Science behind challenge goals?

Is there any scientific reasoning behind the base pair demands in the challenges? If it folds using all GC bonds, why bother with other designs (eg designs with 4 GU bonds, etc)?

One thing to keep in mind is GC Content. In real organisms, they have an average GC content that is roughly around 50%, (give or take 20% based on the organism). For more on GC content, read the Wikipedia entry on it.

Hopefully other people with have other answers as well.

Matt essentially hit the nail on the head. If everything was made of Gs and Cs, the RNA would be so sticky that it would constantly get stuck in misfolded shapes (as we have seen in the RNA lab). Nature gets around this problem by making the RNA flexible to get out of these traps yet still falls into the desired configuration.

There are also some unconventional non GC, AU, GU, pairs that exists. Those may serve other structural roles for the RNA’s function. The game looks more at those situations.