Fig. 6

An example of negative design operator. Here we consider a two-target design. In this example, a parent sequence, target structures 1 and 2, a selected predicted structure, and a child sequence are denoted by Parent, Target1, Target2, Predict1, Child, respectively. First, the Parent sequence is copied to the Child sequence; Step 1) we detect undesired base pairs (positions are denoted in red) in Predict1 which do not appear in the target structures; Step 2) we change the nucleotide(s) of each undesired predicted base pair to disrupt the undesired base pairing. Here, the G in Parent is changed to the C in Child (both are denoted by shadowed characters); Step 3) to repair the base complementarity denoted in red, the shadowed C is changed to the shadowed G