I want to compare the thermodynamics of the two end of the dsRNA. Is there any software available?
Is there any reference paper by which I can find the local thermodynamic parameters of the RNA at its end?
Can I calculate the approximate values on paper by some method, if available?
Any software that is based on the nearest-neighbor model is useful for your purpose e.g. HyTher - Santa Lucia's web site for the prediction of nucleic acid hybridization.
Reference paper: http://pubs.acs.org/doi/abs/10.1021/bi9809425?journalCode=bichaw
The article provides all parameters for prediction of the thermodynamic stability of RNA duplexes - you can calculate it by yourself if you prefer.
Dangling ends stabilize additionally duplexes (e.g. http://www.ncbi.nlm.nih.gov/pubmed/12050013), but you should specify what do you mean by effects of sticky and blunt ends and in reference to what...
Good luck!
Some years ago, I analysed the effects of the different ways to model dangling ends in RNA secondary structure prediction programs http://www.biomedcentral.com/1471-2105/12/429/ In essence: use the OverDangle model, which is now the default in RNAfold of the Vienna Package.
If you are looking for predictions on completely double-stranded RNA (might contain mismatches)l, you might check
http://dx.doi.org/10.1093/nar/22.14.2760
and
http://www.biophys.uni-duesseldorf.de/html/local/POLAND/poland.html
RNAfold will not handle a duplex RNA, but RNAduplex
http://www.tbi.univie.ac.at/RNA/RNAduplex.html
from the Vienna package might be worth a look.
The parameters mentioned by Anna Pasternak are fine, but doing the calculations by hand will give you only the stability of the duplex (Delta G) but not the melting behaviour.
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