Fig. 1. Bead assisted EcoRI-HF SELEX to generate structure-switching aptamers. (a) EcoRI-HF library and capture strand sequences with recognition sites in blue. Cut site is illustrated by dotted line. (b) FAM-labeled DNA library having an N₄₀ random region was hybridized to immobilized capture strand and the complex washed and photocleaved. After target incubation, bound sequences were recovered following EcoRI-HF digestion and PCR amplification. Gel purified library was then carried on to subsequent rounds. ssDNA library was purified by 10% denaturing PAGE and carried on to subsequent selection rounds. (c) Highly enriched sequences did not correctly hybridize the capture strand through the built in EcoRI-HF recognition site (underlined blue) sequences containing partial recognition sites in the N₄₀ region (underlined black) with one or more mismatches (red, bold) were present in predicted structures by NUPACK.