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Phosphorothioate oligonucleotide-directed triple helix formation

J G Hacia1, B J Wold, P B Dervan

  • 1Division of Biology, California Institute of Technology, Pasadena 91125.

Biochemistry
|May 10, 1994
PubMed
Summary

Phosphorothioate oligodeoxyribonucleotides can form triple-helical DNA complexes similar to natural DNA when purine-rich. Pyrimidine-rich versions, however, show no measurable binding affinity.

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Area of Science:

  • Oligonucleotide chemistry
  • Molecular biology
  • Biochemistry

Background:

  • Phosphorothioate oligodeoxyribonucleotides are modified nucleic acids with potential therapeutic applications.
  • Triple helix formation is a DNA structure where a third strand binds to a double helix.

Purpose of the Study:

  • To investigate the DNA binding capabilities of phosphorothioate oligodeoxyribonucleotides in triple helix formation.
  • To compare the binding affinities of purine-rich and pyrimidine-rich phosphorothioate oligonucleotides.

Main Methods:

  • Synthesis of purine-rich and pyrimidine-rich phosphorothioate oligodeoxyribonucleotides with varying linkage stereochemistry.
  • Testing the ability of these modified oligonucleotides to form triple-helical complexes with double-helical DNA.
  • Affinity measurements of triple helix complex formation.

Main Results:

  • Purine-rich phosphorothioate oligonucleotides, both diastereomeric mixtures and stereoregular (all RP) types, formed triple-helical complexes with DNA.
  • The binding affinities of these purine-rich phosphorothioates were comparable to natural phosphodiester oligonucleotides.
  • Pyrimidine-rich phosphorothioate oligonucleotides, regardless of linkage type, did not exhibit measurable binding affinity to double-helical DNA.

Conclusions:

  • The sequence composition (purine-rich vs. pyrimidine-rich) is critical for phosphorothioate oligonucleotide binding in triple helix formation.
  • Stereochemistry of phosphorothioate linkages does not impede binding for purine-rich sequences.
  • Findings impact the design of oligonucleotide-based drugs and the understanding of triple helix structures.

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