Is there a non-enzymatic, non-physical, and preferably a chemical way to efficiently fragment/digest RNA molecules?
Thanks!
Dear Kaveh,
you can use the follwing non enzymatic methods:
Physical Fragmentation
- Acoustic shearing, - Sonication, - Hydrodynamic shear
or Chemical Fragmentation for long RNA strands using Heat and divalent metal cation.
Best,
Frank
Hi Kaveh,
Have a look at the Fragmentation Reagent from Ambion (AM8740):
https://tools.thermofisher.com/content/sfs/manuals/sp_8740.pdf
This is quite efficient.
Mehdi, This looks good., thanks for sharing. Although, I don't know to what degree it would digest the RNA. Do you think a longer exposure would completely digest the RNA? Because that's what I'm trying to get at.
Frank, thanks for your answer. I need to avoid heat, as it would harm other macromolecules in my sample. I have to learn more about "divalent metal cation" digestion. It sounds promising for my application.
I assume that longer incubation would give shorter fragments but I am not really sure if you could reach to mononucleotides. Alternatively, you can try Nuclease P1 which generates mononucleotides, suitable for Mass Spect, for example.
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