Put a fluorophore on your DNA/RNA and visualize by fluorescent scanning. It's as straightforward as using radioisotopes but much safer.

I did it with BET on agarose gel 1% and UV light. You can do it only if you have a lot of DNA/RNA of interest, and if your nucleic acid is (partially) double strand. Maybe precise us the type of nucleic acid you focus. I can send you protocols that could interest you.

Dear Baptiste,

Could you please send me the protocol. If possible, I wanna try it.

Thank you

I am using biotinylated probes with subsequent chemiluminiscent detection. Works very well.

binding buffer: 30mM TrisHCl, pH 7, 0,5 mM MgCl2, 0,1 mM ZnCl2, 50 mM NaCl, 40u/reaction RNAsin.

protocol:

Mix: 100ng of RNA (if 100-1000b length to see it on gel) + approximatively 18 fold more protein ( do a scale of protein quantity from 0,1X to 50X if you can, base you calculation in mol of RNA and mol of protein) + 1µl of 10X binding buffer + up to 10µl H2O

incubation 15mn at 37°C

prepare agarose gel 1% with TBE (classical gel for DNA migration after digestion or PCR) + BET inside

Deposite all you reaction before electrophoresis 20mn 100V (maybe more maybe less depending of the length or your nucleic acid)

look the result with UV light

Remember BET is a dsRNA or dsDNA interspersing. The experiment will not work if you work with ssDNA or ssRNA.

cheers

I agree with Jiri. You can just order fluorescently labeled DNA/RNA oligos. I would first prepare a dilution series to figure out which concentration of your fluorescent oligo you need to put on the gel to get a good signal in your fluorescence reader. Then you can use the identical protocol as for radioisotope labeled DNA/RNA.

In case you would like to know more about your interaction (affinity, stoichiometry, etc.) I would recommend to use MST (MicroScale Thermophoresis). It's an easy and fast way to quantify biomolecular interactions. And you can use the same fluorescently labeled oligos as for the EMSA.