Can I label a short sequence of 30nt that forms a hairpin with biotin for EMSA?

Joana Sofia Pereirinha @Joana-Pereirinha

04 March 2025 1 7K Report

I want to do an EMSA using an RNA sequence of 30/40 bp that forms an hairpin in the 3' end. I wanted to avoid to labeled it with radioactivity so I wanted to try the Chemiluminescent assay in which the RNA is labeled with biotin. I am not sure if the biotin can interfere with the structure of the RNA since the RNA is not very long. Does anyone has experience on that?

Péter Gyarmati

If you can attach a spacer arm of >6 nucleotides for biotinylation, you should be fine. Labeling your 30-40bp RNA directly may cause interference as the biotin molecule is pretty large compared to a nucleotide base

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