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Parallel and antiparallel A*A-T intramolecular triple helices

C Dagneaux1, H Gousset, A K Shchyolkina

  • 1Laboratoire CSSB - URA CNRS 1430, UFR de Santé-Médecine-Biologie-Humaine, Université Paris XIII, Bobigny, France.

Nucleic Acids Research
|November 15, 1996
PubMed
Summary

Researchers created intramolecular triple helices using linked oligonucleotides, demonstrating distinct antiparallel and parallel structures. Spectroscopic analysis confirmed their existence and intramolecular nature, revealing differences in stability and sugar conformations between the two triplexes.

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Structural Chemistry

Background:

  • DNA triple helices are complex nucleic acid structures with potential applications in nanotechnology and therapeutics.
  • Understanding the formation and stability of intramolecular triple helices is crucial for their design and application.
  • Previous studies have explored intermolecular triple helix formation, but intramolecular variants present unique structural challenges.

Purpose of the Study:

  • To synthesize and characterize intramolecular DNA triple helices with defined third strand orientations.
  • To investigate the structural and stability differences between antiparallel and parallel intramolecular triple helices.
  • To elucidate the sugar pucker conformations and base-pairing interactions within these novel DNA structures.

Main Methods:

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  • Oligonucleotide synthesis incorporating non-nucleotide linkers to facilitate intramolecular folding.
  • Spectroscopic techniques including FTIR, UV, and fluorescence spectroscopy to confirm triple helix formation and analyze melting temperatures.
  • Fourier Transform Infrared (FTIR) spectroscopy for sugar conformation analysis and molecular modeling for structural insights.

Main Results:

  • Successfully formed intramolecular antiparallel (apA*A-T) and parallel (pA*A-T) triple helices from folded oligonucleotides.
  • Spectroscopic data confirmed the intramolecular nature of the triple helices, independent of concentration.
  • The antiparallel triplex exhibited slightly higher stability (ΔTm = 6°C) and exclusively South-type sugar conformations.
  • The parallel triplex showed a mix of South- and North-type sugar conformations, with specific assignments for thymidine and adenosine strands.
  • Experimental and modeling data supported a reverse-Hoogsteen-like pairing for the antiparallel triplex.

Conclusions:

  • Intramolecular triple helices with controlled third strand orientation can be successfully constructed.
  • Distinct structural features, including sugar conformations and stability, differentiate antiparallel and parallel triplexes.
  • The findings provide valuable insights into the structural plasticity of DNA and the formation of higher-order nucleic acid structures.