Cy5 is a blue fluorescent dye by GE Healthcare (Amersham Pharmacia). It can be used for: sequencing (e.g. ALFred), for labeling on DNA-arrays (combined with Cy3), as acceptor for FRET hybridization probes and as a dye for TaqMan® and FRET probes in Real-Time PCR. Cy5 can be attached to the oligonucleotides as an amidite (5'-or 3'-terminal, internally only through a disruption in the structure – during the synthesis) or as an ester (through terminal or internal amino groups – after the synthesis). We recommend BlackBerry quenchers (BBQ) or BHQ-3 (unstable).

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