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Research Papers: Design of Mechanisms and Robotic Systems

The Kinematic Principle for Designing Deoxyribose Nucleic Acid Origami Mechanisms: Challenges and Opportunities1

[+] Author and Article Information
Hai-Jun Su

Department of Mechanical and
Aerospace Engineering,
The Ohio State University,
Columbus, OH 43210
e-mail: su.298@osu.edu

Carlos E. Castro

Department of Mechanical and
Aerospace Engineering,
The Ohio State University,
Columbus, OH 43210
e-mail: castro.39@osu.edu

Alexander E. Marras

Department of Mechanical and
Aerospace Engineering,
The Ohio State University,
Columbus, OH 43210
e-mail: marras.3@osu.edu

Lifeng Zhou

Department of Mechanical and
Aerospace Engineering,
The Ohio State University,
Columbus, OH 43210
e-mail: zhou.809@osu.edu

2Corresponding author.

Contributed by the Mechanisms and Robotics Committee of ASME for publication in the JOURNAL OF MECHANICAL DESIGN. Manuscript received August 28, 2016; final manuscript received March 8, 2017; published online April 6, 2017. Assoc. Editor: David Myszka.

J. Mech. Des 139(6), 062301 (Apr 06, 2017) (9 pages) Paper No: MD-16-1599; doi: 10.1115/1.4036216 History: Received August 28, 2016; Revised March 08, 2017

Deoxyribose nucleic acid (DNA) origami nanotechnology is a recently developed self-assembly process for design and fabrication of complex three-dimensional (3D) nanostructures using DNA as a functional material. This paper reviews our recent progress in applying DNA origami to design kinematic mechanisms at the nanometer scale. These nanomechanisms, which we call DNA origami mechanisms (DOM), are made of relatively stiff bundles of double-stranded DNA (dsDNA), which function as rigid links, connected by highly compliant single-stranded DNA (ssDNA) strands, which function as kinematic joints. The design of kinematic joints including revolute, prismatic, cylindrical, universal, and spherical is presented. The steps as well as necessary software or experimental tools for designing DOM with DNA origami links and joints are detailed. To demonstrate the designs, we presented the designs of Bennett four-bar and crank–slider linkages. Finally, a list of technical challenges such as design automation and computational modeling are presented. These challenges could also be opportunities for mechanism and robotics community to apply well-developed kinematic theories and computational tools to the design of nanorobots and nanomachines.

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Figures

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Fig. 1

Examples of some two-dimensional and three-dimensional static DNA origami nanostructures (Reproduced with permission from Castro et al. [9]. Copyright 2011 by Nature Publishing Group.)

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Fig. 2

DNA origami nanoconstruction utilizes a bottom-up assembly process via base-pairing amino acids A–T, C–G. (a) The scaffold sequence is fully known, and staple strands are designed to be piecewise complementary to the scaffold. (b) The scaffold folds to allow full binding to the staple strands, as illustrated for a single staple; hence, the staple sequences control the folded geometry. For clarity, DNA double helices in scaffolded DNA origami structures are often represented by solid cylinders that are connected at junction points where staples cross over from binding one scaffold section to another. (c) Full DNA origami structures consist of many helices, depicted as cylinders, connected by many junction points (black lines) along their length. (Reproduced with permission from Su and Castro [47]. Copyright 2016 by ASME.)

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Fig. 3

Design of rigid links of various shapes using bundles of dsDNA helices. Each dsDNA helix has a diameter of ∼2 nm.

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Fig. 4

The steps for designing and prototyping a planar plate: (a) build the solid model of the plate, (b) approximate the plate with 2 nm cylinders, (c) design scaffold routing blueprint, (d) produce the complementary staple design, (e) extract staple sequences, and (f) experimental prototyping

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Fig. 5

Five basic kinematic joints and the corresponding DNA origami design. The curves represent ssDNA strands that are very soft. Cylinders represent dsDNA strands that are relatively rigid.

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Fig. 6

The design process of a Bennett four-bar DNA origami mechanism and the tool used in each step in parentheses: (a) the conceptual design, (b) the solid model embodiment using cad software, (c) geometry approximation with 2 nm cylinders, (d) scaffold blueprint and staple sequence design using cadnano software, (e) simulation of self-assembled 3D structures using cando software, and (f) transmission electron microscopy (TEM) images of fabricated prototypes. Note the scaffold connection points (short curves) are made of very short ssDNA strands.

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Fig. 7

A DNA origami crank–slider mechanism: (a) the solid model, (b) the cylinder model, and (c) the TEM image of the fabricated prototype [8]

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Fig. 8

Strand-based actuation approach. (Left) DNA origami joint components are modified to include ssDNA staple overhangs which protrude from the rigid arms in a specified direction and location (red and blue). Closing strands (green) can then be introduced to bind to multiple overhangs, bringing the overhangs and their components together. Additional unpaired bases on the closing strand, called a toehold, can be used to remove closing strands and release the components via DNA strand displacement. Opening strands (orange) are designed to be fully complementary to entire closing strand including the toehold and will peel, or displace the closing strand from the overhangs. The fully paired duplex (green and orange) is now inert in solution.

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Fig. 9

Examples of strand-based actuation. (a) The strand-based actuation approach detailed in Fig. 8 used to reversibly control a four-bar Bennett linkage [8]. (b) TEM images of compacted and unconstrained conformations verify the effectiveness of this method with over 90% of structures observed in the desired conformation. (c) The unconstrained slider uses a similar approach to control its conformation [36]. (d) Actuation strands (blue) were programed to bind to specific sites on the scaffold, fixing the slider in this contracted conformation. (e) Another set of strands (red) can be used to fix the slider in the extended conformation. Scale bars = 50 nm (Reproduced with permission from Marras et al. [8,36]. Copyright 2015 by IOPScience and 2016 by United States National Academy of Sciences.)

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Fig. 10

A DNA origami Stewart–Gough six-axis platform (left) and a DNA origami robotic manipulator for precise molecular positioning (right)

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