Nanomechanical DNA origami 'single-molecule beacons' directly imaged by atomic force microscopy

Kuzuya, Akinori; Sakai, Yusuke; Yamazaki, Takahiro; Xu, Yan; Komiyama, Makoto

doi:10.1038/ncomms1452

Cited by 265 publications

(284 citation statements)

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“…In nanoscale design, specific mechanical motion has seldom been explored. Whereas rotational (19,20,32,41,44,[46][47][48][49] and small linear motions (36,(50)(51)(52)(53)(54)(55)(56) have been demonstrated, the mechanics of this motion have not been studied in any detail. Here we use scaffolded DNA origami to integrate stiff double-stranded DNA (dsDNA) and Significance Folding DNA into complex 3D shapes (DNA origami) has emerged as a powerful method for the precise design and fabrication of self-assembled nanodevices.…”

Section: Dna Origami Mechanism Designmentioning

confidence: 99%

“…The largest triggerable structural change was achieved by Han et al in a DNA origami Möbius strip (one-sided ribbon structure) that could be opened to approximately double in size (45). Constrained motion has been achieved in systems with rotational motion (19,20,32,41,44,46,47) in some cases to open lid-like components (19,20,41) or detect molecular binding (44,48,49). A few of these systems achieved reversible conformational changes (32,41,44,46), although the motion path and flexibility were not studied.…”

mentioning

confidence: 99%

“…Since then, efforts to fabricate dynamic DNA systems have primarily focused on strand displacement approaches (30) mainly on systems comprising a few strands or arrays of strands undergoing ∼nm-scale motions (31-37) in some cases guided by DNA origami templates (38)(39)(40). More recently, strand displacement has been used to reconfigure DNA origami nanostructures, for example opening DNA containers (19,41,42), controlling molecular binding (43,44), or reconfiguring structures (45). The largest triggerable structural change was achieved by Han et al in a DNA origami Möbius strip (one-sided ribbon structure) that could be opened to approximately double in size (45).…”

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confidence: 99%

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Programmable motion of DNA origami mechanisms

Marras

Zhou

et al. 2015

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

375

388

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DNA origami enables the precise fabrication of nanoscale geometries. We demonstrate an approach to engineer complex and reversible motion of nanoscale DNA origami machine elements. We first design, fabricate, and characterize the mechanical behavior of flexible DNA origami rotational and linear joints that integrate stiff double-stranded DNA components and flexible single-stranded DNA components to constrain motion along a single degree of freedom and demonstrate the ability to tune the flexibility and range of motion. Multiple joints with simple 1D motion were then integrated into higher order mechanisms. One mechanism is a crank-slider that couples rotational and linear motion, and the other is a Bennett linkage that moves between a compacted bundle and an expanded frame configuration with a constrained 3D motion path. Finally, we demonstrate distributed actuation of the linkage using DNA input strands to achieve reversible conformational changes of the entire structure on ∼minute timescales. Our results demonstrate programmable motion of 2D and 3D DNA origami mechanisms constructed following a macroscopic machine design approach.T he ability to control, manipulate, and organize matter at the nanoscale has demonstrated immense potential for advancements in industrial technology, medicine, and materials (1-3). Bottom-up self-assembly has become a particularly promising area for nanofabrication (4, 5); however, to date designing complex motion at the nanoscale remains a challenge (6-9). Amino acid polymers exhibit well-defined and complex dynamics in natural systems and have been assembled into designed structures including nanotubes, sheets, and networks (10-12), although the complexity of interactions that govern amino acid folding make designing complex geometries extremely challenging. DNA nanotechnology, on the other hand, has exploited well-understood assembly properties of DNA to create a variety of increasingly complex designed nanostructures (13-15).Scaffolded DNA origami, the process of folding a long singlestranded DNA (ssDNA) strand into a custom structure (16-18), has enabled the fabrication of nanoscale objects with unprecedented geometric complexity that have recently been implemented in applications such as containers for drug delivery (19,20), nanopores for single-molecule sensing (21-23), and templates for nanoparticles (24, 25) or proteins (26-28). The majority of these and other applications of DNA origami have largely focused on static structures. Natural biomolecular machines, in contrast, have a rich diversity of functionalities that rely on complex but well-defined and reversible conformational changes. Currently, the scope of biomolecular nanotechnology is limited by an inability to achieve similar motion in designed nanosystems.DNA nanotechnology has enabled critical steps toward that goal starting with the work of Mao et al. (29), who developed a DNA nanostructure that took advantage of the B-Z transition of DNA to switch states. Since then, efforts to fabricate dynamic DNA systems hav...

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Section: Dna Origami Mechanism Designmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Programmable motion of DNA origami mechanisms

Marras

Zhou

et al. 2015

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

375

388

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“…46,47 Recently, we have constructed nanomechanical DNA origami devices, DNA origami pliers and DNA origami forceps, which consisted of two levers connected at a fulcrum (Figure 7). 48 These nanomechanical origami devices experience a marked shape transition from an X-shaped open form to a parallel closed form (or the reverse) by interacting with various specific chemical/biochemical targets. Attaching multiple AuNPs to such nanomachines may permit the dynamic control of plasmonic resonance between metal NPs/NRs.…”

Section: Dna Nanostructures As Scaffoldsmentioning

confidence: 99%

“…In addition, the AuNP helices Figure 7 Nanomechanical DNA origami (DNA origami pliers) that pinch precisely one target molecule. 48 The two levers were modified with a biotin group. Such biotinylated DNA origami pliers markedly change their structure from an X-shaped open form (left) to a parallel closed form (center) by pinching an SA.…”

Section: Dna Nanostructures As Scaffolds a Kuzuya Et Almentioning

confidence: 99%

DNA nanostructures as scaffolds for metal nanoparticles

Kuzuya

Ohya

2012

Polym J

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The rapid development of DNA nanotechnology has enabled the precise bottom-up integration of metal nanoparticles (NPs) on a nanometer scale. The recent introduction of the DNA origami technique has facilitated even more complicated control of the positioning of not only 2 dimensional (D) but also 3D structures. INTRODUCTIONAlthough top-down fabrications, such as photolithography and etching, have long driven advances in nanotechnology, they are now approaching their physical limits. Bottom-up fabrication techniques are expected to break through these limitations. However, these approaches cannot yet replace top-down techniques. Colloidal nanocrystals, including metals and semiconductors, exhibit distinctive properties not observed in the bulk state. Therefore, they are of particular interest for nanotechnology and nanoscience. For example, gold nanoparticles (AuNPs) exhibit unique optical and electrical properties, such as surface plasmon resonance. 1,2 On the basis of their distinctive properties, metal NPs have been applied for biological sensing, diagnosis and other applications. 3,4 Moreover, as new properties not observed in the distributed state are expected to emerge in the organized states, 5 the precise arrangement of metal NPs in 1 dimensional (D) to 3D is one of the important technical objectives of bottom-up nanotechnology. 6,7 On the other hand, DNA is the ideal building block for the construction of self-organized nanostructures. A strand of DNA can specifically bind with its complementary counter strand by WatsonCrick base pairing to form a B-type double helix, which is most common for a pair of complementary DNA in nature and almost independent of their sequences. This fact is highly convenient for fabricating universal nanostructures, as each double helix consisting of various sequences of DNA has the same diameter and pitch. On the basis of this fact and other advantages, such as sequence programmability, reversible double helix formation and strand exchange, availability by automatic synthesis, the relative rigidity of the double helix, enzymatic scission and ligation ability, and easy amplification by a PCR, many DNA-based approaches to construct highly ordered or well-designed nanostructures have been reported. [8][9][10]

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Construction of Functional DNA Nanostructures for Theranostic Applications

Fan

Pei

et al. 2015

Advanced Theranostic Materials

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Nanomechanical DNA origami 'single-molecule beacons' directly imaged by atomic force microscopy

Cited by 265 publications

References 48 publications

Programmable motion of DNA origami mechanisms

Programmable motion of DNA origami mechanisms

DNA nanostructures as scaffolds for metal nanoparticles

Construction of Functional DNA Nanostructures for Theranostic Applications

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