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D
DNA Mechanisms
and Machines for
Nanorobotics
Lifeng Zhou
The RNA Institute, The State University of New
York at Albany, Albany, NY, USA
Synonyms
DNA nanomachines;DNA-based molecular ma-
chines;DNA-based nanorobots;Dynamic DNA
nanostructures
Definitions
DNA Mechanisms and Machines
DNA mechanisms and machines are made by
using DNA as materials to build the assembled
links and joints. The links are formed by
relatively rigid double-stranded DNA (dsDNA)
bundles and the joints are constructed by flexible
single-stranded DNA (ssDNA) segments or rigid
components with geometrical constraints. Also,
complaint DNA mechanisms can be designed by
gently tuning the stiffness of dsDNA bundles.
Driven by one or more linear or rotatory
actuators, these DNA mechanisms can achieve
a predetermined motion pattern much like
macromachines. These DNA machines have
shown promising applications in targeted drug
delivery and biosensors.
Overview
In the macroscopic world, a mechanism is an
assembly of mechanical parts linked together by
joints in an open or closed chain, for example, the
arm of a robot and four-bar linkage (McCarthy
2006). Mechanisms are used in machines so that
they can successfully transmit forces, motion, and
energy from the input to the output components.
Similarly, machines can also be constructed at
the nanoscale and researchers from many disci-
plines have contributed their efforts to the de-
velopment of nanomachines. For example, Dr.
Jean-Pierre Sauvage, Dr. Sir J. Fraser Stoddart,
and Dr. Bernard L. Feringa, who are chemists,
won the 2016 Nobel Prize in Chemistry because
of their pioneering work on nanomachines con-
structed by small chemical molecules (Toumey
2017). Also, in a long period of time, the kine-
matics and mechanism community tried to de-
sign mechanisms at nanoscale by using proteins
whose structures can be modeled via kinematic
linkages (Kazerounian 2004; Chirikjian et al.
2005). Protein-based nanomotors and nanorobots
could be designed based on the investigation of
the mechanical properties of biological motors
that exist in nature, such as ATP, kinesin, and
myosin (Mavroidis and Ferreira 2013). However,
there were many challenges for engineers to build
nanomachines by using proteins or small chemi-
cal molecules due to the extremely complex and
costly fabrications. At almost the same period,
the rise of DNA nanotechnology provided a much
easier and feasible approach to build complex
© Springer-Verlag GmbH Germany, part of Springer Nature 2021
M. H. Ang et al. (eds.), Encyclopedia of Robotics,
https://doi.org/10.1007/978-3-642-41610-1_217-1
2 DNA Mechanisms and Machines for Nanorobotics
nanomachines at a relatively low cost due to
the development of the chemical synthesis of
DNA oligos. The recent design process primar-
ily developed by research groups at The Ohio
State University lays out the key foundation for
formalizing the design of DNA mechanisms and
machines (Huang et al. 2020).
DNA Nanotechnology
DNA nanotechnology uses DNA as materials
to design and build nanostructures with vari-
ous chemical, biological, and physical proper-
ties. Proposed first in the 1980s by Dr. Nadrian
C. Seeman, DNA strands with meticulously de-
signed sequences could self-assemble into immo-
bile junctions (Seeman 1982), such as the Holli-
day Junction (Liu and West 2004), by following
the Watson-Crick base pairing principle, A-T
and G-C. Based on these junctions, 2D and 3D
lattices and higher-order nanostructures could be
assembled. Thereafter, DNA-based mechanical
devices that could achieve simple rotation and
translation motions were also constructed, mainly
by self-assembling of quite a few oligos. For
example, flexible ssDNA segments, usually 2 to
4 nucleotides, were used to connect relatively
rigid short dsDNA links to form a pair of tweez-
ers that could accomplish “scissors-like” opening
and closing (Simmel and Yurke 2002). Besides,
the dsDNA segment with the “proto-Z” sequence
could be triggered by high ionic strength to twist
from B-DNA to Z-DNA (Mao et al. 1999). Ex-
tension and contraction motion had also been
achieved by using G-quadruplex (Alberti and
Mergny 2003) that had a duplex (extension)–
quadruplex (contraction) equilibrium fueled by a
complementary ssDNA. However, the motions of
these DNA-based mechanical devices are mainly
realized by the change of their configurations,
lacking the fidelity of kinematic joints used in
macroscopic mechanisms. Also, made by single
or several DNA duplexes, their degrees of free-
dom and mechanical properties are limited.
In one of the landmark papers of DNA nan-
otechnology published in 2006, Dr. Rothemund
introduced the scaffolded DNA origami which
was then evolved rapidly into a powerful tech-
nique for constructing 2D and 3D nanostructures
with unprecedented geometries (Rothemund
2006). Illustrated in Fig. 1a, the scaffolded DNA
origami uses a bunch of shorter (∼30–50 bases)
ssDNA, named staples, to fold a long (∼7000–
8000 bases) ssDNA template, named scaffold,
into the designed geometry driven by Watson
and Crick base pairing principle. The sequences
of the DNA staples are strategically designed so
that they can be piecewise complementary to the
scaffold and bring spatially distant sections of
the scaffold together. With the synergistic work
of all staples, the scaffold could be folded into a
compact and stable DNA nanostructure. Usually,
most of those DNA origami nanostructures
are constructed by dsDNA bundles, straight or
curved (Fig. 1b).
DNA Mechanisms and Machines for Nanorobotics,
Fig. 1 DNA origami and examples. (A) Fundamental
steps of DNA origami. (B,C,D,E)ExamplesofDNA
origami nanostructures: smiley face (Rothemund 2006),
octahedra (Douglas et al. 2009a), gear (Castro et al. 2011),
and sphere (Han et al. 2011). The oversizes of these DNA
origami nanostructures are smaller than 100 nanometers
DNA Mechanisms and Machines for Nanorobotics 3
D
DNA Mechanical Properties
Experiments have shown that DNA bundles can
be bent and twisted by either internal stresses
or external forces (Dietz et al. 2009; Liedl et al.
2010; Kauert et al. 2011). The mechanical prop-
erties of DNA bundles could be partially charac-
terized by their persistence length (LP), defined as
LP=KB/(kBT), where KB=EI,Eis the effective
Young’s module of dsDNA and Iis the area
moment of inertia, kBis Boltzmann’s constant,
and Tis absolute temperature (Schiffels et al.
2013), the dsDNA bundle can be modeled as a
continuous beam when its length is shorter than
its persistence length. Experiments found that
the persistence length of single dsDNA is about
50 nm at room temperature, varied a little bit
under different chemical conditions (Bustamante
et al. 2000).
Realizing that the DNA origami can have rel-
atively rigid dsDNA bundles and flexible ssDNA
assembled on the same nanostructure, Dr. Hai-jun
Su and Dr. Carlos E. Castro et al. pioneered in the
design and fabrication of DNA mechanisms by
mimicking the counterpart concepts of links and
joints used in the macroscopic world (Su et al.
2012).
Key Research Findings
DNA Kinematic Joints
To distinguish from the “dynamic DNA nanos-
tructures” used in many publications, here the
DNA mechanisms are defined like the macro-
scopic mechanisms that have rigid or compliant
links connected by kinematic joints with at least
one degree of freedom. The links are usually
formed by relatively rigid dsDNA bundles and
the joints are designed by mimicking their macro-
scopic counterparts with necessary geometrical
modifications that do not influence their mobility.
Constrained by their links’ geometries and/or po-
sitions of ssDNA connections which are usually
short segments of the long scaffold, the DNA
joints can achieve the predetermined motions as
their macroscopic counterparts. Though ssDNA
connections can also be constructed by short
DNA staples, this kind of connection is always
weaker than the scaffold connections due to their
shorter binding region. Figure 2shows the five
classic kinematic joints, including revolute (R),
prismatic (P), cylindrical (C), universal (U), and
spherical (S) joints, their degrees of freedom,
and their DNA origami design and fabrication re-
sults shown by transmission electron microscope
(TEM) images.
DNA Mechanisms Made of Kinematic
Linkages
Currently, several classic DNA mechanisms have
been designed and fabricated, including the Ben-
nett linkage (Su et al. 2012), a slider-crank mech-
anism (Marras et al. 2015), a four-bar straight-
line mechanism (Huang et al. 2019), the wa-
terbomb base which is a classic element used
in paper origami (Zhou et al. 2018), and the
Stewart platform (Huang et al. 2020). Here, like
the macroscale mechanisms, those DNA mecha-
nisms were summarized and categorized as open
chain and closed chain, planar, and spatial mech-
anisms shown in Fig. 3.
Compliant DNA Joints and Mechanisms
Compliant mechanisms have found many appli-
cations in the design of microscale machines
(Howell 2001). The complaint DNA mechanisms
can also be designed according to their macro-
scopic counterparts because the stiffness of ds-
DNA bundles can be tuned by changing the
dimensions and formats of their cross-sections.
Fig. 4a shows the design of a DNA complaint
joint whose complaint element is a single layer
of six dsDNA helices, connecting two relatively
rigid links whose cross-section has 18 helices
organized in three layers (Zhou et al. 2014). Its
bending was induced by the long ssDNA connec-
tions placed under the compliant element. Fig. 4b
shows a compound joint constructed by serially
assembling a compliant crossed leaf-type hinge
with a rotation degree of freedom and a compli-
ant prismatic joint whose motion is induced by
the bending of the two plates between the top
and bottom links (Huang et al. 2020). Figure 4c
shows a four-bar bistable mechanism that can
switch between the two stable configurations by
overcoming the energy barrier induced from the
4 DNA Mechanisms and Machines for Nanorobotics
DNA Mechanisms and Machines for Nanorobotics, Fig. 2 Five basic kinematic joints and the corresponding DNA
origami design and fabrication results shown by TEM images. N/A not available
deformation of the compliant link which is fixed
on the bottom frame link (Zhou et al. 2015). Fig-
ure 4d,e, respectively, shows a compliant DNA
gripper and a compliant robotic arm with multiple
compliant joints and links (Huang et al. 2020).
Also, the Holliday junction can be modeled
as a compliant mechanism with four complaint
joints and four rigid links and its two configu-
rations correspond to the two minimum energy
positions. The interconversion of the Holliday
junction between its two configurations can be
triggered by an auxiliary ssDNA staple (Song
et al. 2017).
Actuation of DNA Joints and Mechanisms
DNA mechanisms are self-assembled in solutions
with a variety of chemical substances. Without
extra control and actuation, their motions are
dominated by thermal fluctuation and their con-
figurations vary over time with freely moving
joints. In macroscale, kinematic joints are usually
actuated by electric or hydraulic motors. How-
ever, molecular motors that can be assembled
with DNA mechanisms are still under develop-
ment.
Currently, the most popular method to control
revolute joints of DNA mechanisms is to have
ssDNA overhangs hybridized with actuation
oligos (Fig. 5a,b). Briefly, ssDNA overhangs
are segments of DNA staples extended from
the DNA links. The hybridization of overhangs
and the actuation (closing and opening) DNA
strands can drag the two DNA links together
by rotating about the revolute joint axis. The
actuation of a prismatic joint can be achieved
by shortening the long ssDNA connections,
portions of the scaffold, tied between the slide
and its track (Fig. 5c). The shortening can
be achieved by the binding of DNA oligos
that can fold the long ssDNA connections
into a small DNA loop. On the other side,
the actuation DNA strands can be released by
DNA Mechanisms and Machines for Nanorobotics 5
D
DNA Mechanisms and Machines for Nanorobotics, Fig. 3 DNA mechanisms with more than one kinematic joint
DNA Mechanisms and Machines for Nanorobotics,
Fig. 4 Compliant DNA joints and mechanisms. (a)
Compliant DNA revolute joint(Zhou et al. 2014). (b)A
DNA compliant compound joint constructed by a crossed
leaf-type hinge and a compliant prismatic joint (Huang
et al. 2020). (c) DNA four-bar bistable mechanism(Zhou
et al. 2015). (d,e) Compliant DNA gripper and robotic
arm (Huang et al. 2020). Scale bars: 20 nm
the DNA displacement reaction (Fig. 5a) and
have the DNA mechanisms back to their free
configurations. This kind of DNA strand-based
actuation method has many advantages: first,
it can be easily designed and assembled with
the DNA mechanisms; second, it can be easily
reprogrammed by just varying the sequences of
overhangs and actuation strands; third and most
important, it can be used to program stepwise
6 DNA Mechanisms and Machines for Nanorobotics
DNA Mechanisms and Machines for Nanorobotics, Fig. 5 Actuation of DNA
joints. (a) DNA strand-based actuation. (b,c) DNA strand-based actuation of revolute
and prismatic joints (Marras et al. 2015,2016). (d) DNA base-stacking actuation
(Gerling et al. 2015). (e) Electric field actuation (Kopperger et al. 2018). (f) Magnetic
field actuation with the help of an attached magnetic bead (Lauback et al. 2018). Scale
bars: 50 nm
DNA Mechanisms and Machines for Nanorobotics 7
D
actuation of individual joints. Additionally, the
actuation DNA strands can be eliminated by hav-
ing the pair of overhangs hybridized into a ds-
DNA with the assistance of high ion concen-
trations, including mono-, di-, and trivalent ions
(Marras et al. 2018).
Moreover, the base-stacking between two ad-
jacent dsDNA blunt ends can be used to actuate
and assemble DNA mechanisms (Fig. 5d) and
the attraction force of base-stacking can be tuned
by varying the concentration of Mg2+(Gerling
et al. 2015). This kind of approach could actu-
ate many joints in a single reaction, losing the
control of individual joints independently. On
the other side, rotating electric fields (Fig. 5e)
had been employed to actuate and control the
rotation of a DNA link that was connected to
a fixed DNA plate by a revolute joint made
of ssDNA connections (Kopperger et al. 2018).
This method is rooted in the fact that the DNA
molecules are negatively charged. Also, magnetic
fields (Fig. 5f) can be used to control the rota-
tion of a micrometer-long DNA link of a DNA
revolute joint (Lauback et al. 2018) with the
help of an attached magnetic bead. Controlling
the motion of the attached magnetic bead by
external magnetic fields, the long DNA link can
rotate about the rotation axis of the joint with
required rotation range and speed. Both electrical
and magnetic fields can precisely control and
actuate single joint; however, there are still many
challenges lay ahead before they can be used on
the actuation of DNA mechanisms. For example,
both must have the DNA mechanisms fixed on a
platform or surface, the electrical field will have
force applied on the entire mechanism because
the entire DNA mechanism is negative charged,
and it is arduous, sometimes unacceptable by
the application environments, for example, in the
cells, to assemble a DNA mechanism with a
micrometer-long DNA link.
Design and Analysis Tools
Currently, the design of DNA nanostructures has
been greatly simplified over the years with devel-
oped computer-aid-design (CAD) software (Ta-
ble 1). Among them, Tiamat (Williams et al.
2009) is good for the design of DNA motifs
consisting of several oligos, caDNAno (Douglas
et al. 2009b) is the most popular tool for the
design of DNA origami nanostructures, and vHe-
lix (Benson et al. 2015), PERDIX (Jun et al.
2019c), DAEDALUS (Veneziano et al. 2016),
TALOS (Jun et al. 2019a), METIS (Jun et al.
2019b) are good for the design of wireframe
and 3D polyhedral DNA nanostructures. Adenita
can be used to design multilayer DNA origami,
wireframe DNA origami, and DNA tiles (Llano
et al. 2020). MagicDNA is a powerful CAD
tool that can be used to design most types of
DNA origami nanostructures, including static,
dynamic, wireframe nanostructures, and those
with complex curvatures or multiple scaffolds
(Huang et al. 2020). Also, it integrated the DNA
strand-based actuation within the design process,
making the design of DNA mechanisms much
easier and convenient. The MagicDNA also has
a user-friendly Graphical User Interface (GUI)
with a step-by-step design wizard, guiding users
through all the steps of constructing new DNA
nanostructures and mechanisms.
In modern mechanical design, motion
simulation and finite element analysis are
critical and essential steps for optimizing the
design parameters and ensuring the quality
of fabrication. Likewise, several simulation
tools (Table 2), including CanDo (Kim et al.
2012), oxDNA (Doye et al. 2013), and mrDNA
(Maffeo and Aksimentiev 2020), have also
been developed for the analysis of DNA
nanostructures. Among them, CanDo was
developed based on finite element models and
can obtain the stable configuration of the DNA
nanostructures by minimizing the mechanical
stress within the structure and can simulate
the thermally induced shape fluctuations.
oxDNA and mrDNA use coarse-grain models to
characterize, with high agreement to experiment
results, the fundamental structural properties
of DNA nanostructures. In addition, all-atom
molecular dynamics (MD) simulations, such
as NAMD (Yoo and Aksimentiev 2013), have
been used to inspect the mechanical properties
of DNA nanostructure (Yoo and Aksimentiev
2013). Though MD simulations can provide
the most accurate results, they usually require
8 DNA Mechanisms and Machines for Nanorobotics
DNA Mechanisms and Machines for Nanorobotics, Table 1 Tools for the design of DNA mechanisms
Name Application User-friendliness Reference
caDNAno General designs Good GUI Douglas et al. 2009b
Tiamat
Small nanostructures, junctions,
and tiles Good GUI Williams et al. 2009
NanoEngineer-1
Small/big nanostructures,
junctions, and tiles Good GUI Nanorex, Inc.
vHelix Wireframe DNA origami
GUI is not available yet,
automated sequence design Benson et al. 2015
PERDIX 2D wireframe DNA origami
Good GUI, automated
sequence design Jun et al. 2019c
TALO S 3D polyhedral DNA origami
GUI is not available yet,
automated sequence design Jun et al. 2019a
DAEDALUS 3D polyhedral DNA origami
GUI is not available yet,
automated sequence design Veneziano et al. 2016
Nanobricks 3D DNA brick nanostructures
GUI is not available yet,
automated sequence design Ong et al. 2017
Adenita General designs Good GUI Llano et al. 2020
MagicDNA General designs
Good GUI, automated
sequence design Huang et al. 2020
DNA Mechanisms and Machines for Nanorobotics, Table 2 Tools for the simulation of DNA mechanisms
Name Type Accuracy Efficiency and cost Reference
CanDo Continuum mechanics Good <several hours, low cost Kim et al. 2012
oxDNA Coarse-grain model Very good <several days, low cost Doye et al. 2013
MrDNA Coarse-grain model Very good <1 h, low cost Maffeo and Aksimentiev 2020
NAMD All-atomic simulation Perfect <several days, high cost Yoo and Aksimentiev 2013
supercomputers to speed up the calculation and
the computational cost is much higher than finite
element analysis and coarse grain model-based
simulations.
Examples of Applications
Drug Carriers
Targeted drug delivery is one of the promising
applications of DNA mechanisms. DNA, as a
natural polymer, has perfect biocompatible prop-
erties and negligible side effects as materials for
constructing drug carriers. Besides, many kinds
of chemical drugs and antibody drugs can be
covalently attached to ssDNA strands that can
be assembled into DNA mechanisms. So far,
several DNA origami robots have been developed
with the ability to deliver drugs to the targeted
cells in vitro or in vivo. For example, Fig. 6a
shows a barrel shape DNA nanorobot composed
of two links connected by a revolute joint which
can be controlled to open and close by lock
duplexes composed of ssDNA overhangs modi-
fied with DNA aptamers (Douglas et al. 2012).
Antibody drugs were covalently attached to the
free end of ssDNA overhangs assembled inside
the nanorobot. Once the DNA aptamers recognize
their antigens on the surface of targeted cancer
cells, the lock duplexes dissociate and open the
nanorobot to expose the antibody drugs to kill the
cancer cells.
Biosensors
The tunable stiffness of DNA joints can be
employed to design DNA mechanisms as force
sensors, probing the attraction forces between
two proteins or the stability of nucleosomes. For
example, a revolute joint-based DNA origami
nanocaliper had been developed to characterize
DNA Mechanisms and Machines for Nanorobotics 9
D
DNA Mechanisms and Machines for Nanorobotics,
Fig. 6 Application examples of DNA mechanisms. (a)
Hinge-based DNA nanorobot, delivering antibodies to the
targeted cancer cells (Douglas et al. 2012). (b)DNA
origami clipper, probing nucleosome stability, reprinted
with permission from (Le et al. 2016), copyright 2016
American Chemical Society. (c) DNA origami clipper,
uncovering the forces between nucleosomes (Funke et al.
2016), Copyright 2016, The Authors, published by Amer-
ican Association for the Advancement of Science. (D)
Four-bar DNA mechanisms, detecting the concentration
change of K+, the BamHI, and miR-210, respectively (Ke
et al. 2016), Copyright 2016, The Author(s), published by
Springer Nature. Scale bars: 20 nm
the mechanical properties of nucleosomes
attached to the two arms (Fig. 6b)(Le et al.
2016). Also, the forces between nucleosomes
can be quantified by using a similar DNA hinge
mechanism (Fig. 6c)(Funke et al. 2016).
DNA mechanisms can transform into many
configurations, making them perfect for the de-
sign of biosensors. Besides, many diseases as-
sociated biomarkers, such as ssDNA, RNA, and
proteins, can trigger the configuration change
of DNA mechanisms. For example, sequences
of ssDNA overhangs designed for actuation can
be specified as the complementary sequences of
microRNA and viral RNA so that they could
trigger the configuration change and produce the
detection signal that can be verified by gel elec-
trophoresis or microscopies. Also, pairs of an-
tibodies can be covalently linked to the ends
of ssDNA overhangs. Upon the binding of tar-
geted antigens, the DNA mechanism can trans-
form into another configuration indicating the
existence of associated diseases. For example,
a dsDNA-based nanoswitch can be programmed
and modified to detect viral RNA (Zhou et al.
2020), microRNA (Chandrasekaran et al. 2019),
and antigens (Hansen et al. 2017). A DNA four-
bar linkage, shown in Fig. 6d, can function as
biosensors based on its configuration changes, for
example, from open to closed configuration upon
the binding of targeted microRNA or protein, or
the changing of the buffer conditions, determined
by the composition of protruded ssDNA over-
hangs used for actuation.
Future Directions for Research
The basic elements of DNA mechanisms, in-
cluding kinematic joints and links, have been
fabricated and well characterized. Demonstrated
by several classic designs, such as the four-bar
Bennett linkage, crank-slider mechanism, six-
joint waterbomb base, and the Stewart platform,
those joints and links can be assembled into much
more complex planar or spatial DNA mecha-
nisms. Many computer-aided design and simu-
lation tools have been developed, shortening the
design and optimization time, and flattening the
learning curve. Also, smart DNA robots have
been built to deliver drugs to targeted cells or
tumors. Moreover, DNA mechanisms could be
10 DNA Mechanisms and Machines for Nanorobotics
used in the design of biosensors, providing new
diagnostic tools for a variety of diseases.
Though dramatic progress has been achieved
in the past decade, there are still many chal-
lenges in the design and application of DNA
mechanisms. First, the links and joints of DNA
mechanisms are limited by the length of the DNA
scaffold. To overcome this challenge, one promis-
ing approach is to fabricate DNA joints and links
separately and then assemble them into much
more complex DNA mechanisms, like the assem-
bly of macroscopic machines from many individ-
ual parts and subassemblies. Also, multiscaffold
DNA origami (Huang et al. 2020) can be used to
fabricate much large and complex DNA mecha-
nisms and machines in a one-pot reaction. Sec-
ond, the top-down design strategy, started from
targeted application requirements, could be ap-
plied to design new DNA mechanisms. Third, the
mechanical properties of DNA links and joints
have not been well investigated and character-
ized, impeding the design of DNA mechanisms
that can transfer or bear prescribed forces and
deformations. Fourth, much more powerful and
user-friendly engineering (kinematic and or dy-
namics) simulation tools for these DNA mech-
anisms will be another critical milestone. These
simulation tools should give designers a quick
prediction without the time-consuming molecular
dynamic simulation. Fifth, the fabrication yield
of DNA mechanisms is always lower than static
DNA nanostructures because many DNA connec-
tions were removed at the joints’ positions, un-
dermining the entire stiffness and stability. Also,
molecular motors that can be assembled with
DNA mechanisms are still desired. Moreover, as
smart drug carriers for targeted drug delivery,
the stability of DNA nanorobots should be im-
proved so that they could circulate in the blood
longer and it is still unclear whether the DNA
nanorobots could induce dangerous immunore-
action in vivo or not. Solving these challenges
will require interdisciplinary collaborations of
biologists, chemists, and engineers.
The research of DNA mechanisms expanded
the design of nanomachines and nanorobots into
a new era. Also, the “DNA” can be substituted
by many other nucleic-acid-like molecules with
modified backbones and bases, such as the RNA,
PNA, and TNA, bringing more design possibil-
ities and opportunities (Seeman 2020, p. 40).
Notably, the design domain of DNA mechanisms
can be further expanded by integrating well-
established theories of kinematics into the design
process. In the icon paper of kinematics, “21st
Century Kinematics —Synthesis, Compliance,
and Tensegrity,” Dr. McCarthy listed three re-
search trends: (i) spatial mechanisms and robotic
systems, (ii) compliant linkage systems, and (iii)
tensegrity and cable-driven systems (McCarthy
2011). These three research topics, though pro-
posed for macroscopic mechanisms, could also
be applied to the development of new DNA
mechanisms, boosting the research of nanoma-
chines and nanorobots. Further synergizing with
the improvement of chemical, biological, and
mechanical properties, those DNA mechanisms
can enhance their performances in many ap-
plications, including nanomedicine, biosensors,
bioimaging, nanomanipulation, nanofabrication,
and others unlisted, promoting human health and
welfare.
Cross-References
Chemical Molecular Machines and Robots
DNA-Based and Hybrid Biomolecular
Machines and Robots
Molecular Programming
Molecular Robotics
References
Alberti P, Mergny J-L (2003) DNA duplex–quadruplex
exchange as the basis for a nanomolecular ma-
chine. PNAS 100:1569–1573. https://doi.org/10.1073/
pnas.0335459100
Benson E, Mohammed A, Gardell J et al (2015) DNA ren-
dering of polyhedral meshes at the nanoscale. Nature
523:441–444. https://doi.org/10.1038/nature14586
Bustamante C, Smith SB, Liphardt J, Smith
D (2000) Single-molecule studies of DNA
mechanics. Curr Opin Struct Biol 10:279–285.
https://doi.org/10.1016/S0959-440X(00)00085-3
Castro CE, Kilchherr F, Kim D-N et al (2011) A primer
to scaffolded DNA origami. Nat Methods 8:221–229.
https://doi.org/10.1038/nmeth.1570
DNA Mechanisms and Machines for Nanorobotics 11
D
Chandrasekaran AR, MacIsaac M, Dey P, et al
(2019) Cellular microRNA detection with miRacles:
microRNA- activated conditional looping of engi-
neered switches. Sci Adv 5:eaau9443. https://doi.org/
10.1126/sciadv.aau9443
Chirikjian GS, Kazerounian K, Mavroidis C (2005) Anal-
ysis and design of protein based nanodevices: chal-
lenges and opportunities in mechanical design. J Mech
Des 127:695–698
de Llano E, Miao H, Ahmadi Y et al (2020) Adenita:
interactive 3D modelling and visualization of DNA
nanostructures. Nucleic Acids Res 48:8269–8275.
https://doi.org/10.1093/nar/gkaa593
Dietz H, Douglas SM, Shih WM (2009) Folding DNA
into twisted and curved nanoscale shapes. Science
325:725–730. https://doi.org/10.1126/science.1174251
Douglas SM, Dietz H, Liedl T et al (2009a) Self-assembly
of DNA into nanoscale three-dimensional shapes. Na-
ture 459:414–418. https://doi.org/10.1038/nature08016
Douglas SM, Marblestone AH, Teerapittayanon S et al
(2009b) Rapid prototyping of 3D DNA-origami shapes
with caDNAno. Nucleic Acids Res 37:5001–5006.
https://doi.org/10.1093/nar/gkp436
Douglas SM, Bachelet I, Church GM (2012) A logic-
gated nanorobot for targeted transport of molecu-
lar payloads. Science 335:831–834. https://doi.org/
10.1126/science.1214081
Doye JPK, Ouldridge TE, Louis A et al (2013) Coarse-
graining DNA for simulations of DNA nanotech-
nology. Phys Chem Chem Phys 15:20395–20414.
https://doi.org/10.1039/C3CP53545B
Funke JJ, Ketterer P, Lieleg C et al (2016) Un-
covering the forces between nucleosomes using
DNA origami. Sci Adv 2:e1600974. https://doi.org/
10.1126/sciadv.1600974
Gerling T, Wagenbauer KF, Neuner AM, Dietz H
(2015) Dynamic DNA devices and assemblies formed
by shape-complementary, non–base pairing 3D
components. Science 347:1446–1452. https://doi.org/
10.1126/science.aaa5372
Han D, Pal S, Nangreave J et al (2011) DNA
origami with complex curvatures in three-dimensional
space. Science 332:342–346. https://doi.org/10.1126/
science.1202998
Hansen CH, Yang D, Koussa MA, Wong WP
(2017) Nanoswitch-linked immunosorbent assay
(NLISA) for fast, sensitive, and specific protein
detection. PNAS 114:10367–10372. https://doi.org/
10.1073/pnas.1708148114
Howell LL (2001) Compliant mechanisms. Wiley-
Interscience, New York
Huang C-M, Kucinic A, Le JV et al (2019) Uncer-
tainty quantification of a DNA origami mechanism
using a coarse-grained model and kinematic variance
analysis. Nanoscale 11:1647–1660. https://doi.org/
10.1039/C8NR06377J
Huang C-M, Kucinic A, Johnson JA, et al (2020)
Integrating computer-aided engineering and
computer-aided design for DNA assemblies bioRxiv
2020.05.28.119701. https://doi.org/10.1101/2020.05.
28.119701
Jun H, Shepherd TR, Zhang K et al (2019a) Automated
Sequence Design of 3D Polyhedral Wireframe DNA
Origami with Honeycomb Edges. ACS Nano 13:2083–
2093. https://doi.org/10.1021/acsnano.8b08671
Jun H, Wang X, Bricker WP, Bathe M (2019b) Au-
tomated sequence design of 2D wireframe DNA
origami with honeycomb edges. Nat Commun 10:5419.
https://doi.org/10.1038/s41467-019-13457-y
Jun H, Zhang F, Shepherd T et al (2019c)
Autonomously designed free-form 2D DNA
origami. Science Advances 5:eaav0655.
https://doi.org/10.1126/sciadv.aav0655
Kauert DJ, Kurth T, Liedl T, Seidel R (2011) Direct
mechanical measurements reveal the material prop-
erties of three-dimensional DNA origami. Nano Lett
11:5558–5563. https://doi.org/10.1021/nl203503s
Kazerounian K (2004) From mechanisms and robotics
to protein conformation and drug design. J Mech Des
126:40–45
Ke Y, Meyer T, Shih WM, Bellot G (2016) Regulation at
a distance of biomolecular interactions using a DNA
origami nanoactuator. Nat Commun 7:ncomms10935.
https://doi.org/10.1038/ncomms10935
Kim D-N, Kilchherr F, Dietz H, Bathe M (2012) Quan-
titative prediction of 3D solution shape and flexibil-
ity of nucleic acid nanostructures. Nucleic Acids Res
40:2862–2868. https://doi.org/10.1093/nar/gkr1173
Kopperger E, List J, Madhira S et al (2018) A self-
assembled nanoscale robotic arm controlled by electric
fields. Science 359:296–301. https://doi.org/10.1126/
science.aao4284
Lauback S, Mattioli KR, Marras AE et al (2018) Real-
time magnetic actuation of DNA nanodevices via mod-
ular integration with stiff micro-levers. Nat Commun
9:1446. https://doi.org/10.1038/s41467-018-03601-5
Le JV, Luo Y, Darcy MA et al (2016) Prob-
ing nucleosome stability with a DNA origami
nanocaliper. ACS Nano 10:7073–7084. https://doi.org/
10.1021/acsnano.6b03218
Liedl T, Högberg B, Tytell J et al (2010) Self-
assembly of three-dimensional prestressed tenseg-
rity structures from DNA. Nat Nano 5:520–524.
https://doi.org/10.1038/nnano.2010.107
Liu Y, West SC (2004) Happy Hollidays: 40th anniversary
of the Holliday junction. Nat Rev Mol Cell Biol 5:937–
944. https://doi.org/10.1038/nrm1502
Maffeo C, Aksimentiev A (2020) MrDNA: a multi-
resolution model for predicting the structure and dy-
namics of DNA systems. Nucleic Acids Res 48:5135–
5146. https://doi.org/10.1093/nar/gkaa200
Mao C, Sun W, Shen Z, Seeman NC (1999) A nanome-
chanical device based on the B–Z transition of DNA.
Nature 397:144–146. https://doi.org/10.1038/16437
Marras AE, Zhou L, Su H-J, Castro CE (2015)
Programmable motion of DNA origami mecha-
nisms. PNAS 201408869. https://doi.org/10.1073/
pnas.1408869112
12 DNA Mechanisms and Machines for Nanorobotics
Marras AE, Zhou L, Kolliopoulos V et al (2016) Directing
folding pathways for multi-component DNA origami
nanostructures with complex topology. New J Phys
18:055005
Marras AE, Shi Z, Lindell MG et al (2018) Cation-
activated avidity for rapid reconfiguration of DNA nan-
odevices. ACS Nano 12:9484–9494. https://doi.org/
10.1021/acsnano.8b04817
Mavroidis C, Ferreira A (2013) Nanorobotics. Springer,
New York, pp 3–27
McCarthy JM (2006) Geometric design of linkages.
Springer Science & Business Media, Springer-Verlag,
New York
McCarthy JM (2011) 21st century kinematics: synthe-
sis, compliance, and tensegrity. J Mech Robot 3.
https://doi.org/10.1115/1.4003181
Ong LL, Hanikel N, Yaghi OK et al (2017) Pro-
grammable self-assembly of three-dimensional nanos-
tructures from 10,000 unique components. Nature
552:72–77. https://doi.org/10.1038/nature24648
Rothemund PWK (2006) Folding DNA to create
nanoscale shapes and patterns. Nature 440:297–302.
https://doi.org/10.1038/nature04586
Schiffels D, Liedl T, Fygenson DK (2013) Nanoscale
structure and microscale stiffness of DNA nanotubes.
ACS Nano 7:6700–6710
Seeman NC (1982) Nucleic acid junctions and lattices.
J Theor Biol 99:237–247. https://doi.org/10.1016/
0022-5193(82)90002-9
Seeman NC (2020) DNA nanotechnology at 40.
Nano Lett 20:1477–1478. https://doi.org/10.1021/
acs.nanolett.0c00325
Simmel FC, Yurke B (2002) A DNA-based
molecular device switchable between three distinct
mechanical states. Appl Phys Lett 80:883–885.
https://doi.org/10.1063/1.1447008
Song J, Li Z, Wang P, et al (2017) Reconfiguration of DNA
molecular arrays driven by information relay. Science
eaan3377. https://doi.org/10.1126/science.aan3377
Su H-J, Castro CE, Marras AE, Hudoba M (2012) Design
and fabrication of DNA origami mechanisms and ma-
chines. In: Dai JS, Zoppi M, Kong X (eds) Advances
in reconfigurable mechanisms and robots I. Springer,
London, pp 487–500
Toumey C (2017) From nano machines to Nobel prizes.
Nat Nanotechnol 12:1–1. https://doi.org/10.1038/
nnano.2016.289
Veneziano R, Ratanalert S, Zhang K et al (2016)
Designer nanoscale DNA assemblies programmed
from the top down. Science 352:1534–1534.
https://doi.org/10.1126/science.aaf4388
Williams S, Lund K, Lin C et al (2009) Tiamat: a three-
dimensional editing tool for complex DNA structures.
In: Goel A, Simmel FC, Sosík P (eds) DNA computing.
Springer, Berlin/Heidelberg, pp 90–101
Yoo J, Aksimentiev A (2013) In situ structure and dy-
namics of DNA origami determined through molec-
ular dynamics simulations. Proc Natl Acad Sci
U S A 110:20099–20104. https://doi.org/10.1073/
pnas.1316521110
Zhou L, Marras AE, Su H-J, Castro CE (2014) DNA
origami compliant nanostructures with tunable me-
chanical properties. ACS Nano 8:27–34. https://doi.
org/10.1021/nn405408g
Zhou L, Marras AE, Su H-J, Castro CE (2015) Di-
rect design of an energy landscape with bistable
DNA origami mechanisms. Nano Lett 15:1815–1821.
https://doi.org/10.1021/nl5045633
Zhou L, Marras AE, Huang C-M et al (2018)
Paper origami-inspired design and actuation of
DNA nanomachines with complex motions. Small
14:e1802580. https://doi.org/10.1002/smll.201802580
Zhou L, Chandrasekaran AR, Punnoose JA, et al (2020)
Programmable low-cost DNA-based platform for vi-
ral RNA detection. Science Advances eabc6246.
https://doi.org/10.1126/sciadv.abc6246