51
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Wan J, Brož B, Liu Y, Huang SR, Marek A, Tureček F. Resolution of Identity in Gas-Phase Dissociations of Mono- and Diprotonated DNA Trinucleotide Codons by 15N-Labeling and Computational Structure Analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1936-1950. [PMID: 36040435 DOI: 10.1021/jasms.2c00194] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Dissociations of DNA trinucleotide codons as gas-phase singly and doubly protonated ions were studied by tandem mass spectrometry using 15N-labeling to resolve identity in the nucleobase loss and backbone cleavages. The monocations showed different distributions of nucleobase loss from the 5'-, middle, and 3'-positions depending on the nucleobase, favoring cytosine over guanine, adenine, and thymine in an ensemble-averaged 62:27:11:<1 ratio. The distribution for the loss of the 5'-, middle, and 3'-nucleobase was 49:18:33, favoring the 5'-nucleobase, but also depending on its nature. The formation of sequence w2+ ions was unambiguously established for all codon mono- and dications. Structures of low-Gibbs-energy protomers and conformers of dAAA+, dGGG+, dCCC+, dTTT+, dACA+, and dATC+ were established by Born-Oppenheimer molecular dynamics and density functional theory calculations. Monocations containing guanine favored classical structures protonated at guanine N7. Structures containing adenine and cytosine produced classical nucleobase-protonated isomers as well as zwitterions in which two protonated bases were combined with a phosphate anion. Protonation at thymine was disfavored. Low threshold energies for nucleobase loss allowed extensive proton migration to occur prior to dissociation. Loss of the nucleobase from monocations was assisted by neighboring group participation in nucleophilic addition or proton abstraction, as well as allosteric proton migrations remote from the reaction center. The optimized structures of diprotonated isomers for dAAA2+ and dACA2+ revealed combinations of classical and zwitterionic structures. The threshold and transition-state energies for nucleobase-ion loss from dications were low, resulting in facile dissociations involving cytosine, guanine, and adenine.
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Affiliation(s)
- Jiahao Wan
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| | - Břetislav Brož
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic
| | - Yue Liu
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| | - Shu R Huang
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| | - Aleš Marek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic
| | - František Tureček
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
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52
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Koch J, Kerl AC, Schawalder N, Luescher AM, Nguyen BH, Strauss K, Stark WJ, Grass RN. Preserving DNA in Biodegradable Organosilica Encapsulates. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:11191-11198. [PMID: 36083165 DOI: 10.1021/acs.langmuir.2c01167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A core-shell strategy was developed to protect synthetic DNA in organosilica particles encompassing dithiol linkages allowing for a DNA loading of 1.1 wt %. DNA stability tests involving bleach as an oxidant showed that following the procedure DNA was sandwiched between core particles of ca. 450 nm size and a protective outer layer, separating the DNA from the environment. Rapid aging tests at 60 °C and 50% relative humidity revealed that the DNA protected within this material was significantly more stable than nonprotected DNA, with an expected ambient temperature half-life of over 60 years. Still, and due to the presence of the dithiol linkages in the backbone of the organosilica material, the particles degraded in the presence of reducing agents (TCEP and glutathione) and disintegrated within several days in a simulated compost environment, which was employed to test the biodegradability of the material. This is in contrast to DNA encapsulated following state of the art procedures in pure SiO2 particles, which do not biodegrade in the investigated timeframes and conditions. The results show that synthetic DNA protected within dithiol comprising organosilica particles presents a strategy to store digital data at a high storage capacity for long time frames in a fully biodegradable format.
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Affiliation(s)
- Julian Koch
- Institute for Chemical and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg 1, 8093 Zurich, Switzerland
| | - Ann-Christin Kerl
- Institute for Chemical and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg 1, 8093 Zurich, Switzerland
| | - Natascha Schawalder
- Institute for Chemical and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg 1, 8093 Zurich, Switzerland
| | - Anne M Luescher
- Institute for Chemical and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg 1, 8093 Zurich, Switzerland
| | - Bichlien H Nguyen
- Microsoft Research, One Microsoft Way, Redmond, Washington 98052, United States
| | - Karin Strauss
- Microsoft Research, One Microsoft Way, Redmond, Washington 98052, United States
| | - Wendelin J Stark
- Institute for Chemical and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg 1, 8093 Zurich, Switzerland
| | - Robert N Grass
- Institute for Chemical and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg 1, 8093 Zurich, Switzerland
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53
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Luo Y, Wang S, Feng Z, Li J, Mao C, Wang R, Jiang X. Integrated Microfluidic DNA Storage Platform with Automated Sample Handling and Physical Data Partitioning. Anal Chem 2022; 94:13153-13162. [DOI: 10.1021/acs.analchem.2c02667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yuan Luo
- Shenzhen Key Laboratory of Smart Healthcare Engineering, Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, No 1088, Xueyuan Rd., Xili, Nanshan District, Shenzhen518055, Guangdong, P. R. China
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, No 1088, Xueyuan Rd., Xili, Nanshan
District, Shenzhen518055, Guangdong, P. R. China
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai200050, China
| | - Shuchen Wang
- Shenzhen Key Laboratory of Smart Healthcare Engineering, Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, No 1088, Xueyuan Rd., Xili, Nanshan District, Shenzhen518055, Guangdong, P. R. China
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, No 1088, Xueyuan Rd., Xili, Nanshan
District, Shenzhen518055, Guangdong, P. R. China
| | - Zhuowei Feng
- Shenzhen Key Laboratory of Smart Healthcare Engineering, Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, No 1088, Xueyuan Rd., Xili, Nanshan District, Shenzhen518055, Guangdong, P. R. China
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, No 1088, Xueyuan Rd., Xili, Nanshan
District, Shenzhen518055, Guangdong, P. R. China
| | - Jie Li
- Department of Electronic and Electrical Engineering, Southern University of Science and Technology, No 1088, Xueyuan Rd., Xili, Nanshan District, Shenzhen518055, Guangdong, P. R. China
| | - Cuiping Mao
- Shenzhen Key Laboratory of Smart Healthcare Engineering, Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, No 1088, Xueyuan Rd., Xili, Nanshan District, Shenzhen518055, Guangdong, P. R. China
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, No 1088, Xueyuan Rd., Xili, Nanshan
District, Shenzhen518055, Guangdong, P. R. China
| | - Rui Wang
- Department of Electronic and Electrical Engineering, Southern University of Science and Technology, No 1088, Xueyuan Rd., Xili, Nanshan District, Shenzhen518055, Guangdong, P. R. China
| | - Xingyu Jiang
- Shenzhen Key Laboratory of Smart Healthcare Engineering, Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, No 1088, Xueyuan Rd., Xili, Nanshan District, Shenzhen518055, Guangdong, P. R. China
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, No 1088, Xueyuan Rd., Xili, Nanshan
District, Shenzhen518055, Guangdong, P. R. China
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54
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Robust data storage in DNA by de Bruijn graph-based de novo strand assembly. Nat Commun 2022; 13:5361. [PMID: 36097016 PMCID: PMC9468002 DOI: 10.1038/s41467-022-33046-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022] Open
Abstract
DNA data storage is a rapidly developing technology with great potential due to its high density, long-term durability, and low maintenance cost. The major technical challenges include various errors, such as strand breaks, rearrangements, and indels that frequently arise during DNA synthesis, amplification, sequencing, and preservation. In this study, a de novo strand assembly algorithm (DBGPS) is developed using de Bruijn graph and greedy path search to meet these challenges. DBGPS shows substantial advantages in handling DNA breaks, rearrangements, and indels. The robustness of DBGPS is demonstrated by accelerated aging, multiple independent data retrievals, deep error-prone PCR, and large-scale simulations. Remarkably, 6.8 MB of data is accurately recovered from a severely corrupted sample that has been treated at 70 °C for 70 days. With DBGPS, we are able to achieve a logical density of 1.30 bits/cycle and a physical density of 295 PB/g. DNA data storage is a rapidly developing technology with great potential due to its high density, long-term durability, and low maintenance cost. Here the authors present a strand assembly algorithm (DBGPS) using de Bruijn graph and greedy path search.
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55
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Liu Y, Ren Y, Li J, Wang F, Wang F, Ma C, Chen D, Jiang X, Fan C, Zhang H, Liu K. In vivo processing of digital information molecularly with targeted specificity and robust reliability. SCIENCE ADVANCES 2022; 8:eabo7415. [PMID: 35930647 PMCID: PMC9355361 DOI: 10.1126/sciadv.abo7415] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 06/22/2022] [Indexed: 05/28/2023]
Abstract
DNA has attracted increasing interest as an appealing medium for information storage. However, target-specific rewriting of the digital data stored in intracellular DNA remains a grand challenge because the highly repetitive nature and uneven guanine-cytosine content render the encoded DNA sequences poorly compatible with endogenous ones. In this study, a dual-plasmid system based on gene editing tools was introduced into Escherichia coli to process information accurately. Digital data containing large repeat units in binary codes, such as text, codebook, or image, were involved in the realization of target-specific rewriting in vivo, yielding up to 94% rewriting reliability. An optical reporter was introduced as an advanced tool for presenting data processing at the molecular level. Rewritten information was stored stably and amplified over hundreds of generations. Our work demonstrates a digital-to-biological information processing approach for highly efficient data storage, amplification, and rewriting, thus robustly promoting the application of DNA-based information technology.
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Affiliation(s)
- Yangyi Liu
- Department of Chemistry, Tsinghua University, Beijing, China
| | - Yubin Ren
- Department of Chemistry, Tsinghua University, Beijing, China
| | - Jingjing Li
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
| | - Fan Wang
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
| | - Fei Wang
- Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Chao Ma
- Department of Chemistry, Tsinghua University, Beijing, China
| | - Dong Chen
- College of Energy Engineering and State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, Hangzhou, China
| | - Xingyu Jiang
- Department of Biomedical Engineering, Southern University of Science and Technology, No. 1088 Xueyuan Road, Nanshan District, Shenzhen, Guangdong, China
| | - Chunhai Fan
- Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hongjie Zhang
- Department of Chemistry, Tsinghua University, Beijing, China
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
| | - Kai Liu
- Department of Chemistry, Tsinghua University, Beijing, China
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
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56
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Jo S, Lee S, Park S, Tandon A, Nguyen TBN, Vu THN, Raza MT, Park SH. Multi-Domains in a Single Lattice Formed by DNA Self-Assembly. ACS OMEGA 2022; 7:26514-26522. [PMID: 35936484 PMCID: PMC9352336 DOI: 10.1021/acsomega.2c02556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
Using sequence programmability and the characteristics of self-assembly, DNA has been utilized in the construction of various nanostructures and the placement of specific patterns on lattices. Even though many complex structures and patterns formed by DNA assembly have been reported, the fabrication of multi-domain patterns in a single lattice has rarely been discussed. Multi-domains possessing specifically designed patterns in a single lattice provide the possibility to generate multiple patterns that enhance the pattern density in a given single lattice. Here, we introduce boundaries to construct double- and quadruple-domains with specific patterns in a single lattice and verify them with atomic force microscopy. ON, OFF, and ST (stripe) patterns on a lattice are made of DNA tiles with hairpins (ON), without hairpins (OFF), and alternating DNA tiles without and with hairpins (formed as a stripe, ST). For double- and quadruple-domain lattices, linear and cross boundaries were designed to fabricate two (e.g., ON and OFF, ON and ST, and OFF and ST) and four (OFF, ST, OFF, and ON) different types of patterns in single lattices, respectively. In double-domain lattices, each linear boundary is placed between two different domains. Similarly, four linear boundaries connected with a seed tile (i.e., a cross boundary) can separate four domains in a single lattice in quadruple-domain lattices. Due to the presence of boundaries, the pattern growth directions are different in each domain. The experimentally obtained multi-domain patterns agree well with our design. Lastly, we propose the possibility of the construction of a hexadomain lattice through the mapping from hexagonal to square grids converted by using an axial coordinate system. By proposing a hexadomain lattice design, we anticipate the possibility to extend to higher numbers of multi-domains in a single lattice, thereby further increasing the information density in a given lattice.
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Affiliation(s)
- Soojin Jo
- Department
of Physics and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Republic
of Korea
- Institute
of Basic Science, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Sungjin Lee
- Department
of Physics and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Republic
of Korea
- Institute
of Basic Science, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Suyoun Park
- Department
of Physics and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Republic
of Korea
- Institute
of Basic Science, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Anshula Tandon
- Department
of Physics and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Republic
of Korea
- Institute
of Basic Science, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Thi Bich Ngoc Nguyen
- Department
of Physics and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Republic
of Korea
| | - Thi Hong Nhung Vu
- Department
of Physics and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Republic
of Korea
| | - Muhammad Tayyab Raza
- Department
of Physics and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Republic
of Korea
| | - Sung Ha Park
- Department
of Physics and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Republic
of Korea
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57
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Wang P, Mu Z, Sun L, Si S, Wang B. Hidden Addressing Encoding for DNA Storage. Front Bioeng Biotechnol 2022; 10:916615. [PMID: 35928958 PMCID: PMC9344065 DOI: 10.3389/fbioe.2022.916615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 06/21/2022] [Indexed: 11/13/2022] Open
Abstract
DNA is a natural storage medium with the advantages of high storage density and long service life compared with traditional media. DNA storage can meet the current storage requirements for massive data. Owing to the limitations of the DNA storage technology, the data need to be converted into short DNA sequences for storage. However, in the process, a large amount of physical redundancy will be generated to index short DNA sequences. To reduce redundancy, this study proposes a DNA storage encoding scheme with hidden addressing. Using the improved fountain encoding scheme, the index replaces part of the data to realize hidden addresses, and then, a 10.1 MB file is encoded with the hidden addressing. First, the Dottup dot plot generator and the Jaccard similarity coefficient analyze the overall self-similarity of the encoding sequence index, and then the sequence fragments of GC content are used to verify the performance of this scheme. The final results show that the encoding scheme indexes with overall lower self-similarity, and the local thermodynamic properties of the sequence are better. The hidden addressing encoding scheme proposed can not only improve the utilization of bases but also ensure the correct rate of DNA storage during the sequencing and decoding processes.
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58
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Krehenwinkel H, Weber S, Künzel S, Kennedy SR. The bug in a teacup-monitoring arthropod-plant associations with environmental DNA from dried plant material. Biol Lett 2022; 18:20220091. [PMID: 35702982 PMCID: PMC9198770 DOI: 10.1098/rsbl.2022.0091] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Environmental DNA analysis (eDNA) has revolutionized the field of biomonitoring in the past years. Various sources have been shown to contain eDNA of diverse organisms, for example, water, soil, gut content and plant surfaces. Here we show that dried plant material is a highly promising source for arthropod community eDNA. We designed a metabarcoding assay to enrich diverse arthropod communities while preventing amplification of plant DNA. Using this assay, we analysed various commercially produced teas and herbs. These samples recovered ecologically and taxonomically diverse arthropod communities, a total of over a thousand species in more than 20 orders, many of them specific to their host plant and its geographical origin. Atypically for eDNA, arthropod DNA in dried plants shows very high temporal stability, opening up plant archives as a source for historical arthropod eDNA. Considering these results, dried plant material appears excellently suited as a novel tool to monitor arthropods and arthropod–plant interactions, detect agricultural pests and identify the geographical origin of imported plant material. The simplicity of our approach and the ability to detect highly diverse arthropod communities from all over the world in tea bags also highlights its utility for outreach purposes and to raise awareness about biodiversity.
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Affiliation(s)
| | | | - Sven Künzel
- Max Planck Institute for Evolutionary Biology, Ploen, Germany
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59
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Ezekannagha C, Becker A, Heider D, Hattab G. Design considerations for advancing data storage with synthetic DNA for long-term archiving. Mater Today Bio 2022; 15:100306. [PMID: 35677811 PMCID: PMC9167972 DOI: 10.1016/j.mtbio.2022.100306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 05/05/2022] [Accepted: 05/22/2022] [Indexed: 11/22/2022]
Abstract
Deoxyribonucleic acid (DNA) is increasingly emerging as a serious medium for long-term archival data storage because of its remarkable high-capacity, high-storage-density characteristics and its lasting ability to store data for thousands of years. Various encoding algorithms are generally required to store digital information in DNA and to maintain data integrity. Indeed, since DNA is the information carrier, its performance under different processing and storage conditions significantly impacts the capabilities of the data storage system. Therefore, the design of a DNA storage system must meet specific design considerations to be less error-prone, robust and reliable. In this work, we summarize the general processes and technologies employed when using synthetic DNA as a storage medium. We also share the design considerations for sustainable engineering to include viability. We expect this work to provide insight into how sustainable design can be used to develop an efficient and robust synthetic DNA-based storage system for long-term archiving.
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Affiliation(s)
- Chisom Ezekannagha
- Department of Mathematics and Computer Science, Philipps-Universität Marburg, Hans-Meerwein-Str. 6, D-35043, Marburg, Germany
- Corresponding author.
| | - Anke Becker
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Karl-von-Frisch-Str. 14, D-35043, Marburg, Germany
| | - Dominik Heider
- Department of Mathematics and Computer Science, Philipps-Universität Marburg, Hans-Meerwein-Str. 6, D-35043, Marburg, Germany
| | - Georges Hattab
- Department of Mathematics and Computer Science, Philipps-Universität Marburg, Hans-Meerwein-Str. 6, D-35043, Marburg, Germany
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60
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Ping Z, Chen S, Zhou G, Huang X, Zhu SJ, Zhang H, Lee HH, Lan Z, Cui J, Chen T, Zhang W, Yang H, Xu X, Church GM, Shen Y. Towards practical and robust DNA-based data archiving using the yin-yang codec system. NATURE COMPUTATIONAL SCIENCE 2022; 2:234-242. [PMID: 38177542 PMCID: PMC10766522 DOI: 10.1038/s43588-022-00231-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 03/18/2022] [Indexed: 01/06/2024]
Abstract
DNA is a promising data storage medium due to its remarkable durability and space-efficient storage. Early bit-to-base transcoding schemes have primarily pursued information density, at the expense of introducing biocompatibility challenges or decoding failure. Here we propose a robust transcoding algorithm named the yin-yang codec, using two rules to encode two binary bits into one nucleotide, to generate DNA sequences that are highly compatible with synthesis and sequencing technologies. We encoded two representative file formats and stored them in vitro as 200 nt oligo pools and in vivo as a ~54 kbps DNA fragment in yeast cells. Sequencing results show that the yin-yang codec exhibits high robustness and reliability for a wide variety of data types, with an average recovery rate of 99.9% above 104 molecule copies and an achieved recovery rate of 87.53% at ≤102 copies. Additionally, the in vivo storage demonstration achieved an experimentally measured physical density close to the theoretical maximum.
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Affiliation(s)
- Zhi Ping
- BGI-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, China
- George Church Institute of Regenesis, BGI-Shenzhen, Shenzhen, China
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Shihong Chen
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, China
- George Church Institute of Regenesis, BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Guangyu Zhou
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | | | - Sha Joe Zhu
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Haoling Zhang
- BGI-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, China
- George Church Institute of Regenesis, BGI-Shenzhen, Shenzhen, China
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Henry H Lee
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Zhaojun Lan
- School of Mathematical Science, Capital Normal University, Beijing, China
| | - Jie Cui
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, China
- George Church Institute of Regenesis, BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Tai Chen
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, China
- George Church Institute of Regenesis, BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Wenwei Zhang
- BGI-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, China
- George Church Institute of Regenesis, BGI-Shenzhen, Shenzhen, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, China.
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, China.
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
- China National GeneBank, BGI-Shenzhen, Shenzhen, China.
| | - George M Church
- George Church Institute of Regenesis, BGI-Shenzhen, Shenzhen, China.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
| | - Yue Shen
- BGI-Shenzhen, Shenzhen, China.
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, China.
- George Church Institute of Regenesis, BGI-Shenzhen, Shenzhen, China.
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
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61
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Ren Y, Zhang Y, Liu Y, Wu Q, Su J, Wang F, Chen D, Fan C, Liu K, Zhang H. DNA-Based Concatenated Encoding System for High-Reliability and High-Density Data Storage. SMALL METHODS 2022; 6:e2101335. [PMID: 35146964 DOI: 10.1002/smtd.202101335] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 01/05/2022] [Indexed: 05/25/2023]
Abstract
Information storage based on DNA molecules provides a promising solution with advantages of low-energy consumption, high storage efficiency, and long lifespan. However, there are only four natural nucleotides and DNA storage is thus limited by 2 bits per nucleotide. Here, artificial nucleotides into DNA data storage to achieve higher coding efficiency than 2 bits per nucleotide is introduced. To accommodate the characteristics of DNA synthesis and sequencing, two high-reliability encoding systems suitable for four, six, and eight nucleotides, i.e., the RaptorQ-Arithmetic-LZW-RS (RALR) and RaptorQ-Arithmetic-Base64-RS (RABR) systems, are developed. The two concatenated encoding systems realize the advantages of correcting DNA sequence losses, correcting errors within DNA sequences, reducing homopolymers, and controlling specific nucleotide contents. The average coding efficiencies with error correction and without arithmetic compression by the RALR system using four, six, and eight nucleotides reach 1.27, 1.61, and 1.85 bits per nucleotide, respectively. While the average coding efficiencies by the RABR system are up to 1.50, 2.00, and 2.35 bits per nucleotide, respectively. The coding efficiency, versatility, and tunability of the developed artificial DNA systems might provide significant guidance for high-reliability and high-density data storage.
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Affiliation(s)
- Yubin Ren
- Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Yi Zhang
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Yawei Liu
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Qinglin Wu
- Institute of Process Equipment, College of Energy Engineering and State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Juanjuan Su
- College of Materials Science and Opto-Electronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fan Wang
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Dong Chen
- Institute of Process Equipment, College of Energy Engineering and State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Chunhai Fan
- Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Kai Liu
- Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Hongjie Zhang
- Department of Chemistry, Tsinghua University, Beijing, 100084, China
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62
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Garafutdinov RR, Chemeris DA, Sakhabutdinova AR, Kiryanova OY, Mikhaylenko CI, Chemeris AV. Encoding of non-biological information for its long-term storage in DNA. Biosystems 2022; 215-216:104664. [PMID: 35301090 DOI: 10.1016/j.biosystems.2022.104664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 02/28/2022] [Accepted: 03/06/2022] [Indexed: 11/26/2022]
Abstract
In 2019, at the World Economic Forum, DNA data storage was indicated as one of the breakthroughs expected to radically impact the global socio-economic order. Indeed, dry DNA is a relatively stable substance and an extremely capacious information carrier. One gram of DNA can hold up to 455 exabytes, provided that one nucleotide encodes two bits of information. In this critical review, the main attention is paid to nucleinography, meaning the conversion of digital data into nucleotide sequences. The evolution and diversity of approaches intended for encoding data with nucleotides are demonstrated. The most noticeable examples of storing minor as well as considerable quantities of non-biological information in DNA are given. Some issues of DNA data storage are also reported.
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Affiliation(s)
- Ravil R Garafutdinov
- Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences, 450054, 71, prosp. Oktyabrya, Ufa, Bashkortostan, Russian Federation.
| | - Dmitry A Chemeris
- Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences, 450054, 71, prosp. Oktyabrya, Ufa, Bashkortostan, Russian Federation.
| | - Assol R Sakhabutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences, 450054, 71, prosp. Oktyabrya, Ufa, Bashkortostan, Russian Federation.
| | - Olga Yu Kiryanova
- Ufa State Petroleum Technological University, 450064, 1 Kosmonavtov st., Ufa, Bashkortostan, Russian Federation.
| | - Constantin I Mikhaylenko
- Mavlyutov Institute of Mechanics, Ufa Federal Research Center, Russian Academy of Sciences, 450054, 71, prosp. Oktyabrya, Ufa, Bashkortostan, Russia.
| | - Alexey V Chemeris
- Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences, 450054, 71, prosp. Oktyabrya, Ufa, Bashkortostan, Russian Federation.
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63
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Abstract
In this work, we investigated aggregation of native DNA and thiacalix[4]arene derivative bearing eight terminal amino groups in cone configuration using various redox probes on the glassy carbon electrode. It was shown that sorption transfer of the aggregates on the surface of the electrode covered with carbon black resulted in changes in electrostatic interactions and diffusional permeability of the surface layer. Such changes alter the signals of ferricyanide ion, methylene green and hydroquinone as redox probes to a degree depending on their specific interactions with DNA and own charge. Inclusion of DNA in the surface layer was independently confirmed by scanning electron microscopy, electrochemical impedance spectroscopy and experiments with doxorubicin as a model intercalator. Thermal denaturing of DNA affected the charge separation on the electrode interface and the signals of redox probes. Using hydroquinone, less sensitive to electrostatic interactions, made it possible to determine from 10 pM to 1.0 nM doxorubicin (limit of detection 3 pM) after 10 min incubation. Stabilizers present in the commercial medications did not alter the signal. The DNA sensors developed can find future application in the assessment of the complexes formed by DNA and macrocycles as delivery agents for small chemical species.
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64
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Fan C, Deng Q, Zhu TF. Bioorthogonal information storage in L-DNA with a high-fidelity mirror-image Pfu DNA polymerase. Nat Biotechnol 2021; 39:1548-1555. [PMID: 34326549 DOI: 10.1038/s41587-021-00969-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 05/31/2021] [Indexed: 02/07/2023]
Abstract
Natural DNA is exquisitely evolved to store genetic information. The chirally inverted L-DNA, possessing the same informational capacity but resistant to biodegradation, may serve as a robust, bioorthogonal information repository. Here we chemically synthesize a 90-kDa high-fidelity mirror-image Pfu DNA polymerase that enables accurate assembly of a kilobase-sized mirror-image gene. We use the polymerase to encode in L-DNA an 1860 paragraph by Louis Pasteur that first proposed a mirror-image world of biology. We realize chiral steganography by embedding a chimeric D-DNA/L-DNA key molecule in a D-DNA storage library, which conveys a false or secret message depending on the chirality of reading. Furthermore, we show that a trace amount of an L-DNA barcode preserved in water from a local pond remains amplifiable and sequenceable for 1 year, whereas a D-DNA barcode under the same conditions could not be amplified after 1 day. These next-generation mirror-image molecular tools may transform the development of advanced mirror-image biology systems and pave the way for the realization of the mirror-image central dogma and exploration of their applications.
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Affiliation(s)
- Chuyao Fan
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China
| | - Qiang Deng
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China
| | - Ting F Zhu
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China.
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65
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Electronic Sensing Platform (ESP) Based on Open-Gate Junction Field-Effect Transistor (OG-JFET) for Life Science Applications: Design, Modeling and Experimental Results. SENSORS 2021; 21:s21227491. [PMID: 34833566 PMCID: PMC8619415 DOI: 10.3390/s21227491] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/07/2021] [Accepted: 11/08/2021] [Indexed: 12/25/2022]
Abstract
This paper presents a new field-effect sensor called open-gate junction gate field-effect transistor (OG-JFET) for biosensing applications. The OG-JFET consists of a p-type channel on top of an n-type layer in which the p-type serves as the sensing conductive layer between two ohmic contacted sources and drain electrodes. The structure is novel as it is based on a junction field-effect transistor with a subtle difference in that the top gate (n-type contact) has been removed to open the space for introducing the biomaterial and solution. The channel can be controlled through a back gate, enabling the sensor's operation without a bulky electrode inside the solution. In this research, in order to demonstrate the sensor's functionality for chemical and biosensing, we tested OG-JFET with varying pH solutions, cell adhesion (human oral neutrophils), human exhalation, and DNA molecules. Moreover, the sensor was simulated with COMSOL Multiphysics to gain insight into the sensor operation and its ion-sensitive capability. The complete simulation procedures and the physics of pH modeling is presented here, being numerically solved in COMSOL Multiphysics software. The outcome of the current study puts forward OG-JFET as a new platform for biosensing applications.
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66
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Mostovaya O, Padnya P, Shiabiev I, Mukhametzyanov T, Stoikov I. PAMAM-calix-dendrimers: Synthesis and Thiacalixarene Conformation Effect on DNA Binding. Int J Mol Sci 2021; 22:ijms222111901. [PMID: 34769329 PMCID: PMC8585033 DOI: 10.3390/ijms222111901] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 10/29/2021] [Accepted: 10/30/2021] [Indexed: 12/16/2022] Open
Abstract
A convenient method for the synthesis of the first generation PAMAM dendrimers based on the thiacalix[4]arene has been developed for the first time. Three new PAMAM-calix-dendrimers with the macrocyclic core in cone, partial cone, and 1,3-alternate conformations were obtained with high yields. The interaction of the obtained compounds with salmon sperm DNA resulted in the formation of the associates of the size up to 200 nm, as shown by the UV-Vis spectroscopy, DLS, and TEM. It was demonstrated by the CD method that the structure of the DNA did not undergo significant changes upon binding. The PAMAM-calix-dendrimer based on the macrocycle in cone conformation stabilized DNA and prevented its degradation.
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Affiliation(s)
| | - Pavel Padnya
- Correspondence: (P.P.); (I.S.); Tel.: +7-843-233-7241 (I.S.)
| | | | | | - Ivan Stoikov
- Correspondence: (P.P.); (I.S.); Tel.: +7-843-233-7241 (I.S.)
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67
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Rauwolf S, Bag S, Rouqueiro R, Schwaminger SP, Dias-Cabral AC, Berensmeier S, Wenzel W. Insights on Alanine and Arginine Binding to Silica with Atomic Resolution. J Phys Chem Lett 2021; 12:9384-9390. [PMID: 34551250 DOI: 10.1021/acs.jpclett.1c02398] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Interactions of biomolecules with inorganic oxide surfaces such as silica in aqueous solutions are of profound interest in various research fields, including chemistry, biotechnology, and medicine. While there is a general understanding of the dominating electrostatic interactions, the binding mechanism is still not fully understood. Here, chromatographic zonal elution and flow microcalorimetry experiments were combined with molecular dynamic simulations to describe the interaction of different capped amino acids with the silica surface. We demonstrate that ion pairing is the dominant electrostatic interaction. Surprisingly, the interaction strength is more dependent on the repulsive carboxy group than on the attracting amino group. These findings are essential for conducting experimental and simulative studies on amino acids when transferring the results to biomolecule-surface interactions.
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Affiliation(s)
- Stefan Rauwolf
- Department Mechanical Engineering, Bioseparation Engineering Group, Technical University of Munich, Boltzmannstrasse 15, 85748 Garching, Germany
| | - Saientan Bag
- Institute for Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Rodrigo Rouqueiro
- Department of Chemistry, CICS-UBI Health Science Research Center, University Beira Interior, Avenida Infante D. Henrique, 6200-506 Covilhã, Portugal
| | - Sebastian Patrick Schwaminger
- Department Mechanical Engineering, Bioseparation Engineering Group, Technical University of Munich, Boltzmannstrasse 15, 85748 Garching, Germany
| | - Ana Cristina Dias-Cabral
- Department of Chemistry, CICS-UBI Health Science Research Center, University Beira Interior, Avenida Infante D. Henrique, 6200-506 Covilhã, Portugal
| | - Sonja Berensmeier
- Department Mechanical Engineering, Bioseparation Engineering Group, Technical University of Munich, Boltzmannstrasse 15, 85748 Garching, Germany
| | - Wolfgang Wenzel
- Institute for Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
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68
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UV-Vis Spectrophotometric Analysis of DNA Retrieval for DNA Storage Applications. ACTUATORS 2021. [DOI: 10.3390/act10100246] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Informational Deoxyribonucleic Acid (iDNA) has gained the attention of many researchers and pioneer companies for the development of novel storage systems for the long-term and high-density storing of information. This research focuses on the physical storage of iDNA strands to address some of the current challenges by evaluating the accuracy of the process of iDNA retrieval from the surface after the dehydration process. For this aim, a UV-Vis spectrophotometric technique was used to measure the concentration of the DNA samples. Although spectroscopy has been widely employed for the evaluation of DNA concentration and contamination in a solution, it has not been used to investigate dry-state DNA, which is one of the preferred storage formats for the long-term retention of information. These results demonstrate that the UV-Vis spectrophotometric technique can be used to accurately measure dry-state DNA before the retrieval and its residues after the DNA retrieval process. This paper further examines the storage/retrieval process by investigating the relationship between the storage time and the amount of retrieved DNA or the DNA residue left on various surfaces. Based on the experimental results demonstrated and discussed in this paper, UV-Vis spectrophotometry can be used for monitoring dry-state DNA with a high accuracy larger than 98%. Moreover, these results reveal that the hydrophilicity and hydrophobicity of the surface do not significantly affect DNA retrieval over a one-month time period.
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69
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Housh K, Jha JS, Yang Z, Haldar T, Johnson KM, Yin J, Wang Y, Gates KS. Formation and Repair of an Interstrand DNA Cross-Link Arising from a Common Endogenous Lesion. J Am Chem Soc 2021; 143:15344-15357. [PMID: 34516735 DOI: 10.1021/jacs.1c06926] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Interstrand DNA cross-links (ICLs) are cytotoxic because they block the strand separation required for read-out and replication of the genetic information in duplex DNA. The unavoidable formation of ICLs in cellular DNA may contribute to aging, neurodegeneration, and cancer. Here, we describe the formation and properties of a structurally complex ICL derived from an apurinic/apyrimidinic (AP) site, which is one of the most common endogenous lesions in cellular DNA. The results characterize a cross-link arising from aza-Michael addition of the N2-amino group of a guanine residue to the electrophilic sugar remnant generated by spermine-mediated strand cleavage at an AP site in duplex DNA. An α,β-unsaturated iminium ion is the critical intermediate involved in ICL formation. Studies employing the bacteriophage φ29 polymerase provided evidence that this ICL can block critical DNA transactions that require strand separation. The results of biochemical studies suggest that this complex strand break/ICL might be repaired by a simple mechanism in which the 3'-exonuclease action of the enzyme apurinic/apyrimidinic endonuclease (APE1) unhooks the cross-link to initiate repair via the single-strand break repair pathway.
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Affiliation(s)
- Kurt Housh
- University of Missouri Department of Chemistry 125 Chemistry Building Columbia, Missouri 65211, United States
| | - Jay S Jha
- University of Missouri Department of Chemistry 125 Chemistry Building Columbia, Missouri 65211, United States
| | - Zhiyu Yang
- University of Missouri Department of Chemistry 125 Chemistry Building Columbia, Missouri 65211, United States
| | - Tuhin Haldar
- University of Missouri Department of Chemistry 125 Chemistry Building Columbia, Missouri 65211, United States
| | - Kevin M Johnson
- University of Missouri Department of Chemistry 125 Chemistry Building Columbia, Missouri 65211, United States
| | - Jiekai Yin
- Department of Chemistry University of California-Riverside Riverside, California 92521-0403, United States
| | - Yinsheng Wang
- Department of Chemistry University of California-Riverside Riverside, California 92521-0403, United States
| | - Kent S Gates
- University of Missouri Department of Chemistry 125 Chemistry Building Columbia, Missouri 65211, United States.,University of Missouri Department of Biochemistry 125 Chemistry Building Columbia, Missouri 65211, United States
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70
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Tomek KJ, Volkel K, Indermaur EW, Tuck JM, Keung AJ. Promiscuous molecules for smarter file operations in DNA-based data storage. Nat Commun 2021; 12:3518. [PMID: 34112775 PMCID: PMC8192770 DOI: 10.1038/s41467-021-23669-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/12/2021] [Indexed: 11/22/2022] Open
Abstract
DNA holds significant promise as a data storage medium due to its density, longevity, and resource and energy conservation. These advantages arise from the inherent biomolecular structure of DNA which differentiates it from conventional storage media. The unique molecular architecture of DNA storage also prompts important discussions on how data should be organized, accessed, and manipulated and what practical functionalities may be possible. Here we leverage thermodynamic tuning of biomolecular interactions to implement useful data access and organizational features. Specific sets of environmental conditions including distinct DNA concentrations and temperatures were screened for their ability to switchably access either all DNA strands encoding full image files from a GB-sized background database or subsets of those strands encoding low resolution, File Preview, versions. We demonstrate File Preview with four JPEG images and provide an argument for the substantial and practical economic benefit of this generalizable strategy to organize data.
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Affiliation(s)
- Kyle J Tomek
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Kevin Volkel
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, NC, USA
| | - Elaine W Indermaur
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - James M Tuck
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, NC, USA.
| | - Albert J Keung
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA.
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71
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Yoo E, Choe D, Shin J, Cho S, Cho BK. Mini review: Enzyme-based DNA synthesis and selective retrieval for data storage. Comput Struct Biotechnol J 2021; 19:2468-2476. [PMID: 34025937 PMCID: PMC8113751 DOI: 10.1016/j.csbj.2021.04.057] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 04/20/2021] [Accepted: 04/22/2021] [Indexed: 11/26/2022] Open
Abstract
The market for using and storing digital data is growing, with DNA synthesis emerging as an efficient way to store massive amounts of data. Storing information in DNA mainly consists of two steps: data writing and reading. The writing step requires encoding data in DNA, building one nucleotide at a time as a form of single-stranded DNA (ssDNA). Once the data needs to be read, the target DNA is selectively retrieved and sequenced, which will also be in the form of an ssDNA. Recently, enzyme-based DNA synthesis is emerging as a new method to be a breakthrough on behalf of decades-old chemical synthesis. A few enzymatic methods have been presented for data memory, including the use of terminal deoxynucleotidyl transferase. Besides, enzyme-based amplification or denaturation of the target strand into ssDNA provides selective access to the desired dataset. In this review, we summarize diverse enzymatic methods for either synthesizing ssDNA or retrieving the data-containing DNA.
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Affiliation(s)
- Eojin Yoo
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Donghui Choe
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Jongoh Shin
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Suhyung Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea.,Innovative Biomaterials Research Center, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea.,Innovative Biomaterials Research Center, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
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