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This is a step-by-step guide that will help you solve the vast majority of challenge puzzles. Before you begin, be sure to enable base pair numbering, highlighting of restricted sequences, and viewing of free energy in the settings menu. Most puzzles can be solved using the first few steps.

Step 1: Create a starting sequence with AU pairsEdit

Fill the target structure with AU pairs.

Step 2: Boost the design and add any special sequencesEdit

Boost each internal loop and hairpin loop by adding guanine at boost points.

  • If the target structure has features that demand unique solutions (such as like certain zigzags and isolated base pairs), add those as well.
  • Do not boost multiloops or external loops at this time, unless they are sure that they are required.
  • Take advantage of special loop sequences with low energy: GG mismatches in the 1-1 loop and opposing GU mismatches in the 2-2 loop

Step 3: Add stack capsEdit

Look at the outline of the structure at the top left of your workspace. If the puzzle's restrictions permit you to do so, make the closing pair of any misfolded stack a GC pair.

Step 4: Strengthen misfolded regions with GC pairsEdit

Look at the outline of the structure at the top left of your workspace. Add GC pairs to any regions that appear in red, focusing on short stacks between loops with high energy. Do not exceed the GC pair limit of the puzzle at this time.

Step 5: Flip base pairs in misfolded regionsEdit

Look at the outline of the structure at the top left of your workspace. If long regions in a stack are highlighted in red, flip bases within the stacks. If the misfolded region contains bulges or multiloops, try flipping the closing base pair. Multiloop energy is very sensitive to the orientation of closing base pairs.

Step 6: View the structure in natural mode to find sites to changeEdit

Consider flipping base pairs and making base pair substitutions to destabilize the unwanted structure. Pay careful attention to positions in bulges and multiloops that may need to be blocked.

Step 7: Add additional GC pairsEdit

Look at the outline of the structure at the top left of your workspace and add GC pairs to misfolded regions. Do not worry if you slightly exceed the GC pair limit of the puzzle - these pairs can be removed later once the structure is stable.

Step 8: Add/remove any pairs needed to satisfy restrictionsEdit

Long stacks are excellent places to place consecutive GU pairs.

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