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April 30, 2010

DNA construction kit for nanoengines

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There is fresh buzz in nanomechanics. Scientists at the University of Bonn have succeeded for the first time in making, out of DNA double stands, an interlocked molecule (rotaxane) with freely moveable components. As the researchers wrote in the latest edition of the science journal "Nature Nanotechnology" (doi: 10.1038/NNANO.2010.65), this opens up exciting possibilities for nanorobotics and synthetic biology. Researchers give a major boost to nanorobotics: Rotaxane molecules made of genetic material.

Nature Nanotechnology - A double-stranded DNA rotaxane
The Bonn-based biochemists have created a completely new kind of rotaxane. It forms a stable mechanical unit, with a freely moving inner hoop. A great deal can be done with this wheel. "We envisage quite a few things," says Professor Famulok. "Our initial aim is to construct systems in which movement can be controlled at the nano-level. The axle and wheels are now available, and we have some ideas for how to get the wheels turning." These nanoengines might then also be combined with other biological systems, such as proteins.

The researchers now realize that, with their DNA rotaxanes, they have laid the foundations for developing all sorts of different nano-mechanical systems based on mechanically interlocked double-stranded DNA. It remains open what will finally emerge from these efforts, but the important breakthrough has been made. "What matters is that we now have a set of novel components with which we can build things that were previously impossible," says Ackermann: "The boundaries of our imagination have, in a sense, been pushed a little further


Abstract - Mechanically interlocked molecules such as rotaxanes and catenanes have potential as components of molecular machinery. Rotaxanes consist of a dumb-bell-shaped molecule encircled by a macrocycle that can move unhindered along the axle, trapped by bulky stoppers. Previously, rotaxanes have been made from a variety of molecules, but not from DNA. Here, we report the design, assembly and characterization of rotaxanes in which both the dumb-bell-shaped molecule and the macrocycle are made of double-stranded DNA, and in which the axle of the dumb-bell is threaded through the macrocycle by base pairing. The assembly involves the formation of pseudorotaxanes, in which the macrocycle and the axle are locked together by hybridization. Ligation of stopper modules to the axle leads to the characteristic dumb-bell topology. When an oligonucleotide is added to release the macrocycle from the axle, the pseudorotaxanes are either converted to mechanically stable rotaxanes, or they disassemble by means of a slippage mechanism to yield a dumb-bell and a free macrocycle. Our DNA rotaxanes allow the fields of mechanically interlocked molecules and DNA nanotechnology to be combined, thus opening new possibilities for research into molecular machines and synthetic biology.


23 pages of supplemental information

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