Free binding energy in RNA-target

Question

[CikLa]

Hi,

Normally in RNA structure prediction, they will give the free energy for seed and binding site. What is the justification of the free energy, anyone? If we know this RNA-target have this x free energy, so what is that indicate?

[Michael]

I guess you are referring to miRNAs?

Answer 1

[erikvdbergh]

The free energy refers to the amount of energy that is "left" in the molecule if it would be folded like the predicted structure. For example, when 'A' and 'T' nucleotides are opposite from each other and bound by hydrogen bonds, they have low free energy. This is because their hydrogen atoms have formed bonds and are not free to bind with other things.

In contrast, an unpaired nucleotide has high free energy because it can still bind with other nucleotides. This is also the case for phosphate groups and hydrophobic residues.

In RNA structure modeling, we try to find a configuration with the lowest amount of free energy because we assume that in nature the RNA molecule will arrange itself this way. A structure with high free energy would have a lot of energy still available, which means that it will try to form new bonds all the time and that means that it would be unstable.