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Guanidinylated chitosan (GCS) was prepared by grafting guanidine oligomers onto chitosan under microwave irradiation. The structure of GCS characterized by FT-IR and 1H NMR verified the covalent bonding between the guanidine oligomers and chitosan; the effects of molar ratio, reaction temperature, and time were investigated and the degree of substitution of GCS reached a maximum of 25.5% under optimized conditions in this work. The resulting GCS showed significantly enhanced antimicrobial activities. The results obtained from the dynamic UV absorption of Escherichia coli (E. coli) and atomic force microscopy (AFM) revealed that the deactivation of E. coli by GCS was due to the destructing of the cell membrane and the prompt release of cytoplasm from the bacterial cells. The adsorption of GCS onto cellulose fibers and the antimicrobial efficiency of the hygiene papers with GCS were also investigated. Microwave irradiation as a green assisted method was applied to promote this reaction. This facile approach allowed chitosan to be guanidinylated without tedious preparation procedures and thus broadened its application as a biocompatible antimicrobial agent. [ABSTRACT FROM AUTHOR]