We are having 49 base RNA sequences and want to filter out the stable RNA sequances.For that we performed RNA folding through RNAfold tool as a result we got the minimum folding energy(MFE) for each sequence, ranges from 0.5 to 31 Kcal/mol. We searched a lot of literature but do not find the exact MFE in Kcal/mol for a stable RNA.Hence it is a request to all the expert please tell me MEF and provide the supporting literature.
Thanking you
Dear Saurabh,
could you please define what you mean by "stable"? An RNA that does not switch between different possible structures? RNA structures that would be stable in cells? In defined in vitro conditions?
I'm not an expert on RNA structures but as far as I understand the matter, RNAs may exist in a number of structures that constantly interchange (if the difference in MFEs between the structures is small). Very few RNAs will have only 1 definitive structure with no possible alternative structures that have a similar MFE.
Also, please keep in mind that RNAfold and other such programs make computational predictions of the structure. Although the predeictions are based on solved RNA crystal structures they may not actually reflect the real structure an RNA takes in its natural environment such as in cells. In cells, things get really complex with the possibility of proteins or other RNAs binding and influencing the structure. Also, RNAs in cells are subject to endo- and exonuclease digestion unless they have been somewhat stabilized by capping and have a poly-A tail or have been bound by particular proteins.
I'm afraid there is no simple answer to what I think your question is.
Dear Petra Mam,
Given suggestions regarding RNA structures are appreciable but my question is simple regarding RNA structure, after RNA folding by RNAfold it provides MFE and I want the acceptable range of that value.
The MFE is dependent on the length, G/C or A/U content and intra-sequence homology. So again, I'm afraid there is no straight answer - acceptable range for what?
The best you may be able to do is to arbitrarily decide that a particular RNA structure with a (more negative) MFE that is >x% different than a second possible structure's MFE is what you consider stable for your purpose.
It may be worthwhile to contact the people behind RNAfold ([email protected]) or RNAstructure (http://rna.urmc.rochester.edu/index.html) directly and ask them. They are likely to have a much better idea about this particularly if you are doing some computational stuff.
Thank you Mam
I am also thinking in similar way and mail them regarding same.
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