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.