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 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 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 In vivo multi-dimensional information-keeping in Halobacterium salinarum

2020 ◽  
Author(s):  
J. Davis ◽  
A. Bisson-Filho ◽  
D. Kadyrov ◽  
T. M. De Kort ◽  
M. T. Biamonte ◽  
...  
Keyword(s):  
Data Storage ◽  
Raw Materials ◽  
Halobacterium Salinarum ◽  
Memory Storage ◽  
Digital Information ◽  
Mineral Salts ◽  
Coding Schemes ◽  
Data Archives ◽  
Silicon Based

Shortage of raw materials needed to manufacture components for silicon-based digital memory storage has led to a search for alternatives, including systems for storing texts, images, movies and other forms of information in DNA. Use of DNA as a medium for storage of 3-D information has also been investigated. However, two problems have yet to be addressed: first, storage of 3-D information in DNA has used objects and coding schemes which require large volumes of data; second, the medium used for DNA information-keeping has been inconsistent with qualities needed for long-term data storage. Here, we address these problems. First, we created in vivo DNA-encoded digital archives holding precise specifications for 3- and 4-dimensional figures with unprecedented efficiency. Second, we have demonstrated more robust and longer-lasting information-carriers than earlier repositories for DNA-based data archives by inserting digital information into the halophile, Halobacterium salinarum, an extremophilic archaeon. We then embedded Information-keeping halophiles into crystalline mineral salts in which similar organisms have been shown to persist in stasis for hundreds of millions of years. We propose that digital information archives composed in 3 or more dimensions may be inserted into halophilic organisms and preserved intact for indefinite periods of time.

Fabrication of CoPt Nanodot Array with a Pitch of 33 nm Using Pattern-Transfer Technique of PS-PDMS Self-Assembly

2013 ◽  
Vol 596 ◽  
pp. 83-87 ◽  
Author(s):  
Miftakhul Huda ◽  
Zulfakri bin Mohamad ◽  
Takuya Komori ◽  
You Yin ◽  
Sumio Hosaka
Keyword(s):  
Data Storage ◽  
Self Assembly ◽  
Low Cost ◽  
Disk Drive ◽  
Magnetic Data ◽  
Pattern Transfer ◽  
Ion Milling ◽  
Large Area ◽  
Nanodot Array ◽  
Dimethyl Siloxane

The progress of information technology has increased the demand of the capacity of storage media. Bit patterned media (BPM) has been known as a promising method to achieve the magnetic-data-storage capability of more than 1 Tb/in.2. In this work, we demonstrated fabrication of magnetic nanodot array of CoPt with a pitch of 33 nm using a pattern-transfer method of block copolymer (BCP) self-assembly. Carbon hard mask (CHM) was adopted as a mask to pattern-transfer self-assembled nanodot array formed from poly (styrene)-b-poly (dimethyl siloxane) (PS-PDMS) with a molecular weight of 30,000-7,500 mol/g. According to our experiment results, CHM showed its high selectivity against CoPt in Ar ion milling. Therefore, this result boosted the potential of BCP self-assembly technique to fabricate magnetic nanodot array for the next generation of hard disk drive (HDD) due to the ease of large-area fabrication, and low cost.

Low-cost, simple, and scalable self-assembly of DNA origami nanostructures

Nano Research ◽  
2019 ◽  
Vol 12 (5) ◽  
pp. 1207-1215 ◽  
Author(s):  
Patrick D. Halley ◽  
Randy A. Patton ◽  
Amjad Chowdhury ◽  
John C. Byrd ◽  
Carlos E. Castro
Keyword(s):  
Self Assembly ◽  
Low Cost ◽  
Dna Origami

scholarly journals Robust nucleation control via crisscross polymerization of highly coordinated DNA slats

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Dionis Minev ◽  
Christopher M. Wintersinger ◽  
Anastasia Ershova ◽  
William M. Shih
Keyword(s):  
Self Assembly ◽  
Actin Filaments ◽  
Nearest Neighbors ◽  
Growth Conditions ◽  
Dna Origami ◽  
Ultrasensitive Detection ◽  
Single Stranded Dna ◽  
Spontaneous Nucleation ◽  
Coordination Numbers ◽  
Positive Cooperativity

AbstractNatural biomolecular assemblies such as actin filaments or microtubules can exhibit all-or-nothing polymerization in a kinetically controlled fashion. The kinetic barrier to spontaneous nucleation arises in part from positive cooperativity deriving from joint-neighbor capture, where stable capture of incoming monomers requires straddling multiple subunits on a filament end. For programmable DNA self-assembly, it is likewise desirable to suppress spontaneous nucleation to enable powerful capabilities such as all-or-nothing assembly of nanostructures larger than a single DNA origami, ultrasensitive detection, and more robust algorithmic assembly. However, existing DNA assemblies use monomers with low coordination numbers that present an effective kinetic barrier only for slow, near-reversible growth conditions. Here we introduce crisscross polymerization of elongated slat monomers that engage beyond nearest neighbors which sustains the kinetic barrier under conditions that promote fast, irreversible growth. By implementing crisscross slats as single-stranded DNA, we attain strictly seed-initiated nucleation of crisscross ribbons with distinct widths and twists.

Deoxyribonucleic Acid as a Tool for Digital Information Storage: An Overview

2019 ◽  
Vol 15 (01) ◽  
pp. 1-8
Author(s):  
Ashish C Patel ◽  
C G Joshi
Keyword(s):  
Data Storage ◽  
Dna Sequences ◽  
Consensus Sequence ◽  
Random Access ◽  
Information Storage ◽  
Digital Data ◽  
Digital Information ◽  
Multiple Sequence ◽  
Digital World ◽  
Digital File

Current data storage technologies cannot keep pace longer with exponentially growing amounts of data through the extensive use of social networking photos and media, etc. The "digital world” with 4.4 zettabytes in 2013 has predicted it to reach 44 zettabytes by 2020. From the past 30 years, scientists and researchers have been trying to develop a robust way of storing data on a medium which is dense and ever-lasting and found DNA as the most promising storage medium. Unlike existing storage devices, DNA requires no maintenance, except the need to store at a cool and dark place. DNA has a small size with high density; just 1 gram of dry DNA can store about 455 exabytes of data. DNA stores the informations using four bases, viz., A, T, G, and C, while CDs, hard disks and other devices stores the information using 0’s and 1’s on the spiral tracks. In the DNA based storage, after binarization of digital file into the binary codes, encoding and decoding are important steps in DNA based storage system. Once the digital file is encoded, the next step is to synthesize arbitrary single-strand DNA sequences and that can be stored in the deep freeze until use.When there is a need for information to be recovered, it can be done using DNA sequencing. New generation sequencing (NGS) capable of producing sequences with very high throughput at a much lower cost about less than 0.1 USD for one MB of data than the first sequencing technologies. Post-sequencing processing includes alignment of all reads using multiple sequence alignment (MSA) algorithms to obtain different consensus sequences. The consensus sequence is decoded as the reversal of the encoding process. Most prior DNA data storage efforts sequenced and decoded the entire amount of stored digital information with no random access, but nowadays it has become possible to extract selective files (e.g., retrieving only required image from a collection) from a DNA pool using PCR-based random access. Various scientists successfully stored up to 110 zettabytes data in one gram of DNA. In the future, with an efficient encoding, error corrections, cheaper DNA synthesis,and sequencing, DNA based storage will become a practical solution for storage of exponentially growing digital data.

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 mini DNA-RNA hybrid origami nanobrick

2021 ◽  
Author(s):  
Lifeng Zhou ◽  
Arun Richard Chandrasekaran ◽  
Mengwen Yan ◽  
Vibhav A. Valsangkar ◽  
Jeremy I. Feldblyum ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Dna Origami ◽  
Complex Geometries ◽  
Single Stranded Dna ◽  
Dna Scaffold

DNA origami is typically used to fold a long single-stranded DNA scaffold into nanostructures with complex geometries using many short DNA staple strands. Integration of RNA into nucleic acid nanostructures...

scholarly journals Multiscale additive manufacturing of polymers using 3D photo-printable self-assembling ionic liquid monomers

2019 ◽  
Vol 4 (3) ◽  
pp. 580-585 ◽  
Author(s):  
Bineh G. Ndefru ◽  
Bryan S. Ringstrand ◽  
Sokhna I.-Y. Diouf ◽  
Sönke Seifert ◽  
Juan H. Leal ◽  
...  
Keyword(s):  
Ionic Liquid ◽  
Additive Manufacturing ◽  
Self Assembly ◽  
Low Cost ◽  
Low Resolution ◽  
Top Down ◽  
Bottom Up ◽  
Cost Approach ◽  
Self Assembling ◽  
Nanoscale Features

Combining bottom-up self-assembly with top-down 3D photoprinting affords a low cost approach for the introduction of nanoscale features into a build with low resolution features.

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