Tips and Tricks
From EteRNA WiKi
Revision as of 17:16, 19 August 2021 by Anamfija
Puzzles in EteRNA vary widely in difficulty. Many solutions can be found quickly, without using every tactic available. The hardest puzzles often employ creative uses of the "rules" that dictate how RNA folds in EteRNA.
- Creating a good starting sequence can help you solve easy puzzles more quickly.
- Placing GC pairs at the end of stacks can favor the target folding by lowering the energy of both its stems and loops.
- Loop boosting can favor the target folding by lowering the energy of its loops.
- Using special sequences may be required to create certain secondary structures.
- Exchanging the positions of two paired bases can often stabilize long stacks that have mispaired.
- Blocking can prevent the formation of undesired base pairs.
- Deliberately destabilizing unwanted structures may be necessary to prevent the formation of undesired loops.
- Avoid submitting designs with excess AU, GU, or GC pairs!
- Avoid long strings of any one base. Four identical bases in a row seems to be a good limit.
- Leave all loops as adenine, unless you wish to boost your design. Boosting may or may not be helpful in lab.
- Use of secondary structure prediction programs can identify very poor designs, but these programs are of uncertain value in determining which of two reasonable designs is superior.
- Even Energy Distribution is a hypothesis that stabilizing or destabilizing features should not be concentrated in one area of a lab design.
- Copying elements from previously successful designs has been moderately effective.