Powering the nanoworld: DNA-based molecular motors Bernard Yurke 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 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 y i = y i-1 XOR x i Mao, et al. Nature 407, 493 (2000)

DNA nanotechnology DNA directed assembly of gold nanoparticles (Mirkin ‘96, Alivisatos ‘96) and CdSe nanocrystals (Coffer ‘96) Template directed assembly of metal wires (Braun ‘98) Assembly of proteins (Niemeyer ‘99)

Strand displacement via branch migration

Each step in the random walk takes about 10  sec.

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 Alberts, Nature 421, 431 (2003)

Making machines from DNA Utilizing the BZ transition of DNA (Mao et al, 1999): BZ

DNA tweezers Yurke, 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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

Tweezer operation Switching time: 13 s Filter passband nm

DNA nanoactuator A: 40 bases B: 84 bases F: 48 bases Simmel and Yurke, Phys Rev E 63, (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.