Should I add a spacer between the peptide chain and a dye label?
When attach a dye label onto the peptide, it is suggested to insert a spacer between the peptide chain and the ligand. This will minimize the interference in the folding of the peptide and/or its binding to the receptor. However, in some cases the spacer is not needed or should not be added. For example, when studying protein folding, the fluorescent dyes are attached to specific amino acids at specific positions to study how far or close they are in the folded structure, by quantifying fluorescence transfer. Generally, for protein/peptide binding or targeting studies, a spacer is recommended. For purely structural studies, a spacer is not required and can often hinder the response.
