I’m curious about the relative concentrations of RNA shapes in solution. Although EteRNA shows just one shape (Minimum Free Energy?) as “the” shape for a sequence, other tools such as RNAshapes and RNAsubopt show that other shapes with different free energies can also be formed with different probabilities. In EteRNA, the only hint of these other shapes is in the Dot Plot.

My understanding is that in solution you would end up with each of the shapes showing up with a given relative frequencies/probabilities dependent (in part) on the differences in Free Energies between the shapes. Different energy models might estimate these probabilities differently though.

Is there a metric or rule of thumb for the relative concentrations based on the differences in free energies? For example if a sequence had three likely shapes with free energies of -2.0, -1.0 and 0.0 kcal, is there a reasonable estimate for what the relative concentrations would likely be in solution? (E.g. 25:5:1) Or is that too simplistic?

From playing with RNAshapes and some simple sequences it *seems* like each -1.0 of Free Energy difference often seems to be about 5x difference in relative concentration. However that it is not 100% accurate as shape/structure seems to play some role too as sometimes a higher energy shape is also given a higher probability.

AGGGAAACCA

-5.00 .((…)). 0.9997004 []

0.00 … 0.0002996 _

exp(ln(0.9997004/0.0002996)/5.0) = 5.07

AGCAAAAGCA

-1.20 .((…)). 0.8751232 []

0.00 … 0.1248768 _

exp(ln(0.8751232/0.1248768)/1.2) = 5.07

AGCAAAAGCAAAAGCAAAAGCA

-2.30 .((…((…))…)). 0.5711718 []

-2.40 .((…))…((…)). 0.4202706 [][]

0.00 … 0.0085576 _

exp(ln(0.4202706/0.0085576)/2.4) = 5.07

exp(ln(0.5711718/0.4202706)/-0.1) = 0.05

What’s up?