Machines constructed from DNA can be made to walk along self-assembled DNA tracks. The simplest devices are controlled by sequential addition of DNA signals (molecules of single-stranded DNA, or oligonucleotides). Signal strands interact by hybridizing with complementary single-stranded DNA to form a double-helical duplex; they can also displace a strand from an existing duplex. For example, a signal strand can hybridize to bind a foot of the walker to its track. A complementary signal strand can then reverse this reaction by displacing the “binding” strand, forming a double-stranded waste product and freeing the foot to step forward. Such strand-exchange reactions can be accelerated by several orders of magnitude by the provision of “toeholds”—short sections of exposed single-stranded DNA that can initiate hybridization to the invading strand. Strategies for sequestering and activating toeholds, for example in an autonomous reaction cycle where toehold strands are progressively revealed, have progressed to the point where an external operator is no longer required to control the reaction sequence of the walker. Autonomous bipeds that walk on a reusable track have been designed by coordinating the reactions of DNA fuels with the two feet so that the front foot remains bound to the track while the back foot is lifted. Researchers from the same group that demonstrated the biped, R. Muscat, J. Bath, and A. Turberfield of the University of Oxford, recently demonstrated a DNA motor whose sequence of movements can be programmed by instructions embedded in its DNA fuel molecules. Unlike typical bipedal walking devices, this new motor is normally bound to a single anchorage, operates autonomously, and can be programmed to choose between branches on the track.

As reported in the January 28th online edition of Nano Letters (DOI: 10.1021/nl1037165), Turberfield and co-researchers produced a track consisting of addressable anchorages tethered to a double-stranded DNA backbone. The single-stranded cargo can bind to any anchorage. Parts of the anchorage and cargo that remain single-stranded are held together to form a structure the researchers refer to as a “split-toehold,” which not only signals the cargo’s presence but identifies the current anchorage by displaying its address (a specific sequence of nucleotides). Cargo transfer is mediated by a DNA fuel molecule that provides both energy and a routing instruction; it carries address domains that mediate transfer of the cargo between two specific anchorages.

The researchers used a simple two-anchorage track to demonstrate the coupling of fuel hairpins to control cargo movement by sequential activation of split toeholds. A three-anchorage track was then used to demonstrate the control of directional transport by information stored in the fuel hairpins. Furthermore, a T-junction track with four anchorages and branch points was used to demonstrate that the DNA motor could navigate complex paths. The researchers said, “We have made a further step in the development of molecular robotics by showing that the behavior of an autonomous motor on a branched track can be programmed by a rewritable external program encoded in DNA.”