Is there any tool (like available for DNA restriction mapping at NEB) for restriction of RNA? It will be fantastic if I can provide the secondary structure of the RNA and the enzyme cuts accordingly. Need Help!
Thanks
Parijat
Dear Parijat
would you please take time explaining what you are going to do with cut sites and secondary structures?
Cheers
Mohsen
What do you mean by RNA restriction? I'm not sure what you are looking for exactly.
I am not sure exactly what you want to do but a great tool for RNA secondary structure predictions and 'physics where you want it' is MMB (macromolecular builder)
https://simtk.org/home/rnatoolbox
Sorry, if i was not clear to you all.
What I mean is-- Lets say I have a RNA sequence in hand , also with its secondary structure. So basically in a pdb file I have the RNA structure along with the sequence. By structure I mean the double stranded and single stranded regions in the RNA. Now as you know there are various RNase available , some cut single stranded A, some cut double stranded A etc. So experimentally if I treat my RNA with those sort of enzymes I get a pattern on gel according to he sequence and secondary structure. Where double stranded regions are not cut by some RNase and single stranded are cut by some etc etc , along with particular base specificity.
Now, I want a software where I can give input of a RNA sequence with double stranded regions specified in it. I will tell where to cut and where not to (for DNA restriction enzymes like EcoR1 cut at specific sequence of 6 nucleotides). I want to do this entire thing for RNA.
Am I clear now?
Does your RNase recognizes the cut site based on primary sequence? or it cuts exactly at specific epitopes of secondary structures? In case it cuts at specific sequence motifs and you already know the motifs, then it is your opportunity to shoot for creating such a software. Sorry, but, I am not aware of a software which cuts your RNA by predefined sequence motif as is the case with DNA restriction enzymes.
Good luck in this adventure.
Mohsen
The RNase I will use will not cut at any sequence but at a particular base A,C,U or G. Some will not cut A which is double stranded , some will cut it. Also some will cout double stranded A not single stranded.
Usually, people use these RNases the other way: they know the RNA sequence, but not its structure and they determine where these enzymes cut to obtain information about the RNA structure. There are softwares that predict the RNA secondary structure in which you can use the experimental data as constraints (MFold is the most popular one). If you want more information look for reviews on enzymatic and chemical probing of RNA.
To answer your question more directly, it is very difficult to predict where the enzyme will cut if you don't know the exact 3D structure of the RNA. This is because RNases are rather bulky and steric hindrance may prevent cleavage. Also, if you consider RNAse V1, which cuts into double-stranded or stacked regions, it is very difficult to predict where it will cleave. For instance, it does not cleave in the middle of long regular helices, and very often only one strand is cleaved.
Thanks to all for your suggestions.
Thanks Ronald for the valuable insights. Yes exactly, people do it the way to predict the secondary structure.But I just wanted to know if such programs are available.
Good day Parijat,
This is a link to get you started
http://pubs.acs.org/doi/abs/10.1021/ja1008739
Good luck
- Badges
- Science topic
- Similar topics
- Biological Science
- Molecular Biology
- Biomolecules
- Nucleic Acids
- RNA