Preparation of Stable Branched DNA Nanostructures: Process of Cooperative Self-Assembly

2019 ◽  
Vol 123 (17) ◽  
pp. 3591-3597 ◽  
Author(s):  
Ashok Kumar Nayak ◽  
Sakti Kanta Rath ◽  
Umakanta Subudhi
Keyword(s):  
Self Assembly ◽  
Dna Nanostructures ◽  
Branched Dna

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 Geometry-Based Self-Assembly of Histone–DNA Nanostructures at Single-Nucleotide Resolution

ACS Nano ◽  
2019 ◽  
Vol 13 (7) ◽  
pp. 8155-8168 ◽  
Author(s):  
Maged F. Serag ◽  
Aimaiti Aikeremu ◽  
Ryoko Tsukamoto ◽  
Hubert Piwoński ◽  
Maram Abadi ◽  
...  
Keyword(s):  
Self Assembly ◽  
Dna Nanostructures ◽  
Single Nucleotide ◽  
Nucleotide Resolution ◽  
Single Nucleotide Resolution

scholarly journals Lipid–oligonucleotide conjugates for bioapplications

2020 ◽  
Vol 7 (12) ◽  
pp. 1933-1953
Author(s):  
Xiaowei Li ◽  
Kejun Feng ◽  
Long Li ◽  
Lu Yang ◽  
Xiaoshu Pan ◽  
...  
Keyword(s):  
Self Assembly ◽  
Materials Science ◽  
Molecular Engineering ◽  
Dna Nanostructures ◽  
Future Directions ◽  
Intracellular Imaging ◽  
Cell Behaviors ◽  
Dna Strand ◽  
Oligonucleotide Conjugates ◽  
General Synthesis

Abstract Lipid–oligonucleotide conjugates (LONs) are powerful molecular-engineering materials for various applications ranging from biosensors to biomedicine. Their unique amphiphilic structures enable the self-assembly and the conveyance of information with high fidelity. In particular, LONs present remarkable potential in measuring cellular mechanical forces and monitoring cell behaviors. LONs are also essential sensing tools for intracellular imaging and have been employed in developing cell-surface-anchored DNA nanostructures for biomimetic-engineering studies. When incorporating therapeutic oligonucleotides or small-molecule drugs, LONs hold promise for targeted therapy. Moreover, LONs mediate the controllable assembly and fusion of vesicles based on DNA-strand displacements, contributing to nanoreactor construction and macromolecule delivery. In this review, we will summarize the general synthesis strategies of LONs, provide some characterization analysis and emphasize recent advances in bioanalytical and biomedical applications. We will also consider the relevant challenges and suggest future directions for building better functional LONs in nanotechnology and materials-science applications.

scholarly journals Controlling Matter at the Molecular Scale with DNA Circuits

2019 ◽  
Vol 21 (1) ◽  
pp. 469-493 ◽  
Author(s):  
Dominic Scalise ◽  
Rebecca Schulman
Keyword(s):  
Self Assembly ◽  
Dna Computing ◽  
Chemical Information ◽  
Dna Nanostructures ◽  
Program Complex ◽  
Responsive Materials ◽  
Dna Crystals ◽  
Dna Strands ◽  
Particle Assemblies ◽  
Specific Sequences

In recent years, a diverse set of mechanisms have been developed that allow DNA strands with specific sequences to sense information in their environment and to control material assembly, disassembly, and reconfiguration. These sequences could serve as the inputs and outputs for DNA computing circuits, enabling DNA circuits to act as chemical information processors to program complex behavior in chemical and material systems. This review describes processes that can be sensed and controlled within such a paradigm. Specifically, there are interfaces that can release strands of DNA in response to chemical signals, wavelengths of light, pH, or electrical signals, as well as DNA strands that can direct the self-assembly and dynamic reconfiguration of DNA nanostructures, regulate particle assemblies, control encapsulation, and manipulate materials including DNA crystals, hydrogels, and vesicles. These interfaces have the potential to enable chemical circuits to exert algorithmic control over responsive materials, which may ultimately lead to the development of materials that grow, heal, and interact dynamically with their environments.

Colorimetric Nucleic Acid Detection Based on Gold Nanoparticles with Branched DNA

NANO ◽  
2020 ◽  
Vol 15 (08) ◽  
pp. 2050110
Author(s):  
Zhikun Zhang ◽  
Xiaojie Ye ◽  
Qingqing Liu ◽  
Cuixia Hu ◽  
Jimmy Yun ◽  
...  
Keyword(s):  
Gold Nanoparticles ◽  
Nucleic Acid ◽  
Genetic Diseases ◽  
Colorimetric Detection ◽  
Nucleic Acid Detection ◽  
Great Promise ◽  
Dna Nanostructures ◽  
Practical Applications ◽  
Branched Dna ◽  
Target Dna

Nucleic acid detection is becoming increasingly important in the diagnostics of genetic diseases for biological analysis. We herein propose gold nanoparticles as probe for colorimetric detection of nucleic acids with branched DNA nanostructures, which enables a novel and simple colorimetric biosensor. In our system, the target DNA specifically triggered two short-chain ssDNA probes to generate branched DNA nanostructures (Y-shape DNA), which prevent AuNPs from aggregation in aqueous NaCl solution. On the contrary, when the target DNA did not exist, gold nanoparticles were unstable and aggregated easily because there is no anti-aggregation function from Y-shape DNA. Sensor response was found to be proportional to the target DNA concentration from 5 to 100[Formula: see text]nM, with detection limits determined as 5[Formula: see text]nM. The developed platform is for colorimetric nucleic acid detection without enzymes, label and modification holds great promise for practical applications.

scholarly journals Synergy of Two Assembly Languages in DNA Nanostructures: Self-Assembly of Sequence-Defined Polymers on DNA Cages

2016 ◽  
Vol 138 (13) ◽  
pp. 4416-4425 ◽  
Author(s):  
Pongphak Chidchob ◽  
Thomas G. W. Edwardson ◽  
Christopher J. Serpell ◽  
Hanadi F. Sleiman
Keyword(s):  
Self Assembly ◽  
Dna Nanostructures

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

2012 ◽  
Vol 2012 ◽  
pp. 1-5 ◽  
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.

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.

A C-HCR assembly of branched DNA nanostructures for amplified uracil-DNA glycosylase assays

2017 ◽  
Vol 53 (96) ◽  
pp. 12878-12881 ◽  
Author(s):  
Jing Wang ◽  
Min Pan ◽  
Jie Wei ◽  
Xiaoqing Liu ◽  
Fuan Wang
Keyword(s):  
Dna Glycosylase ◽  
Hybridization Chain Reaction ◽  
Selective Detection ◽  
Dna Nanostructures ◽  
Chain Reaction ◽  
Uracil Dna Glycosylase ◽  
Branched Dna

The amplified and selective detection of uracil-DNA glycosylase was enabled by a two-layered cascaded hybridization chain reaction machinery.

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