Статті в журналах: "Data storage into DNA molecules"

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Jiang, Jiao. "Application of gene editing technology to DNA digital data storage." Highlights in Science, Engineering and Technology 73 (November 29, 2023): 452–58. http://dx.doi.org/10.54097/hset.v73i.14051.

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While the archival digital storage industry is approaching its physical limits, demand is increasing significantly, so alternatives are emerging. The modern world is in dire need of durable, scalable and economical alternative storage media. Deoxyribonucleic acid (DNA), a promising storage medium, offers superior information durability, capacity and energy consumption, making it a promising candidate for long-term data storage. However, the design and realization of DNA digital data storage face many problems, but gene editing technology, as a technology that makes modifications to genes directly from the molecular level, provides a breakthrough in solving these problems. In this paper, I show some methods for designing DNA digital data storage based on gene editing technology. The method utilizes gene editing technology to modify DNA molecules to improve their storage capacity and stability. At the same time, this paper also introduces the application cases of gene editing technology in DNA bio storage devices and looks forward to its future development.

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Garafutdinov, R. R., A. R. Sakhabutdinova, and A. V. Chemeris. "Long-term room temperature storage of DNA molecules." Biomics 12, no. 4 (2020): 552–63. http://dx.doi.org/10.31301/2221-6197.bmcs.2020-49.

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The simplest and most common method of long-term storage of DNA samples at present is the storage of their frozen solutions, which, however, has a number of disadvantages, including the destruction of DNA molecules during freezing and thawing, as well as energy consumption and the likelihood of losing valuable samples in the event of possible accidents. In this regard, long-term storage of DNA samples at room temperature in a dried state is preferable, especially since an even greater increase in the number of stored DNA samples is planned due to the planned preservation of non-biological data in this molecule, which is recognized at the International Economic Forum 2019 among the 10 most important innovative technologies as “DNA Data Storage” of the near future of mankind. Such storage requires the exclusion of hydrolysis and oxidation of DNA molecules under the action of water and reactive oxygen species, which can be achieved by placing DNA in an inert anhydrous atmosphere, including in the presence of additional ingredients in the form of, for example, trehalose, imitating wildlife, since it is known that this simple disaccharide, capable of vitrification, protects a wide range of anhydrobiont organisms from adverse environmental conditions. Currently, there are a number of technologies that provide long-term storage of DNA at room temperature, including those available from commercial sources, but not all problems have yet been solved, which is reflected in this review article.

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Ceze, Luis, Jeff Nivala, and Karin Strauss. "Molecular digital data storage using DNA." Nature Reviews Genetics 20, no. 8 (May 8, 2019): 456–66. http://dx.doi.org/10.1038/s41576-019-0125-3.

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4

Zhang, Yun Peng, Feng Ying Tian, Man Hui Sun, Ding Yu, Fei Xiang Fan, and Wei Guo Liu. "Based on DNA OTP Key Generation and Management Research." Applied Mechanics and Materials 427-429 (September 2013): 2470–72. http://dx.doi.org/10.4028/www.scientific.net/amm.427-429.2470.

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With the development of molecular-bio technology, the feature of DNA molecules for ultra-large-scale data storage has created a new approach for data storage. This paper gives a way of strengthening key transport security. Through recombinant DNA technology, use only sender-receiver know restriction enzymes to combine the key DNA and the T vector, to form a recombinant plasmid, making the key DNA bio-hide, and then place the recombinant plasmid in implanted bacteria .

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Coudy, Delphine, Marthe Colotte, Aurélie Luis, Sophie Tuffet, and Jacques Bonnet. "Long term conservation of DNA at ambient temperature. Implications for DNA data storage." PLOS ONE 16, no. 11 (November 11, 2021): e0259868. http://dx.doi.org/10.1371/journal.pone.0259868.

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DNA conservation is central to many applications. This leads to an ever-increasing number of samples which are more and more difficult and costly to store or transport. A way to alleviate this problem is to develop procedures for storing samples at room temperature while maintaining their stability. A variety of commercial systems have been proposed but they fail to completely protect DNA from deleterious factors, mainly water. On the other side, Imagene company has developed a procedure for long-term conservation of biospecimen at room temperature based on the confinement of the samples under an anhydrous and anoxic atmosphere maintained inside hermetic capsules. The procedure has been validated by us and others for purified RNA, and for DNA in buffy coat or white blood cells lysates, but a precise determination of purified DNA stability is still lacking. We used the Arrhenius law to determine the DNA degradation rate at room temperature. We found that extrapolation to 25°C gave a degradation rate constant equivalent to about 1 cut/century/100 000 nucleotides, a stability several orders of magnitude larger than the current commercialized processes. Such a stability is fundamental for many applications such as the preservation of very large DNA molecules (particularly interesting in the context of genome sequencing) or oligonucleotides for DNA data storage. Capsules are also well suited for this latter application because of their high capacity. One can calculate that the 64 zettabytes of data produced in 2020 could be stored, standalone, for centuries, in about 20 kg of capsules.

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Carmean, Douglas, Luis Ceze, Georg Seelig, Kendall Stewart, Karin Strauss, and Max Willsey. "DNA Data Storage and Hybrid Molecular–Electronic Computing." Proceedings of the IEEE 107, no. 1 (January 2019): 63–72. http://dx.doi.org/10.1109/jproc.2018.2875386.

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Xu, Chengtao, Chao Zhao, Biao Ma, and Hong Liu. "Uncertainties in synthetic DNA-based data storage." Nucleic Acids Research 49, no. 10 (April 9, 2021): 5451–69. http://dx.doi.org/10.1093/nar/gkab230.

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Abstract Deoxyribonucleic acid (DNA) has evolved to be a naturally selected, robust biomacromolecule for gene information storage, and biological evolution and various diseases can find their origin in uncertainties in DNA-related processes (e.g. replication and expression). Recently, synthetic DNA has emerged as a compelling molecular media for digital data storage, and it is superior to the conventional electronic memory devices in theoretical retention time, power consumption, storage density, and so forth. However, uncertainties in the in vitro DNA synthesis and sequencing, along with its conjugation chemistry and preservation conditions can lead to severe errors and data loss, which limit its practical application. To maintain data integrity, complicated error correction algorithms and substantial data redundancy are usually required, which can significantly limit the efficiency and scale-up of the technology. Herein, we summarize the general procedures of the state-of-the-art DNA-based digital data storage methods (e.g. write, read, and preservation), highlighting the uncertainties involved in each step as well as potential approaches to correct them. We also discuss challenges yet to overcome and research trends in the promising field of DNA-based data storage.

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8

Solanki, Arnav, Zak Griffin, Purab Ranjan Sutradhar, Karisha Pradhan, Caiden Merritt, Amlan Ganguly, and Marc Riedel. "Neural network execution using nicked DNA and microfluidics." PLOS ONE 18, no. 10 (October 19, 2023): e0292228. http://dx.doi.org/10.1371/journal.pone.0292228.

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DNA has been discussed as a potential medium for data storage. Potentially it could be denser, could consume less energy, and could be more durable than conventional storage media such as hard drives, solid-state storage, and optical media. However, performing computations on the data stored in DNA is a largely unexplored challenge. This paper proposes an integrated circuit (IC) based on microfluidics that can perform complex operations such as artificial neural network (ANN) computation on data stored in DNA. We envision such a system to be suitable for highly dense, throughput-demanding bio-compatible applications such as an intelligent Organ-on-Chip or other biomedical applications that may not be latency-critical. It computes entirely in the molecular domain without converting data to electrical form, making it a form of in-memory computing on DNA. The computation is achieved by topologically modifying DNA strands through the use of enzymes called nickases. A novel scheme is proposed for representing data stochastically through the concentration of the DNA molecules that are nicked at specific sites. The paper provides details of the biochemical design, as well as the design, layout, and operation of the microfluidics device. Benchmarks are reported on the performance of neural network computation.

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Bhattarai-Kline, Santi, Sierra K. Lear, and Seth L. Shipman. "One-step data storage in cellular DNA." Nature Chemical Biology 17, no. 3 (January 26, 2021): 232–33. http://dx.doi.org/10.1038/s41589-021-00737-2.

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10

Zhang, Cheng, Ranfeng Wu, Fajia Sun, Yisheng Lin, Yuan Liang, Jiongjiong Teng, Na Liu, Qi Ouyang, Long Qian, and Hao Yan. "Parallel molecular data storage by printing epigenetic bits on DNA." Nature 634, no. 8035 (October 23, 2024): 824–32. http://dx.doi.org/10.1038/s41586-024-08040-5.

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11

Organick, Lee, Siena Dumas Ang, Yuan-Jyue Chen, Randolph Lopez, Sergey Yekhanin, Konstantin Makarychev, Miklos Z. Racz, et al. "Random access in large-scale DNA data storage." Nature Biotechnology 36, no. 3 (February 19, 2018): 242–48. http://dx.doi.org/10.1038/nbt.4079.

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12

Kumar, ArunH S., and Apostolos Zarros. "Digitization of DNA: Miniaturization of information storage moving toward data in DNA!" Journal of Natural Science, Biology and Medicine 4, no. 1 (2013): 1. http://dx.doi.org/10.4103/0976-9668.107252.

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13

Anavy, Leon, Inbal Vaknin, Orna Atar, Roee Amit, and Zohar Yakhini. "Data storage in DNA with fewer synthesis cycles using composite DNA letters." Nature Biotechnology 37, no. 10 (September 9, 2019): 1229–36. http://dx.doi.org/10.1038/s41587-019-0240-x.

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14

Liu, Wei, Huaichuan Duan, Derong Zhang, Xun Zhang, Qing Luo, Tao Xie, Hailian Yan, et al. "Concepts and Application of DNA Origami and DNA Self-Assembly: A Systematic Review." Applied Bionics and Biomechanics 2021 (November 16, 2021): 1–15. http://dx.doi.org/10.1155/2021/9112407.

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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.

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Goumy, Carole, Zangbéwendé Guy Ouedraogo, Elodie Bellemonte, Eleonore Eymard-Pierre, Gwendoline Soler, Isabelle Perthus, Céline Pebrel-Richard, et al. "Feasibility of Optical Genome Mapping from Placental and Umbilical Cord Sampled after Spontaneous or Therapeutic Pregnancy Termination." Diagnostics 13, no. 23 (November 30, 2023): 3576. http://dx.doi.org/10.3390/diagnostics13233576.

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Optical genome mapping (OGM) is an alternative to classical cytogenetic techniques to improve the detection rate of clinically significant genomic abnormalities. The isolation of high-molecular-weight (HMW) DNA is critical for a successful OGM analysis. HMW DNA quality depends on tissue type, sample size, and storage conditions. We assessed the feasibility of OGM analysis of DNA from nine umbilical cord (UC) and six chorionic villus (CV) samples collected after the spontaneous or therapeutic termination of pregnancy. We analyzed quality control metrics provided by the Saphyr system (Bionano Genomics) and assessed the length of extracted DNA molecules using pulsed-field capillary electrophoresis. OMG data were successfully analyzed for all six CV samples. Five of the UC samples did not meet the Saphyr quality criteria, mainly due to poor DNA quality. In this regard, we found that DNA quality assessment with pulsed-field capillary electrophoresis can predict a successful OGM analysis. OGM data were fully concordant with the results of standard cytogenetic methods. Moreover, OGM detected an average of 14 additional structural variants involving OMIM genes per sample. On the basis of our results, we established the optimal conditions for sample storage and preparation required for a successful OGM analysis. We recommend checking DNA quality before analysis with pulsed-field capillary electrophoresis if the storage conditions were not ideal or if the quality of the sample is poor. OGM can therefore be performed on fetal tissue harvested after the termination of pregnancy, which opens up the perspective for improved diagnostic yield.

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El-Seoud, Samir Abou, Reham Fouad Mohamed, and Samy Ghoneimy. "DNA Computing: Challenges and Application." International Journal of Interactive Mobile Technologies (iJIM) 11, no. 2 (April 11, 2017): 74. http://dx.doi.org/10.3991/ijim.v11i2.6564.

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<p class="Abstract">Much of our scientific, technological, and economic future depends on the availability of an ever-increasing supply of computational power. However, the increasing demand for such power has pushed electronic technology to the limit of physical feasibility and has raised the concern that this technology may not be able to sustain our growth in the near future. It became important to consider an alternative means of achieving computational power. In this regard, DNA computing was introduced based on the usage of DNA and molecular biology hardware instead of the typical silicon based technology. The molecular computers could take advantage of DNA's physical properties to store information and perform calculations. These include extremely dense information storage, enormous parallelism and extraordinary energy efficiency. One of the main advantages that DNA computations would add to computation is its self - parallel processing while most of the electronic computers now use linear processing. In this paper, the DNA computation is reviewed and its state of the art challenges and applications are presented. Some of these applications are those require fast processing, at which DNA computers would be able to solve the hardest problems faster than the traditional ones. For example, 10 trillion DNA molecules can fit in one cubic centimeter that would result in a computer that holds 10 terabytes of data. Moreover, this work focuses on whether a large scale molecular computer can be built.</p>

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Anavy, Leon, Inbal Vaknin, Orna Atar, Roee Amit, and Zohar Yakhini. "Author Correction: Data storage in DNA with fewer synthesis cycles using composite DNA letters." Nature Biotechnology 37, no. 10 (September 16, 2019): 1237. http://dx.doi.org/10.1038/s41587-019-0281-1.

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Et. al., Arsha Kolate,. "An Information Security Using DNA Cryptography along with AES Algorithm." Turkish Journal of Computer and Mathematics Education (TURCOMAT) 12, no. 1S (April 11, 2021): 183–92. http://dx.doi.org/10.17762/turcomat.v12i1s.1607.

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Securing information is the most important need of not only the business world but also it’s highly essential in all the other major sectors. The secured data storage capacity along with security during data transit is also an important factor. In this paper DNA based security technique is proposed as an information carrier, the new data securing method can be adopted by harnessing the advantages of DNA based AES. This technique will provide multilayer security. The proposed system aims to secure transactional data during communication as it is required when message or data transfer between sender and receiver should be confidential along with integrity and availability.AS the data hiding needs a carrier to hold the data, therefore in order to enhance data security and make the data more confidential effective encryption algorithm is proposed using DNA cryptography. DNA molecules, holds an ability to store, process and transfer data, stimulates the notion of DNA cryptography. This amalgamation of the chemical features of genetic DNA structures along with cryptography confirms the non-vulnerable communication. The current features with reference to DNA cryptography are reviewed and presented here.

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Muhammad Zulkifl Hasan, Muhammad Zunnurain Hussain, Zaka Ullah, and Taimoor Hassan. "Future Computing: DNA Hard Drives." Lahore Garrison University Research Journal of Computer Science and Information Technology 3, no. 1 (March 29, 2019): 31–33. http://dx.doi.org/10.54692/lgurjcsit.2019.030165.

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DNA is a hard drive, the memory in every cell of every living organism that has the instructions on how to make that cell. With the exponential growth of our media, the growth of data storage is also increasing. DNA is incredible compact due to its molecular structure and can be used to achieve data attractively through genome sequencing. A raw limit of 1 Exabyte/mm3 (109 GB/mm3) having half-life of over 500 years. With this, all the data of the world can be stored in just a small place of a room.

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Du, Haigui, Shihua Zhou, WeiQi Yan, and Sijie Wang. "Study on DNA Storage Encoding Based IAOA under Innovation Constraints." Current Issues in Molecular Biology 45, no. 4 (April 18, 2023): 3573–90. http://dx.doi.org/10.3390/cimb45040233.

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With the informationization of social processes, the amount of related data has greatly increased, making traditional storage media unable to meet the current requirements for data storage. Due to its advantages of a high storage capacity and persistence, deoxyribonucleic acid (DNA) has been considered the most prospective storage media to solve the data storage problem. Synthesis is an important process for DNA storage, and low-quality DNA coding can increase errors during sequencing, which can affect the storage efficiency. To reduce errors caused by the poor stability of DNA sequences during storage, this paper proposes a method that uses the double-matching and error-pairing constraints to improve the quality of the DNA coding set. First, the double-matching and error-pairing constraints are defined to solve problems of sequences with self-complementary reactions in the solution that are prone to mismatch at the 3′ end. In addition, two strategies are introduced in the arithmetic optimization algorithm, including a random perturbation of the elementary function and a double adaptive weighting strategy. An improved arithmetic optimization algorithm (IAOA) is proposed to construct DNA coding sets. The experimental results of the IAOA on 13 benchmark functions show a significant improvement in its exploration and development capabilities over the existing algorithms. Moreover, the IAOA is used in the DNA encoding design under both traditional and new constraints. The DNA coding sets are tested to estimate their quality regarding the number of hairpins and melting temperature. The DNA storage coding sets constructed in this study are improved by 77.7% at the lower boundary compared to existing algorithms. The DNA sequences in the storage sets show a reduction of 9.7–84.1% in the melting temperature variance, and the hairpin structure ratio is reduced by 2.1–80%. The results indicate that the stability of the DNA coding sets is improved under the two proposed constraints compared to traditional constraints.

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Karakose, Mehmet, and Ugur Cigdem. "QPSO-Based Adaptive DNA Computing Algorithm." Scientific World Journal 2013 (2013): 1–8. http://dx.doi.org/10.1155/2013/160687.

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DNA (deoxyribonucleic acid) computing that is a new computation model based on DNA molecules for information storage has been increasingly used for optimization and data analysis in recent years. However, DNA computing algorithm has some limitations in terms of convergence speed, adaptability, and effectiveness. In this paper, a new approach for improvement of DNA computing is proposed. This new approach aims to perform DNA computing algorithm with adaptive parameters towards the desired goal using quantum-behaved particle swarm optimization (QPSO). Some contributions provided by the proposed QPSO based on adaptive DNA computing algorithm are as follows: (1) parameters of population size, crossover rate, maximum number of operations, enzyme and virus mutation rate, and fitness function of DNA computing algorithm are simultaneously tuned for adaptive process, (2) adaptive algorithm is performed using QPSO algorithm for goal-driven progress, faster operation, and flexibility in data, and (3) numerical realization of DNA computing algorithm with proposed approach is implemented in system identification. Two experiments with different systems were carried out to evaluate the performance of the proposed approach with comparative results. Experimental results obtained with Matlab and FPGA demonstrate ability to provide effective optimization, considerable convergence speed, and high accuracy according to DNA computing algorithm.

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Cao, Ben, Yanfen Zheng, Qi Shao, Zhenlu Liu, Lei Xie, Yunzhu Zhao, Bin Wang, Qiang Zhang, and Xiaopeng Wei. "Efficient data reconstruction: The bottleneck of large-scale application of DNA storage." Cell Reports 43, no. 4 (April 2024): 113699. http://dx.doi.org/10.1016/j.celrep.2024.113699.

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Jiang, Bin, Yikun Zhao, Hongmei Yi, Yongxue Huo, Haotian Wu, Jie Ren, Jianrong Ge, Jiuran Zhao, and Fengge Wang. "PIDS: A User-Friendly Plant DNA Fingerprint Database Management System." Genes 11, no. 4 (March 30, 2020): 373. http://dx.doi.org/10.3390/genes11040373.

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The high variability and somatic stability of DNA fingerprints can be used to identify individuals, which is of great value in plant breeding. DNA fingerprint databases are essential and important tools for plant molecular research because they provide powerful technical and information support for crop breeding, variety quality control, variety right protection, and molecular marker-assisted breeding. Building a DNA fingerprint database involves the production of large amounts of heterogeneous data for which storage, analysis, and retrieval are time and resource consuming. To process the large amounts of data generated by laboratories and conduct quality control, a database management system is urgently needed to track samples and analyze data. We developed the plant international DNA-fingerprinting system (PIDS) using an open source web server and free software that has automatic collection, storage, and efficient management functions based on merging and comparison algorithms to handle massive microsatellite DNA fingerprint data. PIDS also can perform genetic analyses. This system can match a corresponding capillary electrophoresis image on each primer locus as fingerprint data to upload to the server. PIDS provides free customization and extension of back-end functions to meet the requirements of different laboratories. This system can be a significant tool for plant breeders and can be applied in forensic science for human fingerprint identification, as well as in virus and microorganism research.

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Tabatabaei, S. Kasra, Bach Pham, Chao Pan, Jingqian Liu, Shubham Chandak, Spencer A. Shorkey, Alvaro G. Hernandez, et al. "Expanding the Molecular Alphabet of DNA-Based Data Storage Systems with Neural Network Nanopore Readout Processing." Nano Letters 22, no. 5 (February 25, 2022): 1905–14. http://dx.doi.org/10.1021/acs.nanolett.1c04203.

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Marwan, Samiha Abdelrahman Mohammed, Ahmed Shawish, and Khaled Nagaty. "Utilizing DNA Strands for Secured Data-Hiding with High Capacity." International Journal of Interactive Mobile Technologies (iJIM) 11, no. 2 (April 11, 2017): 88. http://dx.doi.org/10.3991/ijim.v11i2.6565.

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There are continuous threats to network technologies due to its rapidly-changing nature, which raises the demand for data-safe transmission. As a result, the need to come up with new techniques for securing data and accommodating the growing quantities of information is crucial. From nature to science, the idea that genes themselves are made of information stimulated the research in molecular deoxyribonucleic acid (DNA). DNA is capable of storing huge amounts of data, which leads to its promising effect in steganography. DNA steganography is the art of using DNA as an information carrier which achieves high data storage capacity as well as high security level. Currently, DNA steganography techniques utilize the properties of only one DNA strand, since the other strand is completely dependent on the first one. This paper presents a DNA-based steganography technique that hides data into both DNA strands with respect to the dependency between the two strands. In the proposed technique, a key of the same length of the reference DNA sequence is generated after using the second DNA strand. The sender sends both the encrypted DNA message and its reference DNA sequence together into a microdot. If the recipient receives this microdot uncontaminated, the sender can safely send the generated key afterwards. The proposed technique doubles the amount of data stored and guarantees a secure transmission process as well, for even if the attacker suspects the first-sent DNA sequence, they will never receive the key, and hence full data extraction is nearly impossible. The conducted experimental study confirms the effectiveness of the proposed.

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Brázda, Václav, Jan Kolomazník, Jiří Lýsek, Martin Bartas, Miroslav Fojta, Jiří Šťastný, and Jean-Louis Mergny. "G4Hunter web application: a web server for G-quadruplex prediction." Bioinformatics 35, no. 18 (February 5, 2019): 3493–95. http://dx.doi.org/10.1093/bioinformatics/btz087.

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Abstract Motivation Expanding research highlights the importance of guanine quadruplex structures. Therefore, easy-accessible tools for quadruplex analyses in DNA and RNA molecules are important for the scientific community. Results We developed a web version of the G4Hunter application. This new web-based server is a platform-independent and user-friendly application for quadruplex analyses. It allows retrieval of gene/nucleotide sequence entries from NCBI databases and provides complete characterization of localization and quadruplex propensity of quadruplex-forming sequences. The G4Hunter web application includes an interactive graphical data representation with many useful options including visualization, sorting, data storage and export. Availability and implementation G4Hunter web application can be accessed at: http://bioinformatics.ibp.cz. Supplementary information Supplementary data are available at Bioinformatics online.

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Schwarz, Michael, Marius Welzel, Tolganay Kabdullayeva, Anke Becker, Bernd Freisleben, and Dominik Heider. "MESA: automated assessment of synthetic DNA fragments and simulation of DNA synthesis, storage, sequencing and PCR errors." Bioinformatics 36, no. 11 (March 4, 2020): 3322–26. http://dx.doi.org/10.1093/bioinformatics/btaa140.

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Abstract Summary The development of de novo DNA synthesis, polymerase chain reaction (PCR), DNA sequencing and molecular cloning gave researchers unprecedented control over DNA and DNA-mediated processes. To reduce the error probabilities of these techniques, DNA composition has to adhere to method-dependent restrictions. To comply with such restrictions, a synthetic DNA fragment is often adjusted manually or by using custom-made scripts. In this article, we present MESA (Mosla Error Simulator), a web application for the assessment of DNA fragments based on limitations of DNA synthesis, amplification, cloning, sequencing methods and biological restrictions of host organisms. Furthermore, MESA can be used to simulate errors during synthesis, PCR, storage and sequencing processes. Availability and implementation MESA is available at mesa.mosla.de, with the source code available at github.com/umr-ds/mesa_dna_sim. Contact dominik.heider@uni-marburg.de Supplementary information Supplementary data are available at Bioinformatics online.

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Li, Jian, Aarif Mohamed Nazeer Batcha, Björn Gaining, and Ulrich R. Mansmann. "An NGS Workflow Blueprint for DNA Sequencing Data and Its Application in Individualized Molecular Oncology." Cancer Informatics 14s5 (January 2015): CIN.S30793. http://dx.doi.org/10.4137/cin.s30793.

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Next-generation sequencing (NGS) technologies that have advanced rapidly in the past few years possess the potential to classify diseases, decipher the molecular code of related cell processes, identify targets for decision-making on targeted therapy or prevention strategies, and predict clinical treatment response. Thus, NGS is on its way to revolutionize oncology. With the help of NGS, we can draw a finer map for the genetic basis of diseases and can improve our understanding of diagnostic and prognostic applications and therapeutic methods. Despite these advantages and its potential, NGS is facing several critical challenges, including reduction of sequencing cost, enhancement of sequencing quality, improvement of technical simplicity and reliability, and development of semiautomated and integrated analysis workflow. In order to address these challenges, we conducted a literature research and summarized a four-stage NGS workflow for providing a systematic review on NGS-based analysis, explaining the strength and weakness of diverse NGS-based software tools, and elucidating its potential connection to individualized medicine. By presenting this four-stage NGS workflow, we try to provide a minimal structural layout required for NGS data storage and reproducibility.

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Salimi, M., S. Fathizadeh, and S. Behnia. "Molecular spin switch triggered by voltage and magnetic field: towards DNA-based molecular devices." Physica Scripta 97, no. 5 (April 4, 2022): 055005. http://dx.doi.org/10.1088/1402-4896/ac5af1.

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Abstract Spin state switching of the DNA sequences due to external stimuli is investigated theoretically. A molecular-based memory or logic device such as a spin switch could be directly realized within an electronic circuit. The DNA system is subjected to an electrical potential difference through the metal leads for controlling the spin transport. The spectral analysis of spin states demonstrates that voltage operates as a crucial tool to turn the switch on. The width of the functional voltage range changes when the system is subjected to an external magnetic field. The magnetic field reduces the system’s symmetry and drives the system to an extended state. Hence, the voltage and magnetic field can modulate the spin transport properties of DNA. The ability to control the spin localization/delocalization states in DNA chains opens up a new approach for efficient computation and data storage.

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Yu, Meng, Xiaohui Tang, Zhenhua Li, Weidong Wang, Shaopeng Wang, Min Li, Qiuliyang Yu, Sijia Xie, Xiaolei Zuo, and Chang Chen. "High-throughput DNA synthesis for data storage." Chemical Society Reviews, 2024. http://dx.doi.org/10.1039/d3cs00469d.

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Using DNA molecules for digital data storage: the writing and reading of the data are realized by high throughput DNA synthesis and sequencing technologies, where high density array-based chips play an important role.

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31

Zhang, Lichao, Yuanyuan Lv, Lei Xu, and Murong Zhou. "A review of DNA data storage technologies based on biomolecules." Current Bioinformatics 16 (August 13, 2021). http://dx.doi.org/10.2174/1574893616666210813101237.

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: In the information age, data storage technology has become the key to improving computer systems. Since traditional storage technologies cannot meet the demand for massive storage, new DNA storage technology based on biomolecules attracts much attentions. DNA storage refers to the technology that uses artificially synthesized deoxynucleotide chains to store and read all information, such as documents, pictures, and audio. First, data are encoded into binary number strings. Then, the four types of base, A(Adenine), T(Thymine), C(Cytosine), and G(Guanine), are used to encode the corresponding binary numbers so that the data can be used to construct the target DNA molecules in the form of deoxynucleotide chains. Subsequently, the corresponding DNA molecules are artificially synthesized, enabling the data to be stored within them. Compared with traditional storage systems, DNA storage has major advantages, such as high storage density, long duration, as well as low hardware cost, high access parallelism, and strong scalability, which satisfies the demands for big data storage. This manuscript first reviews the origin and development of DNA storage technology, then the storage principles, contents and methods are introduced. Finally, the development of DNA storage technology are analyzed. From the initial research to the cutting edge of this field and beyond, the advantages, disadvantages, and practical applications of DNA storage technology require continuous exploration.

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32

Sriram.S and Dr. D. R. Krithika. "DNA as a Storage Medium for Efficient and Reliable Cloud Data Archieving." International Journal of Advanced Research in Science, Communication and Technology, July 4, 2024, 93–100. http://dx.doi.org/10.48175/ijetir-1218.

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On Earth right now, there are about 10 trillion gigabytes of digital data, and every day, humans produce emails, photos, tweets, and other digital files that add up to another 2.5 million gigabytes of data.Much of this data is stored in enormous facilities known as exabyte data centers (an exabyte is 1 billion gigabytes), which can be the size of several football fields and cost around $1 billion to build and maintain.Demand for data storage is growing exponentially, but the capacity of existing storage media is not keeping up.This project enables molecular-level data storage into DNA molecules by leveraging biotechnology advances in synthesizing, manipulating and sequencing DNA to develop archival storage. Additionally an effective algorithm is introduced using deoxyribonucleic acid (DNA)-based cryptography to enhance data security while sharing the data over the cloud

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33

Tomek, Kyle J., Kevin Volkel, Elaine W. Indermaur, James M. Tuck, and Albert J. Keung. "Promiscuous molecules for smarter file operations in DNA-based data storage." Nature Communications 12, no. 1 (June 10, 2021). http://dx.doi.org/10.1038/s41467-021-23669-w.

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AbstractDNA 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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Takahashi, Christopher N., David P. Ward, Carlo Cazzaniga, Christopher Frost, Paolo Rech, Kumkum Ganguly, Sean Blanchard, Steve Wender, Bichlien H. Nguyen, and Jake A. Smith. "Evaluating the risk of data loss due to particle radiation damage in a DNA data storage system." Nature Communications 15, no. 1 (September 14, 2024). http://dx.doi.org/10.1038/s41467-024-51768-x.

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AbstractDNA data storage is a potential alternative to magnetic tape for archival storage purposes, promising substantial gains in information density. Critical to the success of DNA as a storage media is an understanding of the role of environmental factors on the longevity of the stored information. In this paper, we evaluate the effect of exposure to ionizing particle radiation, a cause of data loss in traditional magnetic media, on the longevity of data in DNA data storage pools. We develop a mass action kinetics model to estimate the rate of damage accumulation in DNA strands due to neutron interactions with both nucleotides and residual water molecules, then utilize the model to evaluate the effect several design parameters of a typical DNA data storage scheme have on expected data longevity. Finally, we experimentally validate our model by exposing dried DNA samples to different levels of neutron irradiation and analyzing the resulting error profile. Our results show that particle radiation is not a significant contributor to data loss in DNA data storage pools under typical storage conditions.

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Matange, Karishma, James M. Tuck, and Albert J. Keung. "DNA stability: a central design consideration for DNA data storage systems." Nature Communications 12, no. 1 (March 1, 2021). http://dx.doi.org/10.1038/s41467-021-21587-5.

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AbstractData storage in DNA is a rapidly evolving technology that could be a transformative solution for the rising energy, materials, and space needs of modern information storage. Given that the information medium is DNA itself, its stability under different storage and processing conditions will fundamentally impact and constrain design considerations and data system capabilities. Here we analyze the storage conditions, molecular mechanisms, and stabilization strategies influencing DNA stability and pose specific design configurations and scenarios for future systems that best leverage the considerable advantages of DNA storage.

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36

Kryuchyn, A., Ye V. Belyak, Ye A. Kryuchyna та A. V. Potebnya. "СТАН І ПРОБЛЕМИ СТВОРЕННЯ ДНК-ПАМ'ЯТІ". Medical Informatics and Engineering, № 3 (20 жовтня 2015). http://dx.doi.org/10.11603/mie.1996-1960.2015.3.4997.

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The results of the analysis of the development of storage systems on DNA molecules are given. The considerable potential for such storage systems for the organization of long-term storage of large volumes of information is shown. The conditions for the extensive use of memory on DNA are determined. It is shown that the key to the use of WORM-type memory on DNA molecules is a significant increase in the speed of sequencing nukleatidov recorded sequences. Data on conditions of storage memory chips on DNA, which provide long-term storage of large volumes of information is presented.

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37

Chen, Yuan-Jyue, Christopher N. Takahashi, Lee Organick, Callista Bee, Siena Dumas Ang, Patrick Weiss, Bill Peck, Georg Seelig, Luis Ceze, and Karin Strauss. "Quantifying molecular bias in DNA data storage." Nature Communications 11, no. 1 (June 29, 2020). http://dx.doi.org/10.1038/s41467-020-16958-3.

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38

Bajc, Gregor, Anja Pavlin, Małgorzata Figiel, Weronika Zajko, Marcin Nowotny, and Matej Butala. "Data storage based on the absence of nucleotides using a bacteriophage abortive infection system reverse transcriptase." Lab on a Chip, 2024. http://dx.doi.org/10.1039/d4lc00755g.

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DNA molecules are a promising data storage medium for the future; however, effective de novo synthesis of DNA using an enzyme that catalyzes the polymerization of natural nucleoside triphosphates in...

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39

Volkel, Kevin D., Kevin N. Lin, Paul W. Hook, Winston Timp, Albert J. Keung, and James M. Tuck. "FrameD: Framework for DNA-based Data Storage Design, Verification, and Validation." Bioinformatics, September 15, 2023. http://dx.doi.org/10.1093/bioinformatics/btad572.

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Abstract Motivation DNA-based data storage is a quickly growing field that hopes to harness the massive theoretical information density of DNA molecules to produce a competitive next-generation storage medium suitable for archival data. In recent years, many DNA-based storage system designs have been proposed. Given that no common infrastructure exists for simulating these storage systems, comparing many different designs along with many different error models is increasingly difficult. To address this challenge we introduce FrameD, a simulation infrastructure for DNA storage systems that leverages the underlying modularity of DNA storage system designs to provide a framework to express different designs while being able to reuse common components. Results We demonstrate the utility of FrameD and the need for a common simulation platform using a case study. Our case study compares designs that utilize strand copies differently, some that align strand copies using Multiple Sequence Alignment (MSA) algorithms and others that do not. We found that the choice to include MSA in the pipeline is dependent on the error rate and the type of errors being injected and is not always beneficial. In addition to supporting a wide range of designs, FrameD provides the user with transparent parallelism to deal with a large number of reads from sequencing and the need for many fault injection iterations. We believe that FrameD fills a void in the tools publicly available to the DNA storage community by providing a modular and extensible framework with support for massive parallelism. As a result, it will help accelerate the design process of future DNA-based storage systems. Availability and implementation The source code for FrameD along with the data generated during the demonstration of FrameD is available in a public Github repository at https://github.com/dna-storage/framed (10.5281/zenodo.7757762)

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40

Lee, Howon, Daniel J. Wiegand, Kettner Griswold, Sukanya Punthambaker, Honggu Chun, Richie E. Kohman, and George M. Church. "Photon-directed multiplexed enzymatic DNA synthesis for molecular digital data storage." Nature Communications 11, no. 1 (October 16, 2020). http://dx.doi.org/10.1038/s41467-020-18681-5.

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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.

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Coudy, Delphine, Marthe Colotte, Aurélie Luis, Sophie Tuffet, and Jacques Bonnet. "Long Term Conservation of DNA at Ambient Temperature. Implications for DNA Data Storage." Applied Cell Biology 10, no. 1 (February 7, 2022). http://dx.doi.org/10.53043/2320-1991.acb90017.

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DNA conservation is central to many applications. This leads to an ever-increasing number of samples which are more and more difficult and costly to store or transport. A way to alleviate this problem is to develop procedures for storing samples at room temperature while maintaining their stability. A variety of commercial systems have been proposed but they fail to completely protect DNA from deleterious factors, mainly water. On the other side, Imagene company has developed a procedure for long-term conservation of biospecimen at room temperature based on the confinement of the samples under an anhydrous and anoxic atmosphere maintained inside hermetic capsules. The procedure has been validated by us and others for purified RNA, and DNA in buffy coat or white blood cells lysates, but a precise determination of purified DNA stability is still lacking. We used the Arrhenius law to determine the DNA degradation rate at room temperature. We found that extrapolation to 25°C gave a degradation rate constant equivalent to about 1 cut/century/100 000 nucleotides, a stability several orders of magnitude larger than the current commercialized processes. Such a stability is fundamental for many applications such as the preservation of very large DNA molecules (particularly interesting in the context of genome sequencing) or oligonucleotides for DNA data storage. Capsules are also well suited for this latter application because of their high capacity. One can calculate that the 64 zettabytes of data produced in 2020 could be stored, standalone, for centuries, in about 20 kg of capsules.

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SUNEJA, VAIBHAV. "BIG DATA MANAGEMENT – DNA DATA WAREHOUSE." International Journal of Computer and Communication Technology, July 2015, 170–73. http://dx.doi.org/10.47893/ijcct.2015.1298.

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Big data storage and retrieval is cause of concern for future. This paper proposes to store data by organizing nucleotides (adenine (A) and thymine (T)) to represent binary 0’s and 1’s. Small fragments of high molecular DNA can be achieved by chain termination method and by shotgun sequencing method, we can select the fragments containing A’s and T’s in order we want. This paper demonstrates a python script, which can produce A and T sequence from the sequence of data as input which can be used while using shotgun sequencing for selecting/discarding of strands, script can also be used to query the DNA database by integration with DNA sequencing method. The data will not be written on the nucleotide but nucleotide sequence will be modified to represent the data. This paper further illustrates how sequence of nucleotides can be arranged as logical table with a proper header and how the python script can be used to save and retrieve the data from this table. The storage and retrieval of 24 bits of data can easily be completed in 15-20 minutes under controlled lab conditions which includes manual and mechanical effort. This paper proves how by automation and robotic arms, this delay can be reduced further and how to overcome challenges that can come for preserving the DNA strands. This approach, can lead to development of DNA data warehouse where there will be infinite storage space as the DNA can be obtained virtually free of cost from any living thing.

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Leblanc, Julien, Olivier Boulle, Emeline Roux, Jacques Nicolas, Dominique Lavenier, and Yann Audic. "Fully in vitro iterative construction of a 24 kb-long artificial DNA sequence to store digital information." BioTechniques, April 4, 2024. http://dx.doi.org/10.2144/btn-2023-0109.

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In the absence of a DNA template, the ab initio production of long double-stranded DNA molecules of predefined sequences is particularly challenging. The DNA synthesis step remains a bottleneck for many applications such as functional assessment of ancestral genes, analysis of alternative splicing or DNA-based data storage. In this report we propose a fully in vitro protocol to generate very long double-stranded DNA molecules starting from commercially available short DNA blocks in less than 3 days using Golden Gate assembly. This innovative application allowed us to streamline the process to produce a 24 kb-long DNA molecule storing part of the Declaration of the Rights of Man and of the Citizen of 1789 . The DNA molecule produced can be readily cloned into a suitable host/vector system for amplification and selection.

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Qu, Guanjin, Zihui Yan, and Huaming Wu. "Clover: tree structure-based efficient DNA clustering for DNA-based data storage." Briefings in Bioinformatics, August 16, 2022. http://dx.doi.org/10.1093/bib/bbac336.

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Abstract Deoxyribonucleic acid (DNA)-based data storage is a promising new storage technology which has the advantage of high storage capacity and long storage time compared with traditional storage media. However, the synthesis and sequencing process of DNA can randomly generate many types of errors, which makes it more difficult to cluster DNA sequences to recover DNA information. Currently, the available DNA clustering algorithms are targeted at DNA sequences in the biological domain, which not only cannot adapt to the characteristics of sequences in DNA storage, but also tend to be unacceptably time-consuming for billions of DNA sequences in DNA storage. In this paper, we propose an efficient DNA clustering method termed Clover for DNA storage with linear computational complexity and low memory. Clover avoids the computation of the Levenshtein distance by using a tree structure for interval-specific retrieval. We argue through theoretical proofs that Clover has standard linear computational complexity, low space complexity, etc. Experiments show that our method can cluster 10 million DNA sequences into 50 000 classes in 10 s and meet an accuracy rate of over 99%. Furthermore, we have successfully completed an unprecedented clustering of 10 billion DNA data on a single home computer and the time consumption still satisfies the linear relationship. Clover is freely available at https://github.com/Guanjinqu/Clover.

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Zan, Xiangzhen, Ling Chu, Ranze Xie, Yanqing Su, Xiangyu Yao, Peng Xu, and Wenbin Liu. "An image cryptography method by highly error-prone DNA storage channel." Frontiers in Bioengineering and Biotechnology 11 (April 19, 2023). http://dx.doi.org/10.3389/fbioe.2023.1173763.

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Introduction: Rapid development in synthetic technologies has boosted DNA as a potential medium for large-scale data storage. Meanwhile, how to implement data security in the DNA storage system is still an unsolved problem.Methods: In this article, we propose an image encryption method based on the modulation-based storage architecture. The key idea is to take advantage of the unpredictable modulation signals to encrypt images in highly error-prone DNA storage channels.Results and Discussion: Numerical results have demonstrated that our image encryption method is feasible and effective with excellent security against various attacks (statistical, differential, noise, and data loss). When compared with other methods such as the hybridization reactions of DNA molecules, the proposed method is more reliable and feasible for large-scale applications.

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Lopez, Randolph, Yuan-Jyue Chen, Siena Dumas Ang, Sergey Yekhanin, Konstantin Makarychev, Miklos Z. Racz, Georg Seelig, Karin Strauss, and Luis Ceze. "DNA assembly for nanopore data storage readout." Nature Communications 10, no. 1 (July 3, 2019). http://dx.doi.org/10.1038/s41467-019-10978-4.

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47

Shetty, Urvi. "From megabytes to molecules: The usage of DNA computing for storage and its implications on the future." Scholarly Review Journal SR Online: Showcase, Equinox 2024 (October 20, 2024). http://dx.doi.org/10.70121/001c.124887.

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It is more important now than ever to develop more effective data storage techniques in the constantly advancing field of computers. Due to their limits in terms of durability, information density, and physical space requirements, current storage technologies, such as magnetic and optical media, are finding it difficult to keep up with the global demand for data storage, which is expected to exceed 175 trillion gigabytes by 2025. Nature’s own method of storing genetic information for a long time, deoxyribonucleic acid (DNA), provides great data density, stability, and endurance, making it a viable solution to address this issue. Through a comprehensive analysis of existing literature, this paper aims to provide a nuanced understanding of DNA computing’s current state - mainly its trajectory towards becoming a viable alternative to traditional storage methods - highlighting the history, current developments/challenges, and future prospects.

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Wang, Boya, Siyuan Stella Wang, Cameron Chalk, Andrew D. Ellington, and David Soloveichik. "Parallel molecular computation on digital data stored in DNA." Proceedings of the National Academy of Sciences 120, no. 37 (September 5, 2023). http://dx.doi.org/10.1073/pnas.2217330120.

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DNA is an incredibly dense storage medium for digital data. However, computing on the stored information is expensive and slow, requiring rounds of sequencing, in silico computation, and DNA synthesis. Prior work on accessing and modifying data using DNA hybridization or enzymatic reactions had limited computation capabilities. Inspired by the computational power of “DNA strand displacement,” we augment DNA storage with “in-memory” molecular computation using strand displacement reactions to algorithmically modify data in a parallel manner. We show programs for binary counting and Turing universal cellular automaton Rule 110, the latter of which is, in principle, capable of implementing any computer algorithm. Information is stored in the nicks of DNA, and a secondary sequence-level encoding allows high-throughput sequencing-based readout. We conducted multiple rounds of computation on 4-bit data registers, as well as random access of data (selective access and erasure). We demonstrate that large strand displacement cascades with 244 distinct strand exchanges (sequential and in parallel) can use naturally occurring DNA sequence from M13 bacteriophage without stringent sequence design, which has the potential to improve the scale of computation and decrease cost. Our work merges DNA storage and DNA computing, setting the foundation of entirely molecular algorithms for parallel manipulation of digital information preserved in DNA.

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Pan, Chao, S. Kasra Tabatabaei, S. M. Hossein Tabatabaei Yazdi, Alvaro G. Hernandez, Charles M. Schroeder, and Olgica Milenkovic. "Rewritable two-dimensional DNA-based data storage with machine learning reconstruction." Nature Communications 13, no. 1 (May 27, 2022). http://dx.doi.org/10.1038/s41467-022-30140-x.

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AbstractDNA-based data storage platforms traditionally encode information only in the nucleotide sequence of the molecule. Here we report on a two-dimensional molecular data storage system that records information in both the sequence and the backbone structure of DNA and performs nontrivial joint data encoding, decoding and processing. Our 2DDNA method efficiently stores images in synthetic DNA and embeds pertinent metadata as nicks in the DNA backbone. To avoid costly worst-case redundancy for correcting sequencing/rewriting errors and to mitigate issues associated with mismatched decoding parameters, we develop machine learning techniques for automatic discoloration detection and image inpainting. The 2DDNA platform is experimentally tested by reconstructing a library of images with undetectable or small visual degradation after readout processing, and by erasing and rewriting copyright metadata encoded in nicks. Our results demonstrate that DNA can serve both as a write-once and rewritable memory for heterogenous data and that data can be erased in a permanent, privacy-preserving manner. Moreover, the storage system can be made robust to degrading channel qualities while avoiding global error-correction redundancy.

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Mir, Owais, Upendra Gupta, Gulzar Bhat, Arshad Pandith, and Feroz Ahmad Mir. "Vibrational, Optical, Electrochemical, and Electrical Analysis of Normal and Cancer DNA." ECS Journal of Solid State Science and Technology, December 4, 2023. http://dx.doi.org/10.1149/2162-8777/ad1204.

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Abstract In the current article, we used such characterizations as Fourier-transform infrared (FT-IR) spectroscopy, UV-visible spectroscopy, photoluminescence (PL) spectroscopy, cyclic voltammetry (CV), electrochemical impedance spectroscopy (EIS), current-voltage (I-V) characteristics, dielectric spectroscopy, and transient time spectroscopy on normal and cancerous (esophagus) DNA samples. FT-IR confirms the associated functional groups of DNA. From the analysis of UV data, the various optical parameters like optical band gap and disorder energy were estimated and discussed. PL data demonstrate the various emissions and are described as per the existing structure of the molecule. From the CV plots, the energy levels, like highest occupied molecular orbital and the lowest unoccupied molecular orbital, were also calculated. The EIS data interpretations show well developed changes in various parameters related with nature of the present molecules. Also from I-V characteristics, visible variations were observed and discussed. From the dielectric spectroscopy, a drastic change in the data were seen and described. Dynamic measurements like transient time demonstrates a vital impact on charge storage and hence on the rise and fall time of the molecules.These observed properties shown by these techniques could be explored for further confirmation of the diagnostic of the disease

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