Carbon nanotubes offer exciting opportunities for devising highly-sensitive detectors of specific molecules in biology and the environment. Detection limits as low as 10−11 M have already been achieved using nanotube-based sensors. We propose the design of a biosensor comprised of functionalized carbon nanotube pores embedded in a silicon-nitride or other membrane, fluorofullerene-Fragment antigen-binding (Fab fragment) conjugates, and polymer beads with complementary Fab fragments. We show by using molecular and stochastic dynamics that conduction through the (9, 9) exohydrogenated carbon nanotubes is 20 times larger than through the Ion Channel Switch ICSTM biosensor, and fluorofullerenes block the nanotube entrance with a dissociation constant as low as 37 pM. Under normal operating conditions and in the absence of analyte, fluorofullerenes block the nanotube pores and the polymer beads float around in the reservoir. When analyte is injected into the reservoir the Fab fragments attached to the fluorofullerene and polymer bead crosslink to the analyte. The drag of the much larger polymer bead then acts to pull the fluorofullerene from the nanotube entrance, thereby allowing the flow of monovalent cations across the membrane. Assuming a tight seal is formed between the two reservoirs, such a biosensor would be able to detect one channel opening and thus one molecule of analyte making it a highly sensitive detection design.