Powering the nanoworld: DNA-based
molecular motors
Bernard Yurke
Bell Laboratories, Lucent Technologies, Murray Hill, New Jersey, USA
A. J. Turberfield University of Oxford
J. C. Mitchell
University of Oxford
A. P. Mills Jr
U. C. Riverside
M. I. Blakey
Bell Laboratories
F. C. Simmel
Ludwig-Maximilians University
J. L. Neumann
Rutgers University
N. Langrana
Rutgers University
D. Lin
Rutgers University
R. J. Sanyal
Princeton University
J. R. Fresco
Princeton University
Assembling nanostructures and
nanomotors out of DNA
• DNA as a structural material
• DNA nanostructures
• DNA machines
• Molecular tweezers
• Nanoactuator
• Control of hybridization rate
Double-stranded DNA
base pairing
Linear representation:
5’ TGATCACTTAGAGCAAGC 3’
3’ ACTAGTGAATCTCGTTCG 5’
Two strands of DNA bind most strongly with each other
when their base sequences are complementary.
Assembly of DNA based
nanostructures via hybridization of
complementary DNA sequences.
Chen and Seeman, Nature 350, 631 (1991).
DNA-based self-assembled masks
Gold particles depicted as being 2 nm in size.
DNA self-assembly for
molecular electronics
Assembly of 2D lattices (tilings)
(Winfree, ‘98)
Assembly of a
’
Sierpinski
Triangle
P. Rothemund and E. Winfree, STOC 2000
Logical computation using algorithmic self-assembly of
DNA triple-crossover molecules
yi = yi-1 XOR xi
Mao, et al. Nature 407, 493 (2000)
DNA nanotechnology
DNA directed assembly
of gold nanoparticles
(Mirkin ‘96, Alivisatos ‘96) and
CdSe nanocrystals (Coffer ‘96)
Assembly
of proteins
(Niemeyer ‘99)
Template directed assembly
of metal wires (Braun ‘98)
Strand displacement via branch migration
Each step in the
random walk takes
about 10 msec.
Reversible Gel
3mm
Artificial molecular motors
Artificial molecular motors may be used to
accomplish tasks similar to biological
molecular motors:
1. Transport substances
2. Provide motility
3. Allow the construction of shape changing
materials
Kinesin: A Trucker of the Cell
Vesicle
Kinesin
Microtubule
DNA Replication
Alberts, Nature 421, 431 (2003)
An assembly process with an error rate of 10-9
Making machines from DNA
Utilizing the BZ transition of DNA (Mao et al, 1999):
B
Z
DNA tweezers
Yurke, et al., Nature 406, 605 (2000)
Motor
Hinge
Arms
Fuel strand
Closing the
tweezers
DNA hybridization can do mechanical work
W = F Dx
The free energy available to
do work when a base pair is
formed, averaged over all
types of base pairing, is
0.43 nm
W = DG = 78 meV.
Dx
F
F
The displacement resulting
from forming a base pair is
Dx = 2 X 0.43 nm.
The stall force for a hybridization motor is thus F = DG/Dx = 15 pN.
This is comparable to the stall force of biological molecular motors.
Attached fuel
strand has
single
stranded
extension.
Complement of
fuel strand
attaches to
single stranded
extension of fuel
strand.
Tweezers are
displaced from
fuel strand via
branch migration.
Waste
product,
consisting of
the fuel
strand
hybridized
with its
complement,
is produced
each time the
tweezers are
cycled
between their
open and
closed
states.
Fluorescence resonant energy transfer (FRET)
is used to follow the opening and closing of
the tweezers
Tweezer operation
Fluorescence intensity
FF
open
closed
0
0
5000
Time (s)
Switching time: 13 s
10000
Filter passband
535-545 nm
DNA nanoactuator
A: 40 bases
B: 84 bases
F: 48 bases
Simmel and Yurke, Phys Rev E 63, 041913 (2001).
Actuator operation
Simmel and Yurke, Applied Physics Letters 80, 883 (2002).
A DNA-device based on triplex binding
A robust DNA mechanical device
H. Yan, et al., Nature 415, 62
(2002).
A nanomotor made of a single DNA molecule
Jianwei J. Li, Weihong Tan, Nano Letters, 2002, in press
Conclusion
The molecular recognition properties of DNA can be used to
• build complicated structures by self-assembly
• induce motion on the molecular scale
Therefore, DNA can provide both molecular scaffolding and
molecular machinery for nanotechnology.