Functional DNAzymes Organized into Two-Dimensional Arrays

Garibotti, Alejandra V.; Knudsen, Scott M.; Ellington, and Andrew D.; Seeman, Nadrian C.

doi:10.1021/nl0609955

Cited by 46 publications

(25 citation statements)

References 25 publications

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“…2D arrays of multiple nanoparticles have also been scaffolded on 2D arrays [23]. In addition to nanoparticles, 2D arrays have been used to organize DNAzymes [60]. DNA tweezers [61] and a robust nanomechanical DNA device [62].…”

Section: Dna Arraysmentioning

confidence: 99%

An Overview of Structural DNA Nanotechnology

2007

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Structural DNA Nanotechnology uses unusual DNA motifs to build target shapes and arrangements. These unusual motifs are generated by reciprocal exchange of DNA backbones, leading to branched systems with many strands and multiple helical domains. The motifs may be combined by sticky ended cohesion, involving hydrogen bonding or covalent interactions. Other forms of cohesion involve edge-sharing or paranemic interactions of double helices. A large number of individual species have been developed by this approach, including polyhedral catenanes, a variety of single-stranded knots, and Borromean rings. In addition to these static species, DNA-based nanomechanical devices have been produced that are ultimately targeted to lead to nanorobotics. Many of the key goals of structural DNA nanotechnology entail the use of periodic arrays. A variety of 2D DNA arrays have been produced with tunable features, such as patterns and cavities. DNA molecules have be used successfully in DNA-based computation as molecular representations of Wang tiles, whose self-assembly can be programmed to perform a calculation. About 4 years ago, on the fiftieth anniversary of the double helix, the area appeared to be at the cusp of a truly exciting explosion of applications; this was a correct assessment, and much progress has been made in the intervening period.

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Section: Dna Arraysmentioning

confidence: 99%

An Overview of Structural DNA Nanotechnology

2007

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“…DNA, however, is a robust biopolymer that, through Watson-Crick base pairing and the multitude of sequences that can be formulated, might yield self-assembled protein scaffolds. Indeed, DNA has been used for the organization of proteins (9,10) and elegant, topologically complex 3D architectures, such as Borromean rings (11), nanotubes (12), [2]catenanes (13), 2D tilings (14)(15)(16)(17)(18), and chains (19), onto which nanoparticles (20)(21)(22)(23)(24)(25)(26)(27)(28) and proteins (19,20,(29)(30)(31)(32) have been tethered by using complementary single-stranded DNA (ssDNA), biotin-streptavidin interactions, or gold-thiol bonds. These studies, however, have been limited to the immobilization of a single biomolecule or nanoparticle onto the scaffold or require multistep protocols to organize more than one nanomaterial onto the template.…”

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A polycatenated DNA scaffold for the one-step assembly of hierarchical nanostructures

Weizmann

Braunschweig

Wilner

et al. 2008

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

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A unique DNA scaffold was prepared for the one-step self-assembly of hierarchical nanostructures onto which multiple proteins or nanoparticles are positioned on a single template with precise relative spatial orientation. The architecture is a topologically complex ladder-shaped polycatenane in which the ''rungs'' of the ladder are used to bring together the individual rings of the mechanically interlocked structure, and the ''rails'' are available for hierarchical assembly, whose effectiveness has been demonstrated with proteins, complementary DNA, and gold nanoparticles. The ability of this template to form from linear monomers and simultaneously bind two proteins was demonstrated by chemical force microscopy, transmission electron microscopy, and confocal fluorescence microscopy. Finally, fluorescence resonance energy transfer between adjacent fluorophores confirmed the programmed spatial arrangement between two different nanomaterials. DNA templates that bring together multiple nanostructures with precise spatial control have applications in catalysis, biosensing, and nanomaterials design.chemical force microscopy ͉ proteins ͉ wires ͉ nanoparticle ͉ catenane V ersatile scaffolds for the immobilization of proteins and other nanosized objects are targets of intensive research in the broader field of nanotechnology because of their potential applications (1) in the areas of catalysis, biosensing, and nanomaterials. In nature, complex catalytic cascades, such as the Krebs cycle (2), photosynthesis (3), or glycolysis (4), involve multiple proteins assembled with exact relative spatial orientations to facilitate cooperative binding, to facilitate electron or energy transfer, and to optimize substrate conversion. Enzymatic cascades that are used industrially (5-7) could also benefit from such closely arranged proteins if a template with the ability to fix precisely various proteins were available. Although functional synthetic polymers (8) are potential matrices for forming useful scaffolds, this approach is limited by polymer compatibility with biomolecules and the flexibility of the polymerization protocol to synthesize macromolecules that controllably bind multiple proteins. DNA, however, is a robust biopolymer that, through Watson-Crick base pairing and the multitude of sequences that can be formulated, might yield self-assembled protein scaffolds. Indeed, DNA has been used for the organization of proteins (9, 10) and elegant, topologically complex 3D architectures, such as Borromean rings (11), nanotubes (12), [2]catenanes (13), 2D tilings (14-18), and chains (19), onto which nanoparticles (20-28) and proteins (19,20,(29)(30)(31)(32) have been tethered by using complementary single-stranded DNA (ssDNA), biotin-streptavidin interactions, or gold-thiol bonds. These studies, however, have been limited to the immobilization of a single biomolecule or nanoparticle onto the scaffold or require multistep protocols to organize more than one nanomaterial onto the template. Results and DiscussionsIn this report, we desc...

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“…This is because biological systems provide mature models for the arrangement of macromolecules with precisely controlled positions, distances, and orientations to maximize their functionality. To this end, DNA lattices have been used to organize proteins, such as streptavidin (Park et al 2005), thrombin , and RuvA (Malo et al 2005), and to organize nucleic acid enzymes (DNAzymes; Garibotti et al 2006). Templating can also occur by volume or area, instead of by arrangement, as DNA tetrahedra have been used to encapsulate proteins (Erben et al 2006;Duckworth et al 2007).…”

Section: Functional Templatingmentioning

confidence: 99%

DNA Nanotechnology: From Biology and Beyond

Liu

Ellington

2013

Nucleic Acids and Molecular Biology

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Over the past three decades, tremendous progress has been made in our understanding of how to use DNA molecules to design and construct intricate nanostructures and nanodevices and how to use these nanoconstructs as versatile tools to functionally arrange a variety of molecules and moieties with nanometer spatial resolution. This chapter summarizes recent development in DNA nanotechnology and addresses its potential applications in drug delivery, analysis and diagnosis, electronics, and photovoltaics.

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Functional DNAzymes Organized into Two-Dimensional Arrays

Cited by 46 publications

References 25 publications

An Overview of Structural DNA Nanotechnology

An Overview of Structural DNA Nanotechnology

A polycatenated DNA scaffold for the one-step assembly of hierarchical nanostructures

DNA Nanotechnology: From Biology and Beyond

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