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Labeling DNA Probes

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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.
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Preparation and In Vivo Use of an Activity-based Probe for N-acylethanolamine Acid Amidase

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Published on: November 23, 2016

Peptidic Probes to Capture Enzyme Activity Using Novel Solid Phase Compatible Warheads.

Valerio Cataldi¹, Nikita Ostrovitsa¹, Fangyuan Cao²

¹School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, Pearse St., Dublin 152-160, Ireland.

ACS Chemical Biology

|December 18, 2025

Summary

This summary is machine-generated.

We developed novel peptidic probes using vinyl methyl ester (VME) amino acids for robust activity-based protein profiling. These probes show high reactivity and selectivity for Otubain 1 (OTUB1), a key enzyme in DNA repair and cancer.

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Kinetic Screening of Nuclease Activity using Nucleic Acid Probes

Kinetic Screening of Nuclease Activity using Nucleic Acid Probes

Published on: November 1, 2019

Area of Science:

Biochemistry
Chemical Biology
Proteomics

Background:

Activity-based probes (ABPs) are essential for studying enzyme activity.
Existing ABPs often face challenges with complex synthesis and stability in biological systems.
Deubiquitinating enzyme Otubain 1 (OTUB1) is crucial in DNA repair and immunity and is a cancer biomarker.

Purpose of the Study:

To synthesize and evaluate novel peptidic probes incorporating a vinyl methyl ester (VME) motif.
To assess the reactivity and selectivity of these VME-based probes against OTUB1.
To establish a robust method for creating selective covalent tools for cysteine proteases.

Main Methods:

Synthesis of a novel amino acid bearing a vinyl methyl ester (VME) group, compatible with solid-phase peptide synthesis (SPPS).
Incorporation of the VME motif into novel peptidic probes.
Investigation of labeling activity against Otubain 1 (OTUB1).

Main Results:

Successful synthesis of VME-bearing amino acids compatible with SPPS.
Development of novel peptidic probes featuring the VME motif.
Demonstrated high reactivity and selectivity of a VME-based probe toward OTUB1.

Conclusions:

The VME motif provides a robust and stable warhead for activity-based probes.
Peptidic VME probes are effective tools for selectively targeting cysteine proteases like OTUB1.
This approach offers significant potential for developing advanced covalent tools for biochemical research and diagnostics.