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Table 1 Proposed computational protocol for designing two-input molecular gates

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

Randomisation of lengths for the extension region that is comprised of a helix that attaches to the ribozyme core, two effectors binding regions or OBS (NN NN), and three linker sequences connecting the binding sites with the helix (inside dotted box) are generated. Parameters are restricted to those given in Table 6.
Sequence positions except the binding sites are assigned by searching for a base sequence that will fold into the target structure designed in the previous step using RNAinverse[28] or RNAdesigner from RNAsoft[31], with a non-binding pseudo-base (N) being assigned to all positions in the binding region.
Replacement of the pseudo-bases in the binding regions with real bases. All possible combinations of effector binding are considered using (NN NN) pseudo-bases to represent an unoccupied binding region. This can be verified with MFOLD[32] or RNAfold from Vienna[28].
  1. Proposed computational protocol (P-ER2) for designing two-input molecular gates. This revised procedure differs from the P-ER1 protocol to design molecular PASS gates presented in [30] by adding another effector binding site and a linker in the extension region of helix II.