LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institut für Organische Chemie und Biochemie, University of Bonn, Bonn,
Center of Advanced European Studies and Research (CAESAR), Bonn, Germany.
Single Molecule Analysis Group, Department of Chemistry,
University of Michigan, Ann Arbor, MI, USA.
Present address: Department of Chemistry, Virginia Commonwealth University, Richmond, VA, USA.
ature provides several examples of highly effective biological
motors that consume chemical energy for rotation, move
ment or power transmission
. Living organisms require
motors for essential functions such as cargo transport, cell locomo
tion and division, chemotaxis, ATP synthesis
or flagellar move-
, with the latter two consisting of interacting stator and rotor
components that generate torque. Despite the complexity of most
natural motors, it has been possible to assemble artificial motor sys
tems by employing DNA nanostructures
or bio-hybrid designs
or based entirely upon synthetic organic chemistry
. Apart from
synthetic small-molecule motors
, however, unidirectionally rotat-
ing biomimetic wheel motors with rotor–stator units that consume
chemical energy have not yet been described.
Here, we describe a supramolecular bio-hybrid rotor composed
of a catalytic stator that unidirectionally rotates an interlocked
double-stranded (ds) DNA wheel, powered by the hydrolysis of
nucleotide triphosphates (NTPs). The design of the engine consists
of a static building block with an engineered T7 RNA polymerase
(T7RNAP) fused to a DNA-binding Zn
-finger (ZIF) motif
(T7RNAP-ZIF). T7RNAP-ZIF attaches firmly to a dsDNA nanor
ing, thus constituting a stator unit that is interlocked with a rigid
rotating dsDNA wheel (the rotor unit) to form a catenane. The
wheel motor operates continuously and thereby produces long,
repetitive RNA transcripts by rolling circle transcription (RCT).
Because this RNA byproduct remains attached to the bio-hybrid
nanoengine, it can be used to guide the movement of the entire
engine along predefined single-stranded (ss) DNA tracks arrayed
on a DNA nanotube.
Design, assembly and characterization of the nanoengine
Integrating T7RNAP as a power generator for our wheel motor
offered several design opportunities (Fig. 1). First, because torque
generation requires defined stator–rotor interactions, T7RNAP had
to be firmly attached to a stationary chassis, otherwise the rota
tional motion would become undefined, as is the case in classical
, where either the polymerase or the circular template can
be regarded as the moving part. Second, interlocking of the rings,
each containing a different recognition motif for T7RNAP-ZIF, pro
motes cooperative binding, reducing the probability of polymerase
detachment and thereby boosting processivity. Third, we integrated
means for quantification of the motor rotation (Fig. 1).
The stator chassis is a 168-base-pair (bp) dsDNA circle con
taining the 10 bp sequence that binds the three Zn
of the Zif268 protein (Fig. 1a)
. This sequence has previously been
used for site-specific positioning of Zn
teins on DNA origami
. Here, it serves as a high-affinity docking
site for a T7RNAP N-terminally fused with Zif268 (T7RNAP-ZIF;
Supplementary Fig. 1a). The rotor ring contains a T7 promoter
(red) and a sequence that allows hybridization of a complementary
molecular beacon (MB, green) to the RNA transcript for fluores
cence monitoring of product formation. Assembly of the interlocked
catenane was performed as described previously (Supplementary
Figs. 1b and 2 and Supplementary Table 1)
. Gel electrophoresis
showed that the mechanically interlocked catenane
slightly faster than the corresponding hybridized catenane
(Supplementary Fig. 1c, Cat
), consistent with previous observa-
tions on similar DNA nanostructures
The Zif268 fragment of T7RNAP-ZIF binds sequence-spe
cifically to the 168 bp stator ring with a dissociation constant K
of 1.6 nM, as determined by surface plasmon resonance (SPR)
(Supplementary Fig. 1d), whereas the T7RNAP fragment recog
nizes the T7 promoter in the 126 bp rotor ring, completing the
bio-hybrid nanoengine. In vitro transcription using a non-inter
locked circular DNA template showed that T7RNAP-ZIF per-
forms just like wild-type (wt) T7RNAP (Supplementary Fig. 1e),
thus binding to its corresponding T7 promoter, which dictates
the direction of transcription on the circular dsDNA template.
Atomic force microscopy (AFM) of the isolated catenane (Fig. 1b),
T7RNAP-ZIF (Fig. 1c) and the assembled nanoengine (Fig. 1d and
Supplementary Figs. 3 and 4) demonstrated the structural integrity
A bio-hybrid DNA rotor–stator nanoengine that
moves along predefined tracks
, Nibedita Pal
, Soma Dhakal
, Nils G. Walter
and Michael Famulok
Biological motors are highly complex protein assemblies that generate linear or rotary motion, powered by chemical energy.
Synthetic motors based on DNA nanostructures, bio-hybrid designs or synthetic organic chemistry have been assembled.
However, unidirectionally rotating biomimetic wheel motors with rotor–stator units that consume chemical energy are elusive.
Here, we report a bio-hybrid nanoengine consisting of a catalytic stator that unidirectionally rotates an interlocked DNA wheel,
powered by NTP hydrolysis. The engine consists of an engineered T7 RNA polymerase (T7RNAP-ZIF) attached to a dsDNA
nanoring that is catenated to a rigid rotating dsDNA wheel. The wheel motor produces long, repetitive RNA transcripts that
remain attached to the engine and are used to guide its movement along predefined ssDNA tracks arranged on a DNA nano-
tube. The simplicity of the design renders this walking nanoengine adaptable to other biological nanoarchitectures, facilitating
the construction of complex bio-hybrid structures that achieve NTP-driven locomotion.
© 2018 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.
NATURE NANOTECHNOLOGY | VOL 13 | JUNE 2018 | 496–503 | www.nature.com/naturenanotechnology