RNA fragmentation - (Aug/31/2010 )

Dear all,

I have long RNA more than , I need to use it in EMSA assay but I need to fragment it to get small size RNA's , is restriction digestion in specific sites, can any body explain how to chose the sites?

Restriction digestion of RNA's? Its impossible. You have to amplify smaller DNA templates. Next you can use it for generation of shorter RNA constructs.

blaszcz on Thu Sep 2 15:06:22 2010 said:

I am sorry I didn't mean RNA, I ment DNA plasmid, so if I have long plasmid for RNA can I digest the areas that I need with restriction enzyme, and then I can use T7 for transcription of this fragmnets?

Of course you can do it but there is big probability that you will not find a restriction enzyme that cuts precisely. So you can get then a fragment of interest with for egzample extra 20nt. I think that better method is to amplify your desire constructs from plasmid using PCR and set of primers because you have a certain that your construcst are exactly as you want.