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Related Experiment Video

Updated: May 22, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

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Published on: April 26, 2013

Triplexator: detecting nucleic acid triple helices in genomic and transcriptomic data.

Fabian A Buske1, Denis C Bauer, John S Mattick

  • 1Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072 QLD, Australia.

Genome Research
|May 3, 2012
PubMed
Summary

DNA triple helix formation targets specific genomic sites for gene therapy and regulation. Triplexator software identifies these sites and reveals RNA

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Double-stranded DNA can form triple helices by incorporating a third nucleotide strand into the major groove.
  • This sequence-specific interaction is valuable for targeting genomic loci in biotechnology and gene therapy.
  • Computational studies suggest widespread natural occurrence of triplex target sites, particularly in gene promoters.

Purpose of the Study:

  • To develop a computational framework, Triplexator, integrating all aspects of DNA triple helix formation.
  • To investigate the in vivo role of triplexes in gene regulation and biotechnological applications.
  • To identify sequences capable of forming triplexes and their target sites.

Main Methods:

  • Development of Triplexator, a computational framework for analyzing triplex formation.
  • Analysis of chromatin-associated RNAs for triplex-forming sequence features.
  • Screening of mammalian genomes for high-affinity triplex target sites.

Main Results:

  • Chromatin-associated RNAs show a higher-than-random fraction of triplex-forming sequences, suggesting a role in gene regulation.
  • Hundreds of human genes identified with promoter sequences predicted to form intramolecular triplexes, indicating potential feedback regulation.
  • Triplex formation provides a resolution of approximately 1300 nucleotides for specific genomic locus targeting.

Conclusions:

  • Triplexator is the first framework to comprehensively analyze DNA triple helix formation.
  • Evidence suggests a role for RNA-mediated triplex formation in gene regulation.
  • Triplex formation is a viable strategy for specific genomic targeting in biotechnological applications.