Can I have a dye conjugated to my oligonucleotide internally?

Yes. We use the succinimidyl ester version of the dye and conjugate it to a selective placement linker. We then post-synthetically conjugate the dye to the oligonucleotide. Other options include using a dT-FAM or dT-TAMRA. These dyes are already conjugated to the dT-C6 amino linker.