Programmed Nanopatterning of Organic/Inorganic Nanoparticles Using Nanometer-Scale Wells Embedded in a DNA Origami Scaffold

Small ◽  
2010 ◽  
Vol 6 (23) ◽  
pp. 2664-2667 ◽  
Author(s):  
Akinori Kuzuya ◽  
Naohiro Koshi ◽  
Mayumi Kimura ◽  
Kentaro Numajiri ◽  
Takahiro Yamazaki ◽  
...  
Keyword(s):  
Dna Origami ◽  
Inorganic Nanoparticles ◽  
Nanometer Scale

scholarly journals An electrochemical biosensor exploiting binding-induced changes in electron transfer of electrode-attached DNA origami to detect hundred nanometer-scale targets

Nanoscale ◽  
2020 ◽  
Vol 12 (26) ◽  
pp. 13907-13911 ◽  
Author(s):  
Netzahualcóyotl Arroyo-Currás ◽  
Muaz Sadeia ◽  
Alexander K. Ng ◽  
Yekaterina Fyodorova ◽  
Natalie Williams ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Electrochemical Biosensor ◽  
Direct Detection ◽  
Dna Origami ◽  
Nanometer Scale ◽  
Recognition Element ◽  
Induced Changes

Using DNA origami as the recognition element in an electrochemical biosensor enables the selective and direct detection of “mesoscale” virus-sized analytes.

Precisely Programmed and Robust 2D Streptavidin Nanoarrays by Using Periodical Nanometer-Scale Wells Embedded in DNA Origami Assembly

ChemBioChem ◽  
2009 ◽  
Vol 10 (11) ◽  
pp. 1811-1815 ◽  
Author(s):  
Akinori Kuzuya ◽  
Mayumi Kimura ◽  
Kentaro Numajiri ◽  
Naohiro Koshi ◽  
Toshiyuki Ohnishi ◽  
...  
Keyword(s):  
Dna Origami ◽  
Nanometer Scale

scholarly journals Connecting DNA Origami Structures into a Designed and Functionalized Network

2019 ◽  
Vol 8 (4) ◽  
pp. 14
Author(s):  
George Amoako
Keyword(s):  
Gold Nanoparticles ◽  
Gel Electrophoresis ◽  
Dna Origami ◽  
Nanometer Scale ◽  
Agarose Gel ◽  
Agarose Gel Electrophoresis ◽  
Attachment Sites ◽  
Vis Spectroscopy ◽  
Specific Affinity ◽  
Affinity Interaction

The versatility of the DNA origami approach of organizing nanoparticles at the nanometer scale, together with thiol chemistry have been used. These approaches were used to design DNA origami structures and to functionalize them with gold nanoparticles after designing attachment sites on the DNA origami structures. In all two structures were designed – a cross-like structure and a nanotube but only the nanotube structure was used to form the gold nanoparticle helices. Finally, use was made of the specific affinity interaction between biotin and streptavidin to connect the DNA origami templated AuNP helices to the cross-like structure. Agarose gel electrophoresis, UV-vis spectroscopy and TEM were used to characterize the structure.

scholarly journals DNA origami cryptography for secure communication

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Yinan Zhang ◽  
Fei Wang ◽  
Jie Chao ◽  
Mo Xie ◽  
Huajie Liu ◽  
...  
Keyword(s):  
Information Security ◽  
Protein Binding ◽  
Secure Communication ◽  
Data Encryption ◽  
Dna Origami ◽  
Nanometer Scale ◽  
Next Generation ◽  
Data Formats ◽  
Unique Approach ◽  
Biomolecular Reactions

AbstractBiomolecular cryptography exploiting specific biomolecular interactions for data encryption represents a unique approach for information security. However, constructing protocols based on biomolecular reactions to guarantee confidentiality, integrity and availability (CIA) of information remains a challenge. Here we develop DNA origami cryptography (DOC) that exploits folding of a M13 viral scaffold into nanometer-scale self-assembled braille-like patterns for secure communication, which can create a key with a size of over 700 bits. The intrinsic nanoscale addressability of DNA origami additionally allows for protein binding-based steganography, which further protects message confidentiality in DOC. The integrity of a transmitted message can be ensured by establishing specific linkages between several DNA origamis carrying parts of the message. The versatility of DOC is further demonstrated by transmitting various data formats including text, musical notes and images, supporting its great potential for meeting the rapidly increasing CIA demands of next-generation cryptography.

scholarly journals Autonomously designed free-form 2D DNA origami

2019 ◽  
Vol 5 (1) ◽  
pp. eaav0655 ◽  
Author(s):  
Hyungmin Jun ◽  
Fei Zhang ◽  
Tyson Shepherd ◽  
Sakul Ratanalert ◽  
Xiaodong Qi ◽  
...  
Keyword(s):  
Materials Science ◽  
Dna Origami ◽  
Free Form ◽  
Nanometer Scale ◽  
Dna Duplexes ◽  
Sequence Design ◽  
Internal Structures ◽  
Design Paradigm ◽  
2D And 3D ◽  
Unique Ability

Scaffolded DNA origami offers the unique ability to organize molecules in nearly arbitrary spatial patterns at the nanometer scale, with wireframe designs further enabling complex 2D and 3D geometries with irregular boundaries and internal structures. The sequence design of the DNA staple strands needed to fold the long scaffold strand to the target geometry is typically performed manually, limiting the broad application of this materials design paradigm. Here, we present a fully autonomous procedure to design all DNA staple sequences needed to fold any free-form 2D scaffolded DNA origami wireframe object. Our algorithm uses wireframe edges consisting of two parallel DNA duplexes and enables the full autonomy of scaffold routing and staple sequence design with arbitrary network edge lengths and vertex angles. The application of our procedure to geometries with both regular and irregular external boundaries and variable internal structures demonstrates its broad utility for nanoscale materials science and nanotechnology.

scholarly journals Automated sequence design of 2D wireframe DNA origami with honeycomb edges

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Hyungmin Jun ◽  
Xiao Wang ◽  
William P. Bricker ◽  
Mark Bathe
Keyword(s):  
Design Procedure ◽  
Computational Approach ◽  
Dna Origami ◽  
Nanometer Scale ◽  
Top Down ◽  
Complex Objects ◽  
Sequence Design ◽  
Theoretical Support ◽  
Powerful Approach ◽  
2D And 3D

AbstractWireframe DNA origami has emerged as a powerful approach to fabricating nearly arbitrary 2D and 3D geometries at the nanometer-scale. Complex scaffold and staple routing needed to design wireframe DNA origami objects, however, render fully automated, geometry-based sequence design approaches essential for their synthesis. And wireframe DNA origami structural fidelity can be limited by wireframe edges that are composed only of one or two duplexes. Here we introduce a fully automated computational approach that programs 2D wireframe origami assemblies using honeycomb edges composed of six parallel duplexes. These wireframe assemblies show enhanced structural fidelity from electron microscopy-based measurement of programmed angles compared with identical geometries programmed using dual-duplex edges. Molecular dynamics provides additional theoretical support for the enhanced structural fidelity observed. Application of our top-down sequence design procedure to a variety of complex objects demonstrates its broad utility for programmable 2D nanoscale materials.

scholarly journals Effect of DNA Origami Nanostructures on hIAPP Aggregation

Nanomaterials ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 2200
Author(s):  
Marcel Hanke ◽  
Alejandro Gonzalez Orive ◽  
Guido Grundmeier ◽  
Adrian Keller
Keyword(s):  
Electrostatic Interactions ◽  
Dna Origami ◽  
Inorganic Nanoparticles ◽  
Ex Situ ◽  
Dna Nanostructures ◽  
Islet Amyloid ◽  
Force Microscopy ◽  
Double Stranded Dna ◽  
Atomic Force

The aggregation of human islet amyloid polypeptide (hIAPP) plays a major role in the pathogenesis of type 2 diabetes mellitus (T2DM), and numerous strategies for controlling hIAPP aggregation have been investigated so far. In particular, several organic and inorganic nanoparticles (NPs) have shown the potential to influence the aggregation of hIAPP and other amyloidogenic proteins and peptides. In addition to conventional NPs, DNA nanostructures are receiving more and more attention from the biomedical field. Therefore, in this work, we investigated the effects of two different DNA origami nanostructures on hIAPP aggregation. To this end, we employed in situ turbidity measurements and ex situ atomic force microscopy (AFM). The turbidity measurements revealed a retarding effect of the DNA nanostructures on hIAPP aggregation, while the AFM results showed the co-aggregation of hIAPP with the DNA origami nanostructures into hybrid peptide–DNA aggregates. We assume that this was caused by strong electrostatic interactions between the negatively charged DNA origami nanostructures and the positively charged peptide. Most intriguingly, the influence of the DNA origami nanostructures on hIAPP aggregation differed from that of genomic double-stranded DNA (dsDNA) and appeared to depend on DNA origami superstructure. DNA origami nanostructures may thus represent a novel route for modulating amyloid aggregation in vivo.

The Kinematic Principle for Designing Deoxyribose Nucleic Acid Origami Mechanisms: Challenges and Opportunities1

2017 ◽  
Vol 139 (6) ◽  
Author(s):  
Hai-Jun Su ◽  
Carlos E. Castro ◽  
Alexander E. Marras ◽  
Lifeng Zhou
Keyword(s):  
Nucleic Acid ◽  
Self Assembly ◽  
Three Dimensional ◽  
Dna Origami ◽  
Nanometer Scale ◽  
Computational Tools ◽  
Deoxyribose Nucleic Acid ◽  
Double Stranded Dna ◽  
Kinematic Mechanisms ◽  
And Robotics

Deoxyribose nucleic acid (DNA) origami nanotechnology is a recently developed self-assembly process for design and fabrication of complex three-dimensional (3D) nanostructures using DNA as a functional material. This paper reviews our recent progress in applying DNA origami to design kinematic mechanisms at the nanometer scale. These nanomechanisms, which we call DNA origami mechanisms (DOM), are made of relatively stiff bundles of double-stranded DNA (dsDNA), which function as rigid links, connected by highly compliant single-stranded DNA (ssDNA) strands, which function as kinematic joints. The design of kinematic joints including revolute, prismatic, cylindrical, universal, and spherical is presented. The steps as well as necessary software or experimental tools for designing DOM with DNA origami links and joints are detailed. To demonstrate the designs, we presented the designs of Bennett four-bar and crank–slider linkages. Finally, a list of technical challenges such as design automation and computational modeling are presented. These challenges could also be opportunities for mechanism and robotics community to apply well-developed kinematic theories and computational tools to the design of nanorobots and nanomachines.

The Kinematic Principle for Designing DNA Origami Mechanisms: Challenges and Opportunities

2015 ◽  
Author(s):  
Hai-Jun Su ◽  
Carlos E. Castro ◽  
Alexander E. Marras ◽  
Lifeng Zhou
Keyword(s):  
Self Assembly ◽  
Design Automation ◽  
Functional Materials ◽  
Dna Origami ◽  
Nanometer Scale ◽  
Computational Tools ◽  
Double Stranded Dna ◽  
Challenges And Opportunities ◽  
Kinematic Mechanisms ◽  
And Robotics

DNA origami nanotechnology is a recently developed self-assembly process for design and fabrication of complex 3D nanostructures using DNA as functional materials. This paper aims to review our recent progress in applying DNA origami to design of kinematic mechanisms of nanometer scale. These nanomechanisms, which we call DNA Origami Mechanisms (DOM), are made of relatively stiff bundles of double-stranded DNA (dsDNA) which function as rigid links, connected by highly compliant single-stranded DNA (ssDNA) strands which function as kinematic joints. The designs of kinematic joints such as revolute, prismatic, cylindrical, universal and spherical are presented. The steps as well as necessary software or experimental tools for designing DOM with DNA origami links and joints are detailed. To demonstrate the designs, we presented the designs of Bennett 4-bar and crank-slider linkages. At last, a list of technical challenges such as design automation, computational modeling are presented. These challenges could also be opportunities for mechanism and robotics community to apply the well developed kinematic theories and computational tools to design of nanorobots and nanomachines.

A switchable DNA origami nanochannel for regulating molecular transport at the nanometer scale

Nanoscale ◽  
2016 ◽  
Vol 8 (7) ◽  
pp. 3944-3948 ◽  
Author(s):  
Dianming Wang ◽  
Yiyang Zhang ◽  
Miao Wang ◽  
Yuanchen Dong ◽  
Chao Zhou ◽  
...  
Keyword(s):  
Dna Nanotechnology ◽  
Molecular Transport ◽  
Dna Origami ◽  
Nanometer Scale

A nanochannel with a shutter at one end was built by DNA nanotechnology.

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