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

Comparison of average structural distribution (percent of sequences displaying a given junction order: either one-way, two-way, three-way, four-way, or five-way junction structures) of 1 million sequences for random RNA/DNA pools (dark gray) and RNA/DNA pools generated by our Random Filtering process (light gray). (A) Without primer sites, Random Filtering has greatly increased the percentage of high-complex structures such as 5Js (by 10%) and 4Js (by 15%). (B) With 15-nt primer sites at both ends, “GGAAGAGATGGCGAC” and 15 “AGCTGATCCTGATGG” (light gray). Random Filtering has greatly increased the percentage of high complex structures such as 5Js (by 6%) and 4Js (by 10%).