DNA-based Nanomachine Design

The goal of this work is to create various machine elements with specific motion by adapting an engineering machine design approach to DNA origami. In macroscale engineering, mechanisms and machines are assembled using a combination of joints constrained to allow rotation, linear motion, or combinations thereof.

A series of static TEM snapshots demonstrating the rotational motion of unconstrained DNA origami hinges

Rotation has been demonstrated with DNA nanotechnology1-3, including systems exhibiting reversible motion3, although specific motion was not a focus. Linear motion, however, remained largely unexplored. The concept behind our design approach is to construct stiff components (i.e. links) using bundles of double-stranded DNA and connect those links at joints formed by flexible single-stranded DNA connections. Using this idea we have fabricated hinges4 (1D rotational motion), sliders4, 5 (1D linear motion), universal joints6 (2D rotational motion), and compliant joints7 allowing for tunable flexibility. These joints are depicted in solid models and transmission electron microscopy (TEM) images below.

DNA origami joints. (a) Hinge with 1 degree of rotational freedom (b) Slider with 1 degree of linear motion (c) Universal joint with 2 degrees of rotation (d) Compliant joint allowing for restricted flexibility. Scale bars in (a) and (d) are 20 nm and in (b) and (c) are 50 nm.

Similar to macroscopic engineering, we built higher-order mechanisms with specific motion by integrating several links and joints into one system. The figure below shows examples of these mechanisms, which include a crank-slider4 (coupling rotational and linear motion), a Bennett linkage4 (3D motion), a bi-stable mechanism8, and a scissor mechanism6.

DNA origami mechanisms. (a) Crank-slider coupling rotational and linear motion (b) Bennett linkage moving between an expanded frame configuration and a compacted bundle (c) Bi-stable mechanism using hinges and a compliant joint to cross a designed energy barrier to switch between two stable states (d) Scissor mechanism translated rotational motion to linear motion. This structure can be polymerized to amplify extension. Scale bars are 50 nm except (b) is 100 nm.

Static TEM snapshots demonstrating the 3D motion of DNA origami 4-bar Bennett Linkages

Back cover art for Nanoscale Issue 14, 2015

References:

  1. Andersen, E. S.; Dong, M.; Nielsen, M. M.; Jahn, K.; Subramani, R.; Mamdouh, W.; Golas, M. M.; Sander, B.; Stark, H.; Oliveira, C. L.; Pedersen, J. S.; Birkedal, V.; Besenbacher, F.; Gothelf, K. V.; Kjems, J. Nature 2009, 459, (7243), 73-6.
  2. Douglas, S. M.; Bachelet, I.; Church, G. M. Science 2012, 335, (6070), 831-4.
  3. Kuzuya, A.; Sakai, Y.; Yamazaki, T.; Xu, Y.; Komiyama, M. Nature communications 2011, 2, 449.
  4. 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.
  5. Marras, A. E.; Zhou, L.; Kolliopoulos, V.; Su, H. J.; Castro, C. E. New Journal of Physics 2016, 18, (5), 055005.
  6. Castro, C. E.; Su, H. J.; Marras, A. E.; Zhou, L.; Johnson, J. Nanoscale 2015, 7, (14), 5913-21.
  7. Zhou, L.; Marras, A. E.; Su, H. J.; Castro, C. E. ACS nano 2014, 8, (1), 27-34.
  8. Zhou, L.; Marras, A. E.; Su, H. J.; Castro, C. E. Nano letters 2015, 15, (3), 1815-21.
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