Can you do periodate oxidation with Sodium periodate that converts the 3' vicinal diol of the RNA into aldehydes. Followed by reductive-amination with biotin hydrazide. Life technologies has a nice schematic and also has references:. See Chemical Methods....: http://www.lifetechnologies.com/us/en/home/life-science/protein-biology/protein-biology-learning-center/protein-biology-resource-library/pierce-protein-methods/methods-labeling-nucleic-acids.html