Hi Delasa, among a series of same-sized RNAs, the one with the most negative value of free energy is considered the most structured and the most stable. You can visualize the predicted secondary structure of your RNA using mfold (http://mfold.rna.albany.edu/?q=mfold.)

One thing you should keep in mind is that the term "stability" here describes a "thermodynamic stability" calculated in silico, which does not necessarily reflects a "biological stability". Within the cell, your RNA might form an alternate secondary structure entirely different from the predicted one through interacting with a myriad of RNA-binding proteins.

Hi Delasa, among a series of same-sized RNAs, the one with the most negative value of free energy is considered the most structured and the most stable. You can visualize the predicted secondary structure of your RNA using mfold (http://mfold.rna.albany.edu/?q=mfold.)

One thing you should keep in mind is that the term "stability" here describes a "thermodynamic stability" calculated in silico, which does not necessarily reflects a "biological stability". Within the cell, your RNA might form an alternate secondary structure entirely different from the predicted one through interacting with a myriad of RNA-binding proteins.

Hello Delasa,

The lower the thermodynamic energy of the structure the more stable it generally is. However, we have to keep in mind that this is calculated using Zuker's algorithm which is accurate for secondary structure predictions. If you are working with specific family or group of RNAs then you can attempt to correlate the secondary structural motifs such as stem loops - bulges or junctions in your RNA structure with the free energy value. Generally there is a pattern for similar biomolecules.

You can refer to our groups publications regarding secondary structural analyses of RNAs if you wish.

Tertiary structures of RNAs can be generated at MCSYM or ifoldRNA, and then you can properly predict the biological stability of the transcript.

Please refer to the following articles:

http://www.sciencedirect.com/science/article/pii/S009286741301595X

http://www.biomedcentral.com/1471-2148/11/59/

http://genome.cshlp.org/content/13/9/2042.long

http://nar.oxfordjournals.org/content/27/7/1578.long

http://www.sciencedirect.com/science/article/pii/S0014579305010719

http://epress.com/w3jbio/vol4/seffens/index.html

Thanks so much for your response.