Why are we only folding in two dimensions? Is this how nature really works? Also should it not matter the end that is created first? I think that could change much about how a given RNA strand folds.
Hi justinoman - Remember, EteRNA is brand new (we only just did get from beta to public opening on Jan 11th), and is still in the process of development; but playing in 3 dimensions is already being planned for implementation in a future version - Please see the paragraph entitled “Where are we going?” on this page:
http://eterna.cmu.edu/htmls/abouteter…
…this whole page is fantastically informative on a number of various points of interest regarding EteRNA and RNA in general.
-d9
The interface is in 2D simply because the “rules” for 2D structure (i.e. nothing but base-pairs, loops, and bulges) are well understood, its a very tractable search problem for a computer and straightforward to put the energy function into computer game form. There are several dozen equally good computer algorithms for predicting this, and it is largely considered a mostly solved problem. All of the RNA’s in the challenges actually exist in 3 dimensions in real life, but for the majority of them we can only guess what they really look like the way you can guess what animal you’ve just run over by examining what you peel off the wheels. . .(I’ve heard these RNA pictures called “roadkill plots”).
So yes, real RNA’s exist in 3 dimensions and not two. I doubt the interface will suddenly become holographic, but you can imagine 3D interactions will be like folding an origami shape out of the structure on your screen, so things on opposite ends could start base pairing with each other and you will have to start taking that into account when you design. . .
and that will be really fun because the “rules” for 3-D RNA folding are not known at all and computer predictions of any method pretty much completely fail at this, which is what will make this game very interesting.
Lastly, in a real cell, it certainly might matter that an RNA gets created in a particular direction, as you can imagine certain structures could start to form even before the whole thing is completely made. But in the lab, it will not matter because it is standard protocol to anneal the RNA after it is made, that is, heat it near boiling to get rid of any residual structure that formed during synthesis, and then let it cool down slowly to (hopefully) settle into the most favorable conformation (i.e. the lowest free energy one).