A set of carboxylate-functionalized poly(phenylene ethynylene)s (PPEs) has been synthesized in which the carboxylic acid groups are separated from the polymer backbone by oligo(ethylene glycol) spacer units. These polymers are soluble in water and organic solvents and have photophysical properties that are sensitive to solvent conditions, with high salt content and the absence of surfactant promoting the formation of aggregates of relatively low quantum yield and long fluorescence lifetime. Quenching of these materials by the dinitrophenyl (DNP) chromophore (K(SV) approximately 10(4)) is also highly solvent-dependent. The presence of carboxylate groups far from the polymer backbone appended to each repeating unit allows for the postpolymerization modification of these PPEs with peptides by methods analogous to those described for carboxylate-functionalized small-molecule dyes. Covalent attachment of the fluorescence-quenching 14-mer Lys(DNP)-GPLGMRGLGGGGK to the PPE results in a nonemissive substrate whose fluorescence is restored upon treatment with trypsin. The rate of fluorescence turn-on in this case is increased 3-fold by the presence of surfactant, though the actual rate of peptide hydrolysis remains the same. A small-molecule mimic of the polymer-peptide system shows a smaller fluorescence enhancement upon treatment with trypsin, illustrating the value of polymer-based amplification in this sensory scheme.

Covalent modification of agarose with a 6-bromo-7-hydroxycoumarin (Bhc) sulfide derivative yields a hydrogel that generates bound thiol groups upon excitation with either UV light or a pulsed infrared laser. Using a multiphoton confocal microscope as the patterning platform, intricate internal chemically modified volumes of stable nucleophilic thiol groups are created within these hydrogel samples, which are in turn modified with biomolecules without causing hydrogel cross-linking or changes in its physical properties. The use of automated scripts and microscope stage control allows, for the first time, biologically relevant molecules of interest to be photochemically immobilized within the hydrogel in complex patterns with feature sizes comparable to those of mammalian cells. The resulting chemically patterned hydrogels have applications in tissue engineering, where they can be used to control cell behavior.