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Glycosaminoglycans (GAGs) like chondroitin sulfate (CS) and heparan sulfate (HS) are synthesized on the tetrasaccharide linkage region, GlcAβ1-3Galβ1-3Galβ1-4Xylβ1-O-Ser, of proteoglycans. The Xyl can be modified by 2-O-phosphate in both CS and HS, whereas the Gal residues can be sulfated at C-4 and/or C-6 in CS but not in HS. To study the roles of these modifications, monoclonal antibodies were developed against linkage glycopeptides of shark cartilage CS proteoglycans, and one was characterized in detail. This antibody bound hexa- and pentasaccharide-peptides more strongly than tetrasaccharide-peptides, suggesting the importance of GalNAc. It did not react to the CS linkage region modified by 4-O-sulfation. Its reactivity was not affected by treatment with chondro-4-sulfatase or alkaline phosphatase. The results of an ELISA using various proteoglycans and glycopeptides with different modifications suggested the recognition of 6-O-sulfate on the GalNAc and/or Gal residues. Treatments with exopeptidases did not affect the reactivity of the hexasaccharide-peptide fraction, whereas weak alkali to cleave the Xyl-Ser linkage completely abolished the binding activity, suggesting the importance of the Xy-Ser linkage for the binding. Furthermore, the antibody stained wild-type CHO cells, but not mutant cells deficient in xylosyltransferase required for the synthesis of the linkage region. These results suggest that the antibody recognizes the structure GalNAc-GlcA-Gal-Gal-Xyl-Ser that is modified by 6-O-sulfation on GalNAc and/or Gal. The antibody will be a useful tool for investigating the significance of the linkage region in the biosynthesis and/or intracellular transport of different GAG chains.