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Cy5-YNE is a member of the tetramethylindo(di)-carbocyanine family of fluorescent dyes. It is built of two indole rings that are connected by a chain of five methine groups, and a long chain with a terminal alkyne. It is used for the detection of azido modified peptides, proteins, and oligonucleotides. The terminal alkyne undergoes a Cu(I)-catalyzed azide-alkyne cycloaddition with the target azido group. It has been used in single molecule fluorescence resonance energy transfer with Cy3-maleimide on maltose-binding-protein.