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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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Optimizing the Genetic Incorporation of Chemical Probes into GPCRs for Photo-crosslinking Mapping and Bioorthogonal Chemistry in Live Mammalian Cells

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Fluorogenic Peptide Aptamer Generated Using Bioorthogonal cDNA Display Technology for Cellular Imaging of Heat Shock

Takanori Uzawa^1,2, Seiichi Tada¹, Chinmay Phadke^1,3

¹Emergent Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science, Wako, Saitama, Japan.

Chembiochem : a European Journal of Chemical Biology

|April 25, 2026

Summary

Researchers developed self-reporting fluorogenic peptide probes using cDNA display to detect heat shock protein 90α (Hsp90α). These probes offer a compact alternative to antibodies for bioimaging and diagnostics.

Keywords:

aptamers cDNA display fluorescent probes heat shock protein 90α (Hsp90α)intracellular imaging

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Area of Science:

Biochemistry
Molecular Biology
Biotechnology

Background:

Fluorogenic probes enable rapid detection and bioimaging without separation.
Antibody probes have limitations including size and accessibility.
Fluorogenic peptide aptamers present a compact, synthesizable alternative.

Purpose of the Study:

To develop a method for preparing fluorophore-conjugated peptide libraries using cDNA display.
To select fluorogenic peptides targeting heat shock protein 90α (Hsp90α).
To evaluate the selected peptides as probes for intracellular Hsp90α detection.

Main Methods:

Utilized cDNA display for library preparation and selection.
Employed an environmentally sensitive fluorophore (4-DMN) as a solvatochromic reporter.
Tested selected peptide probes against Hsp90α and Hsp70 in vitro and in fixed cells.

Main Results:

Successfully selected a fluorogenic peptide (Peptide2) that enhances fluorescence in the presence of Hsp90α.
Peptide2 showed minimal response to the homologous Hsp70.
Intracellular fluorescence patterns from Peptide2 partially overlapped with anti-Hsp90α antibody staining, indicating Hsp90α detection.

Conclusions:

Established a proof of concept for generating target-responsive, self-reporting peptide probes via bioorthogonal cDNA display.
Demonstrated the potential of Peptide2 for detecting intracellular Hsp90α signals.
Highlighted potential differences in epitope and intracellular accessibility compared to antibody probes.