An RNA origami robot that traps and releases a fluorescent aptamer

Abstract

RNA nanotechnology aims at using RNA as a programmable material to create self-assembling nanodevices for application in medicine and synthetic biology. RNA devices have been developed by adopting mechanisms such as allosteric binding and toehold-mediated strand displacement. There are, however, no examples of RNA "robotic" devices that sense, compute, and actuate through mechanical reconfiguration as has been demonstrated in DNA nanotechnology. Here we use the RNA origami method to prototype an RNA robotic device, named the "Traptamer", that senses two RNA key strands, acts as a Boolean AND gate, and activates the fluorescent aptamer iSpinach through release from a mechanical trap. The Traptamer depends on binding of two different RNA key strands to achieve full activation and can be reversed by addition of two complementary RNA anti-key strands. Cryo-EM of the closed Traptamer structure at 5.45 [A] resolution reveals a hinge-like mechanical distortion of the iSpinach motif. Our RNA robot prototype opens the door to build more sophisticated RNA machines that use sensing, computing, and acting modules to precisely control RNA functionalities.