Constructing Large 2D Lattices Out of DNA-Tiles

The predictable nature of deoxyribonucleic acid (DNA) interactions enables assembly of DNA into almost any arbitrary shape with programmable features of nanometer precision. The recent progress of DNA nanotechnology has allowed production of an even wider gamut of possible shapes with high-yield and error-free assembly processes. Most of these structures are, however, limited in size to a nanometer scale. To overcome this limitation, a plethora of studies has been carried out to form larger structures using DNA assemblies as building blocks or tiles. Therefore, DNA tiles have become one of the most widely used building blocks for engineering large, intricate structures with nanometer precision. To create even larger assemblies with highly organized patterns, scientists have developed a variety of structural design principles and assembly methods. This review first summarizes currently available DNA tile toolboxes and the basic principles of lattice formation and hierarchical self-assembly using DNA tiles. Special emphasis is given to the forces involved in the assembly process in liquid-liquid and at solid-liquid interfaces, and how to master them to reach the optimum balance between the involved interactions for successful self-assembly. In addition, we focus on the recent approaches that have shown great potential for the controlled immobilization and positioning of DNA nanostructures on different surfaces. The ability to position DNA objects in a controllable manner on technologically relevant surfaces is one step forward towards the integration of DNA-based materials into nanoelectronic and sensor devices.

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Adenita: interactive 3D modelling and visualization of DNA nanostructures

Nucleic Acids Research ◽

10.1093/nar/gkaa593 ◽

2020 ◽

Vol 48 (15) ◽

pp. 8269-8275 ◽

Cited By ~ 3

Author(s):

Elisa de Llano ◽

Haichao Miao ◽

Yasaman Ahmadi ◽

Amanda J Wilson ◽

Morgan Beeby ◽

...

Keyword(s):

Dna Nanotechnology ◽

Software Tool ◽

Building Blocks ◽

Dna Origami ◽

Dna Nanostructures ◽

User Interactions ◽

Dna Nanostructure ◽

Dna Tiles ◽

The Creation ◽

Interactive 3D

Abstract DNA nanotechnology is a rapidly advancing field, which increasingly attracts interest in many different disciplines, such as medicine, biotechnology, physics and biocomputing. The increasing complexity of novel applications requires significant computational support for the design, modelling and analysis of DNA nanostructures. However, current in silico design tools have not been developed in view of these new applications and their requirements. Here, we present Adenita, a novel software tool for the modelling of DNA nanostructures in a user-friendly environment. A data model supporting different DNA nanostructure concepts (multilayer DNA origami, wireframe DNA origami, DNA tiles etc.) has been developed allowing the creation of new and the import of existing DNA nanostructures. In addition, the nanostructures can be modified and analysed on-the-fly using an intuitive toolset. The possibility to combine and re-use existing nanostructures as building blocks for the creation of new superstructures, the integration of alternative molecules (e.g. proteins, aptamers) during the design process, and the export option for oxDNA simulations are outstanding features of Adenita, which spearheads a new generation of DNA nanostructure modelling software. We showcase Adenita by re-using a large nanorod to create a new nanostructure through user interactions that employ different editors to modify the original nanorod.

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High Yield Assembly of Compliant MEMS Snap Fasteners

Volume 4: 20th International Conference on Design Theory and Methodology; Second International Conference on Micro- and Nanosystems ◽

10.1115/detc2008-49232 ◽

2008 ◽

Cited By ~ 2

Author(s):

Rakesh Murthy ◽

Aditya N. Das ◽

Dan O. Popa

Keyword(s):

Self Assembly ◽

Building Blocks ◽

Deformation Energy ◽

High Yield ◽

3 Dimensional ◽

Lab Experiments ◽

Trade Offs ◽

Robotic Cells ◽

And Performance ◽

Important Design

Heterogeneous assembly at the microscale has recently emerged as a viable pathway to constructing 3-dimensional microrobots and other miniaturized devices. In contrast to self-assembly, this method is directed and deterministic, and is based on serial or parallel microassembly. Whereas at the meso and macro scales, automation is often undertaken after, and often benchmarked against manual assembly, we demonstrate that deterministic automation at the MEMS scale can be completed with higher yields through the use of engineered compliance and precision robotic cells. Snap fasteners have long been used as a way to exploit the inherent stability of local minima of the deformation energy caused by interference during part mating. In this paper we assume that the building blocks are 2 1/2 -dimensional, as is the case with lithographically microfabricated MEMS parts. The assembly of the snap fasteners is done using μ3, a multi-robot microassembly station with unique characteristics located at our ARRI’s Texas Microfactory lab. Experiments are performed to demonstrate that fast and reliable assemblies can be expected if the microparts and the robotic cell satisfy a so-called “High Yield Assembly Condition” (H.Y.A.C.). Important design trade-offs for assembly and performance of microsnap fasteners are discussed and experimentally evaluated.

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Self-Assembly, Dynamics, and Polymorphism of hIAPP(20–29) Aggregates at Solid–Liquid Interfaces

Langmuir ◽

10.1021/acs.langmuir.6b03288 ◽

2016 ◽

Vol 33 (1) ◽

pp. 372-381 ◽

Cited By ~ 6

Author(s):

Roozbeh Hajiraissi ◽

Ignacio Giner ◽

Guido Grundmeier ◽

Adrian Keller

Keyword(s):

Self Assembly ◽

Liquid Interfaces ◽

Solid Liquid

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Bio-surface engineering with DNA scaffolds for theranostic applications

Nanofabrication ◽

10.1515/nanofab-2018-0001 ◽

2018 ◽

Vol 4 (1) ◽

pp. 1-16 ◽

Cited By ~ 4

Author(s):

Xiwei Wang ◽

Wei Lai ◽

Tiantian Man ◽

Xiangmeng Qu ◽

Li Li ◽

...

Keyword(s):

Recent Progress ◽

Surface Engineering ◽

Dna Nanotechnology ◽

Three Dimensions ◽

High Yield ◽

Biological Applications ◽

Dna Nanostructures ◽

Surface Functionality ◽

Recognition Ability ◽

Theranostic Applications

Abstract Biosensor design is important to bioanalysis yet challenged by the restricted target accessibility at the biomolecule-surface (bio-surface). The last two decades have witnessed the appearance of various “art-like” DNA nanostructures in one, two, or three dimensions, and DNA nanostructures have attracted tremendous attention for applications in diagnosis and therapy due to their unique properties (e.g., mechanical flexibility, programmable control over their shape and size, easy and high-yield preparation, precise spatial addressability and biocompatibility). DNA nanotechnology is capable of providing an effective approach to control the surface functionality, thereby increasing the molecular recognition ability at the biosurface. Herein, we present a critical review of recent progress in the development of DNA nanostructures in one, two and three dimensions and highlight their biological applications including diagnostics and therapeutics. We hope that this review provides a guideline for bio-surface engineering with DNA nanostructures.

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Potential- and concentration-dependent self-assembly structures at solid/liquid interfaces

Nanoscale ◽

10.1039/c7nr08475g ◽

2018 ◽

Vol 10 (7) ◽

pp. 3438-3443 ◽

Cited By ~ 6

Author(s):

Zhen-Feng Cai ◽

Hui-Juan Yan ◽

Dong Wang ◽

Li-Jun Wan

Keyword(s):

Scanning Tunneling Microscopy ◽

Self Assembly ◽

Scanning Tunneling ◽

Liquid Interfaces ◽

Tunneling Microscopy ◽

Controlled Assembly ◽

Electrochemical Scanning Tunneling Microscopy ◽

Solid Liquid

We report the potential and concentration controlled assembly of an alkyl-substituted benzo[1,2-b:4,5-b′]dithiophene (DDBDT) on an Au(111) electrode byin situelectrochemical scanning tunneling microscopy (ECSTM).

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Engineering Biomolecular Self‐Assembly at Solid–Liquid Interfaces

Advanced Materials ◽

10.1002/adma.201905784 ◽

2020 ◽

pp. 1905784

Author(s):

Shuai Zhang ◽

Jiajun Chen ◽

Jianli Liu ◽

Harley Pyles ◽

David Baker ◽

...

Keyword(s):

Self Assembly ◽

Liquid Interfaces ◽

Solid Liquid

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Fluorosurfactant Self-Assembly at Solid/Liquid Interfaces

Langmuir ◽

10.1021/la025989c ◽

2002 ◽

Vol 18 (21) ◽

pp. 8085-8095 ◽

Cited By ~ 19

Author(s):

Orlando J. Rojas ◽

Lubica Macakova ◽

Eva Blomberg ◽

Åsa Emmer ◽

Per M. Claesson

Keyword(s):

Self Assembly ◽

Liquid Interfaces ◽

Solid Liquid

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Novel roles for well-known players: from tobacco mosaic virus pests to enzymatically active assemblies

Beilstein Journal of Nanotechnology ◽

10.3762/bjnano.7.54 ◽

2016 ◽

Vol 7 ◽

pp. 613-629 ◽

Cited By ~ 29

Author(s):

Claudia Koch ◽

Fabian J Eber ◽

Carlos Azucena ◽

Alexander Förste ◽

Stefan Walheim ◽

...

Keyword(s):

Tobacco Mosaic Virus ◽

Mosaic Virus ◽

Self Assembly ◽

Building Blocks ◽

Mosaic Disease ◽

Inorganic Materials ◽

High Yield ◽

External Control ◽

Immobilization Of Enzymes

The rod-shaped nanoparticles of the widespread plant pathogentobacco mosaic virus(TMV) have been a matter of intense debates and cutting-edge research for more than a hundred years. During the late 19th century, their behavior in filtration tests applied to the agent causing the 'plant mosaic disease' eventually led to the discrimination of viruses from bacteria. Thereafter, they promoted the development of biophysical cornerstone techniques such as electron microscopy and ultracentrifugation. Since the 1950s, the robust, helically arranged nucleoprotein complexes consisting of a single RNA and more than 2100 identical coat protein subunits have enabled molecular studies which have pioneered the understanding of viral replication and self-assembly, and elucidated major aspects of virus–host interplay, which can lead to agronomically relevant diseases. However, during the last decades, TMV has acquired a new reputation as a well-defined high-yield nanotemplate with multivalent protein surfaces, allowing for an ordered high-density presentation of multiple active molecules or synthetic compounds. Amino acid side chains exposed on the viral coat may be tailored genetically or biochemically to meet the demands for selective conjugation reactions, or to directly engineer novel functionality on TMV-derived nanosticks. The natural TMV size (length: 300 nm) in combination with functional ligands such as peptides, enzymes, dyes, drugs or inorganic materials is advantageous for applications ranging from biomedical imaging and therapy approaches over surface enlargement of battery electrodes to the immobilization of enzymes. TMV building blocks are also amenable to external control of in vitro assembly and re-organization into technically expedient new shapes or arrays, which bears a unique potential for the development of 'smart' functional 3D structures. Among those, materials designed for enzyme-based biodetection layouts, which are routinely applied, e.g., for monitoring blood sugar concentrations, might profit particularly from the presence of TMV rods: Their surfaces were recently shown to stabilize enzymatic activities upon repeated consecutive uses and over several weeks. This review gives the reader a ride through strikingly diverse achievements obtained with TMV-based particles, compares them to the progress with related viruses, and focuses on latest results revealing special advantages for enzyme-based biosensing formats, which might be of high interest for diagnostics employing 'systems-on-a-chip'.

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Self-assembly of large RNA structures: learning from DNA nanotechnology

DNA and RNA Nanotechnology ◽

10.1515/rnan-2015-0002 ◽

2016 ◽

Vol 2 (1) ◽

Cited By ~ 3

Author(s):

Jaimie Marie Stewart ◽

Elisa Franco

Keyword(s):

Self Assembly ◽

De Novo ◽

Dna Nanotechnology ◽

De Novo Design ◽

Dna Nanostructures ◽

Rna Structures ◽

Functional Nanostructures ◽

Rna And Dna ◽

Unique Chemical

AbstractNucleic acid nanotechnology offers many methods to build self-assembled structures using RNA and DNA. These scaffolds are valuable in multiple applications, such as sensing, drug delivery and nanofabrication. Although RNA and DNA are similar molecules, they also have unique chemical and structural properties. RNA is generally less stable than DNA, but it folds into a variety of tertiary motifs that can be used to produce complex and functional nanostructures. Another advantage of using RNA over DNA is its ability to be encoded into genes and to be expressed in vivo. Here we review existing approaches for the self-assembly of RNA and DNA nanostructures and specifically methods to assemble large RNA structures. We describe de novo design approaches used in DNA nanotechnology that can be ported to RNA. Lastly, we discuss some of the challenges yet to be solved to build micron-scale, multi stranded RNA scaffolds.

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