If an RNA has the same number of Cytosines as Guanines, consider it be neutral. If an RNA has fewer Cytosines than guanines, reward it up to a certain point. I would say stop rewarding the structure at 25-50% fewer Cytosines than Guanines. If an RNA has more Cytosines than Guanines, penalize it. Penalize the RNA more severely as that ratio increases. That is, the penalty for 25% more C than G is less harsh than the penalty for 100% more C than G.
I’d also like to see this strategy operate in reverse, if possible- that is, reward the RNA for when C>G and penalize it for when G>C.
The idea is that when there’s fewer Cytosines than Guanines, fewer misfolds tend to occur, it seems. To add to that concept, I’ve used the (RNA) series to illustrate that RNA folds can form quite well without the presence of Cytosine.
The flip side to that coin is that when you add Cytosines to an RNA relative to the number of Guanines, the RNA doesn’t want to fold at all. That is, when C is significantly greater than G, the RNA tends to either want to fold correctly or simply remain a strand. I’m not sure why this is, but that’s how I’ve interpreted the data provided by experimenting with the (RNA) series on low-guanine random structures.
Just bumping to make sure that this doesn’t get overlooked.
And bumping again to see that this doesn’t get overlooked. All this bumping, I feel like I’m in a nightclub >_>