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The DNA Helix01:16

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Deoxyribonucleic acid, or DNA, is the genetic material responsible for passing traits from generation to generation in all organisms and most viruses. DNA is composed of two strands of nucleotides that wind around each other to form a spring-like structure called a double helix. However, the double helix is not perfectly symmetrical. Instead, there are regularly occurring grooves in the structure. The major groove occurs where the sugar-phosphate backbones are relatively far apart. This space...
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Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...
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Analyzing and Building Nucleic Acid Structures with 3DNA
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Cation-DNA outer sphere coordination in DNA polymorphism.

Elena A Zubova1, Ivan A Strelnikov1

  • 1N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 4 Kosygin Street, Moscow 119991, Russia.

The Journal of Chemical Physics
|November 20, 2025
PubMed
Summary

DNA ion interactions influence DNA structure. Outer sphere coordination of ions is key to DNA

Area of Science:

  • Biochemistry
  • Computational Chemistry

Background:

  • DNA exists in various forms (polymorphism).
  • DNA-ion interactions are crucial for its structure and function.
  • Two main approaches describe these interactions: physical and coordination chemistry.

Purpose of the Study:

  • To investigate ion coordination in A-DNA and C-DNA forms.
  • To explore the role of solvents (ethanol-water, methanol-water) in DNA conformational changes.
  • To identify specific ion-binding sites (ionophores) involved in DNA polymorphism.

Main Methods:

  • Molecular dynamics simulations.
  • Analysis of inner- and outer-sphere ion coordination.
  • Study of DNA in low-polarity solvent mixtures.

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Main Results:

  • Outer sphere ion coordination significantly impacts DNA conformation.
  • Specific ionophores were identified for A-DNA and C-DNA complexes.
  • Solvent properties (water and methanol clusters) dictate ion accessibility and binding.
  • Methanol-water mixtures hinder ion coordination in A-DNA, promoting a shift to C-DNA.

Conclusions:

  • Counterion-DNA outer sphere coordination is critical for DNA conformational polymorphism.
  • Solvent composition directly influences ion-DNA interactions and DNA structural transitions.
  • The study elucidates the molecular mechanisms behind DNA form transitions driven by ion-solvent interactions.