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Updated: Jul 18, 2025

RNA Secondary Structure Prediction Using High-throughput SHAPE
Published on: May 31, 2013
TFOFinder: Python program for identifying purine-only double-stranded stretches in the predicted secondary
Atara Neugroschl1, Irina E Catrina2
1Department of Chemistry and Biochemistry, Stern College for Women, Yeshiva University, New York, New York, United States of America.
Researchers developed TFOFinder, a Python tool to identify RNA triplex target sites for novel nucleic acid probes. This enables targeted gene expression modulation and RNA imaging in biological research.
Area of Science:
- Molecular Biology
- Bioinformatics
- RNA Therapeutics
Background:
- Nucleic acid probes are essential for molecular biology techniques like PCR and gene expression analysis.
- Triplex-forming oligonucleotides (TFOs) offer enhanced selectivity and sensitivity for targeting RNA, with applications in cellular imaging and antiviral therapies.
- Existing tools for identifying triplex target sites (TTS) primarily focus on DNA, lacking capabilities for structured RNAs.
Purpose of the Study:
- To introduce TFOFinder, a novel Python program for identifying intramolecular purine-rich RNA regions suitable for parallel triple helix formation.
- To enable the design of corresponding TFOs for targeting structured RNAs.
- To analyze the potential for triplex formation in RNA transcripts across a whole genome and transcriptome.
Main Methods:
- Development of the TFOFinder Python program to identify potential triplex target sites (TTS) in RNA.
- Genome- and transcriptome-wide analysis of TTS in Drosophila melanogaster.
- Utilized minimization algorithms to predict RNA secondary structures and assess TTS accessibility for triple helix formation.
Main Results:
- TFOFinder identified 123 unique transcripts in Drosophila melanogaster with potential for forming 12-purine long triplexes containing at least one guanine.
- Secondary structure prediction revealed that 79% (97 out of 123) of these transcripts are predicted to form at least one TTS for parallel triple helix formation.
- Relaxing search parameters (probe length, allowing inversions/bulges) increased the number of identified potential purine TTS.
Conclusions:
- TFOFinder successfully identifies potential triplex-forming regions in structured RNAs, facilitating the design of novel nucleic acid probes.
- The findings support the potential of modified triplex-forming probes for advanced applications like live imaging of endogenous RNA targets and targeted inhibition of translation.
- This tool opens new avenues for RNA-based therapeutics and diagnostics by enabling precise targeting of structured RNA elements.
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