DNA NANOTECHNOLOGY
DNA walker
Molecular machines have previously been designed that are propelled by DNAzymes, protein enzymes and strand displacement. These engineered machines typically move along precisely defined one- and two-dimensional tracks. Here, we report two different DNA walker systems that use hybridization to drive walking on DNA-coated microparticle surfaces. Through purely DNA:DNA hybridization reactions, the nanoscale movements of the walker can lead to the generation of a single-stranded product and the subsequent immobilization of fluorescent labels on the microparticle surface. The first walker (bipedal) can take more than 30 continuous steps and then it is released from the microparticle surface. The second walker (unipedal) is designed to stay persistently bound to the particle surface through multiple turnovers, and can take at least 47 (and likely more) steps without release. We have developed engineering principles for the unipedal walkers that dictate partition between release, walking, and staying in place. These autonomous walkers may be of use in analytical and diagnostic applications, similar to how strand exchange reactions in solution have been used for transducing and quantifying signals from isothermal molecular amplification assays.
As with other undirected DNA walkers, it is anticipated that the CHA walkers should remain in a local area. To visually demonstrate that the walkers remain bound to their tracks, we performed fluorescence microscopy on a lawn of primed and unprimed microparticles. Microparticles bearing H1 were distributed onto the surface of a well plate. The lawn of microparticles included a small number (1%) of red fluorescent, catalyst-primed microparticles that were distributed randomly among the unprimed, clear microparticles. Walking was initiated by adding the green-fluorescent hairpin, FAM-H2, in solution. Background FAM-H2 was washed away and fluorescence visualised by microscopy. As expected, red microparticles initially primed with single- or double-catalyst became fluorescent. What was interesting to observe, though, was what happened to adjacent microparticles. For single-domain catalysts no adjacent microparticles lit up. This shows that the no significant amount of catalyst could transfer from the (red) particles primed with single-catalyst to adjacent (clear) unprimed particles. However, for double-catalysts (the walker) there were multiple green microparticles adjacent to the red microparticles, indicating that the walkers had crossed between the microparticles, but only in the local, 3D landscape. Arrows show regions where clear particles have taken on green fluorescence. Co-localised green and red fluorescence is expected (yellow in the false-coloured micrographs). Green colour outside of the yellow regions indicates that double-catalysts have transferred away from their red microparticles of origin. This appears in the false-coloured micrographs as green colour outside of the yellow regions (red, primed particles that also develop green fluorescence).
