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Related Experiment Video

Updated: Jul 18, 2026

Method for Labeling Transcripts in Individual Escherichia coli Cells for Single-molecule Fluorescence In Situ Hybridization Experiments
07:51

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Published on: December 21, 2017

Transcriptome analysis using fluorescence-labeled oligonucleotide.

Naohiko Shimada1, Atsushi Mahara, Takashi Sakamoto

  • 1Department of Polymer Science and Engineering, Kyoto Institute of Technology, Matsugasaki, Sakyoku, Kyoto 606-8585, Japan.

Nucleic Acids Symposium Series (2004)
|December 8, 2006
PubMed
Summary

Bispyrene-labeled 2'-O-methyl-oligoribonucleotide (OMUpy2) shows enhanced fluorescence upon hybridization with complementary RNA. This study validates OMUpy2 for transcriptome analysis in cell-free and living cell systems.

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Area of Science:

  • Molecular Biology
  • Biochemistry
  • Genomics

Background:

  • Bispyrene-labeled 2'-O-methyl-oligoribonucleotide (OMUpy2) exhibits fluorescence enhancement upon hybridization with complementary RNA.
  • This phenomenon suggests potential applications in nucleic acid detection and analysis.

Purpose of the Study:

  • To demonstrate the utility of OMUpy2 for transcriptome analysis.
  • To evaluate OMUpy2's performance in both cell-free and living cell environments.
  • To establish the detection limit of OMUpy2 for target RNA.

Main Methods:

  • Design and utilization of a micro-chamber for cell-free RNA analysis.
  • Introduction of C-OMUpy2 into cervical carcinoma cells (C4II) for in vivo monitoring.
  • Fluorescence monitoring of C-OMUpy2 in living cells post-serum stimulation.
  • Comparison of fluorescence data with Reverse Transcription Polymerase Chain Reaction (RT-PCR) results.

Main Results:

  • The detection limit for oligo-RNA in a cell-free system was determined to be approximately 15 femtomoles (fmol).
  • In living cervical carcinoma cells, fluorescence from C-OMUpy2 was observed starting 5 minutes after serum stimulation.
  • The observed fluorescence signal decreased after 20 minutes, indicating dynamic changes within the cells.
  • Results from fluorescence monitoring were consistent with those obtained from RT-PCR analysis.

Conclusions:

  • OMUpy2 demonstrates significant potential as a tool for transcriptome analysis.
  • The OMUpy2 system is effective in both cell-free and living cell settings.
  • Further development of OMUpy2 could advance RNA analysis techniques.