Model Railways

I’ve been in Leeds for a few days for the biennial conference of the Polymer Physics Group of the UK’s Institute of Physics. Among many interesting talks, the one that stood out for me was the first – an update from Andrew Turberfield on his efforts to make a molecular motor from DNA.

Turberfield, who is at the Oxford IRC in Bionanotechnology, is building on the original work from Ned Seeman, exploiting the remarkable self-assembling properties of DNA to make nanoscale structures and devices. A few years ago, Turberfield, working with Bernie Yurke at Lucent Bell Labs, designed and built a DNA nano-machine (see here for a PDF preprint of the original Nature paper), and in 2003 they published a paper describing a free-running motor powered by the energy released when two complementary strands of DNA meet to make a section of double helix (abstract here).

This motor doesn’t actually do anything, apart from sit around in solution cyclically changing shape. What Turberfield wants to do now is make something a bit like the linear motors common in cell biology, in which the motor molecule moves along a track, often carrying a cargo. To make this kind of molecular railway, Turberfield’s scheme is to prepare a track along a surface by grafting strands of DNA to it. The engine is another DNA molecule; what needs to be done is get some scheme whereby the engine molecule is systematically passed along from strand to strand.

His first effort, in collaboration with Duke University’s John Reif, involves using enzymes to alternately cut DNA strands and rejoin them in a sequence that has the effect of making a short strand of DNA move linearly in one direction. In this case, it’s the energy used by the enzyme that joins two bits of DNA that makes the motor run. The full paper is here (PDF). In motor mark 2, it’s a so-called nicking enzyme that makes the engine move, and the directionality is imposed by the fact that the track is destroyed in the path of the engine (abstract here, subscription probably required for full article). What Andrew really wants to do, though, is have a motor that is solely powered by the energy released when DNA strands make a helix, which doesn’t chew up the track behind it, and which doesn’t involve the use of any biological components like enzymes. He has a scheme, and he is confident that it’s not far off working.

These motors are inefficient and slow in their current form. But they are important, because they work on the same basic principles as biological motors, principles which are very different to the mechanical principles that underly the motors we are familiar with. They rely on the Brownian motion and stickiness of the nanoscale environment. But because of the simplicity of the base pair interaction, the calculations you need to do to predict whether the motor will work or not are feasibly simple. By learning to make model railways from these simple, modular components, we’ll learn the design rules that will enable us to make a wider variety of practical nanoscale motors.

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