scholarly journals Concepts and Application of DNA Origami and DNA Self-Assembly: A Systematic Review

2021 ◽  
Vol 2021 ◽  
pp. 1-15
Author(s):  
Wei Liu ◽  
Huaichuan Duan ◽  
Derong Zhang ◽  
Xun Zhang ◽  
Qing Luo ◽  
...  
Keyword(s):  
Systematic Review ◽  
Data Storage ◽  
Computer Technology ◽  
Self Assembly ◽  
Dna Computing ◽  
Dna Origami ◽  
Computing Technology ◽  
Good Biocompatibility ◽  
Material Physics ◽  
Silicon Based

With the arrival of the post-Moore Era, the development of traditional silicon-based computers has reached the limit, and it is urgent to develop new computing technology to meet the needs of science and life. DNA computing has become an essential branch and research hotspot of new computer technology because of its powerful parallel computing capability and excellent data storage capability. Due to good biocompatibility and programmability properties, DNA molecules have been widely used to construct novel self-assembled structures. In this review, DNA origami is briefly introduced firstly. Then, the applications of DNA self-assembly in material physics, biogenetics, medicine, and other fields are described in detail, which will aid the development of DNA computational model in the future.

scholarly journals Bioproduction of single-stranded DNA from isogenic miniphage

2019 ◽  
Author(s):  
Tyson R. Shepherd ◽  
Rebecca R. Du ◽  
Hellen Huang ◽  
Eike-Christian Wamhoff ◽  
Mark Bathe
Keyword(s):  
Data Storage ◽  
Self Assembly ◽  
Low Cost ◽  
Antibiotic Resistance Gene ◽  
Dna Origami ◽  
Memory Storage ◽  
Digital Information ◽  
Single Stranded Dna ◽  
Protein Coding ◽  
Bacteriophage M13

AbstractScalable production of gene-length single-stranded DNA (ssDNA) with sequence control has applications in homology directed repair templating, gene synthesis and sequencing, scaffolded DNA origami, and archival DNA memory storage. Biological production of circular single-stranded DNA (cssDNA) using bacteriophage M13 addresses these needs at low cost. A primary goal toward this end is to minimize the essential protein coding regions of the produced, exported sequence while maintaining its infectivity and production purity, with engineered regions of sequence control. Synthetic miniphage constitutes an ideal platform for bacterial production of isogenic cssDNA, using inserts of custom sequence and size to attain this goal, offering an inexpensive resource at milligram and higher synthesis scales. Here, we show that the Escherichia coli (E. coli) helper strain M13cp combined with a miniphage genome carrying only an f1 origin and a β-lactamase-encoding (bla) antibiotic resistance gene enables the production of pure cssDNA with a minimum sequence genomic length of 1,676 nt directly from bacteria, without the need for additional purification from contaminating dsDNA, genomic DNA, or fragmented DNAs. Low-cost scalability of isogenic, custom-length cssDNA is also demonstrated for a sequence of 2,520 nt using a commercial bioreactor. We apply this system to generate cssDNA for the programmed self-assembly of wireframe DNA origami objects with exonuclease-resistant, custom-designed circular scaffolds that are purified with low endotoxin levels (<5 E.U./ml) for therapeutic applications. We also encode digital information that is stored on the genome with application to write-once, read-many archival data storage.

scholarly journals SELF-RECOGNITION OF DNA FROM LIFE PROCESSES TO DNA COMPUTATION

2007 ◽  
Vol 02 (02) ◽  
pp. 123-137 ◽  
Author(s):  
WEI DA NG ◽  
CHEE KEONG BENJAMIN WONG
Keyword(s):  
Nucleic Acid ◽  
Self Assembly ◽  
Dna Computing ◽  
Dna Nanotechnology ◽  
Computing Technology ◽  
Dna Computation ◽  
Dna Codes ◽  
Self Recognition ◽  
Dna Strands ◽  
Adenine Thymine

Ever since the first appearance of deoxyribose nucleic acid (DNA) in 1953, it has fascinated multitudes with its simplicity. With a modest syllabus of four nucleotides (adenine, thymine, cytosine and guanine), it codes for the complexity of life around us. In this paper, we investigate how the structure of DNA codes for life processes and how we can take advantage of its minuscule size, mechanism of self-recognition and self-assembly for "bottom-up" nanotechnology. High hopes are also placed on miniaturizing present computing technology using DNA computing based on two fundamental features; massive parallelism of DNA strands and Watson–Crick complementarity. Advances in DNA-based computation and algorithmic assembly are then used to complement researches in DNA nanotechnology.

scholarly journals Co-self-assembly of multiple DNA origami nanostructures in a single pot

2021 ◽  
Author(s):  
Joshua A. Johnson ◽  
Vasiliki Kolliopoulos ◽  
Carlos E. Castro
Keyword(s):  
Self Assembly ◽  
Dna Origami ◽  
Folding Pathways

We demonstrate co-self-assembly of two distinct DNA origami structures with a common scaffold strand through programmable bifurcation of folding pathways.

scholarly journals A Structurally Variable Hinged Tetrahedron Framework from DNA Origami

2011 ◽  
Vol 2011 ◽  
pp. 1-9 ◽  
Author(s):  
David M. Smith ◽  
Verena Schüller ◽  
Carsten Forthmann ◽  
Robert Schreiber ◽  
Philip Tinnefeld ◽  
...  
Keyword(s):  
Self Assembly ◽  
Gel Electrophoresis ◽  
Imaging Techniques ◽  
Building Blocks ◽  
Dna Origami ◽  
Microscopy Technique ◽  
Wire Frame ◽  
Wide Range ◽  
Potential Applications ◽  
Linker Molecules

Nanometer-sized polyhedral wire-frame objects hold a wide range of potential applications both as structural scaffolds as well as a basis for synthetic nanocontainers. The utilization of DNA as basic building blocks for such structures allows the exploitation of bottom-up self-assembly in order to achieve molecular programmability through the pairing of complementary bases. In this work, we report on a hollow but rigid tetrahedron framework of 75 nm strut length constructed with the DNA origami method. Flexible hinges at each of their four joints provide a means for structural variability of the object. Through the opening of gaps along the struts, four variants can be created as confirmed by both gel electrophoresis and direct imaging techniques. The intrinsic site addressability provided by this technique allows the unique targeted attachment of dye and/or linker molecules at any point on the structure's surface, which we prove through the superresolution fluorescence microscopy technique DNA PAINT.

Self-assembly of carbon nanotubes into two-dimensional geometries using DNA origami templates

2009 ◽  
Vol 5 (1) ◽  
pp. 61-66 ◽  
Author(s):  
Hareem T. Maune ◽  
Si-ping Han ◽  
Robert D. Barish ◽  
Marc Bockrath ◽  
William A. Goddard III ◽  
...  
Keyword(s):  
Carbon Nanotubes ◽  
Self Assembly ◽  
Dna Origami ◽  
Two Dimensional

scholarly journals Modelling DNA origami self-assembly at the domain level

2015 ◽  
Vol 143 (16) ◽  
pp. 165102 ◽  
Author(s):  
Frits Dannenberg ◽  
Katherine E. Dunn ◽  
Jonathan Bath ◽  
Marta Kwiatkowska ◽  
Andrew J. Turberfield ◽  
...  
Keyword(s):  
Self Assembly ◽  
Dna Origami ◽  
Domain Level

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.

Research of Android Platform Application Based on HTML5

2014 ◽  
Vol 651-653 ◽  
pp. 1901-1904
Author(s):  
Xian Wei Li
Keyword(s):  
Data Storage ◽  
Computer Technology ◽  
High Efficiency ◽  
Rapid Development ◽  
Management Information ◽  
Development Environment ◽  
Android Platform ◽  
User Data ◽  
Realization Process ◽  
Application Module

In the society with the rapid development and popularization of computer technology, the management information system has become the hot field of software development. It runs stably in the browsers, like IE6, IE7, IE8, IE9 and FireFox, with high efficiency, sound security, friendly interface and simple operation. It has done research on the design and realization process of HTML5 off-line data storage on the Android platform. Under the Eclipse integrated development environment, with Android SDK and HTML5 grammar, develop the system, which realize the functions of off-line storage, addition, deletion and modification of user data. It enables the application of HTML5 of Android platform and has made detailed analysis on the Android platform and HTML5 application module. The result indicates, the webpage application design of HTML5 conducted on the Android platform, is simple and fast, which can better meet the demand of Android cellphone users.

scholarly journals Self-assembly of highly ordered DNA origami lattices at solid-liquid interfaces by controlling cation binding and exchange

Nano Research ◽  
2020 ◽  
Vol 13 (11) ◽  
pp. 3142-3150 ◽  
Author(s):  
Yang Xin ◽  
Salvador Martinez Rivadeneira ◽  
Guido Grundmeier ◽  
Mario Castro ◽  
Adrian Keller
Keyword(s):  
Correlation Length ◽  
Self Assembly ◽  
High Speed ◽  
Time Course ◽  
Divalent Cations ◽  
Topological Analysis ◽  
Monovalent Cation ◽  
Cation Binding ◽  
Dna Origami ◽  
Lattice Order

Abstract The surface-assisted hierarchical self-assembly of DNA origami lattices represents a versatile and straightforward method for the organization of functional nanoscale objects such as proteins and nanoparticles. Here, we demonstrate that controlling the binding and exchange of different monovalent and divalent cation species at the DNA-mica interface enables the self-assembly of highly ordered DNA origami lattices on mica surfaces. The development of lattice quality and order is quantified by a detailed topological analysis of high-speed atomic force microscopy (HS-AFM) images. We find that lattice formation and quality strongly depend on the monovalent cation species. Na+ is more effective than Li+ and K+ in facilitating the assembly of high-quality DNA origami lattices, because it is replacing the divalent cations at their binding sites in the DNA backbone more efficiently. With regard to divalent cations, Ca2+ can be displaced more easily from the backbone phosphates than Mg2+ and is thus superior in guiding lattice assembly. By independently adjusting incubation time, DNA origami concentration, and cation species, we thus obtain a highly ordered DNA origami lattice with an unprecedented normalized correlation length of 8.2. Beyond the correlation length, we use computer vision algorithms to compute the time course of different topological observables that, overall, demonstrate that replacing MgCl2 by CaCl2 enables the synthesis of DNA origami lattices with drastically increased lattice order.

Use DNA origami as a scaffold for self-assembly of optical metamolecules

2015 ◽  
Author(s):  
Yoon Jo Hwang ◽  
Shelley F. J. Wickham ◽  
Steven D. Perrault ◽  
Sanghyun Yoo ◽  
Sung Ha Park ◽  
...  
Keyword(s):  
Self Assembly ◽  
Dna Origami
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