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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].
  1. Constraints imposed on candidate sequences following [15].