DNA Engineering: the goal is to design a bifunctional aptamer. Part of that bifunctionality hinges on a good reporter blockade (with stationary toggling). Such a blockade is partly brought about by having the Y-molecule caught at the mouth of the channel (such that the terminus of the dsDNA is over the limiting aperture). The other functionality is to bind to some target. The aptamer shown is designed to have a TATA box for TBP binding (the region indicated in the yellow circle).