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

Sample secondary structure of the RFPool A DNA sequence including primer sites “GGAAGAGATGGCGAC” and “AGCTGATCCTGATGG” designed to generate the highest percentage of 5J sequences (31.13%). Image generated by Mfold. The sequence has 19 single-stranded positions, excluding primer sites (noted as “N”). As a starting pool for SELEX experiments, these 19 single-stranded positions are considered as random (N) and the other positions are considered as fixed.