Real-time magnetic actuation of DNA nanodevices via modular integration with stiff micro-levers

Abstract

DNA nanotechnology has enabled complex nanodevices, but the ability to directly manipulate systems with fast response times remains a key challenge. Current methods of actuation are relatively slow and only direct devices into one or two target configurations. Here we report an approach to control DNA origami assemblies via externally applied magnetic fields using a low-cost platform that enables actuation into many distinct configurations with sub-second response times. The nanodevices in these assemblies are manipulated via mechanically stiff micron-scale lever arms, which rigidly couple movement of a micron size magnetic bead to reconfiguration of the nanodevice while also enabling direct visualization of the conformation. We demonstrate control of three assemblies-a rod, rotor, and hinge-at frequencies up to several Hz and the ability to actuate into many conformations. This level of spatiotemporal control over DNA devices can serve as a foundation for real-time manipulation of molecular and atomic systems.

Fig. 1

Components for actuated assemblies. The prototype nanomachines include a a nano-rotor composed of two separate constructs, the nano-brick and a nano platform, which are connected together via single-stranded DNA (ssDNA) overhang and b nano-hinge consisting of two stiff nano-rods with 36 double-stranded DNA (dsDNA) helices joined at one end by 8 ssDNA strand connections. c A 56-helix nano-brick composed of 56 dsDNA helices bundled together was used as a basis for a lever arm. d The DNA mechanical lever arm for actuation is a 1D array of nano-bricks. Cylindrical models are shown for each with each cylinder representing a DNA helix. AFM and TEM images are shown with scale bar 50 nm for images a–c and 500 nm for image d

Fig. 2

Schematic illustrations of three DNA microsystems. a DNA Lever System, b DNA Rotor System, and c DNA Hinge System—were assembled from DNA nanostructures to actuate three DNA nano constructs—56 Helix nano-brick, nano-rotor and nano-hinge. a The nano-brick was attached to the surface via biotin-streptavidin affinity while a micro-lever arm attached to the other end. b The nano-platform in the nano-rotor was attached to the surface via biotin-streptavidin affinity, while two micro-lever arms were attached on both sides of the nano-rotor arm. c Two micro-lever arms are attached to the nano-hinge. The entire bottom arm of the hinge is fixed to the surface via biotin-streptavidin affinity, while the top micro-arm is free to fluctuate. Micromagnetic beads are attached to the free end of the micro-lever arm in each system. Rotating in-plane fields apply a torque on the bead, precessing the nano-rod and nano-rotor, and opening and closing the nano-hinge

Fig. 3

Assembly of systems. a ssDNA connecting two structures (polymerization strands) were designed with a u-shaped motif where half have a higher affinity to attach to one side of the interface while the other half have higher affinity to the other side of the interface. b Stiff micro levers are assembled by attaching 56 helix nano-bricks end-to-end using polymerization strands. AFM and TEM images show micro-levers. Scale bar is 1 μm. c The nano-rotor is assembled by attaching a nano-platform to a nano-brick via a single ssDNA overhang. AFM and TEM images show the nano-rotor construct. Scale bar is 50 nm. d Stiff micro-levers are formed off the arm of the nano-rotor using polymerization stands to connect the nano-arm to micro levers. AFM and TEM images show the assembled micro-rotor. Scale bar is 100 nm. e A single nano-brick is attached initially to the top and bottom of the nano-hinge using two separate sets of polymerization strands for top (green-blue) and bottom (red-blue). AFM and TEM images show the hinge with top and bottom nano-bricks attached. Scale bar is 50 nm. f Stiff micro-levers are formed off the initial nano-bricks by attaching top nano-rods (green) and bottom nano-rods (red) using two separate sets of polymerization staples for the top (green) and the bottom (red). Zoomed out image of AFM and TEM image show a polymerized nano-hinge (scale bars are 500 nm, left and right). Zoomed in image of the nano-hinge from in the AFM image (scale bar is 50 nm, middle)

Fig. 4

Actuation of micro-lever. a Images of the micro-lever rotated over 360 degrees at 1 Hz shown rotating 90° every fourth of a second corresponding to 0, 0.25, 0.5, 0.75, and 1 s. Scale bar is 1 μm. b Levers were actuated at four frequencies 0.1, 0.5, 1, and 2 Hz (black, blue, green and red) with rotation traces overlaid for 17 different beads. Inset: Representative tracking of one micro-bead attached to the micro-lever. c External in-plane magnetic fields were applied in four orthogonal directions to reorient the lever. d Representative tracking of bead fluctuations in an in-plane external magnetic field oriented in the +y direction with strengths 10, 20, 30, 40, 50 and 100 Oe (black, blue, green, red, yellow, and cyan). The asterisk indicates the origin. The standard deviation of the e in-plane and f out-of-plane fluctuations of 13 lever arms, each tested at four orthogonal orientations at every field strength (each color indicates a different lever arm-bead construct, and error bars indicate s.d. over four orientations). Insets show the average and standard deviation of the e in-plane and f out-of-plane angular fluctuations across all 13 micro-levers (black trace), and the red traces represent the average of the four longest micro-levers. g The in-plane angular distribution of the bead shown in purple in e and f shows greater confinement at 100 Oe (cyan in d) compared to 10 Oe (black in d). h The free energy landscape assuming Boltzmann weighting was calculated from the probability distributions for the same bead at 10 Oe and 100 Oe. i The torque on the same magnetic bead was also calculated at 10 Oe (purple circles) and 100 Oe (purple diamonds) by differentiating the free energy landscapes

Fig. 5

Actuation of prototype nanomachines. a Actuation of nano-rotor. Fluorescence images of nano-rotor magnetically actuated in a flow channel via the micro-lever arm attached to micro-magnetic beads. The nano-platform is falsely colored in blue and arms in red with overlapping positions in white. The nano-rotor is rotated by 360 degrees with a frequency of 1 Hz and rotates by 90° every fourth of a second corresponding to video time frames at 0, 0.25, 0.5, 0.75 and 1 s. b Actuation of nano-hinge. Fluorescence images of nano-hinge magnetically opened and closed in a flow channel using the extension of micro-lever arms attached to micro-magnetic beads. The nano-hinge is falsely colored in blue and arms in red with overlapping positions in white. Video time shots of the hinge closing (0, 0.2, 0.4 s) and reopening (2, 2.2 s) such that the hinge was left closed from 0.4–1.8 s before being reopened. Scale bars are 1 μm