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A proximity-based programmable DNA nanoscale assembly line.

Gu H, Chao J, Xiao SJ, Seeman NC - Nature (2010)

Bottom Line: Here we demonstrate that a nanoscale assembly line can be realized by the judicious combination of three known DNA-based modules: a DNA origami tile that provides a framework and track for the assembly process, cassettes containing three independently controlled two-state DNA machines that serve as programmable cargo-donating devices and are attached in series to the tile, and a DNA walker that can move on the track from device to device and collect cargo.As the walker traverses the pathway prescribed by the origami tile track, it sequentially encounters the three DNA devices, each of which can be independently switched between an 'ON' state, allowing its cargo to be transferred to the walker, and an 'OFF' state, in which no transfer occurs.We use three different types of gold nanoparticle species as cargo and show that the experimental system does indeed allow the controlled fabrication of the eight different products that can be obtained with three two-state devices.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, New York University, New York, New York 10003, USA.

ABSTRACT
Our ability to synthesize nanometre-scale chemical species, such as nanoparticles with desired shapes and compositions, offers the exciting prospect of generating new functional materials and devices by combining them in a controlled fashion into larger structures. Self-assembly can achieve this task efficiently, but may be subject to thermodynamic and kinetic limitations: reactants, intermediates and products may collide with each other throughout the assembly time course to produce non-target species instead of target species. An alternative approach to nanoscale assembly uses information-containing molecules such as DNA to control interactions and thereby minimize unwanted cross-talk between different components. In principle, this method should allow the stepwise and programmed construction of target products by linking individually selected nanoscale components-much as an automobile is built on an assembly line. Here we demonstrate that a nanoscale assembly line can be realized by the judicious combination of three known DNA-based modules: a DNA origami tile that provides a framework and track for the assembly process, cassettes containing three independently controlled two-state DNA machines that serve as programmable cargo-donating devices and are attached in series to the tile, and a DNA walker that can move on the track from device to device and collect cargo. As the walker traverses the pathway prescribed by the origami tile track, it sequentially encounters the three DNA devices, each of which can be independently switched between an 'ON' state, allowing its cargo to be transferred to the walker, and an 'OFF' state, in which no transfer occurs. We use three different types of gold nanoparticle species as cargo and show that the experimental system does indeed allow the controlled fabrication of the eight different products that can be obtained with three two-state devices.

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The Eight Products of the Assembly LineThe small Roman numerals indicate the different pathways illustrated in panels (a), (b) and (c). (a) The eight possible products that can be generated through appropriate programming of the state of the three DNA machines. The walker is shown at the left, without cargo. Each DNA machine is shown twice: in the upper row in the OFF state where no cargo transfer takes place, and in the lower row in the ON state where cargo can be transferred to the walker. The different assembly trajectories are color coded as black, dark blue, rose, brown, yellow, light blue, green, and magenta, giving products i-viii, respectively, shown schematically at right. (b) Schematic of the final state the system reaches for each of the eight assembly pathways. The states of the cassettes and the dispositions of the cargo species (attached to the robot arms or attached to the walker) are visible. (c) TEM images of the products generated in each of the assembly pathways. (Note that TEM resolves the individual gold Nanoparticles.) In each image, several products generated by the given pathway are visible. All scale bars are 50 nm.
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Figure 3: The Eight Products of the Assembly LineThe small Roman numerals indicate the different pathways illustrated in panels (a), (b) and (c). (a) The eight possible products that can be generated through appropriate programming of the state of the three DNA machines. The walker is shown at the left, without cargo. Each DNA machine is shown twice: in the upper row in the OFF state where no cargo transfer takes place, and in the lower row in the ON state where cargo can be transferred to the walker. The different assembly trajectories are color coded as black, dark blue, rose, brown, yellow, light blue, green, and magenta, giving products i-viii, respectively, shown schematically at right. (b) Schematic of the final state the system reaches for each of the eight assembly pathways. The states of the cassettes and the dispositions of the cargo species (attached to the robot arms or attached to the walker) are visible. (c) TEM images of the products generated in each of the assembly pathways. (Note that TEM resolves the individual gold Nanoparticles.) In each image, several products generated by the given pathway are visible. All scale bars are 50 nm.

Mentions: A key feature of the assembly line is the programmability of the cargo-donating DNA machines, which allows the generation of eight different products, as illustrated in Figure 3a. The system can be pre-programmed to produce a desired product, or designated DNA machines can be switched dynamically from OFF to ON as the walker executes its trajectory (Figure S9.) Schematics of the final state of the system, with the eight possible products on the origami tiles, are shown in Figure 3b, while Figure 3c provides the corresponding transmission electron micrograph images. The images clearly illustrate that all assembly pathways function, with programming of the DNA machines as (JX2, JX2, JX2) giving the product (panel I), while programming as (PX, JX2, JX2), (JX2, PX, JX2) or (JX2, JX2, PX), adds cargo to the walker at the first, second or third station (panels ii, iii, iv, respectively). When the DNA machines are set to be in states (PX, PX, JX2), (PX, JX2, PX) or (JX2, PX, PX), cargo is added to the walker twice so that it contains the 5 nm particle + coupled particles, the 5 nm particle + the 10 nm particle or the coupled particles + the 10 nm particle (shown in panels v, vi and vii, respectively). If the system is in a (PX, PX, PX) state, the walker collects cargo at all three stations as was also shown in Figure 1 (panel viii).


A proximity-based programmable DNA nanoscale assembly line.

Gu H, Chao J, Xiao SJ, Seeman NC - Nature (2010)

The Eight Products of the Assembly LineThe small Roman numerals indicate the different pathways illustrated in panels (a), (b) and (c). (a) The eight possible products that can be generated through appropriate programming of the state of the three DNA machines. The walker is shown at the left, without cargo. Each DNA machine is shown twice: in the upper row in the OFF state where no cargo transfer takes place, and in the lower row in the ON state where cargo can be transferred to the walker. The different assembly trajectories are color coded as black, dark blue, rose, brown, yellow, light blue, green, and magenta, giving products i-viii, respectively, shown schematically at right. (b) Schematic of the final state the system reaches for each of the eight assembly pathways. The states of the cassettes and the dispositions of the cargo species (attached to the robot arms or attached to the walker) are visible. (c) TEM images of the products generated in each of the assembly pathways. (Note that TEM resolves the individual gold Nanoparticles.) In each image, several products generated by the given pathway are visible. All scale bars are 50 nm.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2872101&req=5

Figure 3: The Eight Products of the Assembly LineThe small Roman numerals indicate the different pathways illustrated in panels (a), (b) and (c). (a) The eight possible products that can be generated through appropriate programming of the state of the three DNA machines. The walker is shown at the left, without cargo. Each DNA machine is shown twice: in the upper row in the OFF state where no cargo transfer takes place, and in the lower row in the ON state where cargo can be transferred to the walker. The different assembly trajectories are color coded as black, dark blue, rose, brown, yellow, light blue, green, and magenta, giving products i-viii, respectively, shown schematically at right. (b) Schematic of the final state the system reaches for each of the eight assembly pathways. The states of the cassettes and the dispositions of the cargo species (attached to the robot arms or attached to the walker) are visible. (c) TEM images of the products generated in each of the assembly pathways. (Note that TEM resolves the individual gold Nanoparticles.) In each image, several products generated by the given pathway are visible. All scale bars are 50 nm.
Mentions: A key feature of the assembly line is the programmability of the cargo-donating DNA machines, which allows the generation of eight different products, as illustrated in Figure 3a. The system can be pre-programmed to produce a desired product, or designated DNA machines can be switched dynamically from OFF to ON as the walker executes its trajectory (Figure S9.) Schematics of the final state of the system, with the eight possible products on the origami tiles, are shown in Figure 3b, while Figure 3c provides the corresponding transmission electron micrograph images. The images clearly illustrate that all assembly pathways function, with programming of the DNA machines as (JX2, JX2, JX2) giving the product (panel I), while programming as (PX, JX2, JX2), (JX2, PX, JX2) or (JX2, JX2, PX), adds cargo to the walker at the first, second or third station (panels ii, iii, iv, respectively). When the DNA machines are set to be in states (PX, PX, JX2), (PX, JX2, PX) or (JX2, PX, PX), cargo is added to the walker twice so that it contains the 5 nm particle + coupled particles, the 5 nm particle + the 10 nm particle or the coupled particles + the 10 nm particle (shown in panels v, vi and vii, respectively). If the system is in a (PX, PX, PX) state, the walker collects cargo at all three stations as was also shown in Figure 1 (panel viii).

Bottom Line: Here we demonstrate that a nanoscale assembly line can be realized by the judicious combination of three known DNA-based modules: a DNA origami tile that provides a framework and track for the assembly process, cassettes containing three independently controlled two-state DNA machines that serve as programmable cargo-donating devices and are attached in series to the tile, and a DNA walker that can move on the track from device to device and collect cargo.As the walker traverses the pathway prescribed by the origami tile track, it sequentially encounters the three DNA devices, each of which can be independently switched between an 'ON' state, allowing its cargo to be transferred to the walker, and an 'OFF' state, in which no transfer occurs.We use three different types of gold nanoparticle species as cargo and show that the experimental system does indeed allow the controlled fabrication of the eight different products that can be obtained with three two-state devices.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, New York University, New York, New York 10003, USA.

ABSTRACT
Our ability to synthesize nanometre-scale chemical species, such as nanoparticles with desired shapes and compositions, offers the exciting prospect of generating new functional materials and devices by combining them in a controlled fashion into larger structures. Self-assembly can achieve this task efficiently, but may be subject to thermodynamic and kinetic limitations: reactants, intermediates and products may collide with each other throughout the assembly time course to produce non-target species instead of target species. An alternative approach to nanoscale assembly uses information-containing molecules such as DNA to control interactions and thereby minimize unwanted cross-talk between different components. In principle, this method should allow the stepwise and programmed construction of target products by linking individually selected nanoscale components-much as an automobile is built on an assembly line. Here we demonstrate that a nanoscale assembly line can be realized by the judicious combination of three known DNA-based modules: a DNA origami tile that provides a framework and track for the assembly process, cassettes containing three independently controlled two-state DNA machines that serve as programmable cargo-donating devices and are attached in series to the tile, and a DNA walker that can move on the track from device to device and collect cargo. As the walker traverses the pathway prescribed by the origami tile track, it sequentially encounters the three DNA devices, each of which can be independently switched between an 'ON' state, allowing its cargo to be transferred to the walker, and an 'OFF' state, in which no transfer occurs. We use three different types of gold nanoparticle species as cargo and show that the experimental system does indeed allow the controlled fabrication of the eight different products that can be obtained with three two-state devices.

Show MeSH
Related in: MedlinePlus