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Related Experiment Video

Updated: Jan 9, 2026

Split Hybridization Probe Utilizing a DNA Fluorescent Light-up Aptamer as a Signal Reporter for Sequence-Specific Nucleic Acid Analysis

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Detecting tRNA modifications with fluorescent-labeled DNA probes.

Kaushani Misra¹, Mackenzie Dillenbeck¹, Cailyn P Leo¹

¹Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY.

Methods in Enzymology

|December 3, 2025

Summary

This summary is machine-generated.

Researchers developed safer, sensitive fluorescent DNA probes to detect transfer RNA (tRNA) modifications. These methods offer an alternative to radioactive labeling for studying tRNA processing and abundance.

Keywords:

Fluorescent probe Modification Northern blot Primer extension TRNA

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Robust 3D DNA FISH Using Directly Labeled Probes

Robust 3D DNA FISH Using Directly Labeled Probes

Published on: August 15, 2013

Area of Science:

Molecular Biology
Biochemistry
Genetics

Background:

Transfer RNAs (tRNAs) are crucial molecules that undergo numerous post-transcriptional modifications.
These modifications, affecting nucleobases and sugar moieties, are vital for tRNA function.
Detecting these modifications is essential for understanding gene expression and cellular processes.

Purpose of the Study:

To introduce novel, non-radioactive methods for detecting tRNA modifications.
To provide sensitive and high-resolution techniques for analyzing tRNA modification status.
To offer a safer and more convenient alternative to existing radioactive labeling methods.

Main Methods:

Northern blotting combined with differential fluorescent probe hybridization.
Primer extension assay using viral reverse transcriptase to detect modification-induced blocks.
Utilizing fluorescently labeled DNA oligonucleotide probes for detection.

Main Results:

Fluorescent probes demonstrate comparable sensitivity to radioactive probes.
The Northern blot method allows assessment of tRNA processing and abundance alongside modification detection.
The primer extension method provides quantitative, nucleotide-resolution data on tRNA modification status.
Fluorescent probes offer stability for long-term storage and reusability.

Conclusions:

Fluorescence-based detection methods are a convenient, safe, and effective alternative to radioactive labeling for studying tRNA modifications.
These techniques enhance the study of tRNA modification impacts on tRNA processing, abundance, and function.
The described methods offer high sensitivity and resolution for molecular biology research.