Loops Guide

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  • Updated 5 years ago
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mpb21's Loop Guide:

When solving challenge puzzles and submitting solutions for the RNA Lab, it is important to pay attention to the loops. Because it is just as important to make sure that the pairs stay together as it is to make sure that the loops stay apart.

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The general method for solving a loop is to place the pairs in the stacks around it, then start on the loop. First, note the free energy contribution of the loop by mousing over the loop and looking at the free energy display in the top left corner. Then mutate the nucleotides that are adjacent to the pairing nucleotides (circled in black in the picture below) to G’s one at a time. I have always gotten the best results by mutating to guanine (G), the reason for that is that guanine is the biggest base so it’s size likely helps stabilize the loop. Do this for each of the adjacent nucleotides hitting undo after each one and paying attention to which makes the free energy of the loop go to the lowest value.

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"Adjacent" nucleotides circled in black.

Common loops

Following are some of the more common loops that you will see and the improvements that can be made by adding one or more G’s to the loop.

1-1 Loop

Before:
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1.7kcal/mol

After:
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-0.4 kcal/mol

2-2 Loop

Before:
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2.8 kcal/mol

After:
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0.5 kcal/mol

1-3 Loop

Before:
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4.1 kcal/mol

After:
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1.9 kcal/mol

4-1 Loop

Before:
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4.7 kcal/mol

After:
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2.5 kcal/mol

4 Loop

Before:
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5.3 kcal/mol

After:
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2.5 kcal/mol

5 Loop

Before:
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5.1 kcal/mol

After:
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4.5 kcal/mol

Putting guanine's in the adjacent positions can be crucial for stabilizing short stacks. For example, the top loop in the Saccharomyces Cerevisiae puzzle requires a G in a particular place to make it fold properly.

Does not fold:
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Folds:
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This is not an exhaustive list of loops, and more will be added to it soon.

mpb21
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Matt Baumgartner [mpb21], Alum

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