Flip Method of Stability

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.

Hi jnicol,

I think this is an interesting idea, and this may in fact, have same principle with the new feature we are designing - showing “alternative structures”

This feature will list alternative structures that the RNA could fold into with small amount of free energy jump from the minimum energy structure. The more alternative structures there are, the less stable the RNA is. This in principle, could be very similar to what you are describing - if the RNA misfolds dramatically with a change in single base pair energy, the misfolded structure will show up as an alternative structure.

This feature has not been implemented yet, but there are many strong advocates of this idea in our team (and Eterna players).We’ll keep this post updated once we make progress.

Eterna team

Include me as a strong advocate, I would love this tool and think it would help immensely with the lab designs. Thanks for the great feedback!

John

Dev can we have an update please

I am so glad to see that someone else has thought of this. I have always wondered if there could be a tool to do what you’re suggesting john . Somehow alter the energy of a stem or portion to see how stable it is. But I thought of it less as I developed a better understanding of the dot plot since this provides you with where the most likely misfold is to occur in a design. What r your thoughts?

The dot plot is the best way to decide stability, but sometimes it is hard to ‘see’ this stability. The flip method provides a quick feedback.

Sorry I never saw this post before - I’ve thought of something like a reverse-acting FMN molecule, or something that adds kcal to the structure until it breaks. How much kcal is required to break the puzzle may tell us something about the overall stability

That’s a great way to describe what we are talking about. A reverse molecule bonus. But not 4.86 kcals. Maybe an incremental 0.5 penalty

yes, the FMN is just for illustration. Ideally we could slide an “add energy to the structure” bar or something gradually whenever we want to see exactly when and by how much the structure breaks

When I first started and even today I often do an all AU design to maximize the portion that is stable under that constraint, then flip tor best energy in the all AU state before proceeding with the rest of the solution. As I finalize I do repeated flips for sensitive area discovery and check long distance effects.

I have also done this all GU but find it more difficult to proceed quickly.

An energy bonus button to discover how much energy (plus or minus) pushes a form unstable in our model would be really interesting.