Hydrophobically modified water-soluble polymers have been prepared by micellar copolymerization of hydrophilic monomer acrylamide and the silicone-containing hydrophobic comonomer, tris(trimethylsiloxy)methacryloxypropylsilane in various molar ratios. Capillary viscometer, FT-IR, gel permeation chromatography-multi-angle laser light scattering, transmission electron microscopy, and H-1 NMR were used to characterize these polymers. The results showed that the resulting copolymers are amphiphilic in nature and associate into micelles in water. 9-chloromethyl-anthracene was used as the fluorescent probe to further confirm the copolymer self-aggregates in water by fluorescence spectroscopy. The fluorescence intensity increased as a function of the hydrophobicity of copolymers. And the critical concentration of the self-aggregate formation of copolymer (molar ratio of acrylamide to hydrophobic silicone monomer being 75:1) determined fluorometrically was 0.5 g l(-1). The amphiphilic copolymers (molar ratio of acrylamide to hydrophobic silicone monomer being 20:1 and 100: 1, respectively) were used as separation media in capillary electrophoresis for the separation of DNA. The experimental results indicate that the copolymer with higher hydrophobe content showed no separation efficient while the lower one separated most DNA fragments clearly in phiX174/Hae III digest at very low copolymer concentration of 0.1 wt%. (C) 2003 Published by Elsevier Ltd.