Assembly and operation of a single stranded DNA catenane
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The creation of molecular machines has been one of the goals of modern nanotechnology for a few decades. Such machines can be assembled from small molecules, as well as DNA. Of particular interest are mechanically interlocked nanoconstructs – catenanes and rotaxanes. These structures offer developments such as nanoswitches and rotational motors. DNA nanotechnology has produced numerous systems that consist of catenanes that could perform programmable switching and stimuli-responsive behaviour, as well as switching between stations in a semi-autonomous, rotary, motor-like behaviour. Energy transduction and the speed of such Brownian ratchet motors are negligible when compared to natural enzymatic activity. Bridging the gap between enzymology and structural DNA nanotechnology, we propose a method to assemble and operate a prototype system of fully complementary interlocked ssDNA rings that can roll against each other as a pair of gears with a ratio 1:2. The directionality and force is proposed to be generated by a strand-displacing polymerase enzyme performing a rolling circle amplification reaction on one of the members of this catenane, generating torque. Computer modelling of this system using oxDNA script package has been carried out, enabling both the topological visualisation and structural inquiry into the system prior to experimental development. Variations to the system such as changing the overall size, gearing ratio and developments towards integration into larger assemblies have also been described and are discussed in detail. Several experimental assembly strategies are described, together with experimental evidence of their outcomes. A method for operation of the single-stranded DNA catenane as a pair of continuously rolling gears has been investigated using strand displacing polymerases. Applications and suggestions for future developments is provided, addressing integration into complex systems. Additional methods of assembly and operation are discussed and compared.