Custom RNA you can SEE

We offer a number of dye modifications for fluorescent labeling of Dharmacon™ custom siRNA and RNA oligonucleotides, enabling visual tracking in your experiment.

Fluorescent labeling of RNA enables many experimental applications with:

• fluorescent microscopy

• fluorescent plate readers

• microarrays



• flow cytometry

Dye label considerations:


Fluorescent dyes at the 5' end of the antisense strand of a siRNA duplex have been shown to interfere with siRNA silencing activity, and therefore this position is not recommended.

We recommend placing the fluorescent dye at the 5' end of the sense strand, as this is the position that provides the most efficient chemical synthesis.

However, modifications at either of the 3' ends have been shown to have minimal to no effect on silencing activity and can be utilized as well.

Single-strand RNA oligos:

Fluorescent dyes located at the 5' end of an RNA oligo are incorporated during solid-phase synthesis and typically do not require purification.

However, purification is recommended or may be required for most dyes located internally or at the 3' end, as these are added post-synthesis. 

Please contact Scientific Support if you would like recommendations regarding the purification of your custom oligo.

Finally, if you do not see what you need on our website, this does not mean that we won't be able to make it for you. We offer larger sizes, additional fluorescent dyes & other chemical modifications, in vivo processing, QC analysis, and special packaging by request. To further discuss your project's feasibility, please contact Scientific Support.

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Our Scientific Support team is here to help!

Written by Samantha Hartin, PhD, Scientific Support Specialist I