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Heparin and heparan sulfate (HS) glycosaminoglycans are linear sulfated polysaccharides located on cell-surface membranes and in extracellular matrices in virtually all animal tissues. Heparin and HS have been implicated in cell-biological processes, cell adhesion and regulation of enzymatic catalysis (1). HS chains have been shown to interact with a variety of growth factors, chemokines, ECM proteins, and enzymes, including antithrombin, fibroblast growth factors and vascular endothelial growth factor (2). Heparin has been widely used as an anticoagulant drug (3,4), and it has been shown to regulate cellular process by binding, stabilizing and activating various growth factors (5).

Heparin/HS chains consist of repeating disaccharide units of GlcA╬▓1-4GlcNAc╬▒1-4 with poly-disperse sulfation, N-acetylation and uronosyl epimerization. Repeating disaccharide residues varying between one to three sulfate groups exist in heparin/HS which results in domains of high and low sulfation. During biosynthesis incomplete sulfation by transferases leads to the creation of more structurally complex polysaccharides than that of other glycan classes. The structural elucidation of such complex and diverse polysaccharides is an exceptionally challenging task and cannot be accomplished without enzyme tools.

Heparin Lyase enzymes, also called Heparinases, are enzymes that cleave the glycosidic linkage between hexosamines and uronic acids and are known to cleave heparin and HS chains selectively, via an elimination mechanism. Heparinase enzymes create a double bond on the non-reducing end of the uronic acid that absorbs at 232 nm and can be used for the detection of oligosaccharide and disaccharide products. Three Heparinase enzymes are available: Bacteroides Heparinase I (NEB #P0735), Heparinase II (NEB #P0736), and Heparinase III (NEB #P0737). Heparinase I cleaves highly sulfated heparin/HS chains, Heparinase III cleaves less sulfated HS chains, while Heparinase II cleaves domains of both high and low sulfation on both heparin and HS. Heparinase I, II and III used in combination can produce a near-complete depolymerization of heparin/HS polysaccharide chains to disaccharides.


  1. Fritz, T. et al. (1994) J. Biol. Chem. 269, 28809-28814. PMID: 7759502
  2. Linhardt, R.J. et al. (1990) Biochemistry 29, 2611-2617. PMID: 2334685
  3. Linhardt, R.J., and Gunay, N.S. (1999) Semin. Thromb. Hemost. 25 Suppl 3, 5-16. PMID: 10549711
  4. Casu, B. et al. (2002) Biochemistry 41, 10519-10528. PMID: 15106730
  5. Knudsen, C.B. and Knudsen, W. (2001) Semin. Cell Dev. Biol. 12, 69-78. PMID: 11292372

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Heparin/HS Degradation via Elimination Method
The eliminative mechanism of a Heparinase enzyme degrading a Heparin/HS polysaccharide into oligosaccharides. The double bond on the non-reducing end of the uronic acid absorbs at 232 nm.

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