Four para-linked or meta-linked cationic water-soluble fluorene-containing poly(aryleneethynylene)s (PAEs) were synthesized to investigate the solvent-induced pi-stacked self-assembly. These PAE backbones are composed of fluorenylene and phenylene units, which are alternatively linked by ethynylene bonds. UV-vis absorption and photoluminescence spectra were used to study their conformational changes as solvent was gradually changed from MeOH to H2O. In pure water, with gradually increased meta-phenylene content (0, 50, and 100%), they underwent a gradual transition process of conformation from disordered aggregate structure to helix structure, which was not compactly folded. Moreover, the polymer with an ammonium-functionalized side chain on the meta-phenylene unit appeared to adopt a more incompact or extended helix conformation than the corresponding one without this side chain. Furthermore, the conformational changes of these cationic PAEs in H2O were used to study their effects on biological detection. Rubredoxin (Rd), a type of anionic iron-sulfur-based electron transfer protein, was chosen to act as biological analyte in the fluorescence quenching experiments of these polymers. Preliminary results suggest that they all exhibit amplified fluorescence quenching, and that the polymer with more features of helix conformation tends to be quenched by Rd more efficiently. (c) 2006 Wiley Periodicals, Inc.