Some known applications of Heparinase II enzyme:

• Production of low- and ultra-low molecular weight heparins (LMWH and ULMWH)
• Characterization of heparin, heparan sulfate (HS) and LMWH,
• Structural analyses of heparin, HS, LMWH, heparosan and Heparin-like GAGs
• Production and isolation of oligosaccharides with novel sequences of GlcNH₃⁺ residues
• Depolymerization of heparin and HS  and chemically modified heparins and molecular weight profiling of heparins and HS and chemically modified heparins
• Quality control testing of heparin and heparin-derived products,
• Quantification of contaminants in heparin such as over-sulfated chondroitin sulfate and persulfonated heparin
• Quantification of process-related impurities
• Glycobiology research,
• In vitro host-pathogen interactions in viral infections, in vitro virus-adhesion inhibition studies, cell culture experiments
• In vitro virus plaque inhibition assays
• Mass spectral analysis of heparins, HS, heparin-like molecules and heparosan
• Cancer biology research
• In vitro immunohistochemistry, immunocytochemistry and flow cytometry
• Circumventing the inhibitory effects of heparin in the PCR reaction, etc.