mpb21’s Strategy Guide for Solving RNA Lab Structures.
If you are new to the game, I recommend reading the strategy guide for solving the challenges:(http://getsatisfaction.com/eternagame/topics/the_strategy_guide_to_solve_eterna_puzzles).
Then play through several of the challenges until you get a feel for the controls and you start to develop some intuition for the process.
Many of the strategies used in the strategy guide will be used here, but not explicitly mentioned, so if you haven’t yet, read both.
The main difference is that for the challenge puzzles, you are only looking for one correct solution to fulfill the requirements for the puzzle (structure, number of bonds etc…). However in the lab puzzles, you are looking for the best solution. This is a crucial distinction that you must be aware of, because currently, for each round, only one (if any) of your solutions will be synthesized. So you need to make sure that it is the best possible.
Something to remember when working in the RNA Lab:
-The scoring function in EteRNA which tells you whether a given sequence will or not is good, but it’s far from perfect.
-So you want to make sure that the sequence that you submit will be safely on the side of folded. This is where steps 3 and 4 (below) come in handy.
Steps for solving:
1. Filling In. Start as you would for a challenge puzzle by filling in U’s to pair with the A’s that are there initially. You will want to do this in randomly alternating segments of 1-3.
2. Structure Stabilization. Then fill in G-C pairs at the base pairs that are adjacent to the loops. Use a minimal amount more if needed to stabilize the structure. In theory, you could submit your score at this point, but there are a few extra things that you can do to make your structure just that much better.
3. Loop Stabilization. The loops of the RNA are the most unstable parts of the structure. You can make the loops a little more stable by adding G’s to them. The procedure works as such, mouse over the loop and note the free energy of the loop. Then mutate each of the adjacent residues in the loop and see which improves (makes smaller or more negative) the free energy. Only mutate one at a time, hitting Undo (Z) after each. Once you determine which positions will be most adventagous, try and mutate as many as needed to minimize the free energy of the loop. Do not bother trying to mutate the nucleotides in the loop that are not adjacent to the stacks, they will have no effect.
4. Checking for Mispairing. This is probably the most important and agrueably most difficult part of the process. The idea is to make each stretch of nucleotides in a stack have a unique sequence. This is where the Flip Nucleotide feature comes in handy. You have to look for sections of nucleotides that might mispair with the wrong nucleotides. Some easier things to look for include dinucleotide repeats (i.e. AUAUAU). This will likely be one of the biggest causes of failure for the RNA synthesis. While you are doing this, you may want to avoid trinucleotide repeats, because if you have a couple of them, they are more likely to mispair, and they are less stable
5. Submit! Look over your RNA one last time and make sure that it looks good. Then click the submit button in the dock, give it an awesome name and send it on it’s way.
