Yes, Cy5 can be used to label DNA oligos. Cy5 is reactive, water-soluble, and has an absorbance maximum of 649 nm and an emission maximum of 670 nm. It is available as both a phosphoramidite and an NHS ester, and is used to fluorescently label oligonucleotides at either the 5' or 3' end, or internally.

DNA oligos labeled with Cy5 are used as hybridization probes in applications such as Fluorescent In-Situ Hybridization (FISH).