scholarly journals Electrochemical DNA synthesis and sequencing on a single electrode with scalability for integrated data storage

2021 ◽  
Vol 7 (46) ◽  
Author(s):  
Chengtao Xu ◽  
Biao Ma ◽  
Zhongli Gao ◽  
Xing Dong ◽  
Chao Zhao ◽  
...  
Keyword(s):  
Dna Synthesis ◽  
Data Storage

scholarly journals Data Storage Based on Combinatorial Synthesis of DNA Shortmers

2021 ◽  
Author(s):  
Inbal Preuss ◽  
Zohar Yakhini ◽  
Leon Anavy
Keyword(s):  
Dna Synthesis ◽  
Data Storage ◽  
Storage Systems ◽  
Cost Effective ◽  
Fold Increase ◽  
Building Blocks ◽  
Error Rates ◽  
High Density ◽  
Digital Data ◽  
Combinatorial Encoding

Storage needs represent a significant burden on the economy and the environment. Some of this can potentially be offset by improved density molecular storage. The potential of using DNA for storing data is immense. DNA can be harnessed as a high density, durable archiving medium for compressing and storing the exponentially growing quantities of digital data that mankind generates. Several studies have demonstrated the potential of DNA-based data storage systems. These include exploration of different encoding and error correction schemes and the use of different technologies for DNA synthesis and sequencing. Recently, the use of composite DNA letters has been demonstrated to leverage the inherent redundancy in DNA based storage systems to achieve higher logical density, offering a more cost-effective approach. However, the suggested composite DNA approach is still limited due to its sensitivity to the stochastic nature of the process. Combinatorial assembly methods were also suggested to encode information on DNA in high density, while avoding the challenges of the stochastic system. These are based on enzynatic assembly processes for producing the synthetic DNA. In this paper, we propose a novel method to encode information into DNA molecules using combinatorial encoding and shortmer DNA synthesis, in compatibility with current chemical DNA synthesis technologies. Our approach is based on a set of easily distinguishable DNA shortmers serving as building blocks and allowing for near-zero error rates. We construct an extended combinatorial alphabet in which every letter is a subset of the set of building blocks. We suggest different combinatorial encoding schemes and explore their theoretical properties and practical implications in terms of error probabilities and required sequencing depth. To demonstrate the feasibility of our approach, we implemented an end-to-end computer simulation of a DNA-based storage system, using our suggested combinatorial encodings. We use simulations to assess the performance of the system and the effect of different parameters. Our simulations suggest that our combinatorial approach can potentially achieve up to 6.5-fold increase in the logical density over standard DNA based storage systems, with near zero reconstruction error. Implementing our approach at scale to perform actual synthesis, requires minimal alterations to current technologies. Our work thus suggests that the combination of combinatorial encoding with standard DNA chemical synthesis technologies can potentially improve current solutions, achieving scalable, efficient and cost- effective DNA-based storage.

scholarly journals Mini review: Enzyme-based DNA synthesis and selective retrieval for data storage

2021 ◽  
Vol 19 ◽  
pp. 2468-2476
Author(s):  
Eojin Yoo ◽  
Donghui Choe ◽  
Jongoh Shin ◽  
Suhyung Cho ◽  
Byung-Kwan Cho
Keyword(s):  
Dna Synthesis ◽  
Data Storage

scholarly journals New Levenshtein-Marker Code for DNA-based Data Storage Capable of Correcting Multiple Edit Errors

2021 ◽  
Author(s):  
Yan Zihui ◽  
Cong Liang
Keyword(s):  
Dna Synthesis ◽  
Data Storage ◽  
Error Rate ◽  
Decoding Algorithm ◽  
Base Pairs ◽  
Sequencing Technologies ◽  
Dna Strands ◽  
Marker Code ◽  
Dna Strand ◽  
Term Data

With the development of DNA synthesis and sequencing technologies, DNA becomes a promising medium forlong-term data storage. Three types of errors may occur in the DNA strand, insertions, deletions and substitutions,which we collectively call edit errors. It is still challenging to design a code that can correct multiple edit errors onnon-binary alphabets. In this paper, we propose a new coding schema for correcting multiple edit errors on DNAstrands by splitting the whole strand into consecutive blocks with appropriate length and correcting a single editerror in each block. Our method, called theDNA-LMcode, could be considered a generalization of the Levenshteincode combined with the marker code. We provide a linear encoding and decoding algorithm for ourDNA-LMcode.Compared to other encoding methods for DNA strands of several hundred base-pairs, ourDNA-LMcode achievedsimilar code rates and a much lower average nucleotide error rate in decoding.

Commercializing the new frontier in DNA writing: Enzymatic synthesis

2020 ◽  
Vol 25 (4) ◽  
Author(s):  
Michael J. Kamdar ◽  
J. William Efcavitch
Keyword(s):  
Dna Synthesis ◽  
Data Storage ◽  
Business Models ◽  
Vaccine Development ◽  
Synthesis Method ◽  
Dna Nanotechnology ◽  
Cost Effective ◽  
Emerging Industries ◽  
High Quality Sequence ◽  
Post Synthesis

This article provides an overview of the emerging technology of enzymatic DNA synthesis, which holds the promise of making the business of writing DNA cost-effective, faster, sustainable, and more accurate compared to the traditional DNA synthesis method of phosphoramidite chemistry. Enzymatic DNA synthesis lends itself to various business models to realize the enormous opportunities across established and emerging industries that can be transformed with the reliable and affordable creation of long, high-quality, sequence specific DNA or, in the case of DNA data storage, the template-independent creation of DNA in nontoxic solutions without the need for post-synthesis processing. This review includes a discussion of potential verticals, such as life sciences – which includes gene editing, synthetic biology, precision medicine, DNA nanotechnology, and RNA vaccine development – as well as DNA data storage. Enzymatic DNA synthesis is being rapidly advanced to a commercial reality, with the first enzymatically synthesized DNA products to enter the market in the next year.

scholarly journals New Levenshtein-Marker Code for DNA-based Data Storage Capable of Correcting Multiple Edit Errors

2021 ◽  
Author(s):  
Yan Zihui ◽  
Cong Liang
Keyword(s):  
Dna Synthesis ◽  
Data Storage ◽  
Error Rate ◽  
Decoding Algorithm ◽  
Base Pairs ◽  
Sequencing Technologies ◽  
Dna Strands ◽  
Marker Code ◽  
Dna Strand ◽  
Term Data

With the development of DNA synthesis and sequencing technologies, DNA becomes a promising medium forlong-term data storage. Three types of errors may occur in the DNA strand, insertions, deletions and substitutions,which we collectively call edit errors. It is still challenging to design a code that can correct multiple edit errors onnon-binary alphabets. In this paper, we propose a new coding schema for correcting multiple edit errors on DNAstrands by splitting the whole strand into consecutive blocks with appropriate length and correcting a single editerror in each block. Our method, called theDNA-LMcode, could be considered a generalization of the Levenshteincode combined with the marker code. We provide a linear encoding and decoding algorithm for ourDNA-LMcode.Compared to other encoding methods for DNA strands of several hundred base-pairs, ourDNA-LMcode achievedsimilar code rates and a much lower average nucleotide error rate in decoding.

scholarly journals Recording Temporal Signals with Minutes Resolution Using Enzymatic DNA Synthesis

2021 ◽  
Author(s):  
Namita J Bhan ◽  
Alec Castinado ◽  
Joshua I Glaser ◽  
Reza Kalhor Kalhor ◽  
Jonathan Strutz ◽  
...  
Keyword(s):  
Dna Synthesis ◽  
Data Storage ◽  
Average Rate ◽  
Single Step ◽  
Terminal Deoxynucleotidyl Transferase ◽  
Independent Manner ◽  
Environmental Signals ◽  
Minute Period ◽  
Recording Techniques

Employing DNA as a high-density data storage medium has paved the way for next-generation digital storage and biosensing technologies. However, the multipart architecture of current DNA-based recording techniques renders them inherently slow and incapable of recording fluctuating signals with sub-hour frequencies. To address this limitation, we developed a simplified system employing a single enzyme, terminal deoxynucleotidyl transferase (TdT), to transduce environmental signals into DNA. TdT adds nucleotides to the 3 prime ends of single-stranded DNA (ssDNA) in a template-independent manner, selecting bases according to inherent preferences and environmental conditions. By characterizing TdT nucleotide selectivity under different conditions, we show that TdT can encode various physiologically relevant signals like Co2+, Ca2+, Zn2+ concentrations and temperature changes in vitro. Further, by considering the average rate of nucleotide incorporation, we show that the resulting ssDNA functions as a molecular ticker tape. With this method we accurately encode a temporal record of fluctuations in Co2+ concentration to within 1 minute over a 60-minute period. Finally, we engineer TdT to allosterically turn off in the presence of physiologically relevant concentration of calcium. We use this engineered TdT in concert with a reference TdT to develop a two-polymerase system capable of recording a single step change in Ca2+ signal to within 1 minute over a 60-minute period. This work expands the repertoire of DNA-based recording techniques by developing a novel DNA synthesis-based system that can record temporal environmental signals into DNA with minutes resolution.

scholarly journals Photon-directed Multiplexed Enzymatic DNA Synthesis for Molecular Digital Data Storage

2020 ◽  
Author(s):  
Howon Lee ◽  
Daniel J. Wiegand ◽  
Kettner Griswold ◽  
Sukanya Punthambaker ◽  
Honggu Chun ◽  
...  
Keyword(s):  
Dna Synthesis ◽  
Data Storage ◽  
Video Game ◽  
Uv Light ◽  
Synthesis Method ◽  
Digital Data ◽  
Terminal Deoxynucleotidyl Transferase ◽  
Synthesis Methods ◽  
Data Generation ◽  
Promising Alternative

New storage technologies are needed to keep up with the global demands of data generation. DNA is an ideal storage medium due to its stability, information density and ease of readout with advanced sequencing techniques. However, progress in writing DNA is stifled by the continued reliance on chemical synthesis methods. The enzymatic synthesis of DNA is a promising alternative, but thus far has not been well demonstrated in a highly parallelized manner. Here, we report a novel multiplexed enzymatic DNA synthesis method using maskless photolithography. Rapid uncaging of Co2+ ions by patterned UV light activates Terminal deoxynucleotidyl Transferase (TdT) for spatially-selective synthesis on an array surface. Spontaneous quenching of reactions by the diffusion of excess caging molecules confines synthesis to light patterns and controls the extension length. We show that our multiplexed synthesis method can be used to store digital data by encoding 12 unique DNA oligonucleotide sequences with music from the 1985 Nintendo video game Super Mario Brothers™, which is equivalent to 84 trits or 110 bits of data.

scholarly journals Photon-directed multiplexed enzymatic DNA synthesis for molecular digital data storage

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Howon Lee ◽  
Daniel J. Wiegand ◽  
Kettner Griswold ◽  
Sukanya Punthambaker ◽  
Honggu Chun ◽  
...  
Keyword(s):  
Dna Synthesis ◽  
Data Storage ◽  
Video Game ◽  
Uv Light ◽  
Synthesis Method ◽  
Digital Data ◽  
Terminal Deoxynucleotidyl Transferase ◽  
Synthesis Methods ◽  
Data Generation ◽  
Promising Alternative

Abstract New storage technologies are needed to keep up with the global demands of data generation. DNA is an ideal storage medium due to its stability, information density and ease-of-readout with advanced sequencing techniques. However, progress in writing DNA is stifled by the continued reliance on chemical synthesis methods. The enzymatic synthesis of DNA is a promising alternative, but thus far has not been well demonstrated in a parallelized manner. Here, we report a multiplexed enzymatic DNA synthesis method using maskless photolithography. Rapid uncaging of Co2+ ions by patterned UV light activates Terminal deoxynucleotidyl Transferase (TdT) for spatially-selective synthesis on an array surface. Spontaneous quenching of reactions by the diffusion of excess caging molecules confines synthesis to light patterns and controls the extension length. We show that our multiplexed synthesis method can be used to store digital data by encoding 12 unique DNA oligonucleotide sequences with video game music, which is equivalent to 84 trits or 110 bits of data.

Application of an image management system in microscopy

1992 ◽  
Vol 50 (2) ◽  
pp. 1052-1053
Author(s):  
Richard S. Chemock
Keyword(s):  
Data Storage ◽  
Cost Savings ◽  
Image Data ◽  
Analytical Techniques ◽  
Operational Mode ◽  
Fine Grained ◽  
Image Recording ◽  
Primary Output ◽  
Capacity Data ◽  
Image Management System

One of the most common tasks in a typical analysis lab is the recording of images. Many analytical techniques (TEM, SEM, and metallography for example) produce images as their primary output. Until recently, the most common method of recording images was by using film. Current PS/2R systems offer very large capacity data storage devices and high resolution displays, making it practical to work with analytical images on PS/2s, thereby sidestepping the traditional film and darkroom steps. This change in operational mode offers many benefits: cost savings, throughput, archiving and searching capabilities as well as direct incorporation of the image data into reports.The conventional way to record images involves film, either sheet film (with its associated wet chemistry) for TEM or PolaroidR film for SEM and light microscopy. Although film is inconvenient, it does have the highest quality of all available image recording techniques. The fine grained film used for TEM has a resolution that would exceed a 4096x4096x16 bit digital image.

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