John Reif. The Design of Autonomous DNA Nanomechanical Devices: Walking and Rolling DNA. Duke Univ. DNA Hybridization and Ligation Operations. Hybridization of sticky single-strand DNA segments.
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The Design of Autonomous DNA Nanomechanical Devices:Walking and Rolling DNA
Hybridizationof sticky single-strand DNA segments.
Ligation: If the sticky single-strand segments that anneal abut doubly stranded segments of DNA, you can use an enzymic reaction known as ligation to concatenate these segments.
Bernard Yurke’s Molecular Tweezers (Bell Lab):Composed of DNA and powered by DNA hybridization. -Two dsDNA arms are connected by a ssDNA hinge -Two ssDNA “handles” at the ends of the arms. To close tweezers: -Add a special “fuel” strand of ssDNA. -The “fuel” strand attaches to the handles and draws the two arms together.
Nano-mechanical Rotational Transducers(Seeman, NYU)(a) DNA nanomechanical motor: Rotation via B-Z transition controlled by concentration of Co(NH3)6Cl3 .(b) Device switches between PX and JX2 topological states of DNA controlled via introduction of different strands, using Yurke’s Molecular Tweezers.(c) A test system where switching states alternates between a 'cis' configuration (PX) and a 'trans' configuration (JX2). (d) AFM pictures of four successive states through this system.
Walking Triangles:By binding the short red strand (top figure) versus the long red strand (bottom figure) the orientation of and distance between the triangular tiles is altered.
These changes will be observable by AFM.
Applications: Programmable state control for nanomechanical devices.
Also as a visual output method.
Nanofactory device(Seeman, NYU): PX/JX2 devices with 3 cycles of configurations.(a) Nanogen electrodes control release of hybridized strands into solution.(b) Three augmented device molecules mounted on an lattice. Set strands of device labeled: P(urple)-up and G(reen)-up. Cycle 1: -Three G-up set strands on the device, -P-up set strands released into solution. Cycle 2: -G-up strands for molecules 1 and 3 released, -P-up strand for molecule 2 released. Cycle 3: -P-up set strands for molecules 1 and 3 released, -G-up set strand for molecule 2 released.
Patterned Immobilization of Environmentally-Responsive Peptides.(on-going work in collaboration with Chilkoti, Dept. of Biomedical Eng., Duke University.)Nanoscale actuators that function in an aqueous environment.Molecular basis of nanoactuation: - ELPs are Peptides that undergo a structural transition at a characteristic temperature. - The end-to-end distance of the ELP decreases by ~50% upon collapse of the ELP in response to its phase transition. Hybrid materials composed of : (a) self-assembling DNA nanostructures and (b) elastin-like peptides (ELP) -Attachment of ELP to specific sites on DNA lattice results in arrays of peptide in a monolayer of controlled density. -May use layers of DNA sandwiched between layers of ELP.
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(e.g., so the wheel is not sandwiched between two road strands):
Wheel Movement Fueled by Peptides.Heat Energy
Similar to Branch Migrations
Wheel Movement Fueled by DNA Hybridization:
Used by Yurke and Turberfield [YTM+00,YMT00,TYM00] for DNA tweezer nanomechanical devices but they require heat cycling
We use the hybridization energy of DNA fuel loop strands:
o We require no external environmental changes to induce repetitions of the motions by our DNA devices (no heat cycling).
o We apply DNA catalyst techniques for liberating DNA from these loop conformations.
o We harness their energy as they transition into lower energy conformations.
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(b) Nanofabrication: These capabilities might be used to selectively control nanofabrication stages. The size or shape of the lattice may be programmed through the control of such sequence-dependent devices and this might be used to execute a series of foldings (similar to Japanese paper folding techniques) of the DNA lattice to form a variety of 3D confirmations and geometries.
DNA Lattices Peptides. A New, Powerful Technology for Rendering Patterns at the Molecular LevelA 2D DNA lattice is constructed by a self-assembly process:--Begins with the assembly of DNA tile nanostructures: - DNA tiles of size 14 x 7 nanometers - Composed of short DNA strands with Holliday junctions - These DNA tiles self-assemble to form a 2D lattice:-The Assembly is Programmable: -Tiles have sticky ends that provide programming for the patterns to be formed. -Alternatively:tiles self-assemble around segments of a DNA strand encoding a 2D pattern. - Patterning: Each of these tiles has a surface perturbation depending on the pixel intensity. -pixel distances 7 to 14 nanometers -not diffraction limited Key Application:Molecular robotic components
Biological Protein Motors: Peptides.
manufactured by expression of protein motors and linkers
ADP Protein Motor
[Montemagno, et al,99]
Axonemal Dynein Motor
Kinesin [Stracke, 99]
walks on microtubules
DNA tileDNA Tile Lattice for Templating Molecular Motors (with Dan Kenan, Duke)
A bifunctional antibody (Ab) is shown bound to a DNA aptamer on a tile and to a motor protein, thus immobilizing the motor onto the tile.
An example DNA lattice
More complex patterns of motors on lattices can allow for sophisticated molecular robotics tasks.