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Bicyclo-DNA: a Hoogsteen-selective pairing system

M Bolli1, J C Litten, R Schütz

  • 1Institut für Organische Chemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.

Chemistry & Biology
|March 1, 1996
PubMed
Summary

Modifying the DNA backbone with bicyclo-DNA analogs influences base-pairing preferences, favoring Hoogsteen and reversed Hoogsteen modes. This highlights the backbone

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Area of Science:

  • Molecular Biology
  • Biochemistry
  • Structural Biology

Background:

  • Natural nucleic acids (DNA and RNA) form diverse structures beyond the standard double helix.
  • Base pairing preferences are influenced by base sequence, solvent conditions, and sugar-phosphate backbone flexibility.
  • Understanding the backbone's role is key to predicting DNA structure and function.

Purpose of the Study:

  • To investigate the role of the DNA backbone in nucleic acid complex formation.
  • To design and study DNA analogs with modified backbone structures.
  • To determine how backbone modifications affect base-pairing preferences and structural stability.

Main Methods:

  • Design and synthesis of bicyclo-DNA analogs with fixed backbone torsion angles.
  • Analysis of duplex formation between bicyclo-DNA and natural DNA sequences.
  • Characterization of base-pairing modes (e.g., Watson-Crick, Hoogsteen) and strand orientation.

Main Results:

  • Bicyclo-DNA, with a fixed gamma torsion angle, deviates from B-DNA conformation.
  • This analog preferentially forms A-T and G-C+ base pairs via Hoogsteen and reversed Hoogsteen modes.
  • Base-pair formation is highly selective, though strand orientation in the duplex shows degeneracy.

Conclusions:

  • DNA backbone flexibility and orientation significantly impact base-pairing mode selection.
  • Modifications to the DNA backbone can alter the relative stability of duplex and triplex structures.
  • These findings offer insights into the structural plasticity of nucleic acids.

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