Computational approaches toward the design of pools for the in vitro selection of complex aptamers

The best fitness value observed so far at each generation of Genetic Filtering (primer sites “ATACCAGCTTATTCAATT” and “AGATAGTAAGTGCAATCT”) Parameters: NG = 10,000 NoChargeCutoff = 500 P_crossover = 0.0 P_mutation = 0.9 P_position = 0.0156 P_copy = 0.1 (see Materials and Methods). The best fitness score (i.e., smallest value), which indicates its closeness to the desired uniform structure distribution, decreases steadily with each generation until it remains steady after ∼500 generations. (Inset) Sample secondary structure of the DNA pool sequence (GFPool1). This 100-nt in-length pool, containing 24 random nucleotide positions, was synthesized and used in selection experiments against ATP. Image generated by Mfold.