I’m curious about how the EteRNA interface works in determining a stable design. That is, does the interface merely predict if the design will STAY in the desired state, or does it also take into account the probability of completing the folding process and settling into the desired state?
I have no background in RNA folding nor have I had the time to do some background reading (yet). So this is all just speculation; please correct me if I’ve gone astray. I also know that what seems should be the case is not necessarily that way in practice. However…
It seems that there are 2 aspects of creating a design that will successfully fold during synthesis.
The design must be stable in the desired shape.
The design must be able to complete the folding process the get into the stable state without getting sidetracked.
Nature doesn’t provide a jig (I don’t think) into which all the nucleotides are placed and, once the jig is removed, the shape must merely be stable and maintain that shape. Instead nature (again, I think) just copies the proper sequence from the DNA template and, once completed and released, the molecule is on its own to fold up into the desired shape. Please tell me if I’m wrong about that.
So, does the EteRNA interface predict BOTH the stable state AND the probability of the RNA successfully folding up into the desired state (without getting stuck or sidetracked into some other, suboptimal, shape along the way?)
Are we putting too much emphasis on just one aspect of a multi-step process?
This is an interesting question – especially for larger RNAs with complex 3D folds, it ends up being non-trivial for the RNA chain to find the right shape.
After about 10-15 years of RNA biophysical work, the problem for these larger RNAs is not the difficulty of finding base pairs (simple hairpins actually fold in microseconds), but that if the RNA finds the wrong fold, such misfolds can be really stable. For example a helix of longer than 10-15 base pairs can be very stable – for seconds or hours at room temperature. That’s good if its the designed shape – but bad if its an alternative helix that you didn’t want! When players look at ‘dot plots’ they can get a sense if there are these potential ‘traps’ out there, but its very hard to estimate the kinetics of folding.
[There are also likely further complications in 3D folds, where the RNA can get topologically tangled; this hasn’t been proven, but is an interesting hypothesis out there. Here’s a link to a paper I helped write a while back on this idea: Link]
[Another parenthetical comment: its thought that in living cells there are proteins whose jobs are to occasionally disrupt RNA helices to get RNAs out of kinetic traps. In fact some scientists have suggested that proteins originally evolved as RNA-folding helpers (“chaperones”) in the primordial RNA World, and then they took over many of RNA’s roles.]
Anyway, good question – and something we will likely need to revisit carefully as we get to more complex designs (switches and 3D structures) as EteRNA advances…