New Tools for Cost-Effective DNA Synthesis

Tang, Nicholas; Ma, Siying; Tian, Jiajun

doi:10.1016/b978-0-12-394430-6.00001-7

Cited by 15 publications

(8 citation statements)

References 96 publications

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“…Analysis of cells produced by SCRaMbLE can reveal how changes in genome structure influence particular phenotypes or can be used to screen for Box 1 | Methods for building and activating chromosomes Assembly of large DNA molecules: Chromosomes are synthesized through the hierarchical assembly of smaller DNA molecules into progressively larger ones. This process begins with molecules that are hundreds of base pairs in length ("fragments"), which can be readily ordered from commercial vendors and are reviewed elsewhere 134,135 . Fragments are typically combined together and cloned into bacterial plasmids by Gibson 113,136,137 or Golden Gate 138,139 assembly.…”

Section: Genetic Manipulations Enabled By Synthetic Genomicsmentioning

confidence: 99%

Building genomes to understand biology

2020

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Genetic manipulation is one of the central strategies that biologists use to investigate the molecular underpinnings of life and its diversity. Thus, advances in genetic manipulation usually lead to a deeper understanding of biological systems. During the last decade, the construction of chromosomes, known as synthetic genomics, has emerged as a novel approach to genetic manipulation. By facilitating complex modifications to chromosome content and structure, synthetic genomics opens new opportunities for studying biology through genetic manipulation. Here, we discuss different classes of genetic manipulation that are enabled by synthetic genomics, as well as biological problems they each can help solve.

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Section: Genetic Manipulations Enabled By Synthetic Genomicsmentioning

confidence: 99%

Building genomes to understand biology

2020

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“…Once the digital file is encoded, the next step is to synthesize arbitrary single-strand DNA sequences chemically, nucleotide by nucleotide. There are several methods for de novo DNA sequence synthesis chemical oligonucleotide synthesis (phosphoramidite oligonucleotide synthesis) and oligo synthesis platforms using ink-jet printing (Agilent, Protogene), photosensitive 5' deprotection (Nimblegen, Affymetrix), photolithography (Invitrogen) and electrochemical arrays (Oxamer) with 20 to 90 oligomers synthesizing capacity at least error rate (Tang et al, 2013). Once we generate DNA oligomers or sequence that coded for digital information, DNA can be deep freeze at -20° to -80°C temperatures for a long time or till needed to decode through sequencing to recovered digital information.…”

Section: How D I G I Ta L I N F O R M At I O N C a N B E S To R E D Imentioning

confidence: 99%

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

Patel

Joshi

2019

IJVSBT

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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.

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“…While further reduction of the synthesis cost using the traditional column-based methods is unlikely, microarray-based technologies provide great potential for high-throughput and cost-effective DNA synthesis, as discussed in details elsewhere (Mueller, Coleman, 2009, Tang et al, 2013). Here we will focus on two recent advances in microarray-based DNA synthesis, highlighting the importance of technology integration.…”

Section: Genome Synthesismentioning

confidence: 99%

Rapid prototyping of microbial cell factories via genome-scale engineering

Xiao

Zhao

2015

Biotechnology Advances

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Advances in reading, writing and editing genetic materials have greatly expanded our ability to reprogram biological systems at the resolution of a single nucleotide and on the scale of a whole genome. Such capacity has greatly accelerated the cycles of design, build and test to engineer microbes for efficient synthesis of fuels, chemicals and drugs. In this review, we summarize the emerging technologies that have been applied, or are potentially useful for genome-scale engineering in microbial systems. We will focus on the development of high-throughput methodologies, which may accelerate the prototyping of microbial cell factories.

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New Tools for Cost-Effective DNA Synthesis

Cited by 15 publications

References 96 publications

Building genomes to understand biology

Building genomes to understand biology

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

Rapid prototyping of microbial cell factories via genome-scale engineering

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