scholarly journals DNA-Programmed Chemical Synthesis of Polymers and Inorganic Nanomaterials

2020 ◽  
pp. 57-81
Author(s):  
Xuemei Xu ◽  
Pia Winterwerber ◽  
David Ng ◽  
Yuzhou Wu
Keyword(s):  
Chemical Synthesis ◽  
Single Molecule ◽  
Self Assembly ◽  
Dna Recognition ◽  
Dna Nanotechnology ◽  
Nanometer Scale ◽  
Dna Nanostructures ◽  
Future Outlook ◽  
Inorganic Nanomaterials ◽  
Nanofabrication Technique

Abstract DNA nanotechnology, based on sequence-specific DNA recognition, could allow programmed self-assembly of sophisticated nanostructures with molecular precision. Extension of this technique to the preparation of broader types of nanomaterials would significantly improve nanofabrication technique to lower nanometer scale and even achieve single molecule operation. Using such exquisite DNA nanostructures as templates, chemical synthesis of polymer and inorganic nanomaterials could also be programmed with unprecedented accuracy and flexibility. This review summarizes recent advances in the synthesis and assembly of polymer and inorganic nanomaterials using DNA nanostructures as templates, and discusses the current challenges and future outlook of DNA templated nanotechnology.

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 3D DNA structural barcode copying and random access

2020 ◽  
Author(s):  
Filip Bošković ◽  
Alexander Ohmann ◽  
Ulrich F. Keyser ◽  
Kaikai Chen
Keyword(s):  
Data Storage ◽  
Single Molecule ◽  
Self Assembly ◽  
Large Scale ◽  
Three Dimensional ◽  
Random Access ◽  
Scale Production ◽  
Digital Information ◽  
Dna Nanostructures ◽  
Large Scale Production

AbstractThree-dimensional (3D) DNA nanostructures built via DNA self-assembly have established recent applications in multiplexed biosensing and storing digital information. However, a key challenge is that 3D DNA structures are not easily copied which is of vital importance for their large-scale production and for access to desired molecules by target-specific amplification. Here, we build 3D DNA structural barcodes and demonstrate the copying and random access of the barcodes from a library of molecules using a modified polymerase chain reaction (PCR). The 3D barcodes were assembled by annealing a single-stranded DNA scaffold with complementary short oligonucleotides containing 3D protrusions at defined locations. DNA nicks in these structures are ligated to facilitate barcode copying using PCR. To randomly access a target from a library of barcodes, we employ a non-complementary end in the DNA construct that serves as a barcode-specific primer template. Readout of the 3D DNA structural barcodes was performed with nanopore measurements. Our study provides a roadmap for convenient production of large quantities of self-assembled 3D DNA nanostructures. In addition, this strategy offers access to specific targets, a crucial capability for multiplexed single-molecule sensing and for DNA data storage.

scholarly journals Single-Molecule Accommodation of Streptavidin in Nanometer-Scale Wells Formed in DNA Nanostructures

2008 ◽  
Vol 52 (1) ◽  
pp. 681-682 ◽  
Author(s):  
A. Kuzuya ◽  
K. Numajiri ◽  
M. Kimura ◽  
M. Komiyama
Keyword(s):  
Single Molecule ◽  
Nanometer Scale ◽  
Dna Nanostructures

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

2016 ◽  
Vol 2 (1) ◽  
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.

scholarly journals Review of the Electrical Characterization of Metallic Nanowires on DNA Templates

2018 ◽  
Vol 19 (10) ◽  
pp. 3019 ◽  
Author(s):  
Türkan Bayrak ◽  
Nagesh Jagtap ◽  
Artur Erbe
Keyword(s):  
Electronic Properties ◽  
Self Assembly ◽  
Dna Nanotechnology ◽  
Electrical Characterization ◽  
Dna Nanostructures ◽  
Metallic Nanowires ◽  
Electronic Circuits ◽  
Electrically Conducting ◽  
Dna Strands

The use of self-assembly techniques may open new possibilities in scaling down electronic circuits to their ultimate limits. Deoxyribonucleic acid (DNA) nanotechnology has already demonstrated that it can provide valuable tools for the creation of nanostructures of arbitrary shape, therefore presenting an ideal platform for the development of nanoelectronic circuits. So far, however, the electronic properties of DNA nanostructures are mostly insulating, thus limiting the use of the nanostructures in electronic circuits. Therefore, methods have been investigated that use the DNA nanostructures as templates for the deposition of electrically conducting materials along the DNA strands. The most simple such structure is given by metallic nanowires formed by deposition of metals along the DNA nanostructures. Here, we review the fabrication and the characterization of the electronic properties of nanowires, which were created using these methods.

scholarly journals 3D DNA Nanostructures: The Nanoscale Architect

2021 ◽  
Vol 11 (6) ◽  
pp. 2624
Author(s):  
Daniel Fu ◽  
John Reif
Keyword(s):  
Single Molecule ◽  
Mechanical Design ◽  
Dna Nanotechnology ◽  
Dna Nanostructures ◽  
Biophysical Studies ◽  
Significant Research ◽  
Core Concepts ◽  
Potential Applications ◽  
The Stability ◽  
Structural Dna Nanotechnology

Structural DNA nanotechnology is a pioneering biotechnology that presents the opportunity to engineer DNA-based hardware that will mediate a profound interface to the nanoscale. To date, an enormous library of shaped 3D DNA nanostructures have been designed and assembled. Moreover, recent research has demonstrated DNA nanostructures that are not only static but can exhibit specific dynamic motion. DNA nanostructures have thus garnered significant research interest as a template for pursuing shape and motion-dependent nanoscale phenomena. Potential applications have been explored in many interdisciplinary areas spanning medicine, biosensing, nanofabrication, plasmonics, single-molecule chemistry, and facilitating biophysical studies. In this review, we begin with a brief overview of general and versatile design techniques for 3D DNA nanostructures as well as some techniques and studies that have focused on improving the stability of DNA nanostructures in diverse environments, which is pivotal for its reliable utilization in downstream applications. Our main focus will be to compile a wide body of existing research on applications of 3D DNA nanostructures that demonstrably rely on the versatility of their mechanical design. Furthermore, we frame reviewed applications into three primary categories, namely encapsulation, surface templating, and nanomechanics, that we propose to be archetypal shape- or motion-related functions of DNA nanostructures found in nanoscience applications. Our intent is to identify core concepts that may define and motivate specific directions of progress in this field as we conclude the review with some perspectives on the future.

Single Molecule Super-Resolution Microscopy Study on the Precision with Which DNA Nanostructures Can Orient Fluorescent Dyes

2020 ◽  
Author(s):  
Brett Michael Ward
Keyword(s):  
Single Molecule ◽  
Dna Nanotechnology ◽  
Super Resolution ◽  
Fluorescent Dye ◽  
Molecular Networks ◽  
Moderate Degree ◽  
Dna Nanostructures ◽  
Dye Molecules ◽  
Super Resolution Microscopy ◽  
Fluorescent Molecules

DNA nanotechnology enables the rapid, programmable self-assembly of novel structures and devices at the nanoscale. Utilizing the simplicity of Watson-Crick base pairing, DNA nanostructures are capable of assembling a variety of nanoparticles in arbitrary configurations with relative ease. Several emerging opto-electronic systems require a high degree of control of both the position and orientation of component fluorescent molecules, and while DNA nanostructures have demonstrated these capabilities, the precision with which DNA can orient fluorescent molecules is not well understood. Determining these bounds is critical in establishing the viability of DNA nanotechnology as a method of assembling fluorescent molecular networks. In this work, using a combination of single molecule emission dipole imaging and super-resolution microscopy techniques, we correlate the orientations of fluorescent dye molecules to the orientations of their DNA substrates along five degrees of freedom. Several species of dyes were embedded within a DNA sequence using either one or two covalent tethers. These strands were incorporated directly into DNA origami structures to investigate the dependence of the location and binding architecture of the dye on the orientational precision of DNA nanostructures. Dye functionalized strands were also folded into a simpler four-arm junction, which was then immobilized on an origami structure to study the influence of the DNA substrate on dye orientation. Correlated analysis of super-resolution images of origami structures and single molecule emission dipole images from the embedded fluorescent molecule within the same structure allowed us to directly measure the relative orientations of dye molecules within DNA nanostructures. The resulting measurements revealed a moderate degree of polar angle control but a large variation in azimuthal control for the majority of structures examined. These measurements establish a single-molecule method for measurement of correlated orientations and provide a powerful approach for future studies on increasing the precision in the orientational control of fluorescent dye molecule monomers by DNA nanostructures.

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.

Single-molecule methods in structural DNA nanotechnology

2020 ◽  
Vol 49 (13) ◽  
pp. 4220-4233 ◽  
Author(s):  
Casey M. Platnich ◽  
Felix J. Rizzuto ◽  
Gonzalo Cosa ◽  
Hanadi F. Sleiman
Keyword(s):  
Single Molecule ◽  
Method Development ◽  
Dna Nanotechnology ◽  
Dna Nanostructures ◽  
Structural Dna Nanotechnology ◽  
The Relationship

In this tutorial review, we explore the suite of single-molecule techniques currently available to probe DNA nanostructures and highlight the relationship between single-molecule method development and DNA nanotechology.

scholarly journals Endogenous Stimuli-Responsive DNA Nanostructures Toward Cancer Theranostics

2020 ◽  
Vol 2 ◽  
Author(s):  
Xiaoxue Hu ◽  
Ziqi Xu ◽  
Qianhao Min ◽  
Chao Teng ◽  
Ye Tian
Keyword(s):  
Drug Release ◽  
Self Assembly ◽  
Targeted Delivery ◽  
Dna Nanotechnology ◽  
Controlled Drug Release ◽  
Research Direction ◽  
Dna Nanostructures ◽  
Stimuli Responsive ◽  
Cancer Theranostics

Nanostructures specifically responsive to endogenous biomolecules hold great potential in accurate diagnosis and precision therapy of cancers. In the pool of nanostructures with responsiveness to unique triggers, nanomaterials derived from DNA self-assembly have drawn particular attention due to their intrinsic biocompatibility and structural programmability, enabling the selective bioimaging, and site-specific drug delivery in cancer cells and tumor tissues. In this mini review, we summarize the most recent advances in the development of endogenous stimuli-responsive DNA nanostructures featured with precise self-assembly, targeted delivery, and controlled drug release for cancer theranostics. This mini review briefly discusses the diverse dynamic DNA nanostructures aiming at bioimaging and biomedicine, including DNA self-assembling materials, DNA origami structures, DNA hydrogels, etc. We then elaborate the working principles of DNA nanostructures activated by biomarkers (e.g., miRNA, mRNA, and proteins) in tumor cells and microenvironments of tumor tissue (e.g., pH, ATP, and redox gradient). Subsequently, applications of the endogenous stimuli-responsive DNA nanostructures in biological imaging probes for detecting cancer hallmarks as well as intelligent carriers for drug release in vivo are discussed. In the end, we highlight the current challenges of DNA nanotechnology and the further development of this promising research direction.

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