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Table 5 Computational protocol (P-ERM)

From: In-silico design of computational nucleic acids for molecular information processing

Generate all “partial” meta-stable conformations (refer Figure 4 for details) for the molecules. The length of the receptor sites or OBS (bold lines), the helix II (short crinkled lines), and the linkers (cf. Table 1) are randomised within the constraints detailed in Table 6. For instance, to design an XOR gate, four meta-stable partial conformations are provided. Two inactive states where the hammerhead ribozyme motif is distorted (top left and bottom right) and two active states where the hammerhead ribozyme motif is formed when only one of the effectors is present (top right and bottom left).
Using multiSrch[38], generate sequences that conform to the meta-stable conformations from the previous step. Bases are assigned for positions in the bold regions.
  1. Computational protocol (P-ERM) for designing two-input molecular gates based on a multi-stable sequence design algorithm (multiSrch) developed in [38].