Hello, Bharti Singal,

you can easily predict RNA binding residues in your protein of interest using this user-friendly web server as an alternative (additional) method to wet lab experiments - http://rbpmap.technion.ac.il/. For wet lab experiments I would recommend NMR or X-ray crystallography.

Martin

Bioinformatics and sequence analysis as suggested by @Martin would be the first thing to do to give you a rough idea about the potential RNA-binding regions/domains of your protein. You can then recombinantly express and purified those regions of your protein and perform gel shift assays to see if they really binds to RNA. To determine precisely which amino acids contact RNA, you will need structural analysis such as NMR.

Thank you Martin Bartas and Hua Xiao I am familiar with bioinformatics and structural techniques. May be I should elaborate my concern more.

in EMSA do I need to use specific RNA sequence to which it binds or it doesn’t matter. I am naive in RNA field. So to check for specific residues responsible to bind RNA I need not to have that particular RNA sequence. I can simply use the kit! is it?