Table 4 Filter cascade for candidate sequences
From: In-silico design of computational nucleic acids for molecular information processing
Stage | Filter | Condition to satisfy |
|---|---|---|
   1 | Identical nucleotides | No more than three identical consecutive nucleotides in the oligonucleotide binding site(s) |
   2 | Active state conformation | The formation of an active hammerhead conformation based on the truth table condition (cf. Table 2) |
   3 | Base-pairing percentage | In the absence of effector(s) 30%–70% of the oligonucleotide binding region is hybridised |
   4 | Energy gap | Energy gap between the inactive and active state is within -6 kcal/mol to -10 kcal/mol |
   5 | Temperature tolerance | Structure is preserved over a temperature range of 20°– 40°C |
   6 | Ensemble diversity | For neither active nor inactive state the ensemble diversity (cf. [33]) exceeds 9 units |
   7 | Folding efficiency | The RNA molecule must fold, in the absence of the effector, to the inactive conformation within 480 units in Kinfold[34]. |