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Fucosylated chondroitin sulfate (fCS) from sea cucumberIsostichopusbadionotus (fCS-Ib) with a choncdroitin sulfate type E (CSE) backhoneand 2, 4-O-sulfofucose brancheshas shown excellent anticoagulant activityalthough show severe adverse effect.Depolymerization represents aneffective methodtodiminishthis polysaccharides side effects.The present study reports a modified controlled Fenton system for degradation of fCS-Iband the anticoagulant activity of the resulting fragments.MonosaccharidesandNMRanalysis of the resulting fragments indicate thatno significant chemical changes in the backbone of fCS-Iband no loss of sulfo groups take place during depolymerization.Areduction in the molecular weight of fCS-Ibshould result in a dramatic decrease inprolonging activated partial thromboplastin time and thrombin time.A decrease in the inhibition of thrombin by anttithromin ⅢT and heparin cofactor Ⅱ and the slight decrease of the inhibition of factor X activity results in a significant increase of anti-FXa/anti-FIIa activity ratio.The controlled free-radical depolymerization method enables preparation of GAG oligosaccharides suitable for investigation of clinical anticoagulant application.