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Related Experiment Videos

Single-stranded nucleic acid helical secondary structure stabilized by ionic bonds: d(A(+)-G)10.

N G Dolinnaya1, J R Fresco

  • 1Department of Molecular Biology, Princeton University, NJ 08544.

Proceedings of the National Academy of Sciences of the United States of America
|October 1, 1992
PubMed
Summary

Researchers discovered a new DNA structure, d(A(+)-G)10, in homopurine oligomers. This helix forms at low pH and is stabilized by protonated adenine residues and ionic bonds, offering insights into DNA stability.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Structural Biology

Background:

  • Homopurine and homopyrimidine sequences can adopt non-B-DNA structures.
  • Protonation of DNA bases can significantly alter DNA structure and stability.
  • Understanding DNA secondary structures is crucial for comprehending genetic processes.

Purpose of the Study:

  • To identify and characterize a novel secondary structure in the homopurine oligomer d(A-G)10.
  • To investigate the factors influencing the stability of this DNA helix.
  • To elucidate the structural model and stabilizing forces of the identified helix.

Main Methods:

  • Circular Dichroism (CD) spectroscopy to analyze DNA structure and transitions.
  • UV-Vis spectroscopy (hypochromicity) to monitor base stacking and melting.

Related Experiment Videos

  • Varying pH and ionic strength to determine structural stability parameters.
  • Analysis of dinucleoside monophosphates to understand sequence-specific contributions.

    • Main Results:

    • A novel helix, d(A(+)-G)10, was identified in d(A-G)10 below pH 6, exhibiting intense CD signals.
    • Helix stability increased with decreasing pH and ionic strength, with optimal formation at pH 4.0 (Tm = 37°C).
    • The structure involves protonated adenine (dA) residues, with guanine (dG) residues external to the helix, stabilized by ionic interactions.

    Conclusions:

    • The d(A(+)-G)10 helix is an intramolecular structure stabilized by protonated dA residues and phosphate interactions.
    • This structure's stability is influenced by pH and ionic strength, with a high pKa (5.3 at 25°C).
    • The findings suggest a potential role for such protonated structures in stabilizing biologically relevant non-B-DNA conformations.