Loops versus stacks

In tutorial 4 there is a formula with 12 nucleotides which can be arranged in several ways: each with a loop in positions 5,6,7,8.

  1. UUUUGGGGGGGG–> free energy 4.3 kCal
  2. GGGGGGGGCCCC -->free energy -5.7 kCal
  3. GGGGCGCGCCCC -->free energy -6.7 kCal
    Why does this configuration not form 6 stacks, but retains a loop?

Hi mgbunem,

Good question! A short digression - in EteRNA, we focus on how the nucleotide sequence affects the structure of an RNA - but the sequence isn’t the only thing that affects structure! If you zoom in and look closely at a puzzle in the game, you’ll see a little, white triangle and a little, white circle between nucleotides 1 & 2, 2 & 3, etc. These symbols represent the RNA “backbone,” which holds the all the bases in an RNA together. This backbone is made up of alternating phosphate and sugar groups, and you can find lots about it online.

Now, back to your question. The RNA backbone doesn’t like to twist certain ways - it is energetically bad for it to twist too much, as in the case of a super short loop (loops of < 4 nucleotides are rare in natural RNAs). So, even though it is bad energy-wise to have 4 unpaired nucleotides in a row, it is energetically worse to twist the RNA backbone too much. The energetic effects of the backbone are not very clear in the game, unfortunately! However, because the nucleotide sequence is what makes a given RNA unique, we pay much more attention to that EteRNA.

I hope this answers your question!

Thank you for explaining this Tom. You enhanced my understanding of the game.