Base pair flipping, usually referred to as simply "flipping," refers to switching the two nucleotides that are paired in a structure. The flipping tool in EteRNA can be selected by clicking the two white dots at the right of the base toolbar. Flipping bases in misfolded regions is often an effective approach to solving puzzles.
In the example to the right, flipping a single base pair solves the puzzle. Using the flip tool to do this can save time.
In the second example, note that the puzzle outline is mostly red. Flipping a single base pair in misfolded region breaks up a repetitive stretch of AU pairs - and solves the puzzle.
Base pair flipping in EteRNA has no relationship to base flipping, a process (usually in DNA) where a base is rotated out of the helix.