I am carrying out UV cross-linking assays to characterise a RNA binding protein. Unusually, I have labelled my RNA oligo with a fluorochrome (IRDye800), instead of using the more conventional use of radioprobes.
The technique seems to be working. However, I am finding it hard to optimise my technique (the correct levels of RNA and protein, non-specificity etc).
Has anyone used fluorescently labelled probes for RNA-Protein cross-linking and would be so kind to share their experiences?