Cellular processing and destinies of artificial DNA nanostructures

2016 ◽  
Vol 45 (15) ◽  
pp. 4199-4225 ◽  
Author(s):  
Di Sheng Lee ◽  
Hang Qian ◽  
Chor Yong Tay ◽  
David Tai Leong
Keyword(s):  
Dna Nanotechnology ◽  
Dna Nanostructures ◽  
Panoramic View ◽  
Artificial Dna ◽  
Cellular Processing ◽  
Mechanistic Understanding ◽  
The Many ◽  
In Cells

This review gives a panoramic view of the many DNA nanotechnology applications in cells, mechanistic understanding of how and where their interactions occur and their subsequent outcomes.

ARTIFICIALLY DESIGNED DNA NANOSTRUCTURES

NANO ◽  
2009 ◽  
Vol 04 (03) ◽  
pp. 119-139 ◽  
Author(s):  
RASHID AMIN ◽  
SOYEON KIM ◽  
SUNG HA PARK ◽  
THOMAS HENRY LABEAN
Keyword(s):  
Dna Sequences ◽  
Self Assembly ◽  
Dna Nanotechnology ◽  
Medical Applications ◽  
Dna Nanostructures ◽  
Base Pairing ◽  
Assembly Instructions ◽  
Artificial Dna ◽  
Structural Dna Nanotechnology ◽  
Complex Nanostructures

In the field of structural DNA nanotechnology, researchers create artificial DNA sequences to self-assemble into target molecular superstructures and nanostructures. The well-understood Watson–Crick base-pairing rules are used to encode assembly instructions directly into the DNA molecules. A wide variety of complex nanostructures has been created using this method. DNA directed self-assembly is now being adapted for use in the nanofabrication of functional structures for use in electronics, photonics, and medical applications.

scholarly journals In vivo cloning of artificial DNA nanostructures

2008 ◽  
Vol 105 (46) ◽  
pp. 17626-17631 ◽  
Author(s):  
Chenxiang Lin ◽  
Sherri Rinker ◽  
Xing Wang ◽  
Yan Liu ◽  
Nadrian C. Seeman ◽  
...  
Keyword(s):  
Dna Nanotechnology ◽  
Dna Nanostructures ◽  
Scientific Enterprise ◽  
Dna Nanostructure ◽  
Copy Numbers ◽  
Artificial Dna ◽  
Difficult Challenge ◽  
Endonuclease Vii

Mimicking nature is both a key goal and a difficult challenge for the scientific enterprise. DNA, well known as the genetic-information carrier in nature, can be replicated efficiently in living cells. Today, despite the dramatic evolution of DNA nanotechnology, a versatile method that replicates artificial DNA nanostructures with complex secondary structures remains an appealing target. Previous success in replicating DNA nanostructures enzymatically in vitro suggests that a possible solution could be cloning these nanostructures by using viruses. Here, we report a system where a single-stranded DNA nanostructure (Holliday junction or paranemic cross-over DNA) is inserted into a phagemid, transformed into XL1-Blue cells and amplified in vivo in the presence of helper phages. High copy numbers of cloned nanostructures can be obtained readily by using standard molecular biology techniques. Correct replication is verified by a number of assays including nondenaturing PAGE, Ferguson analysis, endonuclease VII digestion, and hydroxyl radical autofootprinting. The simplicity, efficiency, and fidelity of nature are fully reflected in this system. UV-induced psoralen cross-linking is used to probe the secondary structure of the inserted junction in infected cells. Our data suggest the possible formation of the immobile four-arm junction in vivo.

scholarly journals Exceptional biostability of paranemic crossover (PX) DNA, crossover-dependent nuclease resistance, and implications for DNA nanotechnology

2019 ◽  
Author(s):  
Arun Richard Chandrasekaran ◽  
Javier Vilcapoma ◽  
Paromita Dey ◽  
SiuWah Wong-Deyrup ◽  
Bijan K. Dey ◽  
...  
Keyword(s):  
Biomedical Applications ◽  
Biological Fluids ◽  
Dna Nanotechnology ◽  
Full Potential ◽  
Dna Nanostructures ◽  
Double Stranded Dna ◽  
Nuclease Resistance ◽  
Order Of Magnitude ◽  
Paranemic Crossover ◽  
The Many

AbstractInherent nanometer-sized features and molecular recognition properties make DNA a useful material in constructing nanoscale objects, with alluring applications in biosensing and drug delivery. However, DNA can be easily degraded by nucleases present in biological fluids, posing a considerable roadblock to realizing the full potential of DNA nanotechnology for biomedical applications. Here we investigated the nuclease resistance and biostability of the multi-stranded motif called paranemic crossover (PX) DNA and discovered a remarkable and previously unreported resistance to nucleases. We show that PX DNA has more than an order of magnitude increased resistance to degradation by DNase I, serum, and urine compared to double stranded DNA. We further demonstrate that the degradation resistance decreases monotonically as DNA crossovers are removed from the structure, suggesting that frequent DNA crossovers disrupt either the binding or catalysis of nucleases or both. Further, we show using mouse and human cell lines that PX DNA does not affect cell proliferation or interfere with biological processes such as myogenesis. These results have important implications for building DNA nanostructures with enhanced biostability, either by adopting PX-based architectures or by carefully engineering crossovers. We contend that such crossover-dependent nuclease resistance could potentially be used to add “tunable biostability” to the many features of DNA nanotechnology.

scholarly journals Strategies to Build Hybrid Protein–DNA Nanostructures

Nanomaterials ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 1332
Author(s):  
Armando Hernandez-Garcia
Keyword(s):  
Dynamic Systems ◽  
Dna Nanotechnology ◽  
Chemical Properties ◽  
Hybrid Nanostructures ◽  
Advanced Materials ◽  
Dna Nanostructures ◽  
Hybrid Protein ◽  
Structural Protein ◽  
The Individual ◽  
Structural Dna Nanotechnology

Proteins and DNA exhibit key physical chemical properties that make them advantageous for building nanostructures with outstanding features. Both DNA and protein nanotechnology have growth notably and proved to be fertile disciplines. The combination of both types of nanotechnologies is helpful to overcome the individual weaknesses and limitations of each one, paving the way for the continuing diversification of structural nanotechnologies. Recent studies have implemented a synergistic combination of both biomolecules to assemble unique and sophisticate protein–DNA nanostructures. These hybrid nanostructures are highly programmable and display remarkable features that create new opportunities to build on the nanoscale. This review focuses on the strategies deployed to create hybrid protein–DNA nanostructures. Here, we discuss strategies such as polymerization, spatial directing and organizing, coating, and rigidizing or folding DNA into particular shapes or moving parts. The enrichment of structural DNA nanotechnology by incorporating protein nanotechnology has been clearly demonstrated and still shows a large potential to create useful and advanced materials with cell-like properties or dynamic systems. It can be expected that structural protein–DNA nanotechnology will open new avenues in the fabrication of nanoassemblies with unique functional applications and enrich the toolbox of bionanotechnology.

scholarly journals Hybrid Nanoassemblies from Viruses and DNA Nanostructures

Nanomaterials ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1413
Author(s):  
Sofia Ojasalo ◽  
Petteri Piskunen ◽  
Boxuan Shen ◽  
Mauri A. Kostiainen ◽  
Veikko Linko
Keyword(s):  
Cell Activation ◽  
Immune Cell ◽  
Dna Nanotechnology ◽  
Biological Properties ◽  
Dna Nanostructures ◽  
Dna Structures ◽  
Nanoscale Structures ◽  
Immune Cell Activation ◽  
Wide Range ◽  
Structural Dna Nanotechnology

Viruses are among the most intriguing nanostructures found in nature. Their atomically precise shapes and unique biological properties, especially in protecting and transferring genetic information, have enabled a plethora of biomedical applications. On the other hand, structural DNA nanotechnology has recently emerged as a highly useful tool to create programmable nanoscale structures. They can be extended to user defined devices to exhibit a wide range of static, as well as dynamic functions. In this review, we feature the recent development of virus-DNA hybrid materials. Such structures exhibit the best features of both worlds by combining the biological properties of viruses with the highly controlled assembly properties of DNA. We present how the DNA shapes can act as “structured” genomic material and direct the formation of virus capsid proteins or be encapsulated inside symmetrical capsids. Tobacco mosaic virus-DNA hybrids are discussed as the examples of dynamic systems and directed formation of conjugates. Finally, we highlight virus-mimicking approaches based on lipid- and protein-coated DNA structures that may elicit enhanced stability, immunocompatibility and delivery properties. This development also paves the way for DNA-based vaccines as the programmable nano-objects can be used for controlling immune cell activation.

scholarly journals Constructing Large 2D Lattices Out of DNA-Tiles

Molecules ◽  
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.

scholarly journals Spatiotemporally programmable cascade hybridization of hairpin DNA in polymeric nanoframework for precise siRNA delivery

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Feng Li ◽  
Wenting Yu ◽  
Jiaojiao Zhang ◽  
Yuhang Dong ◽  
Xiaohui Ding ◽  
...  
Keyword(s):  
Steric Effect ◽  
Sirna Delivery ◽  
Dna Nanotechnology ◽  
Hybridization Chain Reaction ◽  
Dna Nanostructures ◽  
Chain Reaction ◽  
Dna Hairpins ◽  
In Vivo Experiments ◽  
Dna And Rna

AbstractDNA nanostructures have been demonstrated as promising carriers for gene delivery. In the carrier design, spatiotemporally programmable assembly of DNA under nanoconfinement is important but has proven highly challenging due to the complexity–scalability–error of DNA. Herein, a DNA nanotechnology-based strategy via the cascade hybridization chain reaction (HCR) of DNA hairpins in polymeric nanoframework has been developed to achieve spatiotemporally programmable assembly of DNA under nanoconfinement for precise siRNA delivery. The nanoframework is prepared via precipitation polymerization with Acrydite-DNA as cross-linker. The potential energy stored in the loops of DNA hairpins can overcome the steric effect in the nanoframework, which can help initiate cascade HCR of DNA hairpins and achieve efficient siRNA loading. The designer tethering sequence between DNA and RNA guarantees a triphosadenine triggered siRNA release specifically in cellular cytoplasm. Nanoframework provides stability and ease of functionalization, which helps address the complexity–scalability–error of DNA. It is exemplified that the phenylboronate installation on nanoframework enhanced cellular uptake and smoothed the lysosomal escape. Cellular results show that the siRNA loaded nanoframework down-regulated the levels of relevant mRNA and protein. In vivo experiments show significant therapeutic efficacy of using siPLK1 loaded nanoframework to suppress tumor growth.

scholarly journals Bio-surface engineering with DNA scaffolds for theranostic applications

2018 ◽  
Vol 4 (1) ◽  
pp. 1-16 ◽  
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.

Cellular uptake of covalent and non-covalent DNA nanostructures with different sizes and geometries

Nanoscale ◽  
2019 ◽  
Vol 11 (22) ◽  
pp. 10808-10818 ◽  
Author(s):  
Sofia Raniolo ◽  
Stefano Croce ◽  
Rasmus P. Thomsen ◽  
Anders H. Okholm ◽  
Valeria Unida ◽  
...  
Keyword(s):  
Cellular Uptake ◽  
Dna Nanostructures ◽  
Intracellular Fate ◽  
In Cells

DNA nanostructures of different sizes and forms are internalized in cells through the LOX-1 receptor with different intracellular fate and lifetime.

scholarly journals DNA Nanotechnology: Progress toward Understanding the Interactions between DNA Nanostructures and the Cell (Small 26/2019)

Small ◽  
2019 ◽  
Vol 15 (26) ◽  
pp. 1970137
Author(s):  
Yee Ting Elaine Chiu ◽  
Huize Li ◽  
Chung Hang Jonathan Choi
Keyword(s):  
Dna Nanotechnology ◽  
Dna Nanostructures
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