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Propargyl-PEG5-acid has a propargyl group at one end and an acid group at the other end. The acid can react with primary amines to form a stable amide bond, activation will be needed. The PEG units enhances solubility of the molecule in aqueous environment. The propargyl group can be linked to azide-containing biomolecules via Click Chemistry.

Alkyne-PEG5-acid may be used in the synthesis of peptide nucleic acid (PNA) oligomers that can conjugate with vitamin B₁₂ via Cu-catalyzed 1,3-dipolar cycloaddition in order to study if vitamin B₁₂ to transport PNA oligonucleotides into bacterial cells.

Propargyl-peg5 Acid is used as a reactant in the preparation of site-specific antibody-pyrrolobenzodiazepine conjugates.