How do you introduce the dye when making fluorescently-labeled peptides?

When making fluorescently-labeled peptides, we always suggest that you add a spacer such as Aminoethyloxy-ethyloxy-acetic acid (Aeea) or Amino caproic acid (Aca) between the peptide and the dye molecule. This helps to minimize the possibility that the dye may affect peptide folding and/or binding to its receptors. If a dye is incorporated as an isothiocyanate linkage (fluorescein isothiocyanate, FITC) to an N-terminal residue, it is imperative to use a linker such as β-Ala, Aca or Aeea to avoid Edman Degradation of the dye and first amino acid from the peptide.

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