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Jo S, Shin H, Joe SY, Baek D, Park C, Chun H. Recent progress in DNA data storage based on high-throughput DNA synthesis. Biomed Eng Lett 2024; 14:993-1009. [PMID: 39220021 PMCID: PMC11362454 DOI: 10.1007/s13534-024-00386-z] [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: 02/21/2024] [Revised: 04/24/2024] [Accepted: 04/26/2024] [Indexed: 09/04/2024] Open
Abstract
DNA data storage has emerged as a solution for storing massive volumes of data by utilizing nucleic acids as a digital information medium. DNA offers exceptionally high storage density, long durability, and low maintenance costs compared to conventional storage media such as flash memory and hard disk drives. DNA data storage consists of the following steps: encoding, DNA synthesis (i.e., writing), preservation, retrieval, DNA sequencing (i.e., reading), and decoding. Out of these steps, DNA synthesis presents a bottleneck due to imperfect coupling efficiency, low throughput, and excessive use of organic solvents. Overcoming these challenges is essential to establish DNA as a viable data storage medium. In this review, we provide the overall process of DNA data storage, presenting the recent progress of each step. Next, we examine a detailed overview of DNA synthesis methods with an emphasis on their limitations. Lastly, we discuss the efforts to overcome the constraints of each method and their prospects.
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Affiliation(s)
- Seokwoo Jo
- Department of Biomedical Engineering, Korea University, 466 Hana Science Hall, Seoul, 02841 Korea
- Interdisciplinary Program in Precision Public Health, Korea University, 466 Hana Science Hall, Seoul, 02841 Korea
| | - Haewon Shin
- Department of Biomedical Engineering, Korea University, 466 Hana Science Hall, Seoul, 02841 Korea
- Interdisciplinary Program in Precision Public Health, Korea University, 466 Hana Science Hall, Seoul, 02841 Korea
| | - Sung-yune Joe
- Department of Biomedical Engineering, Korea University, 466 Hana Science Hall, Seoul, 02841 Korea
- Interdisciplinary Program in Precision Public Health, Korea University, 466 Hana Science Hall, Seoul, 02841 Korea
| | - David Baek
- Department of Biomedical Engineering, Korea University, 466 Hana Science Hall, Seoul, 02841 Korea
- Interdisciplinary Program in Precision Public Health, Korea University, 466 Hana Science Hall, Seoul, 02841 Korea
| | - Chaewon Park
- Department of Biomedical Engineering, Korea University, 466 Hana Science Hall, Seoul, 02841 Korea
- Interdisciplinary Program in Precision Public Health, Korea University, 466 Hana Science Hall, Seoul, 02841 Korea
| | - Honggu Chun
- Department of Biomedical Engineering, Korea University, 466 Hana Science Hall, Seoul, 02841 Korea
- Interdisciplinary Program in Precision Public Health, Korea University, 466 Hana Science Hall, Seoul, 02841 Korea
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2
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Zimmermann A, Prieto-Vivas JE, Voordeckers K, Bi C, Verstrepen KJ. Mutagenesis techniques for evolutionary engineering of microbes - exploiting CRISPR-Cas, oligonucleotides, recombinases, and polymerases. Trends Microbiol 2024; 32:884-901. [PMID: 38493013 DOI: 10.1016/j.tim.2024.02.006] [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: 10/12/2023] [Revised: 02/07/2024] [Accepted: 02/09/2024] [Indexed: 03/18/2024]
Abstract
The natural process of evolutionary adaptation is often exploited as a powerful tool to obtain microbes with desirable traits. For industrial microbes, evolutionary engineering is often used to generate variants that show increased yields or resistance to stressful industrial environments, thus obtaining superior microbial cell factories. However, even in large populations, the natural supply of beneficial mutations is typically low, which implies that obtaining improved microbes is often time-consuming and inefficient. To overcome this limitation, different techniques have been developed that boost mutation rates. While some of these methods simply increase the overall mutation rate across a genome, others use recent developments in DNA synthesis, synthetic biology, and CRISPR-Cas techniques to control the type and location of mutations. This review summarizes the most important recent developments and methods in the field of evolutionary engineering in model microorganisms. It discusses how both in vitro and in vivo approaches can increase the genetic diversity of the host, with a special emphasis on in vivo techniques for the optimization of metabolic pathways for precision fermentation.
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Affiliation(s)
- Anna Zimmermann
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium; CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, 3001, Belgium
| | - Julian E Prieto-Vivas
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium; CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, 3001, Belgium
| | - Karin Voordeckers
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium; CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, 3001, Belgium
| | - Changhao Bi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; College of Life Science, Tianjin Normal University, Tianjin, China
| | - Kevin J Verstrepen
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium; CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, 3001, Belgium; VIB-VIB Joint Center of Synthetic Biology, National Center of Technology Innovation for Synthetic Biology, Tianjin, China.
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3
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Khanzode R, Soni G, Srivastava S, Pawar S, Wadapurkar R, Singh A. Combinative workflow for mRNA vaccine development. Biochem Biophys Rep 2024; 39:101766. [PMID: 39040540 PMCID: PMC11261026 DOI: 10.1016/j.bbrep.2024.101766] [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: 03/20/2024] [Accepted: 06/25/2024] [Indexed: 07/24/2024] Open
Abstract
Recently, mRNA has gained a lot of attention in the field of vaccines, gene therapy, and protein replacement therapies. Herein, we are demonstrating a comprehensive approach to designing, cloning, and characterizing an antigenic cassette for the development of mRNA vaccine for COVID-19. The gene encoding the antigenic spike protein of the SARS-CoV-2 Omicron variant (B.1.1.529) was designed using the databases, characterized by in-silico tools, and assembled using overlapping oligonucleotide-based assembly by PCR. Next, the gene was cloned, mRNA was synthesized, and characterized using orthogonal approaches (Capillary electrophoresis, Sanger DNA sequencing, Next-generation sequencing, HPLC, qPCR, etc.). Furthermore, the antigen expression was monitored in-vitro using an animal cell model by western blot, flow cytometer, and surface plasmon resonance. The demonstrated approach has also been followed for developing the mRNA vaccines for various other indications such as Malaria, Herpes, Dengue, HPV, etc.
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Affiliation(s)
| | | | - Shalini Srivastava
- Gennova Biopharmaceuticals Ltd, ITBT Park, Rajiv Gandhi Infotech Park, Hinjawadi, Phase-2, Pune, Maharashtra, 411057, India
| | - Sharad Pawar
- Gennova Biopharmaceuticals Ltd, ITBT Park, Rajiv Gandhi Infotech Park, Hinjawadi, Phase-2, Pune, Maharashtra, 411057, India
| | - Rucha Wadapurkar
- Gennova Biopharmaceuticals Ltd, ITBT Park, Rajiv Gandhi Infotech Park, Hinjawadi, Phase-2, Pune, Maharashtra, 411057, India
| | - Ajay Singh
- Gennova Biopharmaceuticals Ltd, ITBT Park, Rajiv Gandhi Infotech Park, Hinjawadi, Phase-2, Pune, Maharashtra, 411057, India
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4
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Walther RE, Hrabak M, Bernstein DA. How advancements in molecular biology impact education and training. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2024; 25:e0006124. [PMID: 38975770 PMCID: PMC11360415 DOI: 10.1128/jmbe.00061-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 06/04/2024] [Indexed: 07/09/2024]
Abstract
Molecular biology, broadly defined as the investigation of complex biomolecules in the laboratory, is a rapidly advancing field and as such the technologies available to investigators are constantly evolving. This constant advancement has obvious advantages because it allows students and researchers to perform more complex experiments in shorter periods of time. One challenge with such a rapidly advancing field is that techniques that had been vital for students to learn how to perform are now not essential for a laboratory scientist. For example, while cloning a gene in the past could have led to a publication and form the bulk of a PhD thesis project, technology has now made this process only a step toward one of these larger goals and can, in many cases, be performed by a company or core facility. As teachers and mentors, it is imperative that we understand that the technologies we teach in the lab and classroom must also evolve to match these advancements. In this perspective, we discuss how the rapid advances in gene synthesis technologies are affecting curriculum and how our classrooms should evolve to ensure our lessons prepare students for the world in which they will do science.
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Li K, Lu X, Liao J, Chen H, Lin W, Zhao Y, Tang D, Li C, Tian Z, Zhu Z, Jiang H, Sun J, Zhang H, Yang C. DNA-DISK: Automated end-to-end data storage via enzymatic single-nucleotide DNA synthesis and sequencing on digital microfluidics. Proc Natl Acad Sci U S A 2024; 121:e2410164121. [PMID: 39145927 PMCID: PMC11348301 DOI: 10.1073/pnas.2410164121] [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: 05/22/2024] [Accepted: 07/21/2024] [Indexed: 08/16/2024] Open
Abstract
In the age of information explosion, the exponential growth of digital data far exceeds the capacity of current mainstream storage media. DNA is emerging as a promising alternative due to its higher storage density, longer retention time, and lower power consumption. To date, commercially mature DNA synthesis and sequencing technologies allow for writing and reading of information on DNA with customization and convenience at the research level. However, under the disconnected and nonspecialized mode, DNA data storage encounters practical challenges, including susceptibility to errors, long storage latency, resource-intensive requirements, and elevated information security risks. Herein, we introduce a platform named DNA-DISK that seamlessly streamlined DNA synthesis, storage, and sequencing on digital microfluidics coupled with a tabletop device for automated end-to-end information storage. The single-nucleotide enzymatic DNA synthesis with biocapping strategy is utilized, offering an ecofriendly and cost-effective approach for data writing. A DNA encapsulation using thermo-responsive agarose is developed for on-chip solidification, not only eliminating data clutter but also preventing DNA degradation. Pyrosequencing is employed for in situ and accurate data reading. As a proof of concept, DNA-DISK successfully stored and retrieved a musical sheet file (228 bits) with lower write-to-read latency (4.4 min of latency per bit) as well as superior automation compared to other platforms, demonstrating its potential to evolve into a DNA Hard Disk Drive in the future.
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Affiliation(s)
- Kunjie Li
- Key Laboratory of Spectrochemical Analysis and Instrumentation, Ministry of Education, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Discipline Intelligent Instrument & Equipment, Xiamen University, Xiamen361005, China
| | - Xiaoyun Lu
- Zhonghe Gene Technology Co., Ltd., Tianjin300308, China
| | - Jiaqi Liao
- Key Laboratory of Spectrochemical Analysis and Instrumentation, Ministry of Education, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Discipline Intelligent Instrument & Equipment, Xiamen University, Xiamen361005, China
| | - Heng Chen
- Key Laboratory of Spectrochemical Analysis and Instrumentation, Ministry of Education, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Discipline Intelligent Instrument & Equipment, Xiamen University, Xiamen361005, China
| | - Wei Lin
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen361005, China
| | - Yuhan Zhao
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen361005, China
| | - Dongbao Tang
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen361005, China
| | - Congyu Li
- Zhonghe Gene Technology Co., Ltd., Tianjin300308, China
| | - Zhenyang Tian
- Zhonghe Gene Technology Co., Ltd., Tianjin300308, China
| | - Zhi Zhu
- Key Laboratory of Spectrochemical Analysis and Instrumentation, Ministry of Education, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Discipline Intelligent Instrument & Equipment, Xiamen University, Xiamen361005, China
| | - Huifeng Jiang
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin300308, China
| | - Jun Sun
- Zhonghe Gene Technology Co., Ltd., Tianjin300308, China
| | - Huimin Zhang
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen361005, China
| | - Chaoyong Yang
- Key Laboratory of Spectrochemical Analysis and Instrumentation, Ministry of Education, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Discipline Intelligent Instrument & Equipment, Xiamen University, Xiamen361005, China
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen361005, China
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Milisavljevic M, Rodriguez TR, Carlson CK, Liu CC, Tyo KEJ. Engineering the Activity of a Template-Independent DNA Polymerase. ACS Synth Biol 2024; 13:2492-2504. [PMID: 39083642 DOI: 10.1021/acssynbio.4c00255] [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: 08/02/2024]
Abstract
Enzymatic DNA writing technologies based on the template-independent DNA polymerase terminal deoxynucleotidyl transferase (TdT) have the potential to advance DNA information storage. TdT is unique in its ability to synthesize single-stranded DNA de novo but has limitations, including catalytic inhibition by ribonucleotide presence and slower incorporation rates compared to replicative polymerases. We anticipate that protein engineering can improve, modulate, and tailor the enzyme's properties, but there is limited information on TdT sequence-structure-function relationships to facilitate rational approaches. Therefore, we developed an easily modifiable screening assay that can measure the TdT activity in high-throughput to evaluate large TdT mutant libraries. We demonstrated the assay's capabilities by engineering TdT mutants that exhibit both improved catalytic efficiency and improved activity in the presence of an inhibitor. We screened for and identified TdT variants with greater catalytic efficiency in both selectively incorporating deoxyribonucleotides and in the presence of deoxyribonucleotide/ribonucleotide mixes. Using this information from the screening assay, we rationally engineered other TdT homologues with the same properties. The emulsion-based assay we developed is, to the best of our knowledge, the first high-throughput screening assay that can measure TdT activity quantitatively and without the need for protein purification.
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Affiliation(s)
- Marija Milisavljevic
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Teresa Rojas Rodriguez
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Courtney K Carlson
- Department of Biomedical Engineering, University of California, Irvine, California 92697, United States
- Center for Synthetic Biology, University of California, Irvine, California 92697, United States
| | - Chang C Liu
- Department of Biomedical Engineering, University of California, Irvine, California 92697, United States
- Center for Synthetic Biology, University of California, Irvine, California 92697, United States
| | - Keith E J Tyo
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
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7
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Padhy P, Zaman MA, Jensen MA, Cheng YT, Huang Y, Wu M, Galambos L, Davis RW, Hesselink L. Dielectrophoretic bead-droplet reactor for solid-phase synthesis. Nat Commun 2024; 15:6159. [PMID: 39039069 PMCID: PMC11263596 DOI: 10.1038/s41467-024-49284-z] [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: 05/06/2023] [Accepted: 05/29/2024] [Indexed: 07/24/2024] Open
Abstract
Solid-phase synthesis underpins many advances in synthetic and combinatorial chemistry, biology, and material science. The immobilization of a reacting species on the solid support makes interfacing of reagents an important challenge in this approach. In traditional synthesis columns, this leads to reaction errors that limit the product yield and necessitates excess consumption of the mobile reagent phase. Although droplet microfluidics can mitigate these problems, its adoption is fundamentally limited by the inability to controllably interface microbeads and reagent droplets. Here, we introduce Dielectrophoretic Bead-Droplet Reactor as a physical method to implement solid-phase synthesis on individual functionalized microbeads by encapsulating and ejecting them from microdroplets by tuning the supply voltage. Proof-of-concept demonstration of the enzymatic coupling of fluorescently labeled nucleotides onto the bead using this reactor yielded a 3.2-fold higher fidelity over columns through precise interfacing of individual microreactors and beads. Our work combines microparticle manipulation and droplet microfluidics to address a long-standing problem in solid-phase synthesis with potentially wide-ranging implications.
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Affiliation(s)
- Punnag Padhy
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA.
| | - Mohammad Asif Zaman
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Michael Anthony Jensen
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, 94304, USA.
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA.
| | - Yao-Te Cheng
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Yogi Huang
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Mo Wu
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Ludwig Galambos
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Ronald Wayne Davis
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, 94304, USA
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Lambertus Hesselink
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA.
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8
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Hollenstein M. Enzymatic synthesis of RNA oligonucleotides. Nat Biotechnol 2024:10.1038/s41587-024-02322-z. [PMID: 38997580 DOI: 10.1038/s41587-024-02322-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2024]
Affiliation(s)
- Marcel Hollenstein
- Institut Pasteur, Université Paris Cité, CNRS UMR 3523, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, Paris, France.
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9
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Boehm E, Summermatter K, Kaiser L. Orthopox viruses: is the threat growing? Clin Microbiol Infect 2024; 30:883-887. [PMID: 38387500 DOI: 10.1016/j.cmi.2024.02.011] [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: 11/21/2023] [Revised: 02/09/2024] [Accepted: 02/14/2024] [Indexed: 02/24/2024]
Abstract
BACKGROUND Smallpox was a major cause of human mortality until its eradication, but the threat of orthopox viruses has not disappeared. Since the eradication of smallpox and the cessation of the related vaccination campaigns, the threat has been growing, as evidenced by the currently ongoing worldwide Mpox outbreak. In addition to threats of an evolving Mpox, we must also be aware of a myriad of other threats that remain. Many countries still lack biosecurity regulations reflecting the recent technological advances, and the threat of bioterrorism remains ever present. Reconstruction of smallpox is a distinct possibility, as are other scenarios whereby other orthopox viruses may be made more fit for transmission in humans. OBJECTIVES To outline and discuss potential biosafety and biosecurity threats posed by orthopox viruses. SOURCES Published scientific literature, news articles, and international agreements. CONTENT AND IMPLICATIONS It would be wise to take steps to mitigate these threats now. Vaccination campaigns should be considered in areas with frequent orthopox outbreaks, and more efforts must be made to put a final end to the Mpox outbreak. In many countries, national biosafety and biosecurity regulations may need to be revised and strengthened to better reflect the threats posed by new technologies, including controls on synthesis of smallpox sequences. Furthermore, more international cooperation and aid is needed. The present global Mpox outbreak could likely have been prevented had areas where Mpox is endemic not been neglected. Future outbreaks could be much worse.
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Affiliation(s)
- Erik Boehm
- Centre for Emerging Viral Diseases, Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland.
| | | | - Laurent Kaiser
- Centre for Emerging Viral Diseases, Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
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10
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Fernandez‐Moreno J, Yaschenko AE, Neubauer M, Marchi AJ, Zhao C, Ascencio‐Ibanez JT, Alonso JM, Stepanova AN. A rapid and scalable approach to build synthetic repetitive hormone-responsive promoters. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1942-1956. [PMID: 38379432 PMCID: PMC11182585 DOI: 10.1111/pbi.14313] [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: 12/21/2023] [Revised: 02/04/2024] [Accepted: 02/06/2024] [Indexed: 02/22/2024]
Abstract
Advancement of DNA-synthesis technologies has greatly facilitated the development of synthetic biology tools. However, high-complexity DNA sequences containing tandems of short repeats are still notoriously difficult to produce synthetically, with commercial DNA synthesis companies usually rejecting orders that exceed specific sequence complexity thresholds. To overcome this limitation, we developed a simple, single-tube reaction method that enables the generation of DNA sequences containing multiple repetitive elements. Our strategy involves commercial synthesis and PCR amplification of padded sequences that contain the repeats of interest, along with random intervening sequence stuffers that include type IIS restriction enzyme sites. GoldenBraid molecular cloning technology is then employed to remove the stuffers, rejoin the repeats together in a predefined order, and subclone the tandem(s) in a vector using a single-tube digestion-ligation reaction. In our hands, this new approach is much simpler, more versatile and efficient than previously developed solutions to this problem. As a proof of concept, two different phytohormone-responsive, synthetic, repetitive proximal promoters were generated and tested in planta in the context of transcriptional reporters. Analysis of transgenic lines carrying the synthetic ethylene-responsive promoter 10x2EBS-S10 fused to the GUS reporter gene uncovered several developmentally regulated ethylene response maxima, indicating the utility of this reporter for monitoring the involvement of ethylene in a variety of physiologically relevant processes. These encouraging results suggest that this reporter system can be leveraged to investigate the ethylene response to biotic and abiotic factors with high spatial and temporal resolution.
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Affiliation(s)
| | - Anna E. Yaschenko
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNCUSA
| | - Matthew Neubauer
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNCUSA
| | - Alex J. Marchi
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNCUSA
| | - Chengsong Zhao
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNCUSA
| | - José T. Ascencio‐Ibanez
- Department of Molecular and Structural BiochemistryNorth Carolina State UniversityRaleighNCUSA
| | - Jose M. Alonso
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNCUSA
| | - Anna N. Stepanova
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNCUSA
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11
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Zhu Y, Lin Y, Gong B, Zhang Y, Su G, Yu Y. Dual toeholds regulated CRISPR-Cas12a sensing platform for ApoE single nucleotide polymorphisms genotyping. Biosens Bioelectron 2024; 255:116255. [PMID: 38565025 DOI: 10.1016/j.bios.2024.116255] [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: 12/24/2023] [Revised: 03/13/2024] [Accepted: 03/26/2024] [Indexed: 04/04/2024]
Abstract
Single nucleotide polymorphisms (SNPs) are closely associated with many biological processes, including genetic disease, tumorigenesis, and drug metabolism. Accurate and efficient SNP determination has been proved pivotal in pharmacogenomics and diagnostics. Herein, a universal and high-fidelity genotyping platform is established based on the dual toeholds regulated Cas12a sensing methodology. Different from the conventional single stranded or double stranded activation mode, the dual toeholds regulated mode overcomes protospacer adjacent motif (PAM) limitation via cascade toehold mediated strand displacement reaction, which is highly universal and ultra-specific. To enhance the sensitivity for biological samples analysis, a modified isothermal recombinant polymerase amplification (RPA) strategy is developed via utilizing deoxythymidine substituted primer and uracil-DNA glycosylase (UDG) treatment, designated as RPA-UDG. The dsDNA products containing single stranded toehold domain generated in the RPA-UDG allow further incorporation with dual toeholds regulated Cas12a platform for high-fidelity human sample genotyping. We discriminate all the single-nucleotide polymorphisms of ApoE gene at rs429358 and rs7412 loci with human buccal swab samples with 100% accuracy. Furthermore, we engineer visual readout of genotyping results by exploiting commercial lateral flow strips, which opens new possibilities for field deployable implementation.
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Affiliation(s)
- Yuedong Zhu
- School of Pharmacy, Nantong University, Nantong, Jiangsu, 226001, China
| | - Yanan Lin
- School of Pharmacy, Nantong University, Nantong, Jiangsu, 226001, China
| | - Bin Gong
- School of Pharmacy, Nantong University, Nantong, Jiangsu, 226001, China
| | - Yan Zhang
- School of Pharmacy, Nantong University, Nantong, Jiangsu, 226001, China
| | - Gaoxing Su
- School of Pharmacy, Nantong University, Nantong, Jiangsu, 226001, China.
| | - Yanyan Yu
- School of Pharmacy, Nantong University, Nantong, Jiangsu, 226001, China.
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12
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Norton-Baker B, Denton MCR, Murphy NP, Fram B, Lim S, Erickson E, Gauthier NP, Beckham GT. Enabling high-throughput enzyme discovery and engineering with a low-cost, robot-assisted pipeline. Sci Rep 2024; 14:14449. [PMID: 38914665 PMCID: PMC11196671 DOI: 10.1038/s41598-024-64938-0] [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: 04/08/2024] [Accepted: 06/14/2024] [Indexed: 06/26/2024] Open
Abstract
As genomic databases expand and artificial intelligence tools advance, there is a growing demand for efficient characterization of large numbers of proteins. To this end, here we describe a generalizable pipeline for high-throughput protein purification using small-scale expression in E. coli and an affordable liquid-handling robot. This low-cost platform enables the purification of 96 proteins in parallel with minimal waste and is scalable for processing hundreds of proteins weekly per user. We demonstrate the performance of this method with the expression and purification of the leading poly(ethylene terephthalate) hydrolases reported in the literature. Replicate experiments demonstrated reproducibility and enzyme purity and yields (up to 400 µg) sufficient for comprehensive analyses of both thermostability and activity, generating a standardized benchmark dataset for comparing these plastic-degrading enzymes. The cost-effectiveness and ease of implementation of this platform render it broadly applicable to diverse protein characterization challenges in the biological sciences.
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Grants
- DE-SC0022024 U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research (BER), Genomic Science Program
- DE-SC0022024 U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research (BER), Genomic Science Program
- DE-SC0022024 U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research (BER), Genomic Science Program
- DE-SC0022024 U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research (BER), Genomic Science Program
- DE-SC0022024 U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research (BER), Genomic Science Program
- DE-AC36-08GO28308 Advanced Materials and Manufacturing Technologies Office (AMMTO)
- DE-AC36-08GO28308 Advanced Materials and Manufacturing Technologies Office (AMMTO)
- DE-AC36-08GO28308 Advanced Materials and Manufacturing Technologies Office (AMMTO)
- DE-AC36-08GO28308 Advanced Materials and Manufacturing Technologies Office (AMMTO)
- U.S. Department of Energy Office of Energy Efficiency and Renewable Energy Bioenergy Technologies Office (BETO)
- Bio-Optimized Technologies to keep Thermoplastics out of Landfills and the Environment (BOTTLE) Consortium
- Dana-Farber Cancer Institute
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Affiliation(s)
- Brenna Norton-Baker
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
- BOTTLE Consortium, Golden, CO, USA
- Agile BioFoundry, Emeryville, CA, USA
| | - Mackenzie C R Denton
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
- BOTTLE Consortium, Golden, CO, USA
| | - Natasha P Murphy
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
- BOTTLE Consortium, Golden, CO, USA
| | - Benjamin Fram
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Samuel Lim
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Erika Erickson
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
- BOTTLE Consortium, Golden, CO, USA
| | - Nicholas P Gauthier
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Gregg T Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA.
- BOTTLE Consortium, Golden, CO, USA.
- Agile BioFoundry, Emeryville, CA, USA.
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13
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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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14
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Hersch SJ, Chandrasekaran S, Lam J, Nafissi N, Slavcev RA. Manufacturing DNA in E. coli yields higher-fidelity DNA than in vitro enzymatic synthesis. Mol Ther Methods Clin Dev 2024; 32:101227. [PMID: 38516691 PMCID: PMC10951457 DOI: 10.1016/j.omtm.2024.101227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 02/26/2024] [Indexed: 03/23/2024]
Abstract
Biotechnologies such as gene therapy have brought DNA vectors to the forefront of pharmaceuticals. The quality of starting material plays a pivotal role in determining final product quality. Here, we examined the fidelity of DNA replication using enzymatic methods (in vitro) compared to plasmid DNA produced in vivo in E. coli. Next-generation sequencing approaches rely on in vitro polymerases, which have inherent limitations in sensitivity. To address this challenge, we introduce a novel assay based on loss-of-function (LOF) mutations in the conditionally toxic sacB gene. Our findings show that DNA production in E. coli results in significantly fewer LOF mutations (80- to 3,000-fold less) compared to enzymatic DNA replication methods such as polymerase chain reaction (PCR) and rolling circle amplification (RCA). These results suggest that using DNA produced by PCR or RCA may introduce a substantial number of mutation impurities, potentially affecting the quality and yield of final pharmaceutical products. Our study underscores that DNA synthesized in vitro has a significantly higher mutation rate than DNA produced traditionally in E. coli. Therefore, utilizing in vitro enzymatically produced DNA in biotechnology and biomanufacturing may entail considerable fidelity-related risks, while using DNA starting material derived from E. coli substantially mitigates this risk.
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Affiliation(s)
| | | | - Jamie Lam
- Mediphage Bioceuticals, Inc, Toronto, ON, Canada
| | - Nafiseh Nafissi
- Mediphage Bioceuticals, Inc, Toronto, ON, Canada
- School of Pharmacy, University of Waterloo, Waterloo, ON, Canada
| | - Roderick A. Slavcev
- Mediphage Bioceuticals, Inc, Toronto, ON, Canada
- School of Pharmacy, University of Waterloo, Waterloo, ON, Canada
- Centre for Eye and Vision Research, HKSTP, Ma Liu Shui, Hong Kong
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15
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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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16
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Bains RK, Nasseri SA, Wardman JF, Withers SG. Advances in the understanding and exploitation of carbohydrate-active enzymes. Curr Opin Chem Biol 2024; 80:102457. [PMID: 38657391 DOI: 10.1016/j.cbpa.2024.102457] [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: 02/06/2024] [Revised: 03/29/2024] [Accepted: 04/01/2024] [Indexed: 04/26/2024]
Abstract
Carbohydrate-active enzymes (CAZymes) are responsible for the biosynthesis, modification and degradation of all glycans in Nature. Advances in genomic and metagenomic methodologies, in conjunction with lower cost gene synthesis, have provided access to a steady stream of new CAZymes with both well-established and novel mechanisms. At the same time, increasing access to cryo-EM has resulted in exciting new structures, particularly of transmembrane glycosyltransferases of various sorts. This improved understanding has resulted in widespread progress in applications of CAZymes across diverse fields, including therapeutics, organ transplantation, foods, and biofuels. Herein, we highlight a few of the many important advances that have recently been made in the understanding and applications of CAZymes.
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Affiliation(s)
- Rajneesh K Bains
- Department of Chemistry, University of British Columbia, Vancouver, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - Seyed Amirhossein Nasseri
- Department of Chemistry, University of British Columbia, Vancouver, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - Jacob F Wardman
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada; Department of Biochemistry, University of British Columbia, Vancouver, Canada
| | - Stephen G Withers
- Department of Chemistry, University of British Columbia, Vancouver, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, Canada; Department of Biochemistry, University of British Columbia, Vancouver, Canada.
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17
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Švajger U, Kamenšek U. Interleukins and interferons in mesenchymal stromal stem cell-based gene therapy of cancer. Cytokine Growth Factor Rev 2024; 77:76-90. [PMID: 38508954 DOI: 10.1016/j.cytogfr.2024.03.002] [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: 02/05/2024] [Revised: 03/07/2024] [Accepted: 03/11/2024] [Indexed: 03/22/2024]
Abstract
The tumor microenvironment is importantly shaped by various cytokines, where interleukins (ILs) and interferons (IFNs) shape the balance of immune activity within tumor niche and associated lymphoid organs. Their importance in activation and tuning of both innate and adaptive immune responses prompted their use in several clinical trials, albeit with limited therapeutic efficacy and risk of toxicity due to systemic administration. Increasing preclinical evidence suggests that local delivery of ILs and IFNs could significantly increase their effectiveness, while simultaneously attenuate the known side effects and issues related to their biological activity. A prominent way to achieve this is to use cell-based delivery vehicles. For this purpose, mesenchymal stromal stem cells (MSCs) are considered an almost ideal candidate. Namely, MSCs can be obtained in large quantities and from obtainable sources (e.g. umbilical cord or adipose tissue), their ex vivo expansion is relatively straightforward compared to other cell types and they possess very low immunogenicity making them suitable for allogeneic use. Importantly, MSCs have shown an intrinsic capacity to respond to tumor-directed chemotaxis. This review provides a focused and detailed discussion on MSC-based gene therapy using ILs and IFNs, engineering techniques and insights on potential future advancements.
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Affiliation(s)
- Urban Švajger
- Slovenian Institute for Transfusion Medicine, Department for Therapeutic Services, Šlajmerjeva Ulica 6, Ljubljana SI-1000, Slovenia; Faculty of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, Ljubljana SI-1000, Slovenia.
| | - Urška Kamenšek
- Department of Experimental Oncology, Institute of Oncology Ljubljana, Zaloška Cesta 2, Ljubljana SI-1000, Slovenia; Biotechnical Faculty, University of Ljubljana, Jamnikarjeva Ulica 101, Ljubljana SI-1000, Slovenia
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18
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Rasool A, Hong J, Hong Z, Li Y, Zou C, Chen H, Qu Q, Wang Y, Jiang Q, Huang X, Dai J. An Effective DNA-Based File Storage System for Practical Archiving and Retrieval of Medical MRI Data. SMALL METHODS 2024:e2301585. [PMID: 38807543 DOI: 10.1002/smtd.202301585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/29/2024] [Indexed: 05/30/2024]
Abstract
DNA-based data storage is a new technology in computational and synthetic biology, that offers a solution for long-term, high-density data archiving. Given the critical importance of medical data in advancing human health, there is a growing interest in developing an effective medical data storage system based on DNA. Data integrity, accuracy, reliability, and efficient retrieval are all significant concerns. Therefore, this study proposes an Effective DNA Storage (EDS) approach for archiving medical MRI data. The EDS approach incorporates three key components (i) a novel fraction strategy to address the critical issue of rotating encoding, which often leads to data loss due to single base error propagation; (ii) a novel rule-based quaternary transcoding method that satisfies bio-constraints and ensure reliable mapping; and (iii) an indexing technique designed to simplify random search and access. The effectiveness of this approach is validated through computer simulations and biological experiments, confirming its practicality. The EDS approach outperforms existing methods, providing superior control over bio-constraints and reducing computational time. The results and code provided in this study open new avenues for practical DNA storage of medical MRI data, offering promising prospects for the future of medical data archiving and retrieval.
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Affiliation(s)
- Abdur Rasool
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- Shenzhen College of Advanced Technology, University of Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Jingwei Hong
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- College of Mathematics and Information Science, Hebei University, Baoding, 071002, China
| | - Zhiling Hong
- Quanzhou Development Group Co., Ltd, Quanzhou, 362000, China
| | - Yuanzhen Li
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen, 518055, China
| | - Chao Zou
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Hui Chen
- Shenzhen Polytechnic University, Shenzhen, 518055, China
| | - Qiang Qu
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Yang Wang
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Qingshan Jiang
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Xiaoluo Huang
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen, 518055, China
| | - Junbiao Dai
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518055, China
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19
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Flemmich L, Bereiter R, Micura R. Chemical Synthesis of Modified RNA. Angew Chem Int Ed Engl 2024; 63:e202403063. [PMID: 38529723 DOI: 10.1002/anie.202403063] [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: 02/12/2024] [Revised: 03/16/2024] [Accepted: 03/26/2024] [Indexed: 03/27/2024]
Abstract
Ribonucleic acids (RNAs) play a vital role in living organisms. Many of their cellular functions depend critically on chemical modification. Methods to modify RNA in a controlled manner-both in vitro and in vivo-are thus essential to evaluate and understand RNA biology at the molecular and mechanistic levels. The diversity of modifications, combined with the size and uniformity of RNA (made up of only 4 nucleotides) makes its site-specific modification a challenging task that needs to be addressed by complementary approaches. One such approach is solid-phase RNA synthesis. We discuss recent developments in this field, starting with new protection concepts in the ongoing effort to overcome current size limitations. We continue with selected modifications that have posed significant challenges for their incorporation into RNA. These include deazapurine bases required for atomic mutagenesis to elucidate mechanistic aspects of catalytic RNAs, and RNA containing xanthosine, N4-acetylcytidine, 5-hydroxymethylcytidine, 3-methylcytidine, 2'-OCF3, and 2'-N3 ribose modifications. We also discuss the all-chemical synthesis of 5'-capped mRNAs and the enzymatic ligation of chemically synthesized oligoribonucleotides to obtain long RNA with multiple distinct modifications, such as those needed for single-molecule FRET studies. Finally, we highlight promising developments in RNA-catalyzed RNA modification using cofactors that transfer bioorthogonal functionalities.
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Affiliation(s)
- Laurin Flemmich
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Raphael Bereiter
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
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20
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Abraham GR, Chaderjian AS, N Nguyen AB, Wilken S, Saleh OA. Nucleic acid liquids. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2024; 87:066601. [PMID: 38697088 DOI: 10.1088/1361-6633/ad4662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 05/02/2024] [Indexed: 05/04/2024]
Abstract
The confluence of recent discoveries of the roles of biomolecular liquids in living systems and modern abilities to precisely synthesize and modify nucleic acids (NAs) has led to a surge of interest in liquid phases of NAs. These phases can be formed primarily from NAs, as driven by base-pairing interactions, or from the electrostatic combination (coacervation) of negatively charged NAs and positively charged molecules. Generally, the use of sequence-engineered NAs provides the means to tune microsopic particle properties, and thus imbue specific, customizable behaviors into the resulting liquids. In this way, researchers have used NA liquids to tackle fundamental problems in the physics of finite valence soft materials, and to create liquids with novel structured and/or multi-functional properties. Here, we review this growing field, discussing the theoretical background of NA liquid phase separation, quantitative understanding of liquid material properties, and the broad and growing array of functional demonstrations in these materials. We close with a few comments discussing remaining open questions and challenges in the field.
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Affiliation(s)
- Gabrielle R Abraham
- Physics Department,University of California, Santa Barbara, CA 93106, United States of America
| | - Aria S Chaderjian
- Physics Department,University of California, Santa Barbara, CA 93106, United States of America
| | - Anna B N Nguyen
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106, United States of America
| | - Sam Wilken
- Physics Department,University of California, Santa Barbara, CA 93106, United States of America
- Materials Department, University of California, Santa Barbara, CA 93106, United States of America
| | - Omar A Saleh
- Physics Department,University of California, Santa Barbara, CA 93106, United States of America
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106, United States of America
- Materials Department, University of California, Santa Barbara, CA 93106, United States of America
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21
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Fu X, Shen Y. Synthetic Genomics: Repurposing Biological Systems for Applications in Engineering Biology. ACS Synth Biol 2024; 13:1394-1399. [PMID: 38757697 PMCID: PMC11106769 DOI: 10.1021/acssynbio.4c00006] [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: 01/02/2024] [Indexed: 05/18/2024]
Abstract
Substantial improvements in DNA sequencing and synthesis technologies and increased understanding of genome biology have empowered the development of synthetic genomics. The ability to design and construct engineered living cells boosted up by synthetic chromosomes provides opportunities to tackle enormous current and future challenges faced by humanity and the planet. Here we review the progresses, considerations, challenges, and future direction of the "design-build-test-learn" cycle used in synthetic genomics. We also discuss future applications enabled by synthetic genomics as this emerging field shapes and revolutionizes biomanufacturing and biomedicine.
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Affiliation(s)
- Xian Fu
- BGI
Research, Changzhou 213299, China
- BGI
Research, Shenzhen 518083, China
- Guangdong
Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen 518083, China
| | - Yue Shen
- BGI
Research, Changzhou 213299, China
- BGI
Research, Shenzhen 518083, China
- Guangdong
Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen 518083, China
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22
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Matsuda T, Hori H, Yamagami R. Rational design of oligonucleotides for enhanced in vitro transcription of small RNA. RNA (NEW YORK, N.Y.) 2024; 30:710-727. [PMID: 38423625 PMCID: PMC11098460 DOI: 10.1261/rna.079923.123] [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: 12/10/2023] [Accepted: 02/14/2024] [Indexed: 03/02/2024]
Abstract
All kinds of RNA molecules can be produced by in vitro transcription using T7 RNA polymerase using DNA templates obtained by solid-phase chemical synthesis, primer extension, PCR, or DNA cloning. The oligonucleotide design, however, is a challenge to nonexperts as this relies on a set of rules that have been established empirically over time. Here, we describe a Python program to facilitate the rational design of oligonucleotides, calculated with kinetic parameters for enhanced in vitro transcription (ROCKET). The Python tool uses thermodynamic parameters, performs folding-energy calculations, and selects oligonucleotides suitable for the polymerase extension reaction. These oligonucleotides improve yields of template DNA. With the oligonucleotides selected by the program, the tRNA transcripts can be prepared by a one-pot reaction of the DNA polymerase extension reaction and the transcription reaction. Also, the ROCKET-selected oligonucleotides provide greater transcription yields than that from oligonucleotides selected by Primerize, a leading software for designing oligonucleotides for in vitro transcription, due to the enhancement of template DNA synthesis. Apart from over 50 tRNA genes tested, an in vitro transcribed self-cleaving ribozyme was found to have catalytic activity. In addition, the program can be applied to the synthesis of mRNA, demonstrating the wide applicability of the ROCKET software.
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MESH Headings
- Transcription, Genetic
- Oligonucleotides/chemistry
- Oligonucleotides/genetics
- Oligonucleotides/chemical synthesis
- Software
- DNA-Directed RNA Polymerases/metabolism
- DNA-Directed RNA Polymerases/genetics
- RNA, Catalytic/genetics
- RNA, Catalytic/metabolism
- RNA, Catalytic/chemistry
- Thermodynamics
- RNA, Transfer/genetics
- RNA, Transfer/chemistry
- RNA, Transfer/metabolism
- Kinetics
- RNA, Messenger/genetics
- RNA, Messenger/chemistry
- RNA, Messenger/metabolism
- Viral Proteins/genetics
- Viral Proteins/metabolism
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Affiliation(s)
- Teppei Matsuda
- Department of Applied Chemistry, Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Hiroyuki Hori
- Department of Applied Chemistry, Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Ryota Yamagami
- Department of Applied Chemistry, Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime 790-8577, Japan
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23
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Yang B, Cui T, Guo L, Dong L, Wu J, Xing Y, Xu Y, Chen J, Wang Y, Cui Z, Dong Y. Advanced Smart Biomaterials for Regenerative Medicine and Drug Delivery Based on Phosphoramidite Chemistry: From Oligonucleotides to Precision Polymers. Biomacromolecules 2024; 25:2701-2714. [PMID: 38608139 DOI: 10.1021/acs.biomac.4c00259] [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: 04/14/2024]
Abstract
Over decades of development, while phosphoramidite chemistry has been known as the leading method in commercial synthesis of oligonucleotides, it has also revolutionized the fabrication of sequence-defined polymers (SDPs), offering novel functional materials in polymer science and clinical medicine. This review has introduced the evolution of phosphoramidite chemistry, emphasizing its development from the synthesis of oligonucleotides to the creation of universal SDPs, which have unlocked the potential for designing programmable smart biomaterials with applications in diverse areas including data storage, regenerative medicine and drug delivery. The key methodologies, functions, biomedical applications, and future challenges in SDPs, have also been summarized in this review, underscoring the significance of breakthroughs in precisely synthesized materials.
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Affiliation(s)
- Bo Yang
- Sinopec (Beijing) Research Institute of Chemical Industry CO., Ltd., Beijing 100013, P. R. China
| | - Ting Cui
- Sinopec (Beijing) Research Institute of Chemical Industry CO., Ltd., Beijing 100013, P. R. China
| | - Liang Guo
- Sinopec (Beijing) Research Institute of Chemical Industry CO., Ltd., Beijing 100013, P. R. China
| | - Lianqiang Dong
- CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Wu
- CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongzheng Xing
- National Engineering Research Center for Colloidal Materials, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Yun Xu
- Center for Medical Device Evaluation, China Food and Drug Administration (CFDA), Beijing 100084, China
| | - Jian Chen
- Sinopec (Beijing) Research Institute of Chemical Industry CO., Ltd., Beijing 100013, P. R. China
| | - Yufei Wang
- Sinopec (Beijing) Research Institute of Chemical Industry CO., Ltd., Beijing 100013, P. R. China
| | - Zhonghui Cui
- Sinopec (Beijing) Research Institute of Chemical Industry CO., Ltd., Beijing 100013, P. R. China
| | - Yuanchen Dong
- CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, China
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24
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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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25
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Kim HS, Halabi EA, Enbergs N, Kohler RH, Fei F, Garris CS, Weissleder R. A non-lipid nucleic acid delivery vector with dendritic cell tropism and stimulation. Theranostics 2024; 14:2934-2945. [PMID: 38773971 PMCID: PMC11103498 DOI: 10.7150/thno.95267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 04/10/2024] [Indexed: 05/24/2024] Open
Abstract
Rationale: Nucleic acid constructs are commonly used for vaccination, immune stimulation, and gene therapy, but their use in cancer still remains limited. One of the reasons is that systemic delivery to tumor-associated antigen-presenting cells (dendritic cells and macrophages) is often inefficient, while off-target nucleic acid-sensing immune pathways can stimulate systemic immune responses. Conversely, certain carbohydrate nanoparticles with small molecule payloads have been shown to target these cells efficiently in the tumor microenvironment. Yet, nucleic acid incorporation into such carbohydrate-based nanoparticles has proven challenging. Methods: We developed a novel approach using cross-linked bis succinyl-cyclodextrin (b-s-CD) nanoparticles to efficiently deliver nucleic acids and small-molecule immune enhancer to phagocytic cells in tumor environments and lymph nodes. Our study involved incorporating these components into the nanoparticles and assessing their efficacy in activating antigen-presenting cells. Results: The multi-modality immune stimulators effectively activated antigen-presenting cells and promoted anti-tumor immunity in vivo. This was evidenced by enhanced delivery to phagocytic cells and subsequent immune response activation in tumor environments and lymph nodes. Conclusion: Here, we describe a new approach to incorporating both nucleic acids and small-molecule immune enhancers into cross-linked bis succinyl-cyclodextrin (b-s-CD) nanoparticles for efficient delivery to phagocytic cells in tumor environments and lymph nodes in vivo. These multi-modality immune stimulators can activate antigen-presenting cells and foster anti-tumor immunity. We argue that this strategy can potentially be used to enhance anti-tumor efficacy.
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Affiliation(s)
| | | | | | | | | | | | - Ralph Weissleder
- ✉ Corresponding author: R. Weissleder, MD, PhD. Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA, 02114. 617-726-8226;
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26
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Leblanc J, Boulle O, Roux E, Nicolas J, Lavenier D, Audic Y. Fully in vitro iterative construction of a 24 kb-long artificial DNA sequence to store digital information. Biotechniques 2024; 76:203-215. [PMID: 38573592 DOI: 10.2144/btn-2023-0109] [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] [Indexed: 04/05/2024] Open
Abstract
In the absence of a DNA template, the ab initio production of long double-stranded DNA molecules of predefined sequences is particularly challenging. The DNA synthesis step remains a bottleneck for many applications such as functional assessment of ancestral genes, analysis of alternative splicing or DNA-based data storage. In this report we propose a fully in vitro protocol to generate very long double-stranded DNA molecules starting from commercially available short DNA blocks in less than 3 days using Golden Gate assembly. This innovative application allowed us to streamline the process to produce a 24 kb-long DNA molecule storing part of the Declaration of the Rights of Man and of the Citizen of 1789 . The DNA molecule produced can be readily cloned into a suitable host/vector system for amplification and selection.
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Affiliation(s)
- Julien Leblanc
- University Rennes, Inria, CNRS, IRISA, Campus de Beaulieu, Rennes, France
| | - Olivier Boulle
- University Rennes, Inria, CNRS, IRISA, Campus de Beaulieu, Rennes, France
| | - Emeline Roux
- Institut NuMeCan, INRAE, INSERM, University Rennes, France
| | - Jacques Nicolas
- University Rennes, Inria, CNRS, IRISA, Campus de Beaulieu, Rennes, France
| | | | - Yann Audic
- CNRS, University Rennes, Institut de Génétique et Développement de Rennes (IGDR) UMR 6290, Rennes, France
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27
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Pichon M, Levi-Acobas F, Kitoun C, Hollenstein M. 2',3'-Protected Nucleotides as Building Blocks for Enzymatic de novo RNA Synthesis. Chemistry 2024; 30:e202400137. [PMID: 38403849 DOI: 10.1002/chem.202400137] [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: 01/12/2024] [Revised: 02/13/2024] [Accepted: 02/20/2024] [Indexed: 02/27/2024]
Abstract
Besides being a key player in numerous fundamental biological processes, RNA also represents a versatile platform for the creation of therapeutic agents and efficient vaccines. The production of RNA oligonucleotides, especially those decorated with chemical modifications, cannot meet the exponential demand. Due to the inherent limits of solid-phase synthesis and in vitro transcription, alternative, biocatalytic approaches are in dire need to facilitate the production of RNA oligonucleotides. Here, we present a first step towards the controlled enzymatic synthesis of RNA oligonucleotides. We have explored the possibility of a simple protection step of the vicinal cis-diol moiety to temporarily block ribonucleotides. We demonstrate that pyrimidine nucleotides protected with acetals, particularly 2',3'-O-isopropylidene, are well-tolerated by the template-independent RNA polymerase PUP (polyU polymerase) and highly efficient coupling reactions can be achieved within minutes - an important feature for the development of enzymatic de novo synthesis protocols. Even though purines are not equally well-tolerated, these findings clearly demonstrate the possibility of using cis-diol-protected ribonucleotides combined with template-independent polymerases for the stepwise construction of RNA oligonucleotides.
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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
| | - Fabienne Levi-Acobas
- 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
| | - Camélia Kitoun
- 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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28
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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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29
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Wagner C, Urquiza-Garcia U, Zurbriggen MD, Beyer HM. GMOCU: Digital Documentation, Management, and Biological Risk Assessment of Genetic Parts. Adv Biol (Weinh) 2024; 8:e2300529. [PMID: 38263723 DOI: 10.1002/adbi.202300529] [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: 09/29/2023] [Revised: 01/02/2024] [Indexed: 01/25/2024]
Abstract
The continuous evolution of molecular biology and gene synthesis methods paired with an ever-increasing potential of synthetic biology approaches and genome engineering toolkits enables the rapid design of genetic bioparts and genetically modified organisms. Although various software solutions assist with specific design tasks and challenges, lab internal documentation and ensuring compliance with governmental regulations on biosafety assessment of the generated organisms remain the responsibility of individual academic researchers. This results in inconsistent and redundant documentation regimes and a significant time and labor burden. GMOCU (GMO documentation) is a standardized semi-automatic user-oriented software approach -written in Python and freely available- that unifies lab internal data documentation on genetic parts and genetically modified organisms (GMOs). It automatizes biological risk evaluations and maintains a shared up-to-date inventory of bioparts for team-wide data navigation and sharing. GMOCU further enables data export into customizable formats suitable for scientific publications, official biosafety documents, and the research community.
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Affiliation(s)
- Christoph Wagner
- Institute of Synthetic Biology, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, D-40225, Düsseldorf, Germany
| | - Uriel Urquiza-Garcia
- Institute of Synthetic Biology, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, D-40225, Düsseldorf, Germany
- CEPLAS-Cluster of Excellence on Plant Sciences, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, D-40225, Düsseldorf, Germany
| | - Matias D Zurbriggen
- Institute of Synthetic Biology, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, D-40225, Düsseldorf, Germany
- CEPLAS-Cluster of Excellence on Plant Sciences, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, D-40225, Düsseldorf, Germany
| | - Hannes M Beyer
- Institute of Synthetic Biology, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, D-40225, Düsseldorf, Germany
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30
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Li S, Tan W, Jia X, Miao Q, Liu Y, Yang D. Recent advances in the synthesis of single-stranded DNA in vitro. Biotechnol J 2024; 19:e2400026. [PMID: 38622795 DOI: 10.1002/biot.202400026] [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: 01/11/2024] [Revised: 03/19/2024] [Accepted: 03/25/2024] [Indexed: 04/17/2024]
Abstract
Single-stranded DNA (ssDNA) is the foundation of modern biology, with wide applications in gene editing, sequencing, DNA information storage, and materials science. However, synthesizing ssDNA with high efficiency, high throughput, and low error rate in vitro remains a major challenge. Various methods have been developed for ssDNA synthesis, and some significant results have been achieved. In this review, six main methods were introduced, including solid-phase oligonucleotide synthesis, terminal deoxynucleotidyl transferase-based ssDNA synthesis, reverse transcription, primer exchange reaction, asymmetric polymerase chain reaction, and rolling circle amplification. The advantages and limitations of each method were compared, as well as illustrate their representative achievements and applications. Especially, rolling circle amplification has received significant attention, including ssDNA synthesis, assembly, and application based on recent work. Finally, the future challenges and opportunities of ssDNA synthesis were summarized and discussed. Envisioning the development of new methods and significant progress will be made in the near future with the efforts of scientists around the world.
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Affiliation(s)
- Shuai Li
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, P.R. China
| | - Wei Tan
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, P.R. China
| | - Xuemei Jia
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, P.R. China
| | - Qing Miao
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, P.R. China
| | - Ying Liu
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, P.R. China
| | - Dayong Yang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, P.R. China
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31
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Ma Y, Zhang Z, Jia B, Yuan Y. Automated high-throughput DNA synthesis and assembly. Heliyon 2024; 10:e26967. [PMID: 38500977 PMCID: PMC10945133 DOI: 10.1016/j.heliyon.2024.e26967] [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: 04/23/2023] [Revised: 02/20/2024] [Accepted: 02/22/2024] [Indexed: 03/20/2024] Open
Abstract
DNA synthesis and assembly primarily revolve around the innovation and refinement of tools that facilitate the creation of specific genes and the manipulation of entire genomes. This multifaceted process encompasses two fundamental steps: the synthesis of lengthy oligonucleotides and the seamless assembly of numerous DNA fragments. With the advent of automated pipetting workstations and integrated experimental equipment, a substantial portion of repetitive tasks in the field of synthetic biology can now be efficiently accomplished through integrated liquid handling workstations. This not only reduces the need for manual labor but also enhances overall efficiency. This review explores the ongoing advancements in the oligonucleotide synthesis platform, automated DNA assembly techniques, and biofoundries. The development of accurate and high-throughput DNA synthesis and assembly technologies presents both challenges and opportunities.
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Affiliation(s)
- Yuxin Ma
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Zhaoyang Zhang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Bin Jia
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yingjin Yuan
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
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32
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Li Y, Zhang H, Chen Y, Shen Y, Ping Z. DNA Bloom Filter enables anti-contamination and file version control for DNA-based data storage. Brief Bioinform 2024; 25:bbae125. [PMID: 38555478 PMCID: PMC10981766 DOI: 10.1093/bib/bbae125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/09/2024] [Accepted: 02/27/2024] [Indexed: 04/02/2024] Open
Abstract
DNA storage is one of the most promising ways for future information storage due to its high data storage density, durable storage time and low maintenance cost. However, errors are inevitable during synthesizing, storing and sequencing. Currently, many error correction algorithms have been developed to ensure accurate information retrieval, but they will decrease storage density or increase computing complexity. Here, we apply the Bloom Filter, a space-efficient probabilistic data structure, to DNA storage to achieve the anti-error, or anti-contamination function. This method only needs the original correct DNA sequences (referred to as target sequences) to produce a corresponding data structure, which will filter out almost all the incorrect sequences (referred to as non-target sequences) during sequencing data analysis. Experimental results demonstrate the universal and efficient filtering capabilities of our method. Furthermore, we employ the Counting Bloom Filter to achieve the file version control function, which significantly reduces synthesis costs when modifying DNA-form files. To achieve cost-efficient file version control function, a modified system based on yin-yang codec is developed.
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Affiliation(s)
- Yiming Li
- BGI Research, Shenzhen, 518083, China
- BGI Research, Changzhou, 213299, China
| | - Haoling Zhang
- BGI Research, Shenzhen, 518083, China
- Living Systems Lab, BESE, CEMSE, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | | | - Yue Shen
- BGI Research, Shenzhen, 518083, China
- BGI Research, Changzhou, 213299, China
| | - Zhi Ping
- BGI Research, Shenzhen, 518083, China
- BGI Research, Changzhou, 213299, China
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, 518172, China
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33
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Houghton MC, Kashanian SV, Derrien TL, Masuda K, Vollmer F. Whispering-Gallery Mode Optoplasmonic Microcavities: From Advanced Single-Molecule Sensors and Microlasers to Applications in Synthetic Biology. ACS PHOTONICS 2024; 11:892-903. [PMID: 38523742 PMCID: PMC10958601 DOI: 10.1021/acsphotonics.3c01570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 03/26/2024]
Abstract
Optical microcavities, specifically, whispering-gallery mode (WGM) microcavities, with their remarkable sensitivity to environmental changes, have been extensively employed as biosensors, enabling the detection of a wide range of biomolecules and nanoparticles. To push the limits of detection down to the most sensitive single-molecule level, plasmonic nanorods are strategically introduced to enhance the evanescent fields of WGM microcavities. This advancement of optoplasmonic WGM sensors allows for the detection of single molecules of a protein, conformational changes, and even atomic ions, marking significant contributions in single-molecule sensing. This Perspective discusses the exciting research prospects in optoplasmonic WGM sensing of single molecules, including the study of enzyme thermodynamics and kinetics, the emergence of thermo-optoplasmonic sensing, the ultrasensitive single-molecule sensing on WGM microlasers, and applications in synthetic biology.
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Affiliation(s)
- Matthew C. Houghton
- Department
of Physics and Astronomy, University of
Exeter, Exeter
Devon EX4 4QL, United Kingdom
- Department
of Life Sciences, University of Bath, Bath BA2 7AX, United Kingdom
| | - Samir Vartabi Kashanian
- Department
of Physics and Astronomy, University of
Exeter, Exeter
Devon EX4 4QL, United Kingdom
| | - Thomas L. Derrien
- Department
of Physics and Astronomy, University of
Exeter, Exeter
Devon EX4 4QL, United Kingdom
| | - Koji Masuda
- Department
of Physics and Astronomy, University of
Exeter, Exeter
Devon EX4 4QL, United Kingdom
| | - Frank Vollmer
- Department
of Physics and Astronomy, University of
Exeter, Exeter
Devon EX4 4QL, United Kingdom
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34
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Lund S, Potapov V, Johnson SR, Buss J, Tanner NA. Highly Parallelized Construction of DNA from Low-Cost Oligonucleotide Mixtures Using Data-Optimized Assembly Design and Golden Gate. ACS Synth Biol 2024; 13:745-751. [PMID: 38377591 PMCID: PMC10949349 DOI: 10.1021/acssynbio.3c00694] [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: 11/20/2023] [Revised: 02/12/2024] [Accepted: 02/13/2024] [Indexed: 02/22/2024]
Abstract
Commercially synthesized genes are typically made using variations of homology-based cloning techniques, including polymerase cycling assembly from chemically synthesized microarray-derived oligonucleotides. Here, we apply Data-optimized Assembly Design (DAD) to the synthesis of hundreds of codon-optimized genes in both constitutive and inducible vectors using Golden Gate Assembly. Starting from oligonucleotide pools, we synthesize genes in three simple steps: (1) amplification of parts belonging to individual assemblies in parallel from a single pool; (2) Golden Gate Assembly of parts for each construct; and (3) transformation. We construct genes from receiving DNA to sequence confirmed isolates in as little as 4 days. By leveraging the ligation fidelity afforded by T4 DNA ligase, we expect to be able to construct a larger breadth of sequences not currently supported by homology-based methods, which require stability of extensive single-stranded DNA overhangs.
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Affiliation(s)
- Sean Lund
- Research
Department, New England Biolabs, Ipswich, Massachusetts 01938, United States
| | - Vladimir Potapov
- Research
Department, New England Biolabs, Ipswich, Massachusetts 01938, United States
| | - Sean R. Johnson
- Research
Department, New England Biolabs, Ipswich, Massachusetts 01938, United States
| | - Jackson Buss
- Research
Department, New England Biolabs, Ipswich, Massachusetts 01938, United States
| | - Nathan A. Tanner
- Research
Department, New England Biolabs, Ipswich, Massachusetts 01938, United States
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35
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Yang S, Bögels BWA, Wang F, Xu C, Dou H, Mann S, Fan C, de Greef TFA. DNA as a universal chemical substrate for computing and data storage. Nat Rev Chem 2024; 8:179-194. [PMID: 38337008 DOI: 10.1038/s41570-024-00576-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2024] [Indexed: 02/12/2024]
Abstract
DNA computing and DNA data storage are emerging fields that are unlocking new possibilities in information technology and diagnostics. These approaches use DNA molecules as a computing substrate or a storage medium, offering nanoscale compactness and operation in unconventional media (including aqueous solutions, water-in-oil microemulsions and self-assembled membranized compartments) for applications beyond traditional silicon-based computing systems. To build a functional DNA computer that can process and store molecular information necessitates the continued development of strategies for computing and data storage, as well as bridging the gap between these fields. In this Review, we explore how DNA can be leveraged in the context of DNA computing with a focus on neural networks and compartmentalized DNA circuits. We also discuss emerging approaches to the storage of data in DNA and associated topics such as the writing, reading, retrieval and post-synthesis editing of DNA-encoded data. Finally, we provide insights into how DNA computing can be integrated with DNA data storage and explore the use of DNA for near-memory computing for future information technology and health analysis applications.
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Affiliation(s)
- Shuo Yang
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, Shanghai, China
| | - Bas W A Bögels
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Fei Wang
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Can Xu
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, Shanghai, China
| | - Hongjing Dou
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, Shanghai, China
| | - Stephen Mann
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, China.
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, Shanghai, China.
- Centre for Protolife Research and Centre for Organized Matter Chemistry, School of Chemistry, University of Bristol, Bristol, UK.
- Max Planck-Bristol Centre for Minimal Biology, School of Chemistry, University of Bristol, Bristol, UK.
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China.
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Tom F A de Greef
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, The Netherlands.
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands.
- Center for Living Technologies, Eindhoven-Wageningen-Utrecht Alliance, Utrecht, The Netherlands.
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36
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Schaudy E, Ibañez-Redín G, Parlar E, Somoza MM, Lietard J. Nonaqueous Oxidation in DNA Microarray Synthesis Improves the Oligonucleotide Quality and Preserves Surface Integrity on Gold and Indium Tin Oxide Substrates. Anal Chem 2024; 96:2378-2386. [PMID: 38285499 PMCID: PMC10867803 DOI: 10.1021/acs.analchem.3c04166] [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: 09/15/2023] [Revised: 12/29/2023] [Accepted: 12/29/2023] [Indexed: 01/30/2024]
Abstract
Nucleic acids attached to electrically conductive surfaces are very frequently used platforms for sensing and analyte detection as well as for imaging. Synthesizing DNA on these uncommon substrates and preserving the conductive layer is challenging as this coating tends to be damaged by the repeated use of iodine and water, which is the standard oxidizing medium following phosphoramidite coupling. Here, we thoroughly investigate the use of camphorsulfonyl oxaziridine (CSO), a nonaqueous alternative to I2/H2O, for the synthesis of DNA microarrays in situ. We find that CSO performs equally well in producing high hybridization signals on glass microscope slides, and CSO also protects the conductive layer on gold and indium tin oxide (ITO)-coated slides. DNA synthesis on conductive substrates with CSO oxidation yields microarrays of quality approaching that of conventional glass with intact physicochemical properties.
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Affiliation(s)
- Erika Schaudy
- Institute
of Inorganic Chemistry, University of Vienna, Josef-Holaubek-Platz 2, Vienna 1090, Austria
| | - Gisela Ibañez-Redín
- Institute
of Inorganic Chemistry, University of Vienna, Josef-Holaubek-Platz 2, Vienna 1090, Austria
| | - Etkin Parlar
- Institute
of Inorganic Chemistry, University of Vienna, Josef-Holaubek-Platz 2, Vienna 1090, Austria
| | - Mark M. Somoza
- Institute
of Inorganic Chemistry, University of Vienna, Josef-Holaubek-Platz 2, Vienna 1090, Austria
- Leibniz-Institute
for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Straße 30, Freising 85354, Germany
- Chair
of Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner-Straße 34, Freising 85354, Germany
| | - Jory Lietard
- Institute
of Inorganic Chemistry, University of Vienna, Josef-Holaubek-Platz 2, Vienna 1090, Austria
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37
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Matteau D, Duval A, Baby V, Rodrigue S. Mesoplasma florum: a near-minimal model organism for systems and synthetic biology. Front Genet 2024; 15:1346707. [PMID: 38404664 PMCID: PMC10884336 DOI: 10.3389/fgene.2024.1346707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 01/24/2024] [Indexed: 02/27/2024] Open
Abstract
Mesoplasma florum is an emerging model organism for systems and synthetic biology due to its small genome (∼800 kb) and fast growth rate. While M. florum was isolated and first described almost 40 years ago, many important aspects of its biology have long remained uncharacterized due to technological limitations, the absence of dedicated molecular tools, and since this bacterial species has not been associated with any disease. However, the publication of the first M. florum genome in 2004 paved the way for a new era of research fueled by the rise of systems and synthetic biology. Some of the most important studies included the characterization and heterologous use of M. florum regulatory elements, the development of the first replicable plasmids, comparative genomics and transposon mutagenesis, whole-genome cloning in yeast, genome transplantation, in-depth characterization of the M. florum cell, as well as the development of a high-quality genome-scale metabolic model. The acquired data, knowledge, and tools will greatly facilitate future genome engineering efforts in M. florum, which could next be exploited to rationally design and create synthetic cells to advance fundamental knowledge or for specific applications.
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Affiliation(s)
- Dominick Matteau
- Département de biologie, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Anthony Duval
- Département de biologie, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Vincent Baby
- Centre de diagnostic vétérinaire de l'Université de Montréal, Université de Montréal, Saint-Hyacinthe, QC, Canada
| | - Sébastien Rodrigue
- Département de biologie, Université de Sherbrooke, Sherbrooke, QC, Canada
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38
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Sun C, Li M, Wang F. Programming and monitoring surface-confined DNA computing. Bioorg Chem 2024; 143:107080. [PMID: 38183684 DOI: 10.1016/j.bioorg.2023.107080] [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: 10/31/2023] [Revised: 12/19/2023] [Accepted: 12/28/2023] [Indexed: 01/08/2024]
Abstract
DNA-based molecular computing has evolved to encompass a diverse range of functions, demonstrating substantial promise for both highly parallel computing and various biomedical applications. Recent advances in DNA computing systems based on surface reactions have demonstrated improved levels of specificity and computational speed compared to their solution-based counterparts that depend on three-dimensional molecular collisions. Herein, computational biomolecular interactions confined by various surfaces such as DNA origamis, nanoparticles, lipid membranes and chips are systematically reviewed, along with their manipulation methodologies. Monitoring techniques and applications for these surface-based computing systems are also described. The advantages and challenges of surface-confined DNA computing are discussed.
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Affiliation(s)
- Chenyun Sun
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mingqiang Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Fei Wang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China.
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39
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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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40
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Lyons-Abbott S, Abramov A, Chan CL, Deer JR, Fu G, Hassouneh W, Koch T, Misquith A, O'Neill J, Simon SA, Wolf A, Yeh R, Vernet E. Choice of fusion proteins, expression host, and analytics solves difficult-to-produce protein challenges in discovery research. Biotechnol J 2024; 19:e2300162. [PMID: 37802118 DOI: 10.1002/biot.202300162] [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: 04/10/2023] [Revised: 09/05/2023] [Accepted: 09/26/2023] [Indexed: 10/08/2023]
Abstract
High quality biological reagents are a prerequisite for pharmacological research. Herein a protein production screening approach, including quality assessment methods, for protein-based discovery research is presented. Trends from 2895 expression constructs representing 253 proteins screened in mammalian and bacterial hosts-91% of which are successfully expressed and purified-are discussed. Mammalian expression combined with the use of solubility-promoting fusion proteins is deemed suitable for most targets. Furthermore, cases utilizing stable cell line generation and choice of fusion protein for higher yield and quality of difficult-to-produce proteins (Leucine-rich repeat-containing G-protein coupled receptor 4 (LGR4) and Neurturin) are presented and discussed. In the case of Neurturin, choice of fusion protein impacted the target binding 80-fold. These results highlight the need for exploration of construct designs and careful Quality Control (QC) of difficult-to-produce protein reagents.
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Affiliation(s)
| | - Ariel Abramov
- Novo Nordisk Research Center Seattle, Inc, Seattle, Washington, USA
| | - Chung-Leung Chan
- Novo Nordisk Research Center Seattle, Inc, Seattle, Washington, USA
| | - Jen Running Deer
- Novo Nordisk Research Center Seattle, Inc, Seattle, Washington, USA
| | - Guangsen Fu
- Novo Nordisk Research Center Seattle, Inc, Seattle, Washington, USA
| | - Wafa Hassouneh
- Novo Nordisk Research Center Seattle, Inc, Seattle, Washington, USA
| | - Tyree Koch
- Novo Nordisk Research Center Seattle, Inc, Seattle, Washington, USA
| | - Ayesha Misquith
- Novo Nordisk Research Center Seattle, Inc, Seattle, Washington, USA
| | - Jason O'Neill
- Novo Nordisk Research Center Seattle, Inc, Seattle, Washington, USA
| | | | - Anitra Wolf
- Novo Nordisk Research Center Seattle, Inc, Seattle, Washington, USA
| | - Ronald Yeh
- Novo Nordisk Research Center Seattle, Inc, Seattle, Washington, USA
| | - Erik Vernet
- Novo Nordisk Research Center Seattle, Inc, Seattle, Washington, USA
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41
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Yin Y, Arneson R, Apostle A, Eriyagama AMDN, Chillar K, Burke E, Jahfetson M, Yuan Y, Fang S. Long oligodeoxynucleotides: chemical synthesis, isolation via catching-by-polymerization, verification via sequencing, and gene expression demonstration. Beilstein J Org Chem 2023; 19:1957-1965. [PMID: 38170048 PMCID: PMC10760481 DOI: 10.3762/bjoc.19.146] [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: 09/03/2023] [Accepted: 12/14/2023] [Indexed: 01/05/2024] Open
Abstract
Long oligodeoxynucleotides (ODNs) are segments of DNAs having over one hundred nucleotides (nt). They are typically assembled using enzymatic methods such as PCR and ligation from shorter 20 to 60 nt ODNs produced by automated de novo chemical synthesis. While these methods have made many projects in areas such as synthetic biology and protein engineering possible, they have various drawbacks. For example, they cannot produce genes and genomes with long repeats and have difficulty to produce sequences containing stable secondary structures. Here, we report a direct de novo chemical synthesis of 400 nt ODNs, and their isolation from the complex reaction mixture using the catching-by-polymerization (CBP) method. To determine the authenticity of the ODNs, 399 and 401 nt ODNs were synthesized and purified with CBP. The two were joined together using Gibson assembly to give the 800 nt green fluorescent protein (GFP) gene construct. The sequence of the construct was verified via Sanger sequencing. To demonstrate the potential use of the long ODN synthesis method, the GFP gene was expressed in E. coli. The long ODN synthesis and isolation method presented here provides a pathway to the production of genes and genomes containing long repeats or stable secondary structures that cannot be produced or are highly challenging to produce using existing technologies.
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Affiliation(s)
- Yipeng Yin
- Department of Chemistry and Health Research Institute, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA,
| | - Reed Arneson
- College of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA
| | - Alexander Apostle
- Department of Chemistry and Health Research Institute, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA,
| | - Adikari M D N Eriyagama
- Department of Chemistry and Health Research Institute, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA,
| | - Komal Chillar
- Department of Chemistry and Health Research Institute, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA,
| | - Emma Burke
- College of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA
| | - Martina Jahfetson
- Department of Chemistry and Health Research Institute, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA,
| | - Yinan Yuan
- College of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA
| | - Shiyue Fang
- Department of Chemistry and Health Research Institute, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA,
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42
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Zhang Y, Takaki Y, Yoshida-Takashima Y, Hiraoka S, Kurosawa K, Nunoura T, Takai K. A sequential one-pot approach for rapid and convenient characterization of putative restriction-modification systems. mSystems 2023; 8:e0081723. [PMID: 37843256 PMCID: PMC10734518 DOI: 10.1128/msystems.00817-23] [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: 08/03/2023] [Accepted: 09/05/2023] [Indexed: 10/17/2023] Open
Abstract
IMPORTANCE The elucidation of the molecular basis of virus-host coevolutionary interactions is boosted with state-of-the-art sequencing technologies. However, the sequence-only information is often insufficient to output a conclusive argument without biochemical characterizations. We proposed a 1-day and one-pot approach to confirm the exact function of putative restriction-modification (R-M) genes that presumably mediate microbial coevolution. The experiments mainly focused on a series of putative R-M enzymes from a deep-sea virus and its host bacterium. The results quickly unveiled unambiguous substrate specificities, superior catalytic performance, and unique sequence preferences for two new restriction enzymes (capable of cleaving DNA) and two new methyltransferases (capable of modifying DNA with methyl groups). The reality of the functional R-M system reinforced a model of mutually beneficial interactions with the virus in the deep-sea microbial ecosystem. The cell culture-independent approach also holds great potential for exploring novel and biotechnologically significant R-M enzymes from microbial dark matter.
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Affiliation(s)
- Yi Zhang
- SUGAR Program, X-star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Yoshihiro Takaki
- SUGAR Program, X-star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Yukari Yoshida-Takashima
- SUGAR Program, X-star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Satoshi Hiraoka
- Research Center for Bioscience and Nanoscience (CeBN), MRU, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Kanako Kurosawa
- SUGAR Program, X-star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), MRU, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Ken Takai
- SUGAR Program, X-star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
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43
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Li Q, Yan H. "Difficult" deoxyribonucleotide sequences in the solid-phase synthesis by the phosphoramidite chemistry. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2023; 43:655-663. [PMID: 38116988 DOI: 10.1080/15257770.2023.2295478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 12/11/2023] [Indexed: 12/21/2023]
Abstract
This work catalogued oligonucleotide sequences and sequence compositions based on the overall yield of full-length product obtained by the phosphoramidite chemistry-based solid phase synthesis. In total, 76 sequences with different dinucleotide and trinucleotide repeats were synthesized, and the fully-deprotected products were analyzed by denaturing anion exchange HPLC. Overall, sequences containing more 2'-deoxyadenosine residues were obtained in relatively lower yields, likely due to the relative ease of 2'-deoxyadenosine to undergo depurination during the detritylation reaction. Furthermore, dinucleotide steps, such as d(CG)/d(GC) and d(AG)/d(GA), likely contribute the overall lower yields of full-length products as well.
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Affiliation(s)
- Quanjian Li
- Department of Chemistry, Brock University, St. Catharines, ON, Canada
| | - Hongbin Yan
- Department of Chemistry, Brock University, St. Catharines, ON, Canada
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44
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Savinov A, Swanson S, Keating AE, Li GW. High-throughput computational discovery of inhibitory protein fragments with AlphaFold. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.19.572389. [PMID: 38187731 PMCID: PMC10769210 DOI: 10.1101/2023.12.19.572389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Peptides can bind to specific sites on larger proteins and thereby function as inhibitors and regulatory elements. Peptide fragments of larger proteins are particularly attractive for achieving these functions due to their inherent potential to form native-like binding interactions. Recently developed experimental approaches allow for high-throughput measurement of protein fragment inhibitory activity in living cells. However, it has thus far not been possible to predict de novo which of the many possible protein fragments bind their protein targets, let alone act as inhibitors. We have developed a computational method, FragFold, that employs AlphaFold to predict protein fragment binding to full-length protein targets in a high-throughput manner. Applying FragFold to thousands of fragments tiling across diverse proteins revealed peaks of predicted binding along each protein sequence. These predictions were compared with experimentally measured peaks of inhibitory activity in E. coli. We establish that our approach is a sensitive predictor of protein fragment function: Evaluating inhibitory fragments derived from known protein-protein interaction interfaces, we found 87% were predicted by FragFold to bind in a native-like mode. Across full protein sequences, 68% of FragFold-predicted binding peaks match experimentally measured inhibitory peaks. This is true even when the underlying inhibitory mechanism is unclear from existing structural data, and we find FragFold is able to predict novel binding modes for inhibitory fragments of unknown structure, explaining previous genetic and biochemical data for these fragments. The success rate of FragFold demonstrates that this computational approach should be broadly applicable for discovering inhibitory protein fragments across proteomes.
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Affiliation(s)
- Andrew Savinov
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sebastian Swanson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Amy E. Keating
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Center for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Gene-Wei Li
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
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45
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Buller R, Lutz S, Kazlauskas RJ, Snajdrova R, Moore JC, Bornscheuer UT. From nature to industry: Harnessing enzymes for biocatalysis. Science 2023; 382:eadh8615. [PMID: 37995253 DOI: 10.1126/science.adh8615] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/17/2023] [Indexed: 11/25/2023]
Abstract
Biocatalysis harnesses enzymes to make valuable products. This green technology is used in countless applications from bench scale to industrial production and allows practitioners to access complex organic molecules, often with fewer synthetic steps and reduced waste. The last decade has seen an explosion in the development of experimental and computational tools to tailor enzymatic properties, equipping enzyme engineers with the ability to create biocatalysts that perform reactions not present in nature. By using (chemo)-enzymatic synthesis routes or orchestrating intricate enzyme cascades, scientists can synthesize elaborate targets ranging from DNA and complex pharmaceuticals to starch made in vitro from CO2-derived methanol. In addition, new chemistries have emerged through the combination of biocatalysis with transition metal catalysis, photocatalysis, and electrocatalysis. This review highlights recent key developments, identifies current limitations, and provides a future prospect for this rapidly developing technology.
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Affiliation(s)
- R Buller
- Competence Center for Biocatalysis, Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences, 8820 Wädenswil, Switzerland
| | - S Lutz
- Codexis Incorporated, Redwood City, CA 94063, USA
| | - R J Kazlauskas
- Department of Biochemistry, Molecular Biology and Biophysics, Biotechnology Institute, University of Minnesota, Saint Paul, MN 55108, USA
| | - R Snajdrova
- Novartis Institutes for BioMedical Research, Global Discovery Chemistry, 4056 Basel, Switzerland
| | - J C Moore
- MRL, Merck & Co., Rahway, NJ 07065, USA
| | - U T Bornscheuer
- Institute of Biochemistry, Dept. of Biotechnology and Enzyme Catalysis, Greifswald University, Greifswald, Germany
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46
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Brzezinska J, Trzciński S, Strzelec J, Chmielewski MK. From CPG to hybrid support: Review on the approaches in nucleic acids synthesis in various media. Bioorg Chem 2023; 140:106806. [PMID: 37660625 DOI: 10.1016/j.bioorg.2023.106806] [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: 06/07/2023] [Revised: 07/26/2023] [Accepted: 08/22/2023] [Indexed: 09/05/2023]
Abstract
Solid-phase synthesis is, to date, the preferred method for the manufacture of oligonucleotides, in quantities ranging from a few micrograms for research purposes to several kilograms for therapeutic or commercial use. But for large-scale oligonucleotide manufacture, scaling up and hazardous waste production pose challenges that necessitate the investigation of alternate synthetic techniques. Despite the disadvantages of glass supports, using soluble supports as a substitute presents difficulties because of their high overall yield and complex purification steps. To address these challenges, various independent approaches have been developed; however, other problems such as insufficient cycle efficiency and synthesis of oligonucleotide chains of desired length continue to exist. In this study, we present a review of the current developments, advantages, and difficulties of recently reported alternatives to supports based on controlled pore glass, and discuss the importance of a support choice to resolve issues arising during oligonucleotide synthesis.
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Affiliation(s)
- Jolanta Brzezinska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Stanisław Trzciński
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Joanna Strzelec
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Marcin K Chmielewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland; FutureSynthesis sp. z o.o., ul. Rubież 46B, 61-612 Poznan, Poland.
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47
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Capponi S, Daniels KG. Harnessing the power of artificial intelligence to advance cell therapy. Immunol Rev 2023; 320:147-165. [PMID: 37415280 DOI: 10.1111/imr.13236] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 06/17/2023] [Indexed: 07/08/2023]
Abstract
Cell therapies are powerful technologies in which human cells are reprogrammed for therapeutic applications such as killing cancer cells or replacing defective cells. The technologies underlying cell therapies are increasing in effectiveness and complexity, making rational engineering of cell therapies more difficult. Creating the next generation of cell therapies will require improved experimental approaches and predictive models. Artificial intelligence (AI) and machine learning (ML) methods have revolutionized several fields in biology including genome annotation, protein structure prediction, and enzyme design. In this review, we discuss the potential of combining experimental library screens and AI to build predictive models for the development of modular cell therapy technologies. Advances in DNA synthesis and high-throughput screening techniques enable the construction and screening of libraries of modular cell therapy constructs. AI and ML models trained on this screening data can accelerate the development of cell therapies by generating predictive models, design rules, and improved designs.
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Affiliation(s)
- Sara Capponi
- Department of Functional Genomics and Cellular Engineering, IBM Almaden Research Center, San Jose, California, USA
- Center for Cellular Construction, San Francisco, California, USA
| | - Kyle G Daniels
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
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48
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Sabra DM, Krin A, Romeral AB, Frieß JL, Jeremias G. Anthrax revisited: how assessing the unpredictable can improve biosecurity. Front Bioeng Biotechnol 2023; 11:1215773. [PMID: 37795173 PMCID: PMC10546327 DOI: 10.3389/fbioe.2023.1215773] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/24/2023] [Indexed: 10/06/2023] Open
Abstract
B. anthracis is one of the most often weaponized pathogens. States had it in their bioweapons programs and criminals and terrorists have used or attempted to use it. This study is motivated by the narrative that emerging and developing technologies today contribute to the amplification of danger through greater easiness, accessibility and affordability of steps in the making of an anthrax weapon. As states would have way better preconditions if they would decide for an offensive bioweapons program, we focus on bioterrorism. This paper analyzes and assesses the possible bioterrorism threat arising from advances in synthetic biology, genome editing, information availability, and other emerging, and converging sciences and enabling technologies. Methodologically we apply foresight methods to encourage the analysis of contemporary technological advances. We have developed a conceptual six-step foresight science framework approach. It represents a synthesis of various foresight methodologies including literature review, elements of horizon scanning, trend impact analysis, red team exercise, and free flow open-ended discussions. Our results show a significant shift in the threat landscape. Increasing affordability, widespread distribution, efficiency, as well as ease of use of DNA synthesis, and rapid advances in genome-editing and synthetic genomic technologies lead to an ever-growing number and types of actors who could potentially weaponize B. anthracis. Understanding the current and future capabilities of these technologies and their potential for misuse critically shapes the current and future threat landscape and underlines the necessary adaptation of biosecurity measures in the spheres of multi-level political decision making and in the science community.
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Affiliation(s)
- Dunja Manal Sabra
- Carl Friedrich von Weizsäcker-Centre for Science and Peace Research (ZNF), University of Hamburg, Bogenallee, Hamburg, Germany
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Wang Y, Zhang K, Zhao Y, Li Y, Su W, Li S. Construction and Applications of Mammalian Cell-Based DNA-Encoded Peptide/Protein Libraries. ACS Synth Biol 2023; 12:1874-1888. [PMID: 37315219 DOI: 10.1021/acssynbio.3c00043] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
DNA-encoded peptide/protein libraries are the starting point for protein evolutionary modification and functional peptide/antibody selection. Different display technologies, protein directed evolution, and deep mutational scanning (DMS) experiments employ DNA-encoded libraries to provide sequence variations for downstream affinity- or function-based selections. Mammalian cells promise the inherent post-translational modification and near-to-natural conformation of exogenously expressed mammalian proteins and thus are the best platform for studying transmembrane proteins or human disease-related proteins. However, due to the current technical bottlenecks of constructing mammalian cell-based large size DNA-encoded libraries, the advantages of mammalian cells as screening platforms have not been fully exploited. In this review, we summarize the current efforts in constructing DNA-encoded libraries in mammalian cells and the existing applications of these libraries in different fields.
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Affiliation(s)
- Yi Wang
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Kaili Zhang
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Yanjie Zhao
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Yifan Li
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Weijun Su
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Shuai Li
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
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Ling N, Liu H, Guo J, Liang Z, Zhang Y, Li H, Wu H, Xie T, Yuan Y, Li X, Peng M, Wei X, Liang L, Liu J, Wu W, Ye M. Generation of DNA Aptamers with Functional Activity in Mammalian Cells by Mimicking Retroviruses. Anal Chem 2023. [PMID: 37327388 DOI: 10.1021/acs.analchem.3c00387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
DNA aptamers are single-stranded DNA oligonucleotide sequences that bind to specific targets with high affinity. Currently, DNA aptamers can be produced only by in vitro synthesis. It is difficult for DNA aptamers to have a sustained impact on intracellular protein activity, which limits their clinical application. In this study, we developed a DNA aptamer expression system to generate DNA aptamers with functional activity in mammalian cells by mimicking retroviruses. Using this system, DNA aptamers targeting intracellular Ras (Ra1) and membrane-bound CD71 (XQ2) were successfully generated in cells. In particular, the expressed Ra1 not only specifically bound to the intracellular Ras protein but also inhibited the phosphorylation of downstream ERK1/2 and AKT. Furthermore, by inserting the DNA aptamer expression system for Ra1 into a lentivirus vector, the system can be delivered into cells and stably produce Ra1 over time, resulting in the inhibition of lung cancer cell proliferation. Therefore, our study provides a novel strategy for the intracellular generation of DNA aptamers with functional activity and opens a new avenue for the clinical application of intracellular DNA aptamers in disease treatment.
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Affiliation(s)
- Neng Ling
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Huiming Liu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Junxiao Guo
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Zhouliang Liang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Yibin Zhang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Hui Li
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Hui Wu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Tiantian Xie
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Yijun Yuan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Xiahui Li
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Menglan Peng
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Xianhua Wei
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Long Liang
- Molecular Biology Research Center and Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Jing Liu
- Molecular Biology Research Center and Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Wencan Wu
- The Eye Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang 325000, China
| | - Mao Ye
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
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