Why is there a limit on GC pairs? Is RNA with fewer GC pairs better?

I’m just wondering about the scoring. It seems like you want us to minimize GC. So is RNA with fewer GC generally better or more stable or easier to synthesize? And this logically raises the question: Is RNA with more GU generally better or more stable or easier to synthesize?
I’ve read on the forum that the free energy needs to be as low as possible for stability. Why not include it in the mission objectives or as a proportional score bonus?

Awesome, awesome, awesome, guys. Thank you.



I see now that those targets are set to teach us not to overuse GC and underuse GU - in order to ultimately achieve balance in the design…

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I concur. It is only when we advance to be able to do the lab puzzles that there is no restrictions except what is needed to create an elegant working design.

I think I will spend this rainy night cuddling up to the excellent strategy guides before I move on…

Yes. Really, you need a good balance. You need enough GC in your design to really do much good in the lab, but at the same time, having too many could make it misfold in *quite* wild ways. Having a minimum GU count is something that helps to flex your proverbial puzzle solving muscle-it gives an extra challenge, as with weaker pairs there is always a higher chance of not having enough bonding power (though this can be helpful at points). Same can be said for GC limits at [points.

But, overall, yes, you wish to achieve a balance in the end. And having the right things in the right places. :slight_smile: