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Related Experiment Videos

Acidic domains around nucleic acids.

G Lamm1, G R Pack

  • 1Department of Biomedical Sciences, University of Illinois College of Medicine, Rockford 61107.

Proceedings of the National Academy of Sciences of the United States of America
|November 1, 1990
PubMed
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This study maps high hydrogen ion concentration near DNA, revealing acidic pockets in grooves. These acidic DNA sites may explain interactions with carcinogens and proteins.

Area of Science:

  • Biophysical Chemistry
  • Computational Biology
  • Molecular Biophysics

Background:

  • The local hydrogen ion concentration (H+) near DNA influences molecular interactions.
  • Understanding these acidic microenvironments is crucial for DNA-related processes.

Purpose of the Study:

  • To map the distribution of hydrogen ion concentration around DNA.
  • To investigate potential acidic domains within DNA grooves.

Main Methods:

  • Utilized the Poisson-Boltzmann approximation to model H+ concentration.
  • Simulated DNA in a buffer solution with specific cation concentrations (Tris and Mg2+) at pH 7.5.

Main Results:

  • Identified three regions of high H+ concentration (>10 microM) near DNA.

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  • These acidic domains were located in the minor groove and at specific sites within the major groove (near guanine and cytosine bases).

    • Conclusions:

    • The predicted acidic domains correlate with known binding sites of DNA-damaging chemical carcinogens.
    • These localized H+ concentrations may play a role in DNA interactions with carcinogens, proteins, and other molecules.