Hidden instabilities are features that indirectly stabilize the target structure by destabilizing misfolded structures. These instabilities are usually only revealed when base pairs in the target structure are broken. In some cases, placing hidden instabilities in your design may increase its energy. This is not problematic so long as the energy of misfolded structures is increased to even greater extent.
|In the example to the right, a GU pair between nucleotides 2 and 78 creates a hidden instability. If the pair between bases 1 and 80 were broken, the resulting external loop would be unstable. The use of a GU pair in this position actually increases the energy of the sequence folded into the target structure. It is most destabilizing, however, to undesired structures.|