DNA nanotechnology for nanophotonic applications

AbstractAlthough the field of structural DNA nanotechnology has been advancing with an astonishing pace, de novo design of complex 3D nanostructures remains a laborious and time-consuming process. One reason for that is the need for multiple cycles of experimental characterization to elucidate the effect of design choices on the actual shape and function of the self-assembled objects. Here, we demonstrate a multi-resolution simulation framework, mrdna, that, in 30 minutes or less, can produce an atomistic-resolution structure of an arbitrary DNA nanostructure with accuracy on par with that of a cryo-electron microscopy (cryo-EM) reconstruction. We demonstrate fidelity of our mrdna framework through direct comparison of the simulation results with the results of cryo-EM reconstruction of multiple 3D DNA origami objects. Furthermore, we show that our approach can characterize an ensemble of conformations adopted by dynamic DNA nanostructures, the equilibrium structure and dynamics of DNA objects constructed using a self-assembly principle other than origami, i.e., wireframe DNA objects, and to study the properties of DNA objects under a variety of environmental conditions, such as applied electric field. Implemented as an open source Python package, our framework can be extended by the community and integrated with DNA design and molecular graphics tools.

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Constructing Large 2D Lattices Out of DNA-Tiles

Molecules ◽

10.3390/molecules26061502 ◽

2021 ◽

Vol 26 (6) ◽

pp. 1502

Author(s):

Johannes M. Parikka ◽

Karolina Sokołowska ◽

Nemanja Markešević ◽

J. Jussi Toppari

Keyword(s):

Self Assembly ◽

Dna Nanotechnology ◽

Building Blocks ◽

High Yield ◽

Dna Nanostructures ◽

Liquid Interfaces ◽

Basic Principles ◽

Dna Tiles ◽

One Step ◽

Solid Liquid

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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Development of RNA/DNA Hydrogel Targeting Toll-Like Receptor 7/8 for Sustained RNA Release and Potent Immune Activation

Molecules ◽

10.3390/molecules25030728 ◽

2020 ◽

Vol 25 (3) ◽

pp. 728 ◽

Cited By ~ 3

Author(s):

Fusae Komura ◽

Kana Okuzumi ◽

Yuki Takahashi ◽

Yoshinobu Takakura ◽

Makiya Nishikawa

Keyword(s):

Immune Cells ◽

Dna Nanotechnology ◽

Dna Assembly ◽

Toll Like Receptor ◽

Immunostimulatory Activity ◽

Dna Nanostructure ◽

High Level ◽

Factor Α ◽

Dna Hydrogel ◽

Necrosis Factor

Guanosine- and uridine-rich single-stranded RNA (GU-rich RNA) is an agonist of Toll-like receptor (TLR) 7 and TLR8 and induces strong immune responses. A nanostructured GU-rich RNA/DNA assembly prepared using DNA nanotechnology can be used as an adjuvant capable of improving the biological stability of RNA and promoting efficient RNA delivery to target immune cells. To achieve a sustained supply of GU-rich RNA to immune cells, we developed a GU-rich RNA/DNA hydrogel (RDgel) using nanostructured GU-rich RNA/DNA assembly, from which GU-rich RNA can be released in a sustained manner. A hexapod-like GU-rich RNA/DNA nanostructure, or hexapodRD6, was designed using a 20-mer phosphorothioate-stabilized GU-rich RNA and six phosphodiester DNAs. Two sets of hexapodRD6 were mixed to obtain RDgel. Under serum-containing conditions, GU-rich RNA was gradually released from the RDgel. Fluorescently labeled GU-rich RNA was efficiently taken up by DC2.4 murine dendritic cells and induced a high level of tumor necrosis factor-α release from these cells when it was incorporated into RDgel. These results indicate that the RDgel constructed using DNA nanotechnology can be a useful adjuvant in cancer therapy with sustained RNA release and high immunostimulatory activity.

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MrDNA: a multi-resolution model for predicting the structure and dynamics of DNA systems

Nucleic Acids Research ◽

10.1093/nar/gkaa200 ◽

2020 ◽

Vol 48 (9) ◽

pp. 5135-5146 ◽

Cited By ~ 7

Author(s):

Christopher Maffeo ◽

Aleksei Aksimentiev

Keyword(s):

Self Assembly ◽

De Novo ◽

Dna Nanotechnology ◽

Equilibrium Structure ◽

Molecular Graphics ◽

Structure And Dynamics ◽

Self Assembled ◽

Actual Shape ◽

And Function ◽

Assembly Principles

Abstract Although the field of structural DNA nanotechnology has been advancing with an astonishing pace, de novo design of complex 3D nanostructures and functional devices remains a laborious and time-consuming process. One reason for that is the need for multiple cycles of experimental characterization to elucidate the effect of design choices on the actual shape and function of the self-assembled objects. Here, we demonstrate a multi-resolution simulation framework, mrdna, that, in 30 min or less, can produce an atomistic-resolution structure of a self-assembled DNA nanosystem. We demonstrate fidelity of our mrdna framework through direct comparison of the simulation results with the results of cryo-electron microscopy (cryo-EM) reconstruction of multiple 3D DNA origami objects. Furthermore, we show that our approach can characterize an ensemble of conformations adopted by dynamic DNA nanostructures, the equilibrium structure and dynamics of DNA objects constructed using off-lattice self-assembly principles, i.e. wireframe DNA objects, and to study the properties of DNA objects under a variety of environmental conditions, such as applied electric field. Implemented as an open source Python package, our framework can be extended by the community and integrated with DNA design and molecular graphics tools.

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Self-Assembly-Based Structural DNA Nanotechnology

Current Organic Chemistry ◽

10.2174/138527211794474429 ◽

2011 ◽

Vol 15 (4) ◽

pp. 534-547 ◽

Cited By ~ 2

Author(s):

Zhao Zhang ◽

Yanming Fu ◽

Baojie Li ◽

Guoyin Feng ◽

Can Li ◽

...

Keyword(s):

Self Assembly ◽

Dna Nanotechnology ◽

Structural Dna Nanotechnology

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FOLDNA, a Web Server for Self-Assembled DNA Nanostructure Autoscaffolds and Autostaples

Journal of Nanotechnology ◽

10.1155/2012/453953 ◽

2012 ◽

Vol 2012 ◽

pp. 1-5 ◽

Cited By ~ 3

Author(s):

Chensheng Zhou ◽

Heng Luo ◽

Xiaolu Feng ◽

Xingwang Li ◽

Jie Zhu ◽

...

Keyword(s):

Drug Delivery ◽

Dna Sequences ◽

Self Assembly ◽

Web Server ◽

Automatic Design ◽

Dna Nanostructures ◽

Complementary Dna ◽

Dna Nanostructure ◽

Comprehensive Information ◽

Self Assembled

DNA self-assembly is a nanotechnology that folds DNA into desired shapes. Self-assembled DNA nanostructures, also known as origami, are increasingly valuable in nanomaterial and biosensing applications. Two ways to use DNA nanostructures in medicine are to form nanoarrays, and to work as vehicles in drug delivery. The DNA nanostructures perform well as a biomaterial in these areas because they have spatially addressable and size controllable properties. However, manually designing complementary DNA sequences for self-assembly is a technically demanding and time consuming task, which makes it advantageous for computers to do this job instead. We have developed a web server, FOLDNA, which can automatically design 2D self-assembled DNA nanostructures according to custom pictures and scaffold sequences provided by the users. It is the first web server to provide an entirely automatic design of self-assembled DNA nanostructure, and it takes merely a second to generate comprehensive information for molecular experiments including: scaffold DNA pathways, staple DNA directions, and staple DNA sequences. This program could save as much as several hours in the designing step for each DNA nanostructure. We randomly selected some shapes and corresponding outputs from our server and validated its performance in molecular experiments.

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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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The biological applications of DNA nanomaterials: current challenges and future directions

Signal Transduction and Targeted Therapy ◽

10.1038/s41392-021-00727-9 ◽

2021 ◽

Vol 6 (1) ◽

Author(s):

Wenjuan Ma ◽

Yuxi Zhan ◽

Yuxin Zhang ◽

Chenchen Mao ◽

Xueping Xie ◽

...

Keyword(s):

Self Assembly ◽

Drug Carrier ◽

Genetic Material ◽

Three Dimensional ◽

Real Life ◽

Dna Nanotechnology ◽

Structural Development ◽

Biological Applications ◽

Dna Materials ◽

Functional Dna

AbstractDNA, a genetic material, has been employed in different scientific directions for various biological applications as driven by DNA nanotechnology in the past decades, including tissue regeneration, disease prevention, inflammation inhibition, bioimaging, biosensing, diagnosis, antitumor drug delivery, and therapeutics. With the rapid progress in DNA nanotechnology, multitudinous DNA nanomaterials have been designed with different shape and size based on the classic Watson–Crick base-pairing for molecular self-assembly. Some DNA materials could functionally change cell biological behaviors, such as cell migration, cell proliferation, cell differentiation, autophagy, and anti-inflammatory effects. Some single-stranded DNAs (ssDNAs) or RNAs with secondary structures via self-pairing, named aptamer, possess the ability of targeting, which are selected by systematic evolution of ligands by exponential enrichment (SELEX) and applied for tumor targeted diagnosis and treatment. Some DNA nanomaterials with three-dimensional (3D) nanostructures and stable structures are investigated as drug carrier systems to delivery multiple antitumor medicine or gene therapeutic agents. While the functional DNA nanostructures have promoted the development of the DNA nanotechnology with innovative designs and preparation strategies, and also proved with great potential in the biological and medical use, there is still a long way to go for the eventual application of DNA materials in real life. Here in this review, we conducted a comprehensive survey of the structural development history of various DNA nanomaterials, introduced the principles of different DNA nanomaterials, summarized their biological applications in different fields, and discussed the current challenges and further directions that could help to achieve their applications in the future.

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