvironment drive this conformational change.

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Computational Chemistry

Background:

  • DNA conformation (B-DNA and A-DNA) is sensitive to solution properties like salt and ethanol.
  • Understanding microenvironmental effects on DNA transitions is crucial but challenging.
  • Previous studies broadly explored environmental impacts on DNA, yet an intuitive picture is lacking.

Purpose of the Study:

  • To analyze the chemical equilibrium of the B- to A-DNA transition at critical concentrations.
  • To provide an intuitive picture of DNA's response to environmental changes.
  • To investigate microenvironmental effects on DNA conformational transitions using simulations.

Main Methods:

  • Employed explicit-solvent simulations to study DNA conformational transitions.
  • Performed free-energy calculations for the B- to A-DNA transition.
  • Analyzed cation distribution and water molecule mobility in varying ethanol concentrations.

Main Results:

  • Increasing ethanol concentration shifts DNA from the B-form to the more stable A-form.
  • A chemical equilibrium between B- and A-DNA was observed at 60% ethanol, indicating reversibility.
  • Cations showed increased affinity for the DNA backbone, and water molecule mobility decreased with higher ethanol levels.

Conclusions:

  • The study provides a free-energy perspective on DNA microenvironments and conformational changes.
  • Cation redistribution and altered water dynamics are key factors in ethanol-induced B- to A-DNA transitions.
  • Findings offer insights into how environmental factors modulate DNA structure at a molecular level.