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Labeling DNA Probes

Labeling DNA Probes

DNA probes are fragments of DNA labeled with a reporter tag to enable their detection or purification. The resulting labeled DNA probes can then hybridize to target nucleic acid sequences through complementary base-pairing, and may be used to recover or identify these regions.
Radioisotopes, fluorophores, or small molecule binding partners like biotin or digoxigenin, are the most widely used reporter tags for labeling DNA probes. These labels can be attached to the probe DNA molecule via...

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Related Experiment Video

Updated: Jun 15, 2026

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

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

Published on: July 8, 2025

Probing the transition state for nucleic acid hybridization using phi-value analysis.

Jandi Kim¹, Jong-Shik Shin

¹Department of Biotechnology, Yonsei University, Shinchon-Dong 134, Seodaemun-Gu, Seoul 120-749, Korea.

|March 10, 2010

Summary

This summary is machine-generated.

This study reveals that the native secondary structure remains intact during RNA hybridization, forming a nativelike transition state. This finding offers new insights into the physical mechanisms of gene silencing by small RNAs like microRNA and siRNA.

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Nanomanipulation of Single RNA Molecules by Optical Tweezers

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Nanomanipulation of Single RNA Molecules by Optical Tweezers

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Published on: August 20, 2014

Area of Science:

Molecular Biology
Biophysics
Biochemistry

Background:

Noncoding RNAs, including microRNA and small interfering RNA (siRNA), regulate gene expression through mRNA hybridization.
The physical basis and transition-state structure of nucleic acid hybridization remain poorly understood.

Purpose of the Study:

To quantitatively analyze the relationship between secondary structure stability and activation free energy in RNA hybridization.
To elucidate the transition-state structure during hybridization of structured nucleic acids.

Main Methods:

Application of transition-state theory, inspired by protein folding phi-value analysis.
Monitoring hybridization reaction kinetics using a single fluorophore under pseudo-steady-state conditions.
Examining the salt dependence of hybridization kinetics.

Main Results:

Phi-value analysis indicated that the native secondary structure is preserved in the transition state.
Salt dependence studies confirmed a nativelike transition state, with minimal changes in associated sodium ions.
The hybridization process involves a transition state forming a nucleation complex, followed by sequential displacement of base pairings.

Conclusions:

The study proposes a mechanism for structured nucleic acid hybridization involving a nativelike transition state.
This mechanism provides physical insights into small RNA-mediated gene silencing and informs siRNA design.