I have an idea that can allow rna shapes to be designed with greater stability.

Many puzzles are right on the edge of folding correctly. A difference of 0.1 kcal or less can cause a shape to be dramatically wrong or to magically snap into place. We get a black and white picture of the result as being unstable or stable (actually red and white in eterna).

However, in nature, with hundreds of thousands of samples, the rna may form as desired 60% of the time and incorrectly 40% of the time with an on the edge design. Even with a great design, it will never be 100% and 0%.

It would be nice to have a tool that could lower the free energy between each base pair to find the value at which it becomes unstable. The greater the difference in energy, the more stable the shape will be.

Well there is a very crude method that can be used to accomplish this with the tools we already have. After a puzzle has become stable, flipping a base pair will cause the bonding energy to be slightly changed between its neighbors. If the shape remains stable, then we know that the shape can withstand small fluctuations in energy and therefore have some measure of stability.

One problem with this method is that many “mismatched” designs will be excluded even though they may have great stability. I define a “mismatch” as when a flipped base is attracted to another base that is many nucleotides away and reshapes the molecule dramatically. The flip method of stability can only test localized energy bonds between neighbors of the flipped base pair.

The lab entry Summers Back is an attempt to use this method to stabilize the switch shape. In the unbound shape, any single base pair can be flipped and still result in a stable unbound shape. Notice that I say the unbound shape only. For this method, each shape is tested individually.

For the lab entry Summers Back, I did not test the locked base pairs properly, since it was a little more difficult to accomplish this. But, by copying the structure and sequence into puzzle maker, these locked bases can also be tested. Unfortunately, my lab entry has some energy instability on a locked base, but it does not seem too severe, so I still have high hopes for this design. I have since found some other solutions that would pass the flip method of stability test for all base pairs.

I hope that this can help with the switch designs. Please forgive my use of lower and raise the free energy, I may have said it backwards, but hopefully the idea is still understandable.