Patent ID: 8778627

Claim:
A substrate selected from a compound having a structural formula, DYE-(B) m , and a pro-enzyme substrate thereof, wherein DYE, when independent of DYE-(B) m , comprises a dye selected from a biologically functional fluorescent dye and a fluorogenic dye, the dye being capable of binding to a partner biomolecule, partner biomolecules, or an assembly of partner biomolecules; wherein m is selected from 1, 2, 3, 4 and 5; and wherein each of at least one B, independently, comprises an enzyme substrate moiety that is capable of enzymatic transformation comprising cleavage of a bond involving the dye and at least one B, cleavage of a bond within at least one B, or formation of a bond involving at least one B; and wherein the dye is a phenanthrodium dye having a structural formula, wherein: B comprises a peptide or an amino acid; at least one ligand of ligands R 1 and R 2 comprises B, where the C-terminal carbonyl of B is capable of forming an enzymatically cleavable peptide bond with an amino group of the dye; if any one ligand of ligands R 1 and R 2 does not comprise B, said any one ligand comprises H; ligand R 3 comprises a substituted or an unsubstituted C1 to C10 alkyl; ψ comprises a cation selected from H+, Na+, K+, NH 4 +, N,N,N-triethylammonium, and N,N-diisopropylethylammonium, or an anion selected from a halide, a sulfate, a phosphate, a perchlorate, a hexafluorophosphate, and a tetrafluoroborate; and d is a number of ψ sufficient to render overall charge of the substrate neutral.