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Li W, Zhang Z, Xie B, He Y, He K, Qiu H, Lu Z, Jiang C, Pan X, He Y, Hu W, Liu W, Que T, Hu Y. HiOmics: A cloud-based one-stop platform for the comprehensive analysis of large-scale omics data. Comput Struct Biotechnol J 2024; 23:659-668. [PMID: 38292471 PMCID: PMC10824657 DOI: 10.1016/j.csbj.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 01/01/2024] [Accepted: 01/02/2024] [Indexed: 02/01/2024] Open
Abstract
Analyzing the vast amount of omics data generated comprehensively by high-throughput sequencing technology is of utmost importance for scientists. In this context, we propose HiOmics, a cloud-based platform equipped with nearly 300 plugins designed for the comprehensive analysis and visualization of omics data. HiOmics utilizes the Element Plus framework to craft a user-friendly interface and harnesses Docker container technology to ensure the reliability and reproducibility of data analysis results. Furthermore, HiOmics employs the Workflow Description Language and Cromwell engine to construct workflows, ensuring the portability of data analysis and simplifying the examination of intricate data. Additionally, HiOmics has developed DataCheck, a tool based on Golang, which verifies and converts data formats. Finally, by leveraging the object storage technology and batch computing capabilities of public cloud platforms, HiOmics enables the storage and processing of large-scale data while maintaining resource independence among users.
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Affiliation(s)
- Wen Li
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, China
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Biological Molecular Medicine Research (Guangxi Medical University), Education Department of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, China
| | - Zhining Zhang
- Guangxi Henbio Biotechnology Co., Ltd., Nanning, Guangxi, China
| | - Bo Xie
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, China
| | - Yunlin He
- Guangxi Henbio Biotechnology Co., Ltd., Nanning, Guangxi, China
| | - Kangming He
- Guangxi Henbio Biotechnology Co., Ltd., Nanning, Guangxi, China
| | - Hong Qiu
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Henbio Biotechnology Co., Ltd., Nanning, Guangxi, China
| | - Zhiwei Lu
- Guangxi Henbio Biotechnology Co., Ltd., Nanning, Guangxi, China
| | - Chunlan Jiang
- Guangxi Henbio Biotechnology Co., Ltd., Nanning, Guangxi, China
| | - Xuanyu Pan
- School of Basic Medicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Yuxiao He
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, China
| | - Wenyu Hu
- Guangxi Henbio Biotechnology Co., Ltd., Nanning, Guangxi, China
| | - Wenjian Liu
- Faculty of Data Science, City University of Macau, Macau, China
| | - Tengcheng Que
- Faculty of Data Science, City University of Macau, Macau, China
- Youjiang Medical University for Nationalities, Baise, Guangxi, China
- Guangxi Zhuang Autonomous Terrestrial Wildlife Rescue Research and Epidemic Diseases Monitoring Center, Nanning, Guangxi, China
| | - Yanling Hu
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, China
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Biological Molecular Medicine Research (Guangxi Medical University), Education Department of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, China
- Guangxi Henbio Biotechnology Co., Ltd., Nanning, Guangxi, China
- Faculty of Data Science, City University of Macau, Macau, China
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2
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Pichon M, Hollenstein M. Controlled enzymatic synthesis of oligonucleotides. Commun Chem 2024; 7:138. [PMID: 38890393 PMCID: PMC11189433 DOI: 10.1038/s42004-024-01216-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 05/24/2024] [Indexed: 06/20/2024] Open
Abstract
Oligonucleotides are advancing as essential materials for the development of new therapeutics, artificial genes, or in storage of information applications. Hitherto, our capacity to write (i.e., synthesize) oligonucleotides is not as efficient as that to read (i.e., sequencing) DNA/RNA. Alternative, biocatalytic methods for the de novo synthesis of natural or modified oligonucleotides are in dire need to circumvent the limitations of traditional synthetic approaches. This Perspective article summarizes recent progress made in controlled enzymatic synthesis, where temporary blocked nucleotides are incorporated into immobilized primers by polymerases. While robust protocols have been established for DNA, RNA or XNA synthesis is more challenging. Nevertheless, using a suitable combination of protected nucleotides and polymerase has shown promises to produce RNA oligonucleotides even though the production of long DNA/RNA/XNA sequences (>1000 nt) remains challenging. We surmise that merging ligase- and polymerase-based synthesis would help to circumvent the current shortcomings of controlled enzymatic synthesis.
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Affiliation(s)
- Maëva Pichon
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, 28, Rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Marcel Hollenstein
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, 28, Rue du Docteur Roux, 75724, Paris Cedex 15, France.
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3
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Carlson CK, Loveless TB, Milisavljevic M, Kelly PI, Mills JH, Tyo KEJ, Liu CC. A massively parallel in vivo assay of TdT mutants yields variants with altered nucleotide insertion biases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.11.598561. [PMID: 38915690 PMCID: PMC11195295 DOI: 10.1101/2024.06.11.598561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Terminal deoxynucleotidyl transferase (TdT) is a unique DNA polymerase capable of template-independent extension of DNA with random nucleotides. TdT's de novo DNA synthesis ability has found utility in DNA recording, DNA data storage, oligonucleotide synthesis, and nucleic acid labeling, but TdT's intrinsic nucleotide biases limit its versatility in such applications. Here, we describe a multiplexed assay for profiling and engineering the bias and overall activity of TdT variants in high throughput. In our assay, a library of TdTs is encoded next to a CRISPR-Cas9 target site in HEK293T cells. Upon transfection of Cas9 and sgRNA, the target site is cut, allowing TdT to intercept the double strand break and add nucleotides. Each resulting insertion is sequenced alongside the identity of the TdT variant that generated it. Using this assay, 25,623 unique TdT variants, constructed by site-saturation mutagenesis at strategic positions, were profiled. This resulted in the isolation of several altered-bias TdTs that expanded the capabilities of our TdT-based DNA recording system, Cell History Recording by Ordered Insertion (CHYRON), by increasing the information density of recording through an unbiased TdT and achieving dual-channel recording of two distinct inducers (hypoxia and Wnt) through two differently biased TdTs. Select TdT variants were also tested in vitro , revealing concordance between each variant's in vitro bias and the in vivo bias determined from the multiplexed high throughput assay. Overall, our work, and the multiplex assay it features, should support the continued development of TdT-based DNA recorders, in vitro applications of TdT, and further study of the biology of TdT.
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Wang Q, Zhang S, Li Y. Efficient DNA Coding Algorithm for Polymerase Chain Reaction Amplification Information Retrieval. Int J Mol Sci 2024; 25:6449. [PMID: 38928155 PMCID: PMC11204281 DOI: 10.3390/ijms25126449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 06/02/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024] Open
Abstract
Polymerase Chain Reaction (PCR) amplification is widely used for retrieving information from DNA storage. During the PCR amplification process, nonspecific pairing between the 3' end of the primer and the DNA sequence can cause cross-talk in the amplification reaction, leading to the generation of interfering sequences and reduced amplification accuracy. To address this issue, we propose an efficient coding algorithm for PCR amplification information retrieval (ECA-PCRAIR). This algorithm employs variable-length scanning and pruning optimization to construct a codebook that maximizes storage density while satisfying traditional biological constraints. Subsequently, a codeword search tree is constructed based on the primer library to optimize the codebook, and a variable-length interleaver is used for constraint detection and correction, thereby minimizing the likelihood of nonspecific pairing. Experimental results demonstrate that ECA-PCRAIR can reduce the probability of nonspecific pairing between the 3' end of the primer and the DNA sequence to 2-25%, enhancing the robustness of the DNA sequences. Additionally, ECA-PCRAIR achieves a storage density of 2.14-3.67 bits per nucleotide (bits/nt), significantly improving storage capacity.
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Affiliation(s)
| | - Shufang Zhang
- School of Electrical Automation and Information Engineering, Tianjin University, Tianjin 300072, China
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5
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Seo S, Tandon A, Lee KW, Lee JH, Park SH. Information Density Enhancement Using Lossy Compression in DNA Data Storage. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024:e2403071. [PMID: 38779945 DOI: 10.1002/adma.202403071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/06/2024] [Indexed: 05/25/2024]
Abstract
This study develops two deoxyribonucleic acid (DNA) lossy compression models, Models A and B, to encode grayscale images into DNA sequences, enhance information density, and enable high-fidelity image recovery. These models, distinguished by their handling of pixel domains and interpolation methods, offer a novel approach to data storage for DNA. Model A processes pixels in overlapped domains using linear interpolation (LI), whereas Model B uses non-overlapped domains with nearest-neighbor interpolation (NNI). Through a comparative analysis with Joint Photographic Experts Group (JPEG) compression, the DNA lossy compression models demonstrate competitive advantages in terms of information density and image quality restoration. The application of these models to the Modified National Institute of Standards and Technology (MNIST) dataset reveals their efficiency and the recognizability of decompressed images, which is validated by convolutional neural network (CNN) performance. In particular, Model B2, a version of Model B, emerges as an effective method for balancing high information density (surpassing over 20 times the typical densities of two bits per nucleotide) with reasonably good image quality. These findings highlight the potential of DNA-based data storage systems for high-density and efficient compression, indicating a promising future for biological data storage solutions.
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Affiliation(s)
- Seongjun Seo
- Department of Physics and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), 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
| | - Keun Woo Lee
- DNASTech, Industry-Academic Cooperation Center, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Jee-Hyong Lee
- Department of Artificial Intelligence, 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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6
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Yu M, Tang X, Li Z, Wang W, Wang S, Li M, Yu Q, Xie S, Zuo X, Chen C. High-throughput DNA synthesis for data storage. Chem Soc Rev 2024; 53:4463-4489. [PMID: 38498347 DOI: 10.1039/d3cs00469d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
With the explosion of digital world, the dramatically increasing data volume is expected to reach 175 ZB (1 ZB = 1012 GB) in 2025. Storing such huge global data would consume tons of resources. Fortunately, it has been found that the deoxyribonucleic acid (DNA) molecule is the most compact and durable information storage medium in the world so far. Its high coding density and long-term preservation properties make itself one of the best data storage carriers for the future. High-throughput DNA synthesis is a key technology for "DNA data storage", which encodes binary data stream (0/1) into quaternary long DNA sequences consisting of four bases (A/G/C/T). In this review, the workflow of DNA data storage and the basic methods of artificial DNA synthesis technology are outlined first. Then, the technical characteristics of different synthesis methods and the state-of-the-art of representative commercial companies, with a primary focus on silicon chip microarray-based synthesis and novel enzymatic DNA synthesis are presented. Finally, the recent status of DNA storage and new opportunities for future development in the field of high-throughput, large-scale DNA synthesis technology are summarized.
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Affiliation(s)
- Meng Yu
- Institute of Medical Chips, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China.
- School of Microelectronics, Shanghai University, 201800, Shanghai, China
- Shanghai Industrial μTechnology Research Institute, 201800, Shanghai, China
| | - Xiaohui Tang
- Institute of Medical Chips, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China.
- Shanghai Industrial μTechnology Research Institute, 201800, Shanghai, China
| | - Zhenhua Li
- Institute of Medical Chips, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China.
- Shanghai Industrial μTechnology Research Institute, 201800, Shanghai, China
| | - Weidong Wang
- Shanghai Industrial μTechnology Research Institute, 201800, Shanghai, China
| | - Shaopeng Wang
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China.
| | - Min Li
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China.
| | - Qiuliyang Yu
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
| | - Sijia Xie
- Institute of Medical Chips, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China.
- School of Microelectronics, Shanghai University, 201800, Shanghai, China
- Shanghai Industrial μTechnology Research Institute, 201800, Shanghai, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China.
| | - Chang Chen
- Institute of Medical Chips, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China.
- School of Microelectronics, Shanghai University, 201800, Shanghai, China
- Shanghai Industrial μTechnology Research Institute, 201800, Shanghai, China
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 200050, Shanghai, China
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7
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Nolte RJM, Elemans JAAW. Artificial Processive Catalytic Systems. Chemistry 2024; 30:e202304230. [PMID: 38314967 DOI: 10.1002/chem.202304230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 02/07/2024]
Abstract
Processive catalysts remain attached to a substrate and perform multiple rounds of catalysis. They are abundant in nature. This review highlights artificial processive catalytic systems, which can be divided into (A) catalytic rings that move along a polymer chain, (B) catalytic pores that hold polymer chains and decompose them, (C) catalysts that remain attached to and move around a cyclic substrate via supramolecular interactions, and (D) anchored catalysts that remain in contact with a substrate via multiple catalytic interactions (see frontispiece).
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Affiliation(s)
- Roeland J M Nolte
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 125, 6525AJ, Nijmegen, The, Netherlands
| | - Johannes A A W Elemans
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 125, 6525AJ, Nijmegen, The, Netherlands
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8
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Cao B, Zheng Y, Shao Q, Liu Z, Xie L, Zhao Y, Wang B, Zhang Q, Wei X. Efficient data reconstruction: The bottleneck of large-scale application of DNA storage. Cell Rep 2024; 43:113699. [PMID: 38517891 DOI: 10.1016/j.celrep.2024.113699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 11/15/2023] [Accepted: 01/05/2024] [Indexed: 03/24/2024] Open
Abstract
Over the past decade, the rapid development of DNA synthesis and sequencing technologies has enabled preliminary use of DNA molecules for digital data storage, overcoming the capacity and persistence bottlenecks of silicon-based storage media. DNA storage has now been fully accomplished in the laboratory through existing biotechnology, which again demonstrates the viability of carbon-based storage media. However, the high cost and latency of data reconstruction pose challenges that hinder the practical implementation of DNA storage beyond the laboratory. In this article, we review existing advanced DNA storage methods, analyze the characteristics and performance of biotechnological approaches at various stages of data writing and reading, and discuss potential factors influencing DNA storage from the perspective of data reconstruction.
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Affiliation(s)
- Ben Cao
- School of Computer Science and Technology, Dalian University of Technology, Lingshui Street, Dalian, Liaoning 116024, China; Centre for Frontier AI Research, Agency for Science, Technology, and Research (A(∗)STAR), 1 Fusionopolis Way, Singapore 138632, Singapore
| | - Yanfen Zheng
- School of Computer Science and Technology, Dalian University of Technology, Lingshui Street, Dalian, Liaoning 116024, China
| | - Qi Shao
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Xuefu Street, Dalian, Liaoning 116622, China
| | - Zhenlu Liu
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Xuefu Street, Dalian, Liaoning 116622, China
| | - Lei Xie
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Xuefu Street, Dalian, Liaoning 116622, China
| | - Yunzhu Zhao
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Xuefu Street, Dalian, Liaoning 116622, China
| | - Bin Wang
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Xuefu Street, Dalian, Liaoning 116622, China
| | - Qiang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Lingshui Street, Dalian, Liaoning 116024, China.
| | - Xiaopeng Wei
- School of Computer Science and Technology, Dalian University of Technology, Lingshui Street, Dalian, Liaoning 116024, China
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9
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Li Y, Yu C, Wang Y, Yu J, Wang H, Li B. Nanopore sensitization based on a double loop hybridization chain reaction and G-quadruplex. Chem Commun (Camb) 2024; 60:4487-4490. [PMID: 38567405 DOI: 10.1039/d4cc00125g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The widespread implementation of solid-state nanopores faces challenges such as lower resolution and increased electrical noise when compared to biological nanopores. Incorporating specific nucleic acid reactions can enhance resolution. In this study, we've developed a nucleic acid amplifier to enhance the sensitivity of solid-state nanopores, utilizing a G-rich sequence and hybridization chain reaction. This amplifier improves target concentration and volume amplification, showing promise in nanopore sensitivity tests.
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Affiliation(s)
- Yanru Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China.
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Chunmiao Yu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China.
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Yesheng Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China.
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Jin Yu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China.
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Huaning Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China.
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Bingling Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China.
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, China
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10
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Bardales AC, Smirnov V, Taylor K, Kolpashchikov DM. DNA Logic Gates Integrated on DNA Substrates in Molecular Computing. Chembiochem 2024; 25:e202400080. [PMID: 38385968 DOI: 10.1002/cbic.202400080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 02/23/2024]
Abstract
Due to nucleic acid's programmability, it is possible to realize DNA structures with computing functions, and thus a new generation of molecular computers is evolving to solve biological and medical problems. Pioneered by Milan Stojanovic, Boolean DNA logic gates created the foundation for the development of DNA computers. Similar to electronic computers, the field is evolving towards integrating DNA logic gates and circuits by positioning them on substrates to increase circuit density and minimize gate distance and undesired crosstalk. In this minireview, we summarize recent developments in the integration of DNA logic gates into circuits localized on DNA substrates. This approach of all-DNA integrated circuits (DNA ICs) offers the advantages of biocompatibility, increased circuit response, increased circuit density, reduced unit concentration, facilitated circuit isolation, and facilitated cell uptake. DNA ICs can face similar challenges as their equivalent circuits operating in bulk solution (bulk circuits), and new physical challenges inherent in spatial localization. We discuss possible avenues to overcome these obstacles.
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Affiliation(s)
- Andrea C Bardales
- Chemistry Department, University of Central Florida, 4111 Libra Drive, Physical Sciences Bld. Rm. 255, Orlando, FL 32816-2366, Florida
| | - Viktor Smirnov
- Laboratory of Molecular Robotics and Biosensor Materials, SCAMT Institute, ITMO University, 9 Lomonosova Str., St. Petersburg, Russian Federation
| | - Katherine Taylor
- Chemistry Department, University of Central Florida, 4111 Libra Drive, Physical Sciences Bld. Rm. 255, Orlando, FL 32816-2366, Florida
| | - Dmitry M Kolpashchikov
- Chemistry Department, University of Central Florida, 4111 Libra Drive, Physical Sciences Bld. Rm. 255, Orlando, FL 32816-2366, Florida
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11
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Soter de Mariz e Miranda L, Schroeder Borges Gonçalves R, Uziel J, Obika S, Lubin-Germain N. Editorial: Nucleosides, nucleotides and nucleic acids: chemistry and biology. Front Chem 2024; 12:1401510. [PMID: 38660568 PMCID: PMC11040680 DOI: 10.3389/fchem.2024.1401510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 03/27/2024] [Indexed: 04/26/2024] Open
Affiliation(s)
| | | | - Jacques Uziel
- CY Cergy-Paris Université, BioCIS, CNRS, Cergy, France
- Université Paris-Saclay, CNRS, BioCIS, Châtenay-Malabry, France
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Japan
| | - Nadege Lubin-Germain
- CY Cergy-Paris Université, BioCIS, CNRS, Cergy, France
- Université Paris-Saclay, CNRS, BioCIS, Châtenay-Malabry, France
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12
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Siripuram V, Sunkari YK, Ma F, Nguyen TL, Flajolet M. Reversible and Fully Controllable Generation of Organo-Soluble DNA (osDNA). ACS OMEGA 2024; 9:14771-14780. [PMID: 38585059 PMCID: PMC10993399 DOI: 10.1021/acsomega.3c06755] [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: 09/06/2023] [Revised: 11/13/2023] [Accepted: 11/16/2023] [Indexed: 04/09/2024]
Abstract
The present work describes a complete and reversible transformation of DNA's properties allowing solubilization in organic solvents and subsequent chemical modifications that are otherwise not possible in an aqueous medium. Organo-soluble DNA (osDNA) moieties are generated by covalently linking a dsDNA fragment to a polyether moiety with a built-in mechanism, rendering the process perfectly reversible and fully controllable. The precise removal of the polyether moiety frees up the initial DNA fragment, unaltered, both in sequence and nature. The solubility of osDNA was confirmed in six organic solvents of decreasing polarity and six types of osDNAs. As a proof of concept, in the context of DNA-encoded library (DEL) technology, an amidation reaction was successfully performed on osDNA in 100% DMSO. The development of osDNA opens up entirely new avenues for any DNA applications that could benefit from working in nonaqueous solutions, including chemical transformations.
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Affiliation(s)
- Vijay
Kumar Siripuram
- Laboratory of Molecular and
Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York City, New York 10065, United States
| | - Yashoda Krishna Sunkari
- Laboratory of Molecular and
Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York City, New York 10065, United States
| | - Fei Ma
- Laboratory of Molecular and
Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York City, New York 10065, United States
| | - Thu-Lan Nguyen
- Laboratory of Molecular and
Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York City, New York 10065, United States
| | - Marc Flajolet
- Laboratory of Molecular and
Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York City, New York 10065, United States
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13
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Gomes CP, Martins AGC, Nunes SE, Ramos B, Wisinewski HR, Reis JLMS, Lima AP, Aoyagi TY, Goncales I, Maia DS, Tunussi AS, Menossi MS, Pereira SM, Turrini PCG, Gervasio JHDB, Verona BM, Cerize NNP. Coding, Decoding and Retrieving a Message Using DNA: An Experience from a Brazilian Center Research on DNA Data Storage. MICROMACHINES 2024; 15:474. [PMID: 38675287 PMCID: PMC11051810 DOI: 10.3390/mi15040474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/21/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024]
Abstract
DNA data storage based on synthetic oligonucleotides is a major attraction due to the possibility of storage over long periods. Nowadays, the quantity of data generated has been growing exponentially, and the storage capacity needs to keep pace with the growth caused by new technologies and globalization. Since DNA can hold a large amount of information with a high density and remains stable for hundreds of years, this technology offers a solution for current long-term data centers by reducing energy consumption and physical storage space. Currently, research institutes, technology companies, and universities are making significant efforts to meet the growing need for data storage. DNA data storage is a promising field, especially with the advancement of sequencing techniques and equipment, which now make it possible to read genomes (i.e., to retrieve the information) and process this data easily. To overcome the challenges associated with developing new technologies for DNA data storage, a message encoding and decoding exercise was conducted at a Brazilian research center. The exercise performed consisted of synthesizing oligonucleotides by the phosphoramidite route. An encoded message, using a coding scheme that adheres to DNA sequence constraints, was synthesized. After synthesis, the oligonucleotide was sequenced and decoded, and the information was fully recovered.
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Affiliation(s)
- Caio P. Gomes
- Bionanomanufacturing Center, Institute for Technological Research—IPT, Sao Paulo 05508-901, SP, Brazil; (A.G.C.M.); (S.E.N.); (H.R.W.); (J.L.M.S.R.); (A.P.L.); (T.Y.A.); (I.G.); (D.S.M.); (A.S.T.); (M.S.M.); (S.M.P.J.); (P.C.G.T.); (B.M.V.); (N.N.P.C.)
| | - André G. C. Martins
- Bionanomanufacturing Center, Institute for Technological Research—IPT, Sao Paulo 05508-901, SP, Brazil; (A.G.C.M.); (S.E.N.); (H.R.W.); (J.L.M.S.R.); (A.P.L.); (T.Y.A.); (I.G.); (D.S.M.); (A.S.T.); (M.S.M.); (S.M.P.J.); (P.C.G.T.); (B.M.V.); (N.N.P.C.)
| | - Sabrina E. Nunes
- Bionanomanufacturing Center, Institute for Technological Research—IPT, Sao Paulo 05508-901, SP, Brazil; (A.G.C.M.); (S.E.N.); (H.R.W.); (J.L.M.S.R.); (A.P.L.); (T.Y.A.); (I.G.); (D.S.M.); (A.S.T.); (M.S.M.); (S.M.P.J.); (P.C.G.T.); (B.M.V.); (N.N.P.C.)
| | - Bruno Ramos
- Microfluidic & Photoelectrocatalytic Engineering Group, Department of Chemical Engineering, FEI University Center, São Bernardo do Campo 09850-901, SP, Brazil;
| | - Henrique R. Wisinewski
- Bionanomanufacturing Center, Institute for Technological Research—IPT, Sao Paulo 05508-901, SP, Brazil; (A.G.C.M.); (S.E.N.); (H.R.W.); (J.L.M.S.R.); (A.P.L.); (T.Y.A.); (I.G.); (D.S.M.); (A.S.T.); (M.S.M.); (S.M.P.J.); (P.C.G.T.); (B.M.V.); (N.N.P.C.)
| | - João L. M. S. Reis
- Bionanomanufacturing Center, Institute for Technological Research—IPT, Sao Paulo 05508-901, SP, Brazil; (A.G.C.M.); (S.E.N.); (H.R.W.); (J.L.M.S.R.); (A.P.L.); (T.Y.A.); (I.G.); (D.S.M.); (A.S.T.); (M.S.M.); (S.M.P.J.); (P.C.G.T.); (B.M.V.); (N.N.P.C.)
| | - Ariel P. Lima
- Bionanomanufacturing Center, Institute for Technological Research—IPT, Sao Paulo 05508-901, SP, Brazil; (A.G.C.M.); (S.E.N.); (H.R.W.); (J.L.M.S.R.); (A.P.L.); (T.Y.A.); (I.G.); (D.S.M.); (A.S.T.); (M.S.M.); (S.M.P.J.); (P.C.G.T.); (B.M.V.); (N.N.P.C.)
| | - Thiago Y. Aoyagi
- Bionanomanufacturing Center, Institute for Technological Research—IPT, Sao Paulo 05508-901, SP, Brazil; (A.G.C.M.); (S.E.N.); (H.R.W.); (J.L.M.S.R.); (A.P.L.); (T.Y.A.); (I.G.); (D.S.M.); (A.S.T.); (M.S.M.); (S.M.P.J.); (P.C.G.T.); (B.M.V.); (N.N.P.C.)
| | - Icaro Goncales
- Bionanomanufacturing Center, Institute for Technological Research—IPT, Sao Paulo 05508-901, SP, Brazil; (A.G.C.M.); (S.E.N.); (H.R.W.); (J.L.M.S.R.); (A.P.L.); (T.Y.A.); (I.G.); (D.S.M.); (A.S.T.); (M.S.M.); (S.M.P.J.); (P.C.G.T.); (B.M.V.); (N.N.P.C.)
| | - Danilo S. Maia
- Bionanomanufacturing Center, Institute for Technological Research—IPT, Sao Paulo 05508-901, SP, Brazil; (A.G.C.M.); (S.E.N.); (H.R.W.); (J.L.M.S.R.); (A.P.L.); (T.Y.A.); (I.G.); (D.S.M.); (A.S.T.); (M.S.M.); (S.M.P.J.); (P.C.G.T.); (B.M.V.); (N.N.P.C.)
| | - Ariane S. Tunussi
- Bionanomanufacturing Center, Institute for Technological Research—IPT, Sao Paulo 05508-901, SP, Brazil; (A.G.C.M.); (S.E.N.); (H.R.W.); (J.L.M.S.R.); (A.P.L.); (T.Y.A.); (I.G.); (D.S.M.); (A.S.T.); (M.S.M.); (S.M.P.J.); (P.C.G.T.); (B.M.V.); (N.N.P.C.)
| | - Marília S. Menossi
- Bionanomanufacturing Center, Institute for Technological Research—IPT, Sao Paulo 05508-901, SP, Brazil; (A.G.C.M.); (S.E.N.); (H.R.W.); (J.L.M.S.R.); (A.P.L.); (T.Y.A.); (I.G.); (D.S.M.); (A.S.T.); (M.S.M.); (S.M.P.J.); (P.C.G.T.); (B.M.V.); (N.N.P.C.)
| | - Sergio M. Pereira
- Bionanomanufacturing Center, Institute for Technological Research—IPT, Sao Paulo 05508-901, SP, Brazil; (A.G.C.M.); (S.E.N.); (H.R.W.); (J.L.M.S.R.); (A.P.L.); (T.Y.A.); (I.G.); (D.S.M.); (A.S.T.); (M.S.M.); (S.M.P.J.); (P.C.G.T.); (B.M.V.); (N.N.P.C.)
| | - Paula C. G. Turrini
- Bionanomanufacturing Center, Institute for Technological Research—IPT, Sao Paulo 05508-901, SP, Brazil; (A.G.C.M.); (S.E.N.); (H.R.W.); (J.L.M.S.R.); (A.P.L.); (T.Y.A.); (I.G.); (D.S.M.); (A.S.T.); (M.S.M.); (S.M.P.J.); (P.C.G.T.); (B.M.V.); (N.N.P.C.)
| | - João H. D. B. Gervasio
- Bionanomanufacturing Center, Institute for Technological Research—IPT, Sao Paulo 05508-901, SP, Brazil; (A.G.C.M.); (S.E.N.); (H.R.W.); (J.L.M.S.R.); (A.P.L.); (T.Y.A.); (I.G.); (D.S.M.); (A.S.T.); (M.S.M.); (S.M.P.J.); (P.C.G.T.); (B.M.V.); (N.N.P.C.)
| | - Bruno M. Verona
- Bionanomanufacturing Center, Institute for Technological Research—IPT, Sao Paulo 05508-901, SP, Brazil; (A.G.C.M.); (S.E.N.); (H.R.W.); (J.L.M.S.R.); (A.P.L.); (T.Y.A.); (I.G.); (D.S.M.); (A.S.T.); (M.S.M.); (S.M.P.J.); (P.C.G.T.); (B.M.V.); (N.N.P.C.)
| | - Natalia N. P. Cerize
- Bionanomanufacturing Center, Institute for Technological Research—IPT, Sao Paulo 05508-901, SP, Brazil; (A.G.C.M.); (S.E.N.); (H.R.W.); (J.L.M.S.R.); (A.P.L.); (T.Y.A.); (I.G.); (D.S.M.); (A.S.T.); (M.S.M.); (S.M.P.J.); (P.C.G.T.); (B.M.V.); (N.N.P.C.)
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14
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Zhang J, Hou C, Liu C. CRISPR-powered quantitative keyword search engine in DNA data storage. Nat Commun 2024; 15:2376. [PMID: 38491032 PMCID: PMC10943086 DOI: 10.1038/s41467-024-46767-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 03/08/2024] [Indexed: 03/18/2024] Open
Abstract
Despite the growing interest of archiving information in synthetic DNA to confront data explosion, quantitatively querying the data stored in DNA is still a challenge. Herein, we present Search Enabled by Enzymatic Keyword Recognition (SEEKER), which utilizes CRISPR-Cas12a to rapidly generate visible fluorescence when a DNA target corresponding to the keyword of interest is present. SEEKER achieves quantitative text searching since the growth rate of fluorescence intensity is proportional to keyword frequency. Compatible with SEEKER, we develop non-collision grouping coding, which reduces the size of dictionary and enables lossless compression without disrupting the original order of texts. Using four queries, we correctly identify keywords in 40 files with a background of ~8000 irrelevant terms. Parallel searching with SEEKER can be performed on a 3D-printed microfluidic chip. Overall, SEEKER provides a quantitative approach to conducting parallel searching over the complete content stored in DNA with simple implementation and rapid result generation.
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Affiliation(s)
- Jiongyu Zhang
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, CT, 06030, USA
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, 06269, USA
| | - Chengyu Hou
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, CT, 06030, USA
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, 06269, USA
| | - Changchun Liu
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, CT, 06030, USA.
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15
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Cui L, Zhang L, Li Z, Jing Z, Huang L, Zeng H. Giant enhancement of fluorescence resonance energy transfer based on nanoporous gold with small amount of residual silver. NANOTECHNOLOGY 2024; 35:195709. [PMID: 38241734 DOI: 10.1088/1361-6528/ad20a0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/19/2024] [Indexed: 01/21/2024]
Abstract
Fluorescence resonance energy transfer (FRET) was found strongly enhanced by plasmon resonance. In this work, Nanoporous Gold with small amount of residual silver was used to form nanoporous gold/organic molecular layer compound with PSS and PAH. The ratio of its specific gold and silver content is achieved by controlling the time of its dealloying. Layered films of polyelectrolyte multilayers were assembled between the donor-acceptor pairs and NPG films to control distance. The maximum of FRET enhancement of 80-fold on the fluorescence intensity between the donor-acceptor pairs (CFP-YFP) is observed at a distance of ∼10.5 nm from the NPG film. This Nanoporous Gold with small amount of residual silver not only enhanced FRET 4-fold more than nanoporous gold of only gold content almost, but also effectively realized the regulation of FRET enhancement. The ability to precisely measure and regulate the enhancement of FRET enables the rational selection of plasmonic nanotransducer dimensions for the particular biosensing application.
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Affiliation(s)
- Lianmin Cui
- School of Optical-Electrical and Computer Engineering, University of Shanghai for Science and Technology, Shanghai 200093, People's Republic of China
| | - Ling Zhang
- School of Optical-Electrical and Computer Engineering, University of Shanghai for Science and Technology, Shanghai 200093, People's Republic of China
| | - Zhexiao Li
- School of Optical-Electrical and Computer Engineering, University of Shanghai for Science and Technology, Shanghai 200093, People's Republic of China
| | - Zhiyu Jing
- School of Optical-Electrical and Computer Engineering, University of Shanghai for Science and Technology, Shanghai 200093, People's Republic of China
| | - Luyi Huang
- CAS Key Laboratory of Nanophotonic Materials and Devices & Key Laboratory of Nanodevices and Applications, i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics (SINANO), Chinese Academy of Sciences, Suzhou 215123, People's Republic of China
| | - Heping Zeng
- Key Laboratory for Ultrafine Materials of Ministry of Education, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China
- Chongqing Key Laboratory of Precision Optics, Chongqing Institute of East China Normal University, Chongqing, People's Republic of China
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16
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Quazi MZ, Choi JH, Kim M, Park N. DNA and Nanomaterials: A Functional Combination for DNA Sensing. ACS APPLIED BIO MATERIALS 2024; 7:778-786. [PMID: 38270150 DOI: 10.1021/acsabm.3c01190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
Recent decades have experienced tough situations due to the lack of reliable diagnostic facilities. The most recent cases occurred during the pandemic, where researchers observed the lack of diagnostic facilities with precision. Microorganisms and viral disease's ability to escape diagnosis has been a global challenge. DNA always has been a unique moiety with a strong and precise base-paired structure. DNA in human and foreign particles makes identification possible through base pairing. Since then, researchers have focused heavily on designing diagnostic assays targeting DNA in particular. Moreover, DNA nanotechnology has contributed vastly to designing composite nanomaterials by combining DNA/nucleic acids with functional nanomaterials and inorganic nanoparticles exploiting their physicochemical properties. These nanomaterials often exhibit unique or enhanced properties due to the synergistic activity of the many components. The capabilities of DNA and additional nanomaterials have shown the combination of robust and advanced tailoring of biosensors. Preceding findings state that the conventional strategies have exhibited certain limitations such as a low range of target detection, less biodegradability, subordinate half-life, and high susceptibility to microenvironments; however, a DNA-nanomaterial-based biosensor has overcome these limitations meaningfully. Additionally, the unique properties of nucleic acids have been studied extensively due to their high signal conduction abilities. Here, we review recent studies on DNA-nanomaterial-based biosensors, their mechanism of action, and improved/updated strategies in vivo and in situ. Furthermore, this review highlights the recent methodologies on DNA utilization to exploit the interfacial properties of nanomaterials in DNA sensing. Lastly, the review concludes with the limitations/challenges and future directions.
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Affiliation(s)
- Mohzibudin Z Quazi
- Department of Chemistry and The Natural Science Research Institute, Myongji University, Myongji-ro, Yongin, Gyeonggi-do 17058, Republic of Korea
| | - Jang Hyeon Choi
- Department of Chemistry and The Natural Science Research Institute, Myongji University, Myongji-ro, Yongin, Gyeonggi-do 17058, Republic of Korea
| | - Minchul Kim
- Department of Chemistry and The Natural Science Research Institute, Myongji University, Myongji-ro, Yongin, Gyeonggi-do 17058, Republic of Korea
| | - Nokyoung Park
- Department of Chemistry and The Natural Science Research Institute, Myongji University, Myongji-ro, Yongin, Gyeonggi-do 17058, Republic of Korea
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17
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Wang S, Mao X, Wang F, Zuo X, Fan C. Data Storage Using DNA. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2307499. [PMID: 37800877 DOI: 10.1002/adma.202307499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/01/2023] [Indexed: 10/07/2023]
Abstract
The exponential growth of global data has outpaced the storage capacities of current technologies, necessitating innovative storage strategies. DNA, as a natural medium for preserving genetic information, has emerged as a highly promising candidate for next-generation storage medium. Storing data in DNA offers several advantages, including ultrahigh physical density and exceptional durability. Facilitated by significant advancements in various technologies, such as DNA synthesis, DNA sequencing, and DNA nanotechnology, remarkable progress has been made in the field of DNA data storage over the past decade. However, several challenges still need to be addressed to realize practical applications of DNA data storage. In this review, the processes and strategies of in vitro DNA data storage are first introduced, highlighting recent advancements. Next, a brief overview of in vivo DNA data storage is provided, with a focus on the various writing strategies developed to date. At last, the challenges encountered in each step of DNA data storage are summarized and promising techniques are discussed that hold great promise in overcoming these obstacles.
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Affiliation(s)
- Shaopeng Wang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Xiuhai Mao
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Fei Wang
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chunhai Fan
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
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18
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Zhou Y, Kathiresan N, Yu Z, Rivera LF, Yang Y, Thimma M, Manickam K, Chebotarov D, Mauleon R, Chougule K, Wei S, Gao T, Green CD, Zuccolo A, Xie W, Ware D, Zhang J, McNally KL, Wing RA. A high-performance computational workflow to accelerate GATK SNP detection across a 25-genome dataset. BMC Biol 2024; 22:13. [PMID: 38273258 PMCID: PMC10809545 DOI: 10.1186/s12915-024-01820-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 01/09/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND Single-nucleotide polymorphisms (SNPs) are the most widely used form of molecular genetic variation studies. As reference genomes and resequencing data sets expand exponentially, tools must be in place to call SNPs at a similar pace. The genome analysis toolkit (GATK) is one of the most widely used SNP calling software tools publicly available, but unfortunately, high-performance computing versions of this tool have yet to become widely available and affordable. RESULTS Here we report an open-source high-performance computing genome variant calling workflow (HPC-GVCW) for GATK that can run on multiple computing platforms from supercomputers to desktop machines. We benchmarked HPC-GVCW on multiple crop species for performance and accuracy with comparable results with previously published reports (using GATK alone). Finally, we used HPC-GVCW in production mode to call SNPs on a "subpopulation aware" 16-genome rice reference panel with ~ 3000 resequenced rice accessions. The entire process took ~ 16 weeks and resulted in the identification of an average of 27.3 M SNPs/genome and the discovery of ~ 2.3 million novel SNPs that were not present in the flagship reference genome for rice (i.e., IRGSP RefSeq). CONCLUSIONS This study developed an open-source pipeline (HPC-GVCW) to run GATK on HPC platforms, which significantly improved the speed at which SNPs can be called. The workflow is widely applicable as demonstrated successfully for four major crop species with genomes ranging in size from 400 Mb to 2.4 Gb. Using HPC-GVCW in production mode to call SNPs on a 25 multi-crop-reference genome data set produced over 1.1 billion SNPs that were publicly released for functional and breeding studies. For rice, many novel SNPs were identified and were found to reside within genes and open chromatin regions that are predicted to have functional consequences. Combined, our results demonstrate the usefulness of combining a high-performance SNP calling architecture solution with a subpopulation-aware reference genome panel for rapid SNP discovery and public deployment.
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Affiliation(s)
- Yong Zhou
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Arizona Genomics Institute (AGI), School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Nagarajan Kathiresan
- KAUST Supercomputing Laboratory (KSL), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Zhichao Yu
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Luis F Rivera
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Yujian Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Manjula Thimma
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Keerthana Manickam
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Dmytro Chebotarov
- International Rice Research Institute (IRRI), Los Baños, Laguna, 4031, Philippines
| | - Ramil Mauleon
- International Rice Research Institute (IRRI), Los Baños, Laguna, 4031, Philippines
| | - Kapeel Chougule
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Sharon Wei
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Tingting Gao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Carl D Green
- Information Technology Department, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Andrea Zuccolo
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Crop Science Research Center (CSRC), Scuola Superiore Sant'Anna, Pisa, 56127, Italy
| | - Weibo Xie
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
- USDA ARS NEA Plant, Soil & Nutrition Laboratory Research Unit, Ithaca, NY, 14853, USA
| | - Jianwei Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Kenneth L McNally
- International Rice Research Institute (IRRI), Los Baños, Laguna, 4031, Philippines
| | - Rod A Wing
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
- Arizona Genomics Institute (AGI), School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA.
- International Rice Research Institute (IRRI), Los Baños, Laguna, 4031, Philippines.
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19
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Stuber A, Schlotter T, Hengsteler J, Nakatsuka N. Solid-State Nanopores for Biomolecular Analysis and Detection. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2024; 187:283-316. [PMID: 38273209 DOI: 10.1007/10_2023_240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
Advances in nanopore technology and data processing have rendered DNA sequencing highly accessible, unlocking a new realm of biotechnological opportunities. Commercially available nanopores for DNA sequencing are of biological origin and have certain disadvantages such as having specific environmental requirements to retain functionality. Solid-state nanopores have received increased attention as modular systems with controllable characteristics that enable deployment in non-physiological milieu. Thus, we focus our review on summarizing recent innovations in the field of solid-state nanopores to envision the future of this technology for biomolecular analysis and detection. We begin by introducing the physical aspects of nanopore measurements ranging from interfacial interactions at pore and electrode surfaces to mass transport of analytes and data analysis of recorded signals. Then, developments in nanopore fabrication and post-processing techniques with the pros and cons of different methodologies are examined. Subsequently, progress to facilitate DNA sequencing using solid-state nanopores is described to assess how this platform is evolving to tackle the more complex challenge of protein sequencing. Beyond sequencing, we highlight the recent developments in biosensing of nucleic acids, proteins, and sugars and conclude with an outlook on the frontiers of nanopore technologies.
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Affiliation(s)
- Annina Stuber
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich, Switzerland
| | - Tilman Schlotter
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich, Switzerland
| | - Julian Hengsteler
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich, Switzerland
| | - Nako Nakatsuka
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich, Switzerland.
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20
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Zheng F, Alawami M, Zhu J, Platnich CM, Sha J, Keyser UF, Chen K. DNA Carrier-Assisted Molecular Ping-Pong in an Asymmetric Nanopore. NANO LETTERS 2023; 23:11145-11151. [PMID: 38033205 PMCID: PMC10722531 DOI: 10.1021/acs.nanolett.3c03605] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/28/2023] [Accepted: 11/28/2023] [Indexed: 12/02/2023]
Abstract
Nanopore analysis relies on ensemble averaging of translocation signals obtained from numerous molecules, requiring a relatively high sample concentration and a long turnaround time from the sample to results. The recapture and subsequent re-reading of the same molecule is a promising alternative that enriches the signal information from a single molecule. Here, we describe how an asymmetric nanopore improves molecular ping-pong by promoting the recapture of the molecule in the trans reservoir. We also demonstrate that the molecular recapture could be improved by linking the target molecule to a long DNA carrier to reduce the diffusion, thereby achieving over 100 recapture events. Using this ping-pong methodology, we demonstrate its use in accurately resolving nanostructure motifs along a DNA scaffold through repeated detection. Our method offers novel insights into the control of DNA polymer dynamics within nanopore confinement and opens avenues for the development of a high-fidelity DNA detection platform.
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Affiliation(s)
- Fei Zheng
- Cavendish Laboratory, University of Cambridge, CB3 0HE Cambridge, United Kingdom
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China
| | - Mohammed Alawami
- Cavendish Laboratory, University of Cambridge, CB3 0HE Cambridge, United Kingdom
| | - Jinbo Zhu
- Cavendish Laboratory, University of Cambridge, CB3 0HE Cambridge, United Kingdom
- School of Biomedical Engineering, Faculty of Medicine, Dalian University of Technology, Dalian 116024, China
| | - Casey M Platnich
- Cavendish Laboratory, University of Cambridge, CB3 0HE Cambridge, United Kingdom
| | - Jingjie Sha
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China
| | - Ulrich F Keyser
- Cavendish Laboratory, University of Cambridge, CB3 0HE Cambridge, United Kingdom
| | - Kaikai Chen
- Cavendish Laboratory, University of Cambridge, CB3 0HE Cambridge, United Kingdom
- School of Nanoscience and Nanotechnology, University of Chinese Academy of Sciences, Beijing 101408, China
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21
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Liu DD, Cheow LF. Rapid Information Retrieval from DNA Storage with Microfluidic Very Large-Scale Integration Platform. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023:e2309867. [PMID: 38048539 DOI: 10.1002/smll.202309867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 11/09/2023] [Indexed: 12/06/2023]
Abstract
Due to its high information density, DNA is very attractive as a data storage system. However, a major obstacle is the high cost and long turnaround time for retrieving DNA data with next-generation sequencing. Herein, the use of a microfluidic very large-scale integration (mVLSI) platform is described to perform highly parallel and rapid readout of data stored in DNA. Additionally, it is demonstrated that multi-state data encoded in DNA can be deciphered with on-chip melt-curve analysis, thereby further increasing the data content that can be analyzed. The pairing of mVLSI network architecture with exquisitely specific DNA recognition gives rise to a scalable platform for rapid DNA data reading.
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Affiliation(s)
- Dong Dong Liu
- Department of Biomedical Engineering and Institute for Health Innovation and Technology, National University of Singapore, Singapore, 119077, Singapore
| | - Lih Feng Cheow
- Department of Biomedical Engineering and Institute for Health Innovation and Technology, National University of Singapore, Singapore, 119077, Singapore
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22
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Yu M, Lim D, Kim J, Song Y. Processing DNA Storage through Programmable Assembly in a Droplet-Based Fluidics System. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303197. [PMID: 37755129 PMCID: PMC10646262 DOI: 10.1002/advs.202303197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/11/2023] [Indexed: 09/28/2023]
Abstract
DNA can be used to store digital data, and synthetic short-sequence DNA pools are developed to store high quantities of digital data. However, synthetic DNA data cannot be actively processed in DNA pools. An active DNA data editing process is developed using splint ligation in a droplet-controlled fluidics (DCF) system. DNA fragments of discrete sizes (100-500 bps) are synthesized for droplet assembly, and programmed sequence information exchange occurred. The encoded DNA sequences are processed in series and parallel to synthesize the determined DNA pools, enabling random access using polymerase chain reaction amplification. The sequencing results of the assembled DNA data pools can be orderly aligned for decoding and have high fidelity through address primer scanning. Furthermore, eight 90 bps DNA pools with pixel information (png: 0.27-0.28 kB), encoded by codons, are synthesized to create eight 270 bps DNA pools with an animation movie chip file (mp4: 12 kB) in the DCF system.
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Affiliation(s)
- Minsang Yu
- Standard Bioelectronics. Co., 511 Michuhol Tower, Gaetbeol-ro 12, Incheon, 21999, South Korea
| | - Doyeon Lim
- Department of Nano-Bioengineering, Incheon National University, Academy-ro 119, Incheon, 22012, South Korea
| | - Jungwoo Kim
- Department of Nano-Bioengineering, Incheon National University, Academy-ro 119, Incheon, 22012, South Korea
| | - Youngjun Song
- Standard Bioelectronics. Co., 511 Michuhol Tower, Gaetbeol-ro 12, Incheon, 21999, South Korea
- Department of Nano-Bioengineering, Incheon National University, Academy-ro 119, Incheon, 22012, South Korea
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23
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Schmid S. An external speed control for nanopore reads. NATURE NANOTECHNOLOGY 2023; 18:1261-1262. [PMID: 37550576 DOI: 10.1038/s41565-023-01477-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Affiliation(s)
- Sonja Schmid
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands.
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24
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Rasool A, Hong J, Jiang Q, Chen H, Qu Q. BO-DNA: Biologically optimized encoding model for a highly-reliable DNA data storage. Comput Biol Med 2023; 165:107404. [PMID: 37666064 DOI: 10.1016/j.compbiomed.2023.107404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 08/13/2023] [Accepted: 08/26/2023] [Indexed: 09/06/2023]
Abstract
DNA data storage is a promising technology that utilizes computer simulation, and synthetic biology, offering high-density and reliable digital information storage. It is challenging to store massive data in a small amount of DNA without losing the original data since nonspecific hybridization errors occur frequently and severely affect the reliability of stored data. This study proposes a novel biologically optimized encoding model for DNA data storage (BO-DNA) to overcome the reliability problem. BO-DNA model is developed by a new rule-based mapping method to avoid data drop during the transcoding of binary data to premier nucleotides. A customized optimization algorithm based on a tent chaotic map is applied to maximize the lower bounds that help to minimize the nonspecific hybridization errors. The robustness of BO-DNA is computed by four bio-constraints to confirm the reliability of newly generated DNA sequences. Experimentally, different medical images are encoded and decoded successfully with 12%-59% improved lower bounds and optimally constrained-based DNA sequences reported with 1.77bit/nt average density. BO-DNA's results demonstrate substantial advantages in constructing reliable DNA data storage.
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Affiliation(s)
- Abdur Rasool
- Shenzhen Key Laboratory for High Performance Data Mining, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; Shenzhen College of Advanced Technology, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Jingwei Hong
- Shenzhen Key Laboratory for High Performance Data Mining, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; College of Mathematics and Information Science, Hebei University, Baoding, 071002, China
| | - Qingshan Jiang
- Shenzhen Key Laboratory for High Performance Data Mining, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Hui Chen
- Shenzhen Polytechnic University, Shenzhen, 518055, Guangdong, China
| | - Qiang Qu
- Shenzhen Key Laboratory for High Performance Data Mining, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
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25
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Gimpel AL, Stark WJ, Heckel R, Grass RN. A digital twin for DNA data storage based on comprehensive quantification of errors and biases. Nat Commun 2023; 14:6026. [PMID: 37758710 PMCID: PMC10533828 DOI: 10.1038/s41467-023-41729-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
Archiving data in synthetic DNA offers unprecedented storage density and longevity. Handling and storage introduce errors and biases into DNA-based storage systems, necessitating the use of Error Correction Coding (ECC) which comes at the cost of added redundancy. However, insufficient data on these errors and biases, as well as a lack of modeling tools, limit data-driven ECC development and experimental design. In this study, we present a comprehensive characterisation of the error sources and biases present in the most common DNA data storage workflows, including commercial DNA synthesis, PCR, decay by accelerated aging, and sequencing-by-synthesis. Using the data from 40 sequencing experiments, we build a digital twin of the DNA data storage process, capable of simulating state-of-the-art workflows and reproducing their experimental results. We showcase the digital twin's ability to replace experiments and rationalize the design of redundancy in two case studies, highlighting opportunities for tangible cost savings and data-driven ECC development.
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Affiliation(s)
- Andreas L Gimpel
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5, 8093, Zürich, Switzerland
| | - Wendelin J Stark
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5, 8093, Zürich, Switzerland
| | - Reinhard Heckel
- Department of Computer Engineering, Technical University of Munich, Arcistrasse 21, 80333, Munich, Germany
| | - Robert N Grass
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5, 8093, Zürich, Switzerland.
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26
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Gao R, Wei XS, Chen Z, Xie A, Dong W. Leveraging DNA-Based Nanostructures for Advanced Error Detection and Correction in Data Communication. ACS NANO 2023; 17:18055-18061. [PMID: 37498772 DOI: 10.1021/acsnano.3c04777] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
This study demonstrates the implementation of the Hamming code using DNA-based nanostructures for error detection and correction in communication systems. The designed DNA nanostructures conduct logical operations to compute check codes and identify and correct erroneous data based on fluorescence signals. The execution of intricate DNA logic operations requires individuals with specialized training. By interpretation of the fluorescence signals generated by the DNA nanostructures, binary language can be extracted, effectively protecting data security. The findings highlight the potential of DNA as a versatile platform for reliable data transmission.
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Affiliation(s)
- Ruru Gao
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Xiu-Shen Wei
- School of Computer Science and Engineering, Southeast University, Nanjing, 210096, China
- Key Laboratory of New Generation Artificial Intelligence Technology and Its Interdisciplinary Applications (Southeast University), Ministry of Education, Nanjing, 210096, China
| | - Zelin Chen
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Aming Xie
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Wei Dong
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
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27
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Zhao Y, Cao B, Wang P, Wang K, Wang B. DBTRG: De Bruijn Trim rotation graph encoding for reliable DNA storage. Comput Struct Biotechnol J 2023; 21:4469-4477. [PMID: 37736298 PMCID: PMC10510065 DOI: 10.1016/j.csbj.2023.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/23/2023] Open
Abstract
DNA is a high-density, long-term stable, and scalable storage medium that can meet the increased demands on storage media resulting from the exponential growth of data. The existing DNA storage encoding schemes tend to achieve high-density storage but do not fully consider the local and global stability of DNA sequences and the read and write accuracy of the stored information. To address these problems, this article presents a graph-based De Bruijn Trim Rotation Graph (DBTRG) encoding scheme. Through XOR between the proposed dynamic binary sequence and the original binary sequence, k-mers can be divided into the De Bruijn Trim graph, and the stored information can be compressed according to the overlapping relationship. The simulated experimental results show that DBTRG ensures base balance and diversity, reduces the likelihood of undesired motifs, and improves the stability of DNA storage and data recovery. Furthermore, the maintenance of an encoding rate of 1.92 while storing 510 KB images and the introduction of novel approaches and concepts for DNA storage encoding methods are achieved.
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Affiliation(s)
- Yunzhu Zhao
- The Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Dalian, Liaoning 116622, China
| | - Ben Cao
- School of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Penghao Wang
- The Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Dalian, Liaoning 116622, China
| | - Kun Wang
- The Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Dalian, Liaoning 116622, China
| | - Bin Wang
- The Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Dalian, Liaoning 116622, China
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28
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He L, Charron M, Mensing P, Briggs K, Adams J, de Haan H, Tabard-Cossa V. DNA origami characterized via a solid-state nanopore: insights into nanostructure dimensions, rigidity and yield. NANOSCALE 2023; 15:14043-14054. [PMID: 37580994 DOI: 10.1039/d3nr01873c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
Due to their programmability via specific base pairing, self-assembled DNA origami structures have proven to be useful for a wide variety of applications, including diagnostics, molecular computation, drug delivery, and therapeutics. Measuring and characterizing these structures is therefore of great interest and an important part of quality control. Here, we show the extent to which DNA nanostructures can be characterized by a solid-state nanopore; a non-destructive, label-free, single-molecule sensor capable of electrically detecting and characterizing charged biomolecules. We demonstrate that in addition to geometrical dimensions, nanopore sensing can provide information on the mechanical properties, assembly yield, and stability of DNA nanostructures. For this work, we use a model structure consisting of a 3 helix-bundle (3HB), i.e. three interconnected DNA double helices using a M13 scaffold folded twice on itself by short DNA staple strands, and translocate it through solid-state nanopores fabricated by controlled breakdown. We present detailed analysis of the passage characteristics of 3HB structures through nanopores under different experimental conditions which suggest that segments of locally higher flexibility are present along the nanostructure contour that allow for the otherwise rigid 3HB to fold inside nanopores. By characterizing partially melted 3HB structures, we find that locally flexible segments are likely due to short staple oligomers missing from the fully assembled structure. The 3HB used herein is a prototypical example to establish nanopores as a sensitive, non-destructive, and label-free alternative to conventional techniques such as gel electrophoresis with which to characterize DNA nanostructures.
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Affiliation(s)
- Liqun He
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada.
| | - Martin Charron
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada.
| | - Philipp Mensing
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada.
| | - Kyle Briggs
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada.
| | - Jonathan Adams
- Faculty of Science, Ontario Tech University, Oshawa, Ontario, Canada
| | - Hendrick de Haan
- Faculty of Science, Ontario Tech University, Oshawa, Ontario, Canada
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29
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Zhang C, Liu H, Li X, Xu F, Li Z. Modularized synthetic biology enabled intelligent biosensors. Trends Biotechnol 2023; 41:1055-1065. [PMID: 36967259 DOI: 10.1016/j.tibtech.2023.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/27/2023] [Accepted: 03/06/2023] [Indexed: 03/29/2023]
Abstract
Biosensors that sense the concentration of a specified target and produce a specific signal output have become important technology for biological analysis. Recently, intelligent biosensors have received great interest due to their adaptability to meet sophisticated demands. Advances in developing standard modules and carriers in synthetic biology have shed light on intelligent biosensors that can implement advanced analytical processing to better accommodate practical applications. This review focuses on intelligent synthetic biology-enabled biosensors (SBBs). First, we illustrate recent progress in intelligent SBBs with the capability of computation, memory storage, and self-calibration. Then, we discuss emerging applications of SBBs in point-of-care testing (POCT) and wearable monitoring. Finally, future perspectives on intelligent SBBs are proposed.
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Affiliation(s)
- Chao Zhang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P.R. China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, P.R. China
| | - Hao Liu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P.R. China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, P.R. China
| | - Xiujun Li
- Department of Chemistry and Biochemistry, University of Texas at El Paso, 500 West University Ave, El Paso, TX 79968, USA
| | - Feng Xu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P.R. China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, P.R. China.
| | - Zedong Li
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P.R. China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, P.R. China; TFX Group-Xi'an Jiaotong University Institute of Life Health, Xi'an 710049, P.R. China.
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30
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Sheng Y, Zhang Y, Xing F, Liu C, Di Y, Yang X, Wei S, Zhang X, Liu Y, Gan Z. Co-multiplexing spectral and temporal dimensions based on luminescent materials. OPTICS EXPRESS 2023; 31:24667-24677. [PMID: 37475287 DOI: 10.1364/oe.495972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 06/30/2023] [Indexed: 07/22/2023]
Abstract
Optical multiplexing is a pivotal technique for augmenting the capacity of optical data storage (ODS) and increasing the security of anti-counterfeiting. However, due to the dearth of appropriate storage media, optical multiplexing is generally restricted to a single dimension, thus curtailing the encoding capacity. Herein, the co-multiplexing spectral and temporal dimensions are proposed for optical encoding based on photoluminescence (PL) and persistent-luminescence (PersL) at four different wavelengths. Each emission color comprises four luminescence modes. The further multiplexing of four wavelengths leads to the maximum encoding capacity of 8 bits at each pixel. The wavelength difference between adjacent peaks is larger than 50 nm. The well-separated emission wavelengths significantly lower the requirements for high-resolution spectrometers. Moreover, the information is unable to be decoded until both PL and PersL spectra are collected, suggesting a substantial improvement in information security and the security level of anti-counterfeiting.
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31
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Polak RE, Keung AJ. A molecular assessment of the practical potential of DNA-based computation. Curr Opin Biotechnol 2023; 81:102940. [PMID: 37058876 PMCID: PMC10229437 DOI: 10.1016/j.copbio.2023.102940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/16/2023] [Accepted: 03/17/2023] [Indexed: 04/16/2023]
Abstract
The immense information density of DNA and its potential for massively parallelized computations, paired with rapidly expanding data production and storage needs, have fueled a renewed interest in DNA-based computation. Since the construction of the first DNA computing systems in the 1990s, the field has grown to encompass a diverse array of configurations. Simple enzymatic and hybridization reactions to solve small combinatorial problems transitioned to synthetic circuits mimicking gene regulatory networks and DNA-only logic circuits based on strand displacement cascades. These have formed the foundations of neural networks and diagnostic tools that aim to bring molecular computation to practical scales and applications. Considering these great leaps in system complexity as well as in the tools and technologies enabling them, a reassessment of the potential of such DNA computing systems is warranted.
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Affiliation(s)
- Rachel E Polak
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27606, USA; Genetics and Genomics Academy, North Carolina State University, Raleigh, NC 27606, USA
| | - Albert J Keung
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27606, USA.
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32
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Buko T, Tuczko N, Ishikawa T. DNA Data Storage. BIOTECH 2023; 12:44. [PMID: 37366792 DOI: 10.3390/biotech12020044] [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: 04/20/2023] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 06/28/2023] Open
Abstract
The demand for data storage is growing at an unprecedented rate, and current methods are not sufficient to accommodate such rapid growth due to their cost, space requirements, and energy consumption. Therefore, there is a need for a new, long-lasting data storage medium with high capacity, high data density, and high durability against extreme conditions. DNA is one of the most promising next-generation data carriers, with a storage density of 10¹⁹ bits of data per cubic centimeter, and its three-dimensional structure makes it about eight orders of magnitude denser than other storage media. DNA amplification during PCR or replication during cell proliferation enables the quick and inexpensive copying of vast amounts of data. In addition, DNA can possibly endure millions of years if stored in optimal conditions and dehydrated, making it useful for data storage. Numerous space experiments on microorganisms have also proven their extraordinary durability in extreme conditions, which suggests that DNA could be a durable storage medium for data. Despite some remaining challenges, such as the need to refine methods for the fast and error-free synthesis of oligonucleotides, DNA is a promising candidate for future data storage.
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Affiliation(s)
- Tomasz Buko
- Department of Molecular Biology, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Miecznikowa 1, PL-02-096 Warsaw, Poland
| | - Nella Tuczko
- Department of Molecular Biology, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Miecznikowa 1, PL-02-096 Warsaw, Poland
| | - Takao Ishikawa
- Department of Molecular Biology, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Miecznikowa 1, PL-02-096 Warsaw, Poland
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33
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Zhuravlev AV. Three levels of information processing in the brain. Biosystems 2023:104934. [PMID: 37245794 DOI: 10.1016/j.biosystems.2023.104934] [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: 03/01/2023] [Revised: 05/25/2023] [Accepted: 05/25/2023] [Indexed: 05/30/2023]
Abstract
Information, the measure of order in a complex system, is the opposite of entropy, the measure of chaos and disorder. We can distinguish several levels at which information is processed in the brain. The first one is the level of serial molecular genetic processes, similar in some aspects to digital computations (DC). At the same time, higher cognitive activity is probably based on parallel neural network computations (NNC). The advantage of neural networks is their intrinsic ability to learn, adapting their parameters to specific tasks and to external data. However, there seems to be a third level of information processing as well, which involves subjective consciousness and its units, so called qualia. They are difficult to study experimentally, and the very fact of their existence is hard to explain within the framework of modern physical theory. Here I propose a way to consider consciousness as the extension of basic physical laws - namely, total entropy dissipation leading to a system simplification. At the level of subjective consciousness, the brain seems to convert information embodied by neural activity to a more simple and compact form, internally observed as qualia. Whereas physical implementations of both DC and NNC are essentially approximate and probabilistic, qualia-associated computations (QAC) make the brain capable of recognizing general laws and relationships. While elaborating a behavioral program, the conscious brain does not act blindly or gropingly but according to the very meaning of such general laws, which gives it an advantage compared to any artificial intelligence system.
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Affiliation(s)
- Aleksandr V Zhuravlev
- I. P. Pavlov Institute of Physiology, nab Makarova 6, 199034, St Petersburg, Russian Federation.
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34
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Zheng LL, Li JZ, Wen M, Xi D, Zhu Y, Wei Q, Zhang XB, Ke G, Xia F, Gao ZF. Enthalpy and entropy synergistic regulation-based programmable DNA motifs for biosensing and information encryption. SCIENCE ADVANCES 2023; 9:eadf5868. [PMID: 37196083 DOI: 10.1126/sciadv.adf5868] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 04/13/2023] [Indexed: 05/19/2023]
Abstract
Deoxyribonucleic acid (DNA) provides a collection of intelligent tools for the development of information cryptography and biosensors. However, most conventional DNA regulation strategies rely solely on enthalpy regulation, which suffers from unpredictable stimuli-responsive performance and unsatisfactory accuracy due to relatively large energy fluctuations. Here, we report an enthalpy and entropy synergistic regulation-based pH-responsive A+/C DNA motif for programmable biosensing and information encryption. In the DNA motif, the variation in loop length alters entropic contribution, and the number of A+/C bases regulates enthalpy, which is verified through thermodynamic characterizations and analyses. On the basis of this straightforward strategy, the performances, such as pKa, of the DNA motif can be precisely and predictably tuned. The DNA motifs are finally successfully applied for glucose biosensing and crypto-steganography systems, highlighting their potential in the field of biosensing and information encryption.
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Affiliation(s)
- Lin Lin Zheng
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Jin Ze Li
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
| | - Mei Wen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Dongmei Xi
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
| | - Yanxi Zhu
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
- Central Laboratory of Linyi People's Hospital, Linyi 276003, P. R. China
| | - Qin Wei
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Xiao-Bing Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Guoliang Ke
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Fan Xia
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, 388 Lumo Road, Wuhan 430074, P. R. China
| | - Zhong Feng Gao
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
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Sun F, Dong Y, Ni M, Ping Z, Sun Y, Ouyang Q, Qian L. Mobile and Self-Sustained Data Storage in an Extremophile Genomic DNA. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2206201. [PMID: 36737843 PMCID: PMC10074078 DOI: 10.1002/advs.202206201] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/11/2023] [Indexed: 06/18/2023]
Abstract
DNA has been pursued as a novel biomaterial for digital data storage. While large-scale data storage and random access have been achieved in DNA oligonucleotide pools, repeated data accessing requires constant data replenishment, and these implementations are confined in professional facilities. Here, a mobile data storage system in the genome of the extremophile Halomonas bluephagenesis, which enables dual-mode storage, dynamic data maintenance, rapid readout, and robust recovery. The system relies on two key components: A versatile genetic toolbox for the integration of 10-100 kb scale synthetic DNA into H. bluephagenesis genome and an efficient error correction coding scheme targeting noisy nanopore sequencing reads. The storage and repeated retrieval of 5 KB data under non-laboratory conditions are demonstrated. The work highlights the potential of DNA data storage in domestic and field scenarios, and expands its application domain from archival data to frequently accessed data.
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Affiliation(s)
- Fajia Sun
- Center for Quantitative BiologyPeking University5 Yiheyuan Road Haidian DistrictBeijing100871P. R. China
| | - Yiming Dong
- Center for Quantitative BiologyPeking University5 Yiheyuan Road Haidian DistrictBeijing100871P. R. China
| | - Ming Ni
- Academician Workstation of BGI Synthetic GenomicsBGI‐ShenzhenHuada Comprehensive ParkYantian DistrictShenzhen518083P. R. China
| | - Zhi Ping
- Academician Workstation of BGI Synthetic GenomicsBGI‐ShenzhenHuada Comprehensive ParkYantian DistrictShenzhen518083P. R. China
| | - Yuhui Sun
- Academician Workstation of BGI Synthetic GenomicsBGI‐ShenzhenHuada Comprehensive ParkYantian DistrictShenzhen518083P. R. China
| | - Qi Ouyang
- Center for Quantitative BiologyPeking University5 Yiheyuan Road Haidian DistrictBeijing100871P. R. China
- The State Key Laboratory for Artificial Microstructures and Mesoscopic PhysicsPeking University5 Yiheyuan Road Haidian DistrictBeijing100871P. R. China
| | - Long Qian
- Center for Quantitative BiologyPeking University5 Yiheyuan Road Haidian DistrictBeijing100871P. R. China
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36
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Peil A, Zhan P, Duan X, Krahne R, Garoli D, M Liz-Marzán L, Liu N. Transformable Plasmonic Helix with Swinging Gold Nanoparticles. Angew Chem Int Ed Engl 2023; 62:e202213992. [PMID: 36423337 DOI: 10.1002/anie.202213992] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/20/2022] [Accepted: 11/24/2022] [Indexed: 11/25/2022]
Abstract
Control over multiple optical elements that can be dynamically rearranged to yield substantial three-dimensional structural transformations is of great importance to realize reconfigurable plasmonic nanoarchitectures with sensitive and distinct optical feedback. In this work, we demonstrate a transformable plasmonic helix system, in which multiple gold nanoparticles (AuNPs) can be directly transported by DNA swingarms to target positions without undergoing consecutive stepwise movements. The swingarms allow for programmable AuNP translocations in large leaps within plasmonic nanoarchitectures, giving rise to tailored circular dichroism spectra. Our work provides an instructive bottom-up solution to building complex dynamic plasmonic systems, which can exhibit prominent optical responses through cooperative rearrangements of the constituent optical elements with high fidelity and programmability.
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Affiliation(s)
- Andreas Peil
- 2. Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany.,Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569, Stuttgart, Germany
| | - Pengfei Zhan
- 2. Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany.,Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569, Stuttgart, Germany
| | - Xiaoyang Duan
- 2. Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany.,Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569, Stuttgart, Germany
| | - Roman Krahne
- Instituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy
| | - Denis Garoli
- Instituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy
| | - Luis M Liz-Marzán
- CIC BiomaGUNE, Paseo Miramón 182, 20014, Donostia/San Sebastián, Spain.,Biomedical Networking Center, Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Paseo Miramón 182, 20014, Donostia/San Sebastián, Spain.,Ikerbasque, Basque Foundation for Science, 43009, Bilbao, Spain
| | - Na Liu
- 2. Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany.,Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569, Stuttgart, Germany
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37
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Sabat N, Katkevica D, Pajuste K, Flamme M, Stämpfli A, Katkevics M, Hanlon S, Bisagni S, Püntener K, Sladojevich F, Hollenstein M. Towards the controlled enzymatic synthesis of LNA containing oligonucleotides. Front Chem 2023; 11:1161462. [PMID: 37179777 PMCID: PMC10172484 DOI: 10.3389/fchem.2023.1161462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/17/2023] [Indexed: 05/15/2023] Open
Abstract
Enzymatic, de novo XNA synthesis represents an alternative method for the production of long oligonucleotides containing chemical modifications at distinct locations. While such an approach is currently developed for DNA, controlled enzymatic synthesis of XNA remains at a relative state of infancy. In order to protect the masking groups of 3'-O-modified LNA and DNA nucleotides against removal caused by phosphatase and esterase activities of polymerases, we report the synthesis and biochemical characterization of nucleotides equipped with ether and robust ester moieties. While the resulting ester-modified nucleotides appear to be poor substrates for polymerases, ether-blocked LNA and DNA nucleotides are readily incorporated into DNA. However, removal of the protecting groups and modest incorporation yields represent obstacles for LNA synthesis via this route. On the other hand, we have also shown that the template-independent RNA polymerase PUP represents a valid alternative to the TdT and we have also explored the possibility of using engineered DNA polymerases to increase substrate tolerance for such heavily modified nucleotide analogs.
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Affiliation(s)
- Nazarii Sabat
- Institut Pasteur, Université de Paris Cité, CNRS UMR3523, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, Paris, France
| | | | | | - Marie Flamme
- Institut Pasteur, Université de Paris Cité, CNRS UMR3523, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, Paris, France
| | - Andreas Stämpfli
- Pharma Research and Early Development, Roche Innovation Center Basel, F Hoffmann-La Roche Ltd., Basel, Switzerland
| | | | - Steven Hanlon
- Pharmaceutical Division, Synthetic Molecules Technical Development, Process Development and Catalysis, F Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Serena Bisagni
- Pharmaceutical Division, Synthetic Molecules Technical Development, Process Development and Catalysis, F Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Kurt Püntener
- Pharmaceutical Division, Synthetic Molecules Technical Development, Process Development and Catalysis, F Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Filippo Sladojevich
- Pharma Research and Early Development, Roche Innovation Center Basel, F Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Marcel Hollenstein
- Institut Pasteur, Université de Paris Cité, CNRS UMR3523, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, Paris, France
- *Correspondence: Marcel Hollenstein,
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38
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Armeni P, Gatti A. Comment on "Emerging Approaches to DNA Data Storage: Challenges and Prospects". ACS NANO 2022; 16:19612-19613. [PMID: 36598758 DOI: 10.1021/acsnano.2c11397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Affiliation(s)
| | - Anna Gatti
- LIFT Lab - SDA Bocconi School of Management
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