An Overview of Structural DNA Nanotechnology

Seeman, Nadrian C.

doi:10.1007/s12033-007-0059-4

Cited by 407 publications

(296 citation statements)

References 88 publications

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“…With such methods, one can make architectures with well-defined lattice parameters (6)(7)(8)(9)(10)(11)(12), symmetries (4,8,10,12), and compositions (10,12,13), but to date they have been confined primarily to the use of hard inorganic nanoparticles (NPs) or highly branched pure nucleic-acid materials (2,14,15). In contrast, Nature's most powerful and versatile nanostructured building blocks are proteins and are used to effect the vast majority of processes in living systems (16).…”

mentioning

confidence: 99%

DNA-mediated engineering of multicomponent enzyme crystals

Brodin

Auyeung

Mirkin

2015

Proc. Natl. Acad. Sci. U.S.A.

129

138

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The ability to predictably control the coassembly of multiple nanoscale building blocks, especially those with disparate chemical and physical properties such as biomolecules and inorganic nanoparticles, has far-reaching implications in catalysis, sensing, and photonics, but a generalizable strategy for engineering specific contacts between these particles is an outstanding challenge. This is especially true in the case of proteins, where the types of possible interparticle interactions are numerous, diverse, and complex. Herein, we explore the concept of trading protein-protein interactions for DNA-DNA interactions to direct the assembly of two nucleic-acid-functionalized proteins with distinct surface chemistries into six unique lattices composed of catalytically active proteins, or of a combination of proteins and DNA-modified gold nanoparticles. The programmable nature of DNA-DNA interactions used in this strategy allows us to control the lattice symmetries and unit cell constants, as well as the compositions and habit, of the resulting crystals. This study provides a potentially generalizable strategy for constructing a unique class of materials that take advantage of the diverse morphologies, surface chemistries, and functionalities of proteins for assembling functional crystalline materials.nanoscience | biomaterials | self-assembly | superlattice | DNA-programmable assembly D NA-mediated assembly strategies (1-3) that take advantage of rigid building blocks, functionalized with oriented oligonucleotides to create entities with well-defined "valencies," have emerged as powerful new ways for programming the formation of crystalline materials (4, 5). With such methods, one can make architectures with well-defined lattice parameters (6-12), symmetries (4,8,10,12), and compositions (10, 12, 13), but to date they have been confined primarily to the use of hard inorganic nanoparticles (NPs) or highly branched pure nucleic-acid materials (2, 14, 15). In contrast, Nature's most powerful and versatile nanostructured building blocks are proteins and are used to effect the vast majority of processes in living systems (16). Unlike most inorganic NP systems, proteins can be made in pure and perfectly monodisperse form, making them ideal synthons for supramolecular assemblies. However, the ability to engineer lattices composed of multiple proteins, or of proteins and inorganic nanomaterials, has been limited, and the choice of protein building blocks is often restricted by structural constraints, which limits the catalytic functionalities that can be incorporated into these structures. Currently, the primary methods for making protein lattices have relied on the use of natural protein-protein interactions (17), interactions between proteins and ligands on the surfaces of inorganic NPs (17, 18), metal coordination chemistry (19), small molecule ligand-protein interactions (20-23), genetically fusing protein complexes with specific symmetries (24, 25), or DNA-mediated assembly of viruses (26,27). Here, we introduce a new...

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mentioning

confidence: 99%

DNA-mediated engineering of multicomponent enzyme crystals

Brodin

Auyeung

Mirkin

2015

Proc. Natl. Acad. Sci. U.S.A.

129

138

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“…Crosstalk is recognized as a potentially significant threat to successful self-assembly. Seeman described this in 2007, as "the key to any successful molecular engineering approach is to design the components of a construction not just so that they are capable of yielding the product, but also to ensure, insofar as possible, that no other product will be competitive with the target" [30].…”

Section: E Requirements Evolutionmentioning

confidence: 99%

Requirements analysis for a product family of DNA nanodevices

Lutz

Lathrop

et al. 2012

2012 20th IEEE International Requirements Engineering Conference (RE)

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Abstract-DNA nanotechnology uses the information processing capabilities of nucleic acids to design self-assembling, programmable structures and devices at the nanoscale. Devices developed to date have been programmed to implement logic circuits and neural networks, capture or release specific molecules, and traverse molecular tracks and mazes.Here we investigate the use of requirements engineering methods to make DNA nanotechnology more productive, predictable, and safe. We use goal-oriented requirements modeling to identify, specify, and analyze a product family of DNA nanodevices, and we use PRISM model checking to verify both common properties across the family and properties that are specific to individual products. Challenges to doing requirements engineering in this domain include the errorprone nature of nanodevices carrying out their tasks in the probabilistic world of chemical kinetics, the fact that roughly a nanomole (a 1 followed by 14 0s) of devices are typically deployed at once, and the difficulty of specifying and achieving modularity in a realm where devices have many opportunities to interfere with each other. Nevertheless, our results show that requirements engineering is useful in DNA nanotechnology and that leveraging the similarities among nanodevices in the product family improves the modeling and analysis by supporting reuse.

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“…Thus, for rigid armed tiles, the octet truss (see Figures 6 and 7) provides a reasonable geometric model. Currently, branched junction molecules with 2, 4, 5, 6, 8, and 12 arms have been fabricated (see [18] for an overview), so the 12-regular octet truss accurately reflects current capacity. All the edges are unit length, and the even spacing of the edges about the vertices prohibits any unattainable angles.…”

Section: Exercise 3 Show That the Chromatic Number Of A Graph Providmentioning

confidence: 99%

“…Because of the great promise of nanotechnology, in particular for biomolecular computing, drug delivery and biosensors (see [1,23,13,18]), recent research has focused on self-assembly of nanoscale geometric constructs, notably graphs. A number of techniques have been developed using the Watson-Crick complementarity properties of DNA strands to achieve the self-assembly.…”

Section: Introductionmentioning

confidence: 99%

Using DNA Self-assembly Design Strategies to Motivate Graph Theory Concepts

Ellis-Monaghan

Pangborn

2011

Math. Model. Nat. Phenom.

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Abstract. A number of exciting new laboratory techniques have been developed using the WatsonCrick complementarity properties of DNA strands to achieve the self-assembly of graphical complexes. For all of these methods, an essential step in building the self-assembling nanostructure is designing the component molecular building blocks. These design strategy problems fall naturally into the realm of graph theory. We describe graph theoretical formalism for various construction methods, and then suggest several graph theory exercises to introduce this application into a standard undergraduate graph theory class. This application provides a natural framework for motivating central concepts such as degree sequence, Eulerian graphs, Fleury's algorithm, trees, graph genus, paths, cycles, etc. There are many open questions associated with these applications which are accessible to students and offer the possibility of exciting undergraduate research experiences in applied graph theory.

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An Overview of Structural DNA Nanotechnology

Cited by 407 publications

References 88 publications

DNA-mediated engineering of multicomponent enzyme crystals

DNA-mediated engineering of multicomponent enzyme crystals

Requirements analysis for a product family of DNA nanodevices

Using DNA Self-assembly Design Strategies to Motivate Graph Theory Concepts

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