An easy, one-pot, high-yield preparation of high molecular weight polyrotaxanes (PRs) from poly(ethylene glycol) (PEG) and alpha-cyclodextrin (alpha-CD) by click chemistry is presented with novel water soluble and clickable end-capping agents containing quaternary ammonium and propargyl groups. The threading numbers of alpha-CD on the PEG chain were investigated by means of H-1 NMR spectroscopy and gel permeation chromatography (GPC). When M-n of the PEG axis is 35 kDa, the yield is up to 614 mg per 100 mg PEG axis and the average number of alpha-CDs on each PEG axis is 193. Wide-angle X-ray diffraction (WAXD) revealed that PRs form a column-type crystalline structure. The prepared PR possesses terminal alkyne groups which can connect with functional molecules to make the PR more useful. As a typical example, fluorescent rhodamine B has been successfully installed on the PR terminals. (C) 2012 Elsevier Ltd. All rights reserved.