Dye to Peptide Conjugation

Peptides are short-chain amino acids that perform numerous functions as chemical messengers, hormones, cellular mediators, highly specific stimulators, inhibitors, and novel treatments for various diseases, including Alzheimer's and cancer. Due to the emerging solid-phase peptide synthesis technologies, synthetic peptides have now been widely used in biochemistry, molecular biology, and pharmaceutical areas. Dye-labeled peptides are powerful tools to investigate the cellular structure, analyze receptor-ligand or protein-protein interactions, study cellular transport, and measure enzymatic activity via FRET analysis.

Fig. 1

Dye-labeled peptides

Tide Fluor™ Dyes

Our Tide Fluor™ dyes are superior peptide labeling dyes with improved characteristics for labeling and detection. The enhanced brightness, photostability, and water solubility of Tide Fluor™ dyes significantly outperform classic peptide labeling dyes and Alexa Fluor^® dyes.

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Tide Quencher™ Dyes

Tide Quencher™ dyes are non-fluorescent acceptors for synthesizing longer wavelength FRET probes. Displaying excellent FRET efficiency, Tide Quencher™ dyes are designed to pair with corresponding Tide Fluor™ dyes to guarantee optimum FRET analysis results.

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Classic Peptide Labeling Dyes

AAT Bioquest offers classic peptide labeling dyes in various chemical reactivities and conjugated to peptide substrates for enzyme activity assays. Choose from our comprehensive portfolio of:

FRET Donor/Acceptor Dyes

In addition to Tide Fluor™ and Tide Quencher™ FRET pairs, we offer various combinations of classic donor and acceptor dyes. Develop FRET peptides for measuring enzyme activity, receptor-ligand interactions, colocalization studies, and much more.

Peptide Labeling Strategies

Labeled peptides can be prepared by either modifying isolated peptides or by incorporating the label during solid-phase synthesis. Common strategies for labeling peptides with fluorophores include:

Labeling during peptide synthesis - dyes that can withstand unblocking procedures can be incorporated onto the amino terminus of the peptide chain.
N-terminal modification: N-terminus refers to the free amine group (-NH2) at the start of a protein or polypeptide chain. It can be modified co- or post-translationally using amine-reactive succinimidyl ester fluorophores.
Lysine residues: the ε-amino group of lysine residues can be modified using amine-reactive succinimidyl ester fluorophores.
C-terminal modification: C-terminus refers to the carboxyl group (-COOH) at the end of a protein or polypeptide chain. It can be modified post-translationally, typically after C-terminal amidation.
Thiol-reactive protein labels can covalently label synthetic peptides if cysteine is available on the peptide chain.
Unnatural amino acids could be incorporated in peptide chains during synthesis and then labeled with dyes or other probes through bioorthogonal reactions, for example, azide and alkyne-based reactions and ketone-aldehyde reactions.

Document: 01.0090.211015r1

Last updated Fri Oct 10 2025