Fig. 2.

RNA selection strategy. (Step 1) RNA is transcribed from a randomized DNA template that contains a T7 RNA polymerase promoter (boxed). Transcription begins at the G immediately following the promoter. N₆₀ is a 60 nucleotide randomized region. (Step 2) Randomized RNA molecules are bound to a stationary phase through base-pairing with an immobilized DNA oligonucleotide. The oligonucleotide is biotinylated at its 3′ end and immobilized by binding to streptavidin-coated magnetic beads. (Step 3) Beads are washed with buffer to remove unbound RNA (Step 4) RNA is eluted with the desired ligand. RNA elution requires that ligand binding disrupts the intermolecular duplex (5′-GGAAUG-3′ paired with 5′-CATTCC-3′). (Step 5) Eluted RNA is converted to cDNA and amplified to produce the transcription template for the next round of selection. Repeated rounds of selection enrich for RNA molecules that can be eluted by the ligand. Selected RNA molecules are converted to beacon aptamers by (Step 6) adding CAUUCC to their 3′ ends and (Step 7) labeling the ends with fluorophore and quencher.