Linkers & spacers

Pepscan (now Biosynth B.V.) is part of Biosynth's Peptide Division. This page will soon be fully integrated into the Biosynth website. Visit and bookmark it.

You can find everything about unusual & non-natural amino acids here.

Linkers, also named spacers, are flexible molecules or stretch of molecules that are used to link 2 molecules of interest together (e.g.: a fluorophore to a peptide or 2 peptides). For instance the presence of a spacer > 4Å (~5 atoms) is crucial between the carboxy group of the biotin and the 1st bulky amino acid of the peptide to allow the biotin to reach the avidin binding pocket. Aliphatic spacers as well as more hydrophilic ones (e.g.: PEG) exist with a length starting from 4 atoms and can exceed 200 atoms. Linkers exceeding 60 atoms in length are generally not well defined or monodisperse. They generally comprise a population of compounds having an average length.

Depending on design and application we can insert a spacer/linker to couple a peptide to biotin, carrier proteins (KLH, BSA), fluorescent dyes or other molecules. Spacers of different lengths or polarity can be incorporated anywhere in the peptide. Spacer attachment is usually through an amide linkage but other functionalities are possible as well. A number of examples from the broad range of available linkers are listed below.

Building Block

Length of bonds

End Structure



4-aminobutyric acid (GABA)


(2-aminoethoxy) acetic acid (AEA)


5-aminovaleric acid (Ava)


6-aminohexanoic acid (Ahx)


PEG2 Spacer or AEEA

 (8-amino-3,6-dioxaoctanoic acid)


PEG3 Spacer

(12-amino-4,7,10-trioxadodecanoic acid)


PEG4 Spacer

(15-amino-4,7,10,13-tetraoxapenta-decanoic acid)


Ttds (Trioxatridecan-succinamic acid)


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