Fluorescent Labeling of Peptides

Methods for Labeling Peptides with Fluorescent Dyes

Labeling peptides with fluorescent dyes or other labels provides powerful tools for investigating biological relevant interactions like receptor-ligand-binding^,1-3 protein structures,^4-6 and enzyme activity. Fluorescence energy transfer (FRET) between a donor and an acceptor label is widely applied for such investigations. It can be determined by a number of different methods, e.g., quenching and other intensity measurements, donor or acceptor depletion kinetics, and fluorescence lifetime or emission anisotropy measurements.^3-13 A variety of enzyme substrates have been designed and used,^14-22 partially based on quenching of emission through a second label, that is eliminated through the separation of label and quencher by cleavage of substrate.

Labeled peptides can be prepared by either modifying isolated peptides or by incorporating the label during solid-phase synthesis. Three strategies are used to label peptides with dyes:

• Labeling during synthesis of peptide. Dyes that are not damaged by unblocking procedures are incorporated onto the amino terminus of the peptide chain.
• Synthetic peptides can be covalently modified on specific residues and labels incorporated following synthesis.
• Synthetic peptides may be covalently labeled by amine- or thiolreactive protein labels.

Fluorophores can be conjugated to the N-terminus of a resin-bound peptide before other protecting groups are removed and the labeled peptide is released from the resin. Amine-reactive fluorophores are used in about five-fold molar excess relative to the amines of the immobilized peptide. Reactive fluorescein, sulforhodamine B, tetramethylrhodamine, coumarin, eosin, dabcyl, dabsyl, or biotin labels, as well as several of our new atto labels, should be stable enough to resist the harsh deprotection conditions. Dabcyl has been frequently used as quencher. Another possibility is the use of fluorescence or chromophore labeled amino acids to incorporate labels at specific sites of peptides.

Labeling can also be achieved indirectly by using a biotinylated amino acid. If, for example, Fmoc-Lys(biotinyl)-OH (Product No. 73749) is used in peptide synthesis, the biotin group enables specific binding of streptavidin or avidin-conjugate to that site. A variety of fluorophores are available as (strept)avidin conjugates.

Following the routine synthesis procedure, peptides can also be labeled by practically all labels used for protein labeling. This means mainly amine reactive labels, or thiol reactive labels, if a cystein has been used for the peptide. Whereas the common standard procedures for protein labeling are based on aqueous solutions of target proteins, labeling peptides in organic solvents like DMSO or DMF requires specific modifications. Use of triethylamine can be added to ensure that the target amino groups of the peptide are deprotonated, which is required for the labeling procedure.