Controlling Motion of DNA Nanomachines

Rotational Control1: Here, we develop methods for controlling the motion of DNA origami mechanisms, with a focus on optimizing speed of actuation. The ability to actuate dynamic systems in real time is crucial to apply them as functional devices, such as manipulators or delivery vehicles. To demonstrate actuation of our Bennett linkage, we modified the links to include ssDNA overhangs distributed across their length (Figure 4a). Closing DNA strands (shown in green) bind to overhangs on opposite arms, thereby pulling the structure closed. Once in the closed state, additional strands (orange) with a higher binding affinity to the closing strands can remove the closing strands and release the mechanism back to the free state. A bulk fluorescence-quenching assay was used to measure the kinetics of these reactions. Compacting and expanding occurs on the timescale of t1/2 ≈ 1 min (Figure 4e-f).

Distributed actuation of DNA Origami Bennett linkage. (a) ssDNA overhangs distributed across the length of mechanism arms come together when closing strands are added. Once closed, additional releasing strands can be added to remove the closing strands via DNA strand displacement, releasing the mechanism back into the free state. This process was verified through TEM (b-d). The actuation timescales measured using a fluorescence-quenching assay reveal a compacting timescale of t1/2,c = 55 s (e) and expanding timescale of t1/2,e = 49 s (f). Scale bars = 100 nm. Figure from 1.

Linear motion2: A properly formed DNA slider serves as a linear joint useful in engineering mechanisms. Here we present a method for controlling the linear motion using DNA inputs. By adding short single-stranded DNA strands designed to pinch together the scaffold connections on each end of the tube (A, below), we can control the configuration of the sliders. As shown in (B), a set of strands was added to close the middle connections, resulting in sliders with the tube contracted. This yields a clear shift of extension lengths in the distributions of (D). Similarly, in (C) strands were added to pinch the connections on the front end of the slider, resulting in mostly extended sliders also evident in the linear distributions. Sliders in these actuated configurations still have some flexibility due to single-stranded DNA slack left between the two components. Some slack is necessary to traverse the distance between the two attachment points.

Linear actuation with a DNA origami slider. (a) The slider was used to demonstrate a strategy for controlling linear motion. In the unconstrained state, the tube can travel along the track with thermal fluctuations. (b) By adding addition strands (red) we pinch the connections closed to force the slider into a contracted state. (c) Similarly, a set of strands (blue) can be added to fix the slider in the extended state. (d) Measuring sliders through TEM we see a shift in the extension distribution for each case compared to the free slider. Scale bars = 50 nm. Figure from 2.

Rapid actuation using buffer exchange3: We modified a DNA origami hinge with short, weakly complementary single-stranded DNA overhangs, whose hybridization is sensitive to cation concentrations in solution. We triggered conformational changes with several different types of ions including mono-, di-, and trivalent ions and also illustrated the ability to engineer the actuation response with design parameters such as number and length of DNA overhangs and hinge torsional stiffness. Single-molecule Förster resonance energy-transfer (smFRET) measurements revealed that closing and opening transitions occur on the millisecond time scale, and these transitions can be repeated with time resolution on the scale of one second. Our results advance capabilities for rapid control of DNA nanodevices, expand the range of triggering mechanisms, and demonstrate DNA nanomachines with tunable analog responses to the local environment.


Cation-Activated Avidity for Rapid Reconfiguration of DNA Nanodevices [3]


  1. Marras, A. E.; Zhou, L.; Su, H. J.; Castro, C. E. Proceedings of the National Academy of Sciences of the United States of America. 2015, 112, (3), 713-8.
  2. Marras, A. E.; Zhou, L.; Kolliopoulos, V.; Su, H. J.; Castro, C. E. New Journal of Physics. 2016, 18, (5), 055005.
  3. Marras, A.E.; Shi, Z., Lindell, M, Patton, R., Huang, C.-M., Zhou, L., Su, H.-J., Arya, G., Castro, C.E. ACS Nano. 2018, 12, (9), 9484-9494.