Powering the nanoworld: DNA-based molecular motors
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Transcript of Powering the nanoworld: DNA-based molecular motors
Powering the nanoworld: DNA-based molecular motors
Bernard Yurke
A. J. Turberfield University of OxfordJ. C. Mitchell University of OxfordA. P. Mills Jr U. C. RiversideM. I. Blakey Bell LaboratoriesF. C. Simmel Ludwig-Maximilians UniversityJ. L. Neumann Rutgers UniversityN. Langrana Rutgers UniversityD. Lin Rutgers UniversityR. J. Sanyal Princeton UniversityJ. R. Fresco Princeton University
Bell Laboratories, Lucent Technologies, Murray Hill, New Jersey, USA
• DNA as a structural material
• DNA nanostructures
• DNA machines• Molecular tweezers• Nanoactuator
• Control of hybridization rate
Assembling nanostructures and nanomotors out of DNA
Double-stranded DNA
Linear representation:
5’ TGATCACTTAGAGCAAGC 3’ 3’ ACTAGTGAATCTCGTTCG 5’
base pairing
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) andCdSe nanocrystals (Coffer ‘96)
Template directed assembly of metal wires (Braun ‘98)
Assemblyof proteins(Niemeyer ‘99)
Strand displacement via branch migration
Each step in the random walk takes about 10sec.
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
Microtubule
Vesicle
Kinesin
DNA Replication
An assembly process with an error rate of 10-9
Alberts, Nature 421, 431 (2003)
Making machines from DNA
Utilizing the BZ transition of DNA (Mao et al, 1999):
B Z
DNA tweezersYurke, et al., Nature 406, 605 (2000)
Arms
Hinge
Motor
Fuel strand
Closing the tweezers
DNA hybridization can do mechanical work
0.43 nm
F
F
x
W = F x
The free energy available to do work when a base pair is formed, averaged over all types of base pairing, is
W = G = 78 meV.
The displacement resulting from forming a base pair is
x = 2 X 0.43 nm.
The stall force for a hybridization motor is thus F = G/x = 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
0 5000 100000
FF
open
closed
Time (s)
Flu
ore
sce
nce
inte
nsi
ty
Tweezer operation
Switching time: 13 s
Filter passband 535-545 nm
DNA nanoactuator
A: 40 basesB: 84 basesF: 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.