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]. |
