Suspending DNA Origami Between Four Gold Nanodots

Morales, P.; Wang, Liqian; Krissanaprasit, Abhichart; Dalmastri, Claudia; Caruso, Mario; Stefano, Mattia De; Mosiello, Lucia; Rapone, Bruno; Rinaldi, Antonio; Vespucci, Stefano; Vinther, Jesper; Retterer, Scott T.; Gothelf, Kurt V.

doi:10.1002/smll.201501782

Cited by 8 publications

(10 citation statements)

References 29 publications

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“…Pearson et al reported a similar strategy to align DNA origami on a gold island, which was patterned with block copolymer . Later on, Morales et al further demonstrated that rectangular DNA origami structures could be suspended on four gold dots …”

Section: Applications Of Dna Origamimentioning

confidence: 99%

“…510 Later on, Morales et al further demonstrated that rectangular DNA origami structures could be suspended on four gold dots. 511 To control the position and orientation of the DNA origami structures on the substrate surface, Kershner et al developed an electron-beam lithography and dry oxidative etching process. This new process helped to create DNA origami-shaped binding sites on SiO 2 to direct the DNA origami positions and orientations with a high selectivity and a proper orientation (Figure 26A).…”

Section: Bioanalysis With Dna Origamimentioning

confidence: 99%

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DNA Origami: Scaffolds for Creating Higher Order Structures

2017

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DNA has become one of the most extensively used molecular building blocks for engineering self-assembling materials. DNA origami is a technique that uses hundreds of short DNA oligonucleotides, called staple strands, to fold a long single-stranded DNA, which is called a scaffold strand, into various designer nanoscale architectures. DNA origami has dramatically improved the complexity and scalability of DNA nanostructures. Due to its high degree of customization and spatial addressability, DNA origami provides a versatile platform with which to engineer nanoscale structures and devices that can sense, compute, and actuate. These capabilities open up opportunities for a broad range of applications in chemistry, biology, physics, material science, and computer science that have often required programmed spatial control of molecules and atoms in three-dimensional (3D) space. This review provides a comprehensive survey of recent developments in DNA origami structure, design, assembly, and directed self-assembly, as well as its broad applications.

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Section: Applications Of Dna Origamimentioning

confidence: 99%

Section: Bioanalysis With Dna Origamimentioning

confidence: 99%

DNA Origami: Scaffolds for Creating Higher Order Structures

2017

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“…This was for instance used by Fan and co-workers for binding a DNA tetrahedron to a gold surface with a specific face of the structure attached to the surface. 534 The gold−thiol interaction was also used for bridging gold islands with DNA origami nanotubes, 535 for trapping rectangular DNA origami with thiol-modified corners between gold islands on a SiO 2surface, 536 and for immobilization of origami using dielectrophoretic trapping between gold electrodes. 537,538 Rothemund and co-workers have further devised a methodology for covalent immobilization of DNA origami on Si/SiO 2 surfaces.…”

Section: Covalent Interactionsmentioning

confidence: 99%

Chemistries for DNA Nanotechnology

2019

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The predictable nature of DNA interactions enables the programmable assembly of highly advanced 2D and 3D DNA structures of nanoscale dimensions. The access to ever larger and more complex structures has been achieved through decades of work on developing structural design principles. Concurrently, an increased focus has emerged on the applications of DNA nanostructures. In its nature, DNA is chemically inert and nanostructures based on unmodified DNA mostly lack function. However, functionality can be obtained through chemical modification of DNA nanostructures and the opportunities are endless. In this review, we discuss methodology for chemical functionalization of DNA nanostructures and provide examples of how this is being used to create functional nanodevices and make DNA nanostructures more applicable. We aim to encourage researchers to adopt chemical modifications as part of their work in DNA nanotechnology and inspire chemists to address current challenges and opportunities within the field.

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“…Approaches which fix the ends of linear nanostructures on metal bars or dots (18,19,21), or align them to chemical stripes (16), add arbitrary control of position and in-plane rotation, but still cannot distinguish the orientations in Fig. 1, D to G. Nor can methods which fix the corners of rectangles (22). Here we show that absolute orientation can be achieved by DOP with suitably asymmetric DNA origami shapes, and demonstrate two applications in which absolute and arbitrary orientation work together to optimize or integrate optical devices.…”

mentioning

confidence: 99%

“…(F) Lithographic patterning of gold dots allows linear DNA structures terminated with thiols to be arbitrarily oriented (19,21) similar work on block copolymers (20) compromises arbitrary x, y, θ control for potential scalability. (G) Extension of the gold-dot/thiol approach to 2D nanostructures (rectangles) allows orientational freedom to be limited to just four degenerate orientations (22). (H) DNA origami placement of equilateral triangles still leaves six degenerate orientations, and orientational fidelity is relatively coarse, allowing only four rotations to be distinguished (24)(25)(26).…”

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confidence: 99%

Absolute and arbitrary orientation of single molecule shapes

Gopinath¹,

Thachuk²,

Mitskovets³

et al. 2018

Preprint

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DNA origami is a modular platform for the combination of molecular and colloidal components to create optical, electronic, and biological devices. Integration of such nanoscale devices with microfabricated connectors and circuits is challenging: large numbers of freely diffusing devices must be fixed at desired locations with desired alignment. We present a DNA origami molecule whose energy landscape on lithographic binding sites has a unique maximum. This property enables device alignment within 3.2 • on SiO 2 . Orientation is absolute (all degrees of freedom are specified) and arbitrary (every molecule's orientation is independently specified). The use of orientation to optimize device performance is shown by aligning fluorescent emission dipoles within microfabricated optical cavities. Large-scale integration is demonstrated via an array of 3,456 DNA origami with 12 distinct orientations, which indicates the polarization of excitation light.The sequential combination of solution-phase self-assembly (SPSA) and directed self-assembly (DSA) provides a general paradigm for the synthesis of nanoscale devices and their large-scale integration with control circuitry, microfluidics, or other conventionally-fabricated structures. SPSA for the creation of sub-lithographic devices via structural DNA nanotechnology (1) is relatively mature. In particular, typical DNA origami (2) allow up to 200 nanoscale components, including carbon nanotubes (3-5), metal nanoparticles (6, 7), fluorescent molecules (6-8), quantum dots (7, 9) and conductive polymers (10) to be simultaneously juxtaposed at 3-5 nm resolution within a 100 nm×70 nm DNA rectangle. DSA uses topographic (11,12) or chemical (13-26) patterning, fields (27-37), or flow (38-46) to control the higher order structure of molecules and particles. Well-developed for continuous block copolymers films (13, 14), spherical nanoparticles (11, 12), and linear nanostructures (16-22, 27-36, 38-46), DSA is less developed for origami-templated devices for which shape and symmetry play an important role in device function and integration. Two challenges arise in the DSA of orgami-templated devices. The first is analogous to the problem of absolute orientation (47) (Fig. 1A) in computational geometry: Given two Cartesian coordinate systems, what translation and rotation can transform the first to the second? Such transformations are key in computer vision and robotics, where they can be used to plan the motion of a virtual camera, or a robot arm. The physical analog for DSA asks: How can an asymmetric device in solution be positioned and aligned relative to a global reference frame in the laboratory? The second challenge is to achieve absolute orientation for many devices at once, such that the position and alignment of each device is arbitrary, i.e. independent of other devices (Fig. 1B). DNA origami placement (DOP) (24-26) is a potential solution to both challenges. In DOP the * Departments of 1 Bioengineering, 2 Computing & Mathematical Science,

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Suspending DNA Origami Between Four Gold Nanodots

Abstract: Rectangular DNA origami functionalized with thiols in each of the four corners immobilizes by self-assembly between lithographically patterned gold nanodots on a silicon oxide surface.

Cited by 8 publications

References 29 publications

DNA Origami: Scaffolds for Creating Higher Order Structures

DNA Origami: Scaffolds for Creating Higher Order Structures

Chemistries for DNA Nanotechnology

Absolute and arbitrary orientation of single molecule shapes

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