I’'d like to understand the pairing probability dot plots provided in the RNA Lab. The Lab Manual says,
“The lower half triangle of the plot only colors pairs that are in the minimum free energy structure.”
Is the “minimum free energy structure” the same as the targeted design shape? Is it correct that the lower left triangle only shows which bases in the design shape have paired with each other? This seems to be independent of the precise sequence of bases. We are given the shape before any bases have even been specified.
Googling this suggests that there is a certain amount of freedom in how dot plots can be generated, depending on what you’re looking at. Is there a more detailed description somewhere of how the upper right triangle of our plot is calculated? This seems to depend on the precise sequence of bases, and allowing the shape to vary. (am i right?)
In nature, RNA does not sit rest in a single shape. Although it would stay longest in the “most stable shape” ( = minimum free energy structure), it rapidly shifts between other shapes as well.
The pair probability shows the the probability of each pair happening in many shapes that the RNA forms. The lower half triangle actually represents an ideal case where your RNA “always” stays in the minimum free energy structure. The upper half triangle shows actual probabilities. So the more your upper triangle looks like the lower triangle, the more likely your RNA stays in the minimum free energy structure.
Hi Jeehyung Lee!
Thanks for your response to my question. I can see that you are describing the behavior of a real molecule that wiggles and bumps into other things in its environment. It can absorb and release a little energy by shifting its shape as it jostles about. I can also imagine how this might be represented in a dot plot where the most stable shape gives the darkest dots and where less frequently occurring shapes give lighter colored dots.
How does EteRNA calculate the dot plots that appear in the RNA Lab? I want to understand how EteRNA generates the dot plots on the fly. This might make the information in the RNA Lab dot plots much more helpful in finding designs that score higher after synthesis.
Take all the possible shapes. Go through every pair in every one of those shapes, and in your dotplot, make the relevant dot for each pairing a little darker. That is all it is. The darker the dot, the more of the possible shapes have a pair there. At least that’s how I understand it. I know this is an old thread, I just figured the explanation wasn’t really clear. I’m also assuming that dots are not generated for structures with >0 total energy.