I would like to block ligation at the 3′ end of an oligo. The traditional way to block described in the literature is C3 spacer. I was wondering if I label the 3′ end of an oligo with the Cy5 dye, would the dye molecule effectively block ligation? -Chun-Nan

Dear Chun-Nan,

The blocking groups most often described in the literature are 3′ dideoxy-C, 3′ C3 Spacer (C3-OH) or 3′ Amino Linker (C6-NH2). All the mentioned modifications permanently block the 3′ hydroxyl group of the 3′ base. We can use the 3′ Amino Linker and label it with the Cyanine 5 dye which would continue to block the 3′ hydroxyl group.

Please contact us if you have any other questions.

Best regards,
Sabrina Shore, MS
Scientist, Research & Development