1
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Bizat PN, Sabat N, Hollenstein M. Recent Advances in Biocatalytic and Chemoenzymatic Synthesis of Oligonucleotides. Chembiochem 2025; 26:e202400987. [PMID: 39854143 DOI: 10.1002/cbic.202400987] [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: 12/02/2024] [Revised: 01/16/2025] [Accepted: 01/24/2025] [Indexed: 01/26/2025]
Abstract
Access to synthetic oligonucleotides is crucial for applications in diagnostics, therapeutics, synthetic biology, and nanotechnology. Traditional solid phase synthesis is limited by sequence length and complexities, low yields, high costs and poor sustainability. Similarly, polymerase-based approaches such as in vitro transcription and primer extension reactions do not permit any control on the positioning of modifications and display poor substrate tolerance. In response, biocatalytic and chemoenzymatic strategies have emerged as promising alternatives, offering selective and efficient pathways for oligonucleotide synthesis. These methods leverage the precision and efficiency of enzymes to construct oligonucleotides with high fidelity. Recent advancements have focused on optimized systems and/or engineered enzymes enabling the incorporation of chemically modified nucleotides. Biocatalytic approaches, particularly those using DNA/RNA polymerases provide advantages in milder reaction conditions and enhanced sustainability. Chemoenzymatic methods, combining chemical synthesis and enzymes, have proven to be effective in overcoming limitations of traditional solid phase synthesis. This review summarizes recent developments in biocatalytic and chemoenzymatic strategies to construct oligonucleotides, highlighting innovations in enzyme engineering, substrate and reaction condition optimization for various applications. We address crucial details of the methods, their advantages, and limitations as well as important insights for future research directions in oligonucleotide production.
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Affiliation(s)
- Pierre Nicolas Bizat
- 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
| | - Nazarii Sabat
- 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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2
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Pant S, Jena NR. Computational predictions of artificial nucleoside triphosphates as potent inhibitors of RNA-dependent RNA polymerase of the ZIKA virus. Hum Immunol 2025; 86:111286. [PMID: 40117673 DOI: 10.1016/j.humimm.2025.111286] [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: 10/21/2024] [Revised: 03/07/2025] [Accepted: 03/08/2025] [Indexed: 03/23/2025]
Abstract
As the RNA-dependent RNA polymerase (RdRp) of the Zika virus (ZIKV) is responsible for replicating the viral RNA genome inside host cells, its inhibition is necessary to control the Zika viral disease. Here, the interactions of 16 artificial RNA and DNA nucleoside triphosphates with the substrate active site of RdRp are studied in detail by using the molecular docking technique. The top 8 hits containing ligands such as ZTP, BTP, STP, XTP, dZTP, dBTP, dSTP, and dXTP were further studied by using molecular dynamics, and MM/GBSA Free-energy methods. It is revealed that among various nucleoside triphosphates studied herein, the dBTP would bind to RdRP most strongly with a binding free energy (ΔGbind) of -70.40 ± 4.6 kcal/mol followed by dZTP with a ΔGbind of -67.37 ± 3.1 kcal/mol. The binding of these artificial nucleoside triphosphates to RdRp is about 22-26 kcal/mol more stable than that of the natural nucleoside triphosphate GTP. Therefore, it is expected that dBTP and dZTP would inhibit the activities of RdRp strongly. The molecular mechanisms of inhibition of RdRp activities are also discussed and compared with experimental studies.
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Affiliation(s)
- S Pant
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Kolkata 700054, India
| | - N R Jena
- Discipline of Natural Sciences, Indian Institute of Information Technology, Design and Manufacturing, Dumna Airport Road, Jabalpur 482005, India.
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3
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Huang X, Hou Z, Qiang W, Wang H, Wang X, Chen X, Hu X, Dai J, Li L, Zhao G. Towards next-generation DNA encryption via an expanded genetic system. Natl Sci Rev 2025; 12:nwae469. [PMID: 40160677 PMCID: PMC11951100 DOI: 10.1093/nsr/nwae469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 11/22/2024] [Accepted: 12/12/2024] [Indexed: 04/02/2025] Open
Abstract
Information encryption based on DNA data archiving, referred to as DNA encryption, has been advocated for decades and has become highly appealing owing to its remarkable advantages, e.g. high storage capacity, complexity and programmability. Early DNA encryption schemes primarily leveraged the natural four-letter genetic alphabet for data storage, with message-storing DNA sequences easily decrypted by routine DNA sequencing, which is consequently vulnerable to attack and faces severe security challenges. Here, an unnatural base pair (UBP), dNaM-dTPT3, was introduced into the message and/or index DNA sequences, which can be stored either in vitro or in vivo; this approach achieved the bioorthogonal encryption of 'secret' messages, where message DNAs could be selectively, faithfully and readily retrieved or read exclusively in the presence of unnatural bases. Furthermore, a separative computational algorithm, named IM-Codec, was developed to encrypt the data into a 'key sequence' and an 'information sequence' through UBP insertion. Finally, a UBP-based multilevel DNA encryption approach was developed and validated for data encryption and decryption. The employment of the UBP expanded genetic system for data encryption should provide valuable solutions for archiving highly confidential data and thus usher in a new era of DNA encryption.
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Affiliation(s)
- Xiaoluo Huang
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Zhaohua Hou
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710129, China
| | - Wei Qiang
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Honglei Wang
- Henan Key Laboratory of Organic Functional Molecule and Drug Innovation, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, School of Chemistry and Chemical Engineering, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Normal University, Xinxiang 453007, China
- State Key Laboratory of Antiviral Drug and Pingyuan Lab, Henan Normal University, Xinxiang 453007, China
| | - Xiangxiang Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710129, China
| | - Xiaoxu Chen
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710129, China
| | - Xin Hu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710129, China
| | - Junbiao Dai
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes 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 518000, China
| | - Lingjun Li
- Henan Key Laboratory of Organic Functional Molecule and Drug Innovation, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, School of Chemistry and Chemical Engineering, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Normal University, Xinxiang 453007, China
- State Key Laboratory of Antiviral Drug and Pingyuan Lab, Henan Normal University, Xinxiang 453007, China
| | - Guanghou Zhao
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710129, China
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4
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Kawabe H, Manfio L, Magana Pena S, Zhou NA, Bradley KM, Chen C, McLendon C, Benner SA, Levy K, Yang Z, Marchand JA, Fuhrmeister ER. Harnessing Non-standard Nucleic Acids for Highly Sensitive Icosaplex (20-Plex) Detection of Microbial Threats for Environmental Surveillance. ACS Synth Biol 2025; 14:470-484. [PMID: 39898969 PMCID: PMC11854376 DOI: 10.1021/acssynbio.4c00619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2024] [Revised: 01/13/2025] [Accepted: 01/17/2025] [Indexed: 02/04/2025]
Abstract
Environmental surveillance and clinical diagnostics heavily rely on the polymerase chain reaction (PCR) for target detection. A growing list of microbial threats warrants new PCR-based detection methods that are highly sensitive, specific, and multiplexable. Here, we introduce a PCR-based icosaplex (20-plex) assay for detecting 18 enteropathogen and two antimicrobial resistance genes. This multiplexed PCR assay leverages the self-avoiding molecular recognition system (SAMRS) to avoid primer dimer formation, the artificially expanded genetic information system (AEGIS) for amplification specificity, and next-generation sequencing for amplicon identification. Using parallelized multitarget TaqMan Array Cards (TAC) to benchmark performance of the 20-plex assay on wastewater, soil, and human stool samples, we found 90% agreement on positive calls and 89% agreement on negative calls. Additionally, we show how long-read and short-read sequencing information from the 20-plex can be used to further classify allelic variants of genes and distinguish subspecies. The strategy presented offers sensitive, affordable, and robust multiplex detection that can be used to support efforts in wastewater-based epidemiology, environmental monitoring, and human/animal diagnostics.
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Affiliation(s)
- Hinako Kawabe
- Chemical
Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Luran Manfio
- Foundation
for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Alachua, Florida 32615, United States
| | - Sebastian Magana Pena
- Foundation
for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Alachua, Florida 32615, United States
| | - Nicolette A. Zhou
- Department
of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Kevin M. Bradley
- Foundation
for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Alachua, Florida 32615, United States
- Firebird
Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, Florida 32615, United States
| | - Cen Chen
- Foundation
for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Alachua, Florida 32615, United States
- Firebird
Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, Florida 32615, United States
| | - Chris McLendon
- Firebird
Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, Florida 32615, United States
| | - Steven A. Benner
- Foundation
for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Alachua, Florida 32615, United States
- Firebird
Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, Florida 32615, United States
| | - Karen Levy
- Department
of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Zunyi Yang
- Foundation
for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Alachua, Florida 32615, United States
- Firebird
Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, Florida 32615, United States
| | - Jorge A. Marchand
- Chemical
Engineering, University of Washington, Seattle, Washington 98195, United States
- Molecular
Engineering and Science Institute, University
of Washington, Seattle, Washington 98195, United States
| | - Erica R. Fuhrmeister
- Department
of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington 98195, United States
- Molecular
Engineering and Science Institute, University
of Washington, Seattle, Washington 98195, United States
- Civil and
Environmental Engineering, University of
Washington, Seattle, Washington 98195, United States
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5
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Shaker S, Li J, Wan S, Xuan H, Long J, Cao H, Wei T, Liu Q, Xu D, Benner S, Zhang L. Cancer cell target discovery: comparing laboratory evolution of expanded DNA six-nucleotide alphabets with standard four-nucleotide alphabets. Nucleic Acids Res 2025; 53:gkaf072. [PMID: 39950344 PMCID: PMC11826092 DOI: 10.1093/nar/gkaf072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2024] [Revised: 01/07/2025] [Accepted: 01/29/2025] [Indexed: 02/17/2025] Open
Abstract
Anthropogenic evolvable genetic information systems (AEGIS) are DNA-like molecules that can be copied, support laboratory in vitro evolution (LIVE), and evolve to give AegisBodies, analogs of antibodies. However, unlike DNA aptamers built from four different nucleotides, AegisBodies are currently built from six different nucleotides. Thus, six-letter AEGIS-LIVE delivers AegisBodies with greater stability in biological mixtures, more folds, and enhanced binding and catalytic power. Unlike DNA however, AEGIS has not benefited from 4 billion years of biological evolution to create AEGIS-specialized enzymes, but only a decade or so of human design. To learn whether AEGIS can nevertheless perform as well as natural DNA as a platform to create functional molecules, we compared two six-letter AegisBodies (LZH5b and LZH8) with a single standard four-letter aptamer, both evolved to bind specific cancer cells with ∼10 cycles of LIVE. Both evolved ∼50 nM affinities. Both discovered proteins on their cancer cell surfaces thought to function only inside of cells. Both can be internalized. Internalizing of LZH5b attached to an AEGIS nanotrain brings attached drugs into the cell. These data show that AEGIS-LIVE can do what four-letter LIVE can do at its limits of performance after 4 billion years of evolution of DNA-specialized enzymes, and better by a few metrics. As synthetic biologists continue to improve enzymology and analytical chemistry to support AEGIS-LIVE, this technology shoud prove increasingly useful as a tool, especially in cancer research.
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Affiliation(s)
- Sharpkate Shaker
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Jun Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Shuo Wan
- Foundation for Applied Molecular Evolution, Alachua, FL 32615, United States
| | - Hong Xuan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Jinchen Long
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Haiyan Cao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Tongxuan Wei
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Qinguo Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Da Xu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Hepatopancreatobiliary Surgery Department I, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, Alachua, FL 32615, United States
| | - Liqin Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
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6
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Mao Y, Zhao Y, Zhou Q, Li W. Chromosome Engineering: Technologies, Applications, and Challenges. Annu Rev Anim Biosci 2025; 13:25-47. [PMID: 39541223 DOI: 10.1146/annurev-animal-111523-102225] [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: 11/16/2024]
Abstract
Chromosome engineering is a transformative field at the cutting edge of biological science, offering unprecedented precision in manipulating large-scale genomic DNA within cells. This discipline is central to deciphering how the multifaceted roles of chromosomes-guarding genetic information, encoding sequence positional information, and influencing organismal traits-shape the genetic blueprint of life. This review comprehensively examines the technological advancements in chromosome engineering, which center on engineering chromosomal rearrangements, generating artificial chromosomes, de novo synthesizing chromosomes, and transferring chromosomes. Additionally, we introduce the application progress of chromosome engineering in basic and applied research fields, showcasing its capacity to deepen our knowledge of genetics and catalyze breakthroughs in therapeutic strategies. Finally, we conclude with a discussion of the challenges the field faces and highlight the profound implications that chromosome engineering holds for the future of modern biology and medical applications.
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Affiliation(s)
- Yihuan Mao
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology and Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing, China;
| | - Yulong Zhao
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology and Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing, China;
| | - Qi Zhou
- University of Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology and Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing, China;
| | - Wei Li
- University of Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology and Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing, China;
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7
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Liu D, Xu D, Shi L, Zhang J, Bi K, Luo B, Liu C, Li Y, Fan G, Wang W, Ping Z. A practical DNA data storage using an expanded alphabet introducing 5-methylcytosine. GIGABYTE 2025; 2025:gigabyte147. [PMID: 39906332 PMCID: PMC11791762 DOI: 10.46471/gigabyte.147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2024] [Accepted: 01/15/2025] [Indexed: 02/06/2025] Open
Abstract
The DNA molecule is a promising next-generation data storage medium. Recently, it has been theoretically proposed that non-natural or modified bases can serve as extra molecular letters to increase the information density. However, this strategy is challenging due to the difficulty in synthesizing non-natural DNA sequences and their complex structure. Here, we described a practical DNA data storage transcoding scheme named R+ based on an expanded molecular alphabet that introduces 5-methylcytosine (5mC). We demonstrated its experimental validation by encoding one representative file into several 1.3∼1.6 kbps in vitro DNA fragments for nanopore sequencing. Our results show an average data recovery rate of 98.97% and 86.91% with and without reference, respectively. Our work validates the practicability of 5mC in DNA storage systems, with a potentially wide range of applications. Availability and implementation R+ is implemented in Python and the code is available under a MIT license at https://github.com/Incpink-Liu/DNA-storage-R_plus.
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Affiliation(s)
- Deruilin Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI Research, Shenzhen, 518083, China
| | - Demin Xu
- BGI Research, Shenzhen, 518083, China
- BGI Research, Beijing, 100101, China
| | | | | | - Kewei Bi
- BGI Research, Changzhou, 213299, China
| | - Bei Luo
- Wuhan BGI Technology Service Co., Ltd., Wuhan, 430073, China
| | - Chen Liu
- Wuhan BGI Technology Service Co., Ltd., Wuhan, 430073, China
| | - Yuxiang Li
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310030, China
| | - Guangyi Fan
- BGI Research, Shenzhen, 518083, China
- BGI Research, Qingdao, 266426, China
| | - Wen Wang
- BGI Research, Shenzhen, 518083, China
- BGI Research, Beijing, 100101, China
| | - Zhi Ping
- BGI Research, Shenzhen, 518083, China
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen, 518172, China
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8
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Blackstock C, Walters-Freke C, Richards N, Williamson A. Nucleic acid joining enzymes: biological functions and synthetic applications beyond DNA. Biochem J 2025; 482:39-56. [PMID: 39840831 DOI: 10.1042/bcj20240136] [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: 09/09/2024] [Revised: 11/21/2024] [Accepted: 12/04/2024] [Indexed: 01/23/2025]
Abstract
DNA-joining by ligase and polymerase enzymes has provided the foundational tools for generating recombinant DNA and enabled the assembly of gene and genome-sized synthetic products. Xenobiotic nucleic acid (XNA) analogues of DNA and RNA with alternatives to the canonical bases, so-called 'unnatural' nucleobase pairs (UBP-XNAs), represent the next frontier of nucleic acid technologies, with applications as novel therapeutics and in engineering semi-synthetic biological organisms. To realise the full potential of UBP-XNAs, researchers require a suite of compatible enzymes for processing nucleic acids on a par with those already available for manipulating canonical DNA. In particular, enzymes able to join UBP-XNA will be essential for generating large assemblies and also hold promise in the synthesis of single-stranded oligonucleotides. Here, we review recent and emerging advances in the DNA-joining enzymes, DNA polymerases and DNA ligases, and describe their applications to UBP-XNA manipulation. We also discuss the future directions of this field which we consider will involve two-pronged approaches of enzyme biodiscovery for natural UBP-XNA compatible enzymes, coupled with improvement by structure-guided engineering.
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Affiliation(s)
- Chelsea Blackstock
- School of Science, University of Waikato, Hamilton, Waikato, 3216, New Zealand
| | | | - Nigel Richards
- Foundation for Applied Molecular Evolution, Alachua, FL, 32615, U.S.A
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, U.K
| | - Adele Williamson
- School of Science, University of Waikato, Hamilton, Waikato, 3216, New Zealand
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9
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Gu R, Lambertsen Larsen K, Wang A, Tan J. Approaching Dynamic Behaviors of Life through Systems Chemistry. Chemistry 2025; 31:e202403083. [PMID: 39485372 DOI: 10.1002/chem.202403083] [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: 08/15/2024] [Revised: 10/20/2024] [Accepted: 10/30/2024] [Indexed: 11/03/2024]
Abstract
The intricate interplay of metabolic reactions and molecular assembly in living systems enables spatiotemporally organization and gives rise to diverse dynamic behaviors that characterize life. Over the last decades, research efforts have increasingly focused on replicating the remarkable properties and characteristics of living systems, driving the rapid growth of systems chemistry. This young discipline which generally studies interacting molecular networks and emergent system-level properties, behaviors, and functions, offers new concepts and tools to tackle the complexity of life. In this review paper, we have explored seminal research and recent advancements in recreating dynamic behaviors of life with systems chemistry. We believe that the recreation of the dynamic behaviors of life through systems chemistry would set the initial steps to obtain synthetic life de novo.
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Affiliation(s)
- Ruirui Gu
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Chemistry and Molecular Engineering, Institute of Fine Chemicals, East China University of Science and Technology, 130 Meilong Road, Shanghai, China
| | - Kim Lambertsen Larsen
- Department of Chemistry and Bioscience, Section of Chemistry Science and Engineering, Aalborg University, Fredrik Bajers Vej 7H, Aalborg Ø, Denmark
| | - Ali Wang
- Department of Chemistry, Section of Biological Chemistry, University of Copenhagen, Universitetsparken 5, København Ø, Denmark
| | - Junjun Tan
- Department of Chemistry, Section of Biological Chemistry, University of Copenhagen, Universitetsparken 5, København Ø, Denmark
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10
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Kompatscher M, Gonnella I, Erlacher M. Studying the Function of tRNA Modifications: Experimental Challenges and Opportunities. J Mol Biol 2025:168934. [PMID: 39756793 DOI: 10.1016/j.jmb.2024.168934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2024] [Revised: 12/19/2024] [Accepted: 12/31/2024] [Indexed: 01/07/2025]
Abstract
tRNAs are essential molecules in protein synthesis, responsible for translating the four-nucleotide genetic code into the corresponding amino acid sequence. RNA modifications play a crucial role in influencing tRNA folding, structure, and function. These modifications, ranging from simple methylations to complex hypermodified species, are distributed throughout the tRNA molecule. Depending on their type and position, they contribute to the accuracy and efficiency of decoding by participating in a complex network of interactions. The enzymatic processes introducing these modifications are equally intricate and diverse, adding further complexity. As a result, studying tRNA modifications faces limitations at multiple levels. This review addresses the challenges involved in manipulating and studying the function of tRNA modifications and discusses experimental strategies and possibilities to overcome these obstacles.
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Affiliation(s)
- Maria Kompatscher
- Institute of Genomics and RNomics, Medical University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Isabell Gonnella
- Institute of Genomics and RNomics, Medical University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Matthias Erlacher
- Institute of Genomics and RNomics, Medical University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria.
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11
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Ward AJ, Partridge BE. Beyond DAD: proposing a one-letter code for nucleobase-mediated molecular recognition. J Mater Chem B 2025; 13:485-495. [PMID: 39569673 DOI: 10.1039/d4tb01999g] [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: 11/22/2024]
Abstract
Nucleobase binding is a fundamental molecular recognition event central to modern biological and bioinspired supramolecular research. Underpinning this recognition is a deceptively simple hydrogen-bonding code, primarily based on the canonical nucleobases in DNA and RNA. Inspired by these biotic structures, chemists and biologists have designed abiotic hydrogen-bonding motifs that can interact with, augment, and reshape native molecular recognition, for applications ranging from genetic code expansion and nucleic acid recognition to supramolecular materials utilizing mono- and bifacial nucleobases. However, as the number of nucleobase-inspired motifs expands, the absence of a standard vocabulary to describe hydrogen bond (HB) patterns has led to a haphazard mixture of shorthand descriptors that are confusing and inconsistent. Alternative notations that specify individual HB sites (such as DAD for donor-acceptor-donor) are cumbersome for biological and supramolecular constructs that contain many such patterns. This situation creates a barrier to sharing and interpreting nucleobase-related research across sub-disciplines, hindering collaboration and innovation. In this perspective, we aim to initiate discourse on this issue by considering what would be needed to formulate a concise one-letter code for the HB patterns associated with synthetic nucleobases. We first summarize some of the issues caused by the current absence of a consistent naming scheme. Subsequently, we discuss some key considerations in designing a coherent naming system. Finally, we leverage chemical rationale and pedagogical mnemonic considerations to propose a succinct and intuitive one-letter code for supramolecular two- and three-HB motifs. We hope that this discussion will spark conversations within our interdisciplinary community, thereby facilitating collaboration and easing communication among researchers engaged in synthetic nucleobase design.
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Affiliation(s)
- Aiden J Ward
- Department of Chemistry, University of Rochester, Rochester, NY 14627-0216, USA.
| | - Benjamin E Partridge
- Department of Chemistry, University of Rochester, Rochester, NY 14627-0216, USA.
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12
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Wang B, Kim HJ, Bradley KM, Chen C, McLendon C, Yang Z, Benner SA. Joining Natural and Synthetic DNA Using Biversal Nucleotides: Efficient Sequencing of Six-Nucleotide DNA. J Am Chem Soc 2024; 146:35129-35138. [PMID: 39625448 DOI: 10.1021/jacs.4c11043] [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: 12/26/2024]
Abstract
By rearranging hydrogen bond donor and acceptor groups within a standard Watson-Crick geometry, DNA can add eight independently replicable nucleotides forming four additional not found in standard Terran DNA. For many applications, the orthogonal pairing of standard and nonstandard pairs offers a key advantage. However, other applications require standard and nonstandard nucleotides to communicate with each other. This is especially true when seeking to recruit high-throughput instruments (e.g., Illumina), designed to sequence standard 4-nucleotide DNA, to sequence DNA that includes added nucleotides. For this purpose, PCR workflows are needed to replace nonstandard nucleotides in (for example) a 6-letter DNA sequence by defined mixtures of standard nucleotides built from 4 nucleotides. High-throughput sequencing can then report the sequences of those mixtures to bioinformatic alignment tools, which infer the original 6-nucleotide sequence by analysis of the mixtures. Unfortunately, the intrinsic orthogonality of standard and nonstandard nucleotides often demand polymerases that violate pairing biophysics to do this replacement, leading to inefficiencies in this "transliteration" process. Thus, laboratory in vitro evolution (LIVE) using "anthropogenic evolvable genetic information systems" (AEGIS), an important "consumer" of new sequencing tools, has been slow to be democratized; robust sequencing is needed to identify the AegisBodies and AegisZymes that AEGIS-LIVE delivers. This work introduces a new way to connect synthetic and standard molecular biology: biversal nucleotides. In an example presented here, a pyrimidine analogue (pyridine-2-one, y) pairs with Watson-Crick geometry to both a nonstandard base (2-amino-8-imidazo-[1,2a]-1,3,5-triazin-[8H]-4-one, P, the Watson-Crick partner of 6-amino-5-nitro-[1H]-pyridin-2-one, Z) and a base that completes the Watson-Crick hydrogen bond pattern (2-amino-2'-deoxyadenosine, amA). PCR amplification of GACTZP DNA with dyTP delivers products where Z:P pairs are cleanly transliterated to A:T pairs. In parallel, PCR of the same GACTZP sample at higher pH delivers products where Z:P pairs are cleanly transliterated to C:G pairs. By allowing robust sequencing of 6-letter GACTZP DNA, this workflow will help democratize AEGIS-LIVE. Further, other implementations of the biversal concept can enable communication across and between standard DNA and synthetic DNA more generally.
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Affiliation(s)
- Bang Wang
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd, Alachua, Florida 32601, United States
- Firebird Biomolecular Sciences, LLC, Alachua, Florida 32601, United States
| | - Hyo-Joong Kim
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd, Alachua, Florida 32601, United States
| | - Kevin M Bradley
- Firebird Biomolecular Sciences, LLC, Alachua, Florida 32601, United States
| | - Cen Chen
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd, Alachua, Florida 32601, United States
| | - Chris McLendon
- Firebird Biomolecular Sciences, LLC, Alachua, Florida 32601, United States
| | - Zunyi Yang
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd, Alachua, Florida 32601, United States
- Firebird Biomolecular Sciences, LLC, Alachua, Florida 32601, United States
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd, Alachua, Florida 32601, United States
- Firebird Biomolecular Sciences, LLC, Alachua, Florida 32601, United States
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13
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Babar V, Sharma S, Shaikh AR, Oliva R, Chawla M, Cavallo L. Sensing Hachimoji DNA Bases with Janus MoSH Monolayer Nanodevice: Insights from Density Functional Theory (DFT) and Non-Equilibrium Green's Function Analysis. ACS OMEGA 2024; 9:48173-48184. [PMID: 39676917 PMCID: PMC11635677 DOI: 10.1021/acsomega.4c05356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Revised: 11/14/2024] [Accepted: 11/19/2024] [Indexed: 12/17/2024]
Abstract
Detection of nucleobases is of great significance in DNA sequencing, which is one of the main goals of the Human Genome Project. The synthesis of Hachimoji DNA, an artificial genetic system with eight nucleotide bases, has induced a transformative shift in genetic research and biosensing. Here, we present a systematic investigation of the adsorption behavior and electronic transport properties of natural and modified DNA bases on a Janus molybdenum sulfur hydride (MoSH) monolayer using density functional theory (DFT) and nonequilibrium Green's function (NEGF) methods. Our results demonstrate that the S side of the MoSH monolayer is more effective as a sensing platform compared to the H side, which undergoes significant structural distortions due to chemisorption. The S side selectively distinguishes natural bases A and T from G and C, and modified bases S and Z from others. However, the negligible changes in current after base adsorption highlight the limitations of relying solely on current sensitivity for detection. Our findings provide valuable insights into the design of MoSH monolayer-based sensing platforms for selective DNA base detection, with potential applications in next-generation DNA sequencing technologies.
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Affiliation(s)
- Vasudeo Babar
- Physical
Sciences and Engineering Division, Kaust Catalysis Center, King Abdullah University of Science and Technology
(KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Sitansh Sharma
- Department
of Research and Innovation, STEMskills Research
and Education Lab Private Limited, Faridabad, Haryana 121002, India
| | - Abdul Rajjak Shaikh
- Department
of Sciences and Technologies, University
Parthenope of Naples, Centro Direzionale Isola C4, Naples 80143, Italy
| | - Romina Oliva
- Department
of Sciences and Technologies, University
Parthenope of Naples, Centro Direzionale Isola C4, Naples 80143, Italy
| | - Mohit Chawla
- Physical
Sciences and Engineering Division, Kaust Catalysis Center, King Abdullah University of Science and Technology
(KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Luigi Cavallo
- Physical
Sciences and Engineering Division, Kaust Catalysis Center, King Abdullah University of Science and Technology
(KAUST), Thuwal 23955-6900, Saudi Arabia
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14
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Fallah A, Imani Fooladi AA, Havaei SA, Mahboobi M, Sedighian H. Recent advances in aptamer discovery, modification and improving performance. Biochem Biophys Rep 2024; 40:101852. [PMID: 39525567 PMCID: PMC11546948 DOI: 10.1016/j.bbrep.2024.101852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2024] [Revised: 10/06/2024] [Accepted: 10/16/2024] [Indexed: 11/16/2024] Open
Abstract
Aptamers are nucleic acid (Ribonucleic acid (RNA) and single strand deoxyribonucleic acid (ssDNA)) with a length of approximately 25-80 bases that can bind to particular target molecules, similar to monoclonal antibodies. Due to their many benefits, which include a long shelf life, minimal batch-to-batch variations, extremely low immunogenicity, the possibility of chemical modifications for improved stability, an extended serum half-life, and targeted delivery, they are receiving a lot of attention in a variety of clinical applications. The development of high-affinity modification approaches has attracted significant attention in aptamer applications. Stable three-dimensional aptamers that have undergone chemical modification can engage firmly with target proteins through improved non-covalent binding, potentially leading to hundreds of affinity improvements. This review demonstrates how cutting-edge methodologies for aptamer discovery are being developed to consistently and effectively construct high-performing aptamers that need less money and resources yet have a high chance of success. Also, High-affinity aptamer modification techniques were discussed.
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Affiliation(s)
- Arezoo Fallah
- Department of Bacteriology and Virology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Abbas Ali Imani Fooladi
- Applied Microbiology Research Center, Biomedicine Technologies Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Seyed Asghar Havaei
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mahdieh Mahboobi
- Applied Microbiology Research Center, Biomedicine Technologies Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Hamid Sedighian
- Applied Microbiology Research Center, Biomedicine Technologies Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
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15
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Xiong Q, Wang P, Ma C, Law ATK, Wang M, Kwok WM. Superior Photostability of the Unnatural Base 6-Amino-5-nitropyridin-2-ol: A Case Study Using Ultrafast Broadband Fluorescence, Transient Absorption, and Theoretical Computation. J Phys Chem Lett 2024; 15:11553-11561. [PMID: 39526600 DOI: 10.1021/acs.jpclett.4c02751] [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: 11/16/2024]
Abstract
6-Amino-5-nitropyridin-2-ol (Z), a nitroaromatic compound and a base for Hachimoji nucleic acids, holds significant potential in expanding the genetic alphabet, as well as in synthetic biology and biotechnology. Despite its promising applications, the spectral characterization and photoinduced properties of Z have remained largely unexplored until now. This study presents a comprehensive investigation into its excited state dynamics in various solvents, utilizing state-of-the-art ultrafast broadband time-resolved fluorescence and transient absorption spectroscopy, complemented by computational methods. The acquired results provide direct experimental evidence that, upon photoexcitation, Z emits prompt fluorescence from a nearly planar structure in its excited state, independent of solvent properties. This state deactivates nonradiatively within sub-picoseconds through internal conversion with a unitary yield, primarily mediated by the rotation of the nitro group. This unusually rapid deactivation pathway entirely excludes the involvement of long-lived nπ* states, triplet states, and photoproducts, which are commonly observed in most nitroaromatic compounds and natural DNA and RNA bases. Our findings underscore that Z, as an unnatural base, exhibits superior photostability compared to canonical natural bases. This provides valuable insights into the photodynamics of nitroaromatic compounds, which is beneficial for strategic substitution design in environmental and biological applications.
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Affiliation(s)
- Qingwu Xiong
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong 518071, People's Republic of China
- College of Physics and optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong 518060, People's Republic of China
| | - Ping Wang
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong 518071, People's Republic of China
| | - Chensheng Ma
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong 518071, People's Republic of China
| | - Alvis Tsz-Kit Law
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong 999077, People's Republic of China
| | - Mingliang Wang
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong 518071, People's Republic of China
| | - Wai-Ming Kwok
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong 999077, People's Republic of China
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16
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Cui X, Fan J, Gao Y, Zhou X, Zhang C, Meng Q. Designing Quasi-Intrinsic Photosensitizers with Dual Function of Fluorescence Imaging and Photodynamic Therapy. J Med Chem 2024; 67:19826-19836. [PMID: 39485727 DOI: 10.1021/acs.jmedchem.4c02213] [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: 11/03/2024]
Abstract
Photosensitizers (PSs) with effective two-photon absorption in the therapeutic window are the key to two-photon photodynamic therapy. However, the traditional exogenous PSs usually lead to rejection in the body. Besides, the precise visualization of treatments proposes new demands and challenges for the design of PSs. Accordingly, in this work, a series of quasi-intrinsic PSs are obtained based on the artificial base 2-amino-8-(1'-β-d-2'-deoxyribofuranosyl)-imidazo[1,2-α]-1,3,5-triazin-4(8H)-one (P). The calculations show that the structural modification could enhance the two-photon absorption and fluorescence emission, which is beneficial for tumor localization. Furthermore, the reduced singlet-triplet energy gaps and enhanced spin-orbit coupling contribute to the rapid intersystem crossing process, which results in a triplet state with high quantum yields. To ensure the phototherapeutic performance of the newly designed PSs, we also examined the vertical electron affinity and vertical ionization potential for generation of superoxide anions, as well as the T1 energy required to produce singlet oxygen.
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Affiliation(s)
- Xixi Cui
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, P. R. China
| | - Jianzhong Fan
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, P. R. China
| | - Yang Gao
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, P. R. China
| | - Xucong Zhou
- School of Basic Medical Sciences, Shandong Second Medical University, Weifang 261053, P. R. China
| | - Changzhe Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, P. R. China
| | - Qingtian Meng
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, P. R. China
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17
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Costello A, Peterson AA, Chen PH, Bagirzadeh R, Lanster DL, Badran AH. Genetic Code Expansion History and Modern Innovations. Chem Rev 2024; 124:11962-12005. [PMID: 39466033 DOI: 10.1021/acs.chemrev.4c00275] [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: 10/29/2024]
Abstract
The genetic code is the foundation for all life. With few exceptions, the translation of nucleic acid messages into proteins follows conserved rules, which are defined by codons that specify each of the 20 proteinogenic amino acids. For decades, leading research groups have developed a catalogue of innovative approaches to extend nature's amino acid repertoire to include one or more noncanonical building blocks in a single protein. In this review, we summarize advances in the history of in vitro and in vivo genetic code expansion, and highlight recent innovations that increase the scope of biochemically accessible monomers and codons. We further summarize state-of-the-art knowledge in engineered cellular translation, as well as alterations to regulatory mechanisms that improve overall genetic code expansion. Finally, we distill existing limitations of these technologies into must-have improvements for the next generation of technologies, and speculate on future strategies that may be capable of overcoming current gaps in knowledge.
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Affiliation(s)
- Alan Costello
- Department of Chemistry The Scripps Research Institute; La Jolla, California 92037, United States
- Department of Integrative Structural and Computational Biology The Scripps Research Institute; La Jolla, California 92037, United States
| | - Alexander A Peterson
- Department of Chemistry The Scripps Research Institute; La Jolla, California 92037, United States
- Department of Integrative Structural and Computational Biology The Scripps Research Institute; La Jolla, California 92037, United States
| | - Pei-Hsin Chen
- Department of Chemistry The Scripps Research Institute; La Jolla, California 92037, United States
- Department of Integrative Structural and Computational Biology The Scripps Research Institute; La Jolla, California 92037, United States
- Doctoral Program in Chemical and Biological Sciences The Scripps Research Institute; La Jolla, California 92037, United States
| | - Rustam Bagirzadeh
- Department of Chemistry The Scripps Research Institute; La Jolla, California 92037, United States
- Department of Integrative Structural and Computational Biology The Scripps Research Institute; La Jolla, California 92037, United States
| | - David L Lanster
- Department of Chemistry The Scripps Research Institute; La Jolla, California 92037, United States
- Department of Integrative Structural and Computational Biology The Scripps Research Institute; La Jolla, California 92037, United States
- Doctoral Program in Chemical and Biological Sciences The Scripps Research Institute; La Jolla, California 92037, United States
| | - Ahmed H Badran
- Department of Chemistry The Scripps Research Institute; La Jolla, California 92037, United States
- Department of Integrative Structural and Computational Biology The Scripps Research Institute; La Jolla, California 92037, United States
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18
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Vecchioni S, Ohayon YP, Hernandez C, Hoshika S, Mao C, Benner SA, Sha R. Six-Letter DNA Nanotechnology: Incorporation of Z- P Base Pairs into Self-Assembling 3D Crystals. NANO LETTERS 2024; 24:14302-14306. [PMID: 39471314 PMCID: PMC11566107 DOI: 10.1021/acs.nanolett.4c03949] [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: 08/14/2024] [Revised: 10/25/2024] [Accepted: 10/25/2024] [Indexed: 11/01/2024]
Abstract
Artificially expanded genetic information systems (AEGIS) were developed to expand the diversity and functionality of biological systems. Recent experiments have shown that these expanded DNA molecular systems are robust platforms for information storage and retrieval as well as useful for basic biotechnologies. In tandem, nucleic acid nanotechnology has seen the use of information-based "semantomorphic" encoding to drive the self-assembly of a vast array of supramolecular devices. To establish the effectiveness of AEGIS toward nanotechnological applications, we investigated the ability of a six-letter alphabet composed of A:T, G:C and synthetic Z:P (Z, 6-amino-3-(1'-β-d-2'-deoxy ribofuranosyl)-5-nitro-(1H)-pyridin-2-one; P, 2-amino-8-(1'-β-d-2'-deoxyribofuranosyl)-imidazo-[1,2a]-1,3,5-triazin-(8H)-4-one) base pairs to engage in 3D self-assembly. We found that crystals could be programmably assembled from AEGIS oligomers. We conclude that unnatural base pairs can be used for the topological self-assembly of crystals. We anticipate the expansion of AEGIS-based nucleic acid nanotechnologies to enable the development of novel nanomaterials, high-fidelity signal cascades, and dynamic nanoscale devices.
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Affiliation(s)
- Simon Vecchioni
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - Yoel P. Ohayon
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - Carina Hernandez
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - Shuichi Hoshika
- Foundation
for Applied Molecular Evolution, Alachua, Florida 32615, United States
| | - Chengde Mao
- Department
of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Steven A. Benner
- Foundation
for Applied Molecular Evolution, Alachua, Florida 32615, United States
| | - Ruojie Sha
- Department
of Chemistry, New York University, New York, New York 10003, United States
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19
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Esposito J, Kakar J, Khokhar T, Noll-Walker T, Omar F, Christen A, James Cleaves H, Sandora M. Comparing the complexity of written and molecular symbolic systems. Biosystems 2024; 244:105297. [PMID: 39154841 DOI: 10.1016/j.biosystems.2024.105297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 08/11/2024] [Accepted: 08/11/2024] [Indexed: 08/20/2024]
Abstract
Symbolic systems (SSs) are uniquely products of living systems, such that symbolism and life may be inextricably intertwined phenomena. Within a given SS, there is a range of symbol complexity over which signaling is functionally optimized. This range exists relative to a complex and potentially infinitely large background of latent, unused symbol space. Understanding how symbol sets sample this latent space is relevant to diverse fields including biochemistry and linguistics. We quantitatively explored the graphic complexity of two biosemiotic systems: genetically encoded amino acids (GEAAs) and written language. Molecular and graphical notions of complexity are highly correlated for GEAAs and written language. Symbol sets are generally neither minimally nor maximally complex relative to their latent spaces, but exist across an objectively definable distribution, with the GEAAs having especially low complexity. The selection pressures guiding these disparate systems are explicable by symbol production and disambiguation efficiency. These selection pressures may be universal, offer a quantifiable metric for comparison, and suggest that all life in the Universe may discover optimal symbol set complexity distributions with respect to their latent spaces. If so, the "complexity" of individual components of SSs may not be as strong a biomarker as symbol set complexity distribution.
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Affiliation(s)
- Julia Esposito
- Blue Marble Space Institute of Science, Seattle, WA, USA
| | - Jyotika Kakar
- Blue Marble Space Institute of Science, Seattle, WA, USA; Department of Computer Engineering, University of Mumbai, MH, India
| | - Tasneem Khokhar
- Blue Marble Space Institute of Science, Seattle, WA, USA; Department of Physics and Astronomy, University of California, Irvine, CA, USA
| | | | - Fatima Omar
- Blue Marble Space Institute of Science, Seattle, WA, USA; Jodrell Bank Centre for Astrophysics, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Anna Christen
- Blue Marble Space Institute of Science, Seattle, WA, USA
| | - H James Cleaves
- Department of Chemistry, Howard University, Washington, DC, 20059, USA; Blue Marble Space Institute of Science, Seattle, WA, USA; Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan.
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20
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Wang H, Tie W, Zhu W, Wang S, Zhang R, Duan J, Ye B, Zhu A, Li L. Recognition and Sequencing of Mutagenic DNA Adduct at Single-Base Resolution Through Unnatural Base Pair. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2404622. [PMID: 39225557 PMCID: PMC11515917 DOI: 10.1002/advs.202404622] [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: 04/30/2024] [Revised: 08/06/2024] [Indexed: 09/04/2024]
Abstract
DNA lesions are linked to cancer, aging, and various diseases. The recognition and sequencing of special DNA lesions are of great interest but highly challenging. In this paper, an unnatural-base-pair-promoting method for sequencing highly mutagenic ethenodeoxycytidine (εC) DNA lesions that occurred frequently is developed. First, a promising unnatural base pair of dεC-dNaM to recognize εC lesions is identified, and then a conversion PCR is developed to site-precise transfer dεC-dNaM to dTPT3-dNaM for convenient Sanger sequencing. The low sequence dependence of this method and its capacity for the enrichment of dεC in the abundance of as low as 1.6 × 10-6 nucleotides is also validated. Importantly, the current method can be smoothly applied for recognition, amplification, enrichment, and sequencing of the real biological samples in which εC lesions are generated in vitro or in vivo, thus offering the first sequencing methodology of εC lesions at single-base resolution. Owing to its simple operations and no destruction of inherent structures of DNA, the unnatural-base-pair strategy may provide a new platform to produce general tools for the sequencing of DNA lesions that are hardly sequenced by traditional strategies.
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Affiliation(s)
- Honglei Wang
- Henan Key Laboratory of Organic Functional Molecule and Drug InnovationCollaborative Innovation Center of Henan Province for Green Manufacturing of Fine ChemicalsSchool of Chemistry and Chemical EngineeringHenan Normal UniversityXinxiangHenan453007China
| | - Wenchao Tie
- Henan Key Laboratory of Organic Functional Molecule and Drug InnovationCollaborative Innovation Center of Henan Province for Green Manufacturing of Fine ChemicalsSchool of Chemistry and Chemical EngineeringHenan Normal UniversityXinxiangHenan453007China
| | - Wuyuan Zhu
- Henan Key Laboratory of Organic Functional Molecule and Drug InnovationCollaborative Innovation Center of Henan Province for Green Manufacturing of Fine ChemicalsSchool of Chemistry and Chemical EngineeringHenan Normal UniversityXinxiangHenan453007China
| | - Shuyuan Wang
- Henan Key Laboratory of Organic Functional Molecule and Drug InnovationCollaborative Innovation Center of Henan Province for Green Manufacturing of Fine ChemicalsSchool of Chemistry and Chemical EngineeringHenan Normal UniversityXinxiangHenan453007China
| | - Ruzhen Zhang
- Henan Key Laboratory of Organic Functional Molecule and Drug InnovationCollaborative Innovation Center of Henan Province for Green Manufacturing of Fine ChemicalsSchool of Chemistry and Chemical EngineeringHenan Normal UniversityXinxiangHenan453007China
| | - Jianlin Duan
- Henan Key Laboratory of Organic Functional Molecule and Drug InnovationCollaborative Innovation Center of Henan Province for Green Manufacturing of Fine ChemicalsSchool of Chemistry and Chemical EngineeringHenan Normal UniversityXinxiangHenan453007China
| | - Bingyu Ye
- State Key Laboratory of Antiviral Drug and Pingyuan LabHenan Normal UniversityXinxiangHenan453007China
| | - Anlian Zhu
- Henan Key Laboratory of Organic Functional Molecule and Drug InnovationCollaborative Innovation Center of Henan Province for Green Manufacturing of Fine ChemicalsSchool of Chemistry and Chemical EngineeringHenan Normal UniversityXinxiangHenan453007China
| | - Lingjun Li
- Henan Key Laboratory of Organic Functional Molecule and Drug InnovationCollaborative Innovation Center of Henan Province for Green Manufacturing of Fine ChemicalsSchool of Chemistry and Chemical EngineeringHenan Normal UniversityXinxiangHenan453007China
- State Key Laboratory of Antiviral Drug and Pingyuan LabHenan Normal UniversityXinxiangHenan453007China
- Henan Key Laboratory of Organic Functional Molecule and Drug InnovationCollaborative Innovation Center of Henan Province for Green Manufacturing of Fine ChemicalsSchool of Chemistry and Chemical EngineeringKey Laboratory of Green Chemical Media and ReactionsMinistry of EducationHenan Normal UniversityXinxiangHenan453007China
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21
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Jann C, Giofré S, Bhattacharjee R, Lemke EA. Cracking the Code: Reprogramming the Genetic Script in Prokaryotes and Eukaryotes to Harness the Power of Noncanonical Amino Acids. Chem Rev 2024; 124:10281-10362. [PMID: 39120726 PMCID: PMC11441406 DOI: 10.1021/acs.chemrev.3c00878] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 06/10/2024] [Accepted: 06/27/2024] [Indexed: 08/10/2024]
Abstract
Over 500 natural and synthetic amino acids have been genetically encoded in the last two decades. Incorporating these noncanonical amino acids into proteins enables many powerful applications, ranging from basic research to biotechnology, materials science, and medicine. However, major challenges remain to unleash the full potential of genetic code expansion across disciplines. Here, we provide an overview of diverse genetic code expansion methodologies and systems and their final applications in prokaryotes and eukaryotes, represented by Escherichia coli and mammalian cells as the main workhorse model systems. We highlight the power of how new technologies can be first established in simple and then transferred to more complex systems. For example, whole-genome engineering provides an excellent platform in bacteria for enabling transcript-specific genetic code expansion without off-targets in the transcriptome. In contrast, the complexity of a eukaryotic cell poses challenges that require entirely new approaches, such as striving toward establishing novel base pairs or generating orthogonally translating organelles within living cells. We connect the milestones in expanding the genetic code of living cells for encoding novel chemical functionalities to the most recent scientific discoveries, from optimizing the physicochemical properties of noncanonical amino acids to the technological advancements for their in vivo incorporation. This journey offers a glimpse into the promising developments in the years to come.
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Affiliation(s)
- Cosimo Jann
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- IMB
Postdoc Programme (IPPro), 55128 Mainz, Germany
| | - Sabrina Giofré
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- IMB
Postdoc Programme (IPPro), 55128 Mainz, Germany
| | - Rajanya Bhattacharjee
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- IMB
International PhD Programme (IPP), 55128 Mainz, Germany
| | - Edward A. Lemke
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- Institute
of Molecular Biology (IMB), 55128 Mainz, Germany
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22
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Le AV, Hartman MCT. Improved synthesis of the unnatural base NaM, and evaluation of its orthogonality in in vitro transcription and translation. RSC Chem Biol 2024; 5:d4cb00121d. [PMID: 39279876 PMCID: PMC11389374 DOI: 10.1039/d4cb00121d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Accepted: 09/04/2024] [Indexed: 09/18/2024] Open
Abstract
Unnatural base pairs (UBP) promise to diversify cellular function through expansion of the genetic code. Some of the most successful UBPs are the hydrophobic base pairs 5SICS:NaM and TPT3:NaM developed by Romesberg. Much of the research on these UBPs has emphasized strategies to enable their efficient replication, transcription and translation in living organisms. These experiments have achieved spectacular success in certain cases; however, the complexity of working in vivo places strong constraints on the types of experiments that can be done to optimize and improve the system. Testing UBPs in vitro, on the other hand, offers advantages including minimization of scale, the ability to precisely control the concentration of reagents, and simpler purification of products. Here we investigate the orthogonality of NaM-containing base pairs in transcription and translation, looking at background readthrough of NaM codons by the native machinery. We also describe an improved synthesis of NaM triphosphate (NaM-TP) and a new assay for testing the purity of UBP containing RNAs.
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Affiliation(s)
- Anthony V Le
- Virginia Commonwealth University, Department of Chemistry 1001 W Main St. Richmond VA 23284 USA
- Virginia Commonwealth University, Massey Cancer Center 401 College St. Richmond VA 23219 USA
| | - Matthew C T Hartman
- Virginia Commonwealth University, Department of Chemistry 1001 W Main St. Richmond VA 23284 USA
- Virginia Commonwealth University, Massey Cancer Center 401 College St. Richmond VA 23219 USA
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23
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Stanisavljević A, Aleksić J, Stojanović M, Baranac-Stojanović M. Solid-state synthesis of polyfunctionalized 2-pyridones and conjugated dienes. Org Biomol Chem 2024; 22:7218-7230. [PMID: 39163014 DOI: 10.1039/d4ob00902a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/21/2024]
Abstract
Functionalized 2-pyridones are important biologically active compounds, DNA base analogues and synthetic intermediates. Herein, we report a simple, green, solid-state synthesis of differently substituted 2-pyridones. It starts from commercially available amines and activated alkynes, uses silica gel (15%Cs2CO3/SiO2) as the solid phase and a reaction vial as the only equipment. If necessary, heating is performed in a laboratory oven. Since most reactions are completed within a few hours, no additional energy consumption is required. The syntheses do not require solvents and other reagents and are easily monitored by standard analytical techniques. The atom economy is high, since all atoms of reactants are present in the products and EtOH is the only by-product. The syntheses produce polyfunctionalized conjugated dienes as the only intermediates, which are also important building blocks.
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Affiliation(s)
- Anđela Stanisavljević
- University of Belgrade - Faculty of Chemistry, Studentski trg 12-16, P.O. Box 158, 11000 Belgrade, Serbia.
| | - Jovana Aleksić
- University of Belgrade - Institute of Chemistry, Technology and Metallurgy - Center for Chemistry, Njegoševa 12, P.O. Box 473, 11000 Belgrade, Serbia.
| | - Milovan Stojanović
- University of Belgrade - Institute of Chemistry, Technology and Metallurgy - Center for Chemistry, Njegoševa 12, P.O. Box 473, 11000 Belgrade, Serbia.
| | - Marija Baranac-Stojanović
- University of Belgrade - Faculty of Chemistry, Studentski trg 12-16, P.O. Box 158, 11000 Belgrade, Serbia.
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24
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Wong TF. Triphasic Development of the Genetic Code. Chem Rev 2024; 124:9866-9872. [PMID: 39088192 PMCID: PMC11393795 DOI: 10.1021/acs.chemrev.3c00915] [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: 08/02/2024]
Abstract
The genetic code contains an alphabet of genetically encoded amino acids. The ten Phase 1 amino acids, including Gly, Ala, Ser, Asp, Glu, Val, Leu, Ile, Pro and Thr, were available from the prebiotic environment, whereas the ten Phase 2 amino acids, including Phe, Tyr, Arg, His, Trp, Asn, Gln, Lys, Cys, and Met, became available only later from amino acid biosyntheses. In the archaeon Methanopyrus kandleri, the oldest organism known, the standard alphabet of 20 amino acids was "frozen" and no additional amino acid was encoded in the subsequent 3 Gyrs. Four decades ago, it was discovered that the code was frozen because all the organisms were so well adapted to the standard amino acids that oligogenic barriers, consisting of genes that are thoroughly dependent on the standard code, would cause loss of viability upon the deletion of any one amino acid from the code. Once the reason for the freezing of the code was ascertained, procedures were devised by scientists worldwide to enable the encoding of novel noncanonical amino acids (ncAAs). These encoded Phase 3 ncAAs now surpass the 20 canonical Phase 2 amino acids in the code.
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Affiliation(s)
- Tze-Fei Wong
- Division of Life Science and Applied Genomics Center, Hong Kong University of Science & Technology Hong Kong, China
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25
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Kawabe H, Manfio L, Pena SM, Zhou NA, Bradley KM, Chen C, McLendon C, Benner SA, Levy K, Yang Z, Marchand JA, Fuhrmeister ER. Harnessing non-standard nucleic acids for highly sensitive icosaplex (20-plex) detection of microbial threats. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.09.09.24313328. [PMID: 39314929 PMCID: PMC11419210 DOI: 10.1101/2024.09.09.24313328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Environmental surveillance and clinical diagnostics heavily rely on the polymerase chain reaction (PCR) for target detection. A growing list of microbial threats warrants new PCR-based detection methods that are highly sensitive, specific, and multiplexable. Here, we introduce a PCR-based icosaplex (20-plex) assay for detecting 18 enteropathogen and two antimicrobial resistance genes. This multiplexed PCR assay leverages the self-avoiding molecular recognition system (SAMRS) to avoid primer dimer formation, the artificially expanded genetic information system (AEGIS) for amplification specificity, and next-generation sequencing for amplicon identification. We benchmarked this assay using a low-cost, portable sequencing platform (Oxford Nanopore) on wastewater, soil, and human stool samples. Using parallelized multi-target TaqMan Array Cards (TAC) to benchmark performance of the 20-plex assay, there was 74% agreement on positive calls and 97% agreement on negative calls. Additionally, we show how sequencing information from the 20-plex can be used to further classify allelic variants of genes and distinguish sub-species. The strategy presented offers sensitive, affordable, and robust multiplex detection that can be used to support efforts in wastewater-based epidemiology, environmental monitoring, and human/animal diagnostics.
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Affiliation(s)
- Hinako Kawabe
- Chemical Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Luran Manfio
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Alachua, FL 32615, USA
| | - Sebastian Magana Pena
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Alachua, FL 32615, USA
| | - Nicolette A. Zhou
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Seattle, WA, 98195, USA
| | - Kevin M. Bradley
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Alachua, FL 32615, USA
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
| | - Cen Chen
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Alachua, FL 32615, USA
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
| | - Chris McLendon
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
| | - Steven A. Benner
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Alachua, FL 32615, USA
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
| | - Karen Levy
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Seattle, WA, 98195, USA
| | - Zunyi Yang
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Alachua, FL 32615, USA
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
| | - Jorge A. Marchand
- Chemical Engineering, University of Washington, Seattle, WA, 98195, USA
- Molecular Engineering and Science Institute, University of Washington, Seattle, Seattle, WA, 98195, USA
| | - Erica R. Fuhrmeister
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Seattle, WA, 98195, USA
- Civil and Environmental Engineering, University of Washington, Seattle, Seattle, WA, 98195, USA
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26
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Gómez-Tatay L, Hernández-Andreu JM. Xenobiology for the Biocontainment of Synthetic Organisms: Opportunities and Challenges. Life (Basel) 2024; 14:996. [PMID: 39202738 PMCID: PMC11355180 DOI: 10.3390/life14080996] [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: 07/24/2024] [Revised: 08/07/2024] [Accepted: 08/09/2024] [Indexed: 09/03/2024] Open
Abstract
Since the development of recombinant DNA technologies, the need to establish biosafety and biosecurity measures to control genetically modified organisms has been clear. Auxotrophies, or conditional suicide switches, have been used as firewalls to avoid horizontal or vertical gene transfer, but their efficacy has important limitations. The use of xenobiological systems has been proposed as the ultimate biosafety tool to circumvent biosafety problems in genetically modified organisms. Xenobiology is a subfield of Synthetic Biology that aims to construct orthogonal biological systems based on alternative biochemistries. Establishing true orthogonality in cell-based or cell-free systems promises to improve and assure that we can progress in synthetic biology safely. Although a wide array of strategies for orthogonal genetic systems have been tested, the construction of a host harboring fully orthogonal genetic system, with all parts operating in an orchestrated, integrated, and controlled manner, still poses an extraordinary challenge for researchers. In this study, we have performed a thorough review of the current literature to present the main advances in the use of xenobiology as a strategy for biocontainment, expanding on the opportunities and challenges of this field of research.
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Affiliation(s)
- Lucía Gómez-Tatay
- Institute of Life Sciences, Universidad Católica de Valencia San Vicente Mártir, 46001 Valencia, Spain;
| | - José Miguel Hernández-Andreu
- Grupo de Investigación en Medicina Molecular y Mitocondrial, Universidad Católica de Valencia San Vicente Mártir, 46001 Valencia, Spain
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27
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Cui X, Fan J, Lyu Y, Zhou X, Meng Q, Zhang C. Quasi-intrinsic thiobase derivatives as potential targeted photosensitizers in two-photon photodynamic therapy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 316:124311. [PMID: 38663131 DOI: 10.1016/j.saa.2024.124311] [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: 01/14/2024] [Revised: 04/08/2024] [Accepted: 04/17/2024] [Indexed: 05/15/2024]
Abstract
In this study, a set of potential quasi-intrinsic photosensitizers for two-photon photodynamic therapy (PDT) are proposed based on the unnatural 2-amino-8-(1'-β-ᴅ-2'-deoxyribofuranosyl)-imidazo[1,2-ɑ]-1,3,5-triazin-4(8H)-one (P), which is paired with the 6-amino-5-nitro-3-(1'-β-ᴅ-2'-deoxyribofuranosyl)-2(1H)-pyridone (Z) and can specifically recognize breast and liver cancer cells. Herein, the effects of sulfur substitution and electron-donating/electron-withdrawing groups on the photophysical properties in aqueous solution are systematically investigated. The one- and two-photon absorption spectra evidence that the modifications could result in red-shifted absorption wavelength and large two-photon absorption cross-section, which contributes to selective excitation and provides effective PDT for deep-seated tissues. To ensure the efficient triplet state population, the singlet-triplet energy gaps and spin-orbit coupling constants were examined, which is responsible for a rapid intersystem crossing rate. Furthermore, these thiobase derivatives are characterized by the long-lived T1 state and the large energy gap for radiationless transition to ensure the generation of cytotoxic singlet oxygen.
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Affiliation(s)
- Xixi Cui
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, PR China
| | - Jianzhong Fan
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, PR China
| | - Yongkang Lyu
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, PR China
| | - Xucong Zhou
- School of Basic Medical Sciences, Shandong Second Medical University, Weifang 261053, PR China
| | - Qingtian Meng
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, PR China.
| | - Changzhe Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, PR China.
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28
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Kehrli J, Husser C, Ryckelynck M. Fluorogenic RNA-Based Biosensors of Small Molecules: Current Developments, Uses, and Perspectives. BIOSENSORS 2024; 14:376. [PMID: 39194605 DOI: 10.3390/bios14080376] [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: 06/05/2024] [Revised: 07/14/2024] [Accepted: 07/19/2024] [Indexed: 08/29/2024]
Abstract
Small molecules are highly relevant targets for detection and quantification. They are also used to diagnose and monitor the progression of disease and infectious processes and track the presence of contaminants. Fluorogenic RNA-based biosensors (FRBs) represent an appealing solution to the problem of detecting these targets. They combine the portability of molecular systems with the sensitivity and multiplexing capacity of fluorescence, as well as the exquisite ligand selectivity of RNA aptamers. In this review, we first present the different sensing and reporting aptamer modules currently available to design an FRB, together with the main methodologies used to discover modules with new specificities. We next introduce and discuss how both modules can be functionally connected prior to exploring the main applications for which FRB have been used. Finally, we conclude by discussing how using alternative nucleotide chemistries may improve FRB properties and further widen their application scope.
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Affiliation(s)
- Janine Kehrli
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France
| | - Claire Husser
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France
| | - Michael Ryckelynck
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France
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29
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Wei K, Ye Z, Dong W, Zhang L, Wang W, Li J, Eltzov E, Wang S, Mao X. Generating robust aptamers for food analysis by sequence-based configuration optimization. Talanta 2024; 275:126044. [PMID: 38626500 DOI: 10.1016/j.talanta.2024.126044] [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: 12/13/2023] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 04/18/2024]
Abstract
Advanced analytical techniques are emerging in the food industry. Aptamer-based biosensors achieve rapid and highly selective analysis, thus drawing particular attention. Aptamers are oligonucleotide probes screened via in vitro Systematic Evolution of Ligands by EXponential Enrichment (SELEX), which can bind with their specific targets by folding into three-dimensional configurations and accept various modifications to be incorporated into biosensors, showing great potential in food analysis. Unfortunately, aptamers obtained by SELEX may not possess satisfactory affinity. Post-SELEX strategies were proposed to optimize aptamers' configuration and enhance the binding affinity, with specificity confirmed. Sequence-based optimization strategies exhibit great advantages in simple operation, good generalization, low cost, etc. This review summarizes the latest study (2015-2023) on generating robust aptamers for food targets by sequence-based configuration optimization, as well as the generated aptamers and aptasensors, with an expectation to provide inspirations for developing aptamer and aptasensors with high performance for food analysis and to safeguard food quality and safety.
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Affiliation(s)
- Kaiyue Wei
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, 266404, PR China; Qingdao Key Laboratory of Food Biotechnology, Qingdao, 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, 266404, PR China
| | - Ziyang Ye
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, 266404, PR China; Qingdao Key Laboratory of Food Biotechnology, Qingdao, 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, 266404, PR China
| | - Wenhui Dong
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, 266404, PR China; Qingdao Key Laboratory of Food Biotechnology, Qingdao, 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, 266404, PR China
| | - Ling Zhang
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, 266404, PR China; Qingdao Key Laboratory of Food Biotechnology, Qingdao, 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, 266404, PR China
| | - Wenjing Wang
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, 266404, PR China; Qingdao Key Laboratory of Food Biotechnology, Qingdao, 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, 266404, PR China
| | - Jiao Li
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, 266404, PR China; Qingdao Key Laboratory of Food Biotechnology, Qingdao, 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, 266404, PR China
| | - Evgeni Eltzov
- Department of Postharvest Science, Institute of Postharvest and Food Sciences, The Volcani Center, Agricultural Research Organization, Bet Dagan, 50250, Israel
| | - Sai Wang
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, 266404, PR China; Qingdao Key Laboratory of Food Biotechnology, Qingdao, 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, 266404, PR China.
| | - Xiangzhao Mao
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, 266404, PR China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, PR China; Qingdao Key Laboratory of Food Biotechnology, Qingdao, 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, 266404, PR China
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30
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Fayaz F, Ganie MA, Kumar S, Raheem S, Rizvi MA, Shah BA. Modular access to sulfur substituted analogues of isocytosine via photoredox catalysis. Chem Commun (Camb) 2024; 60:8256-8259. [PMID: 39011863 DOI: 10.1039/d4cc02076f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
A photoredox approach for synthesizing sulfur-substituted analogues of isocytosine via coupling of modular phenyl propargyl chloride with thiourea has been reported. The resulting product with an amine group was found amenable to various late-stage modifications, providing access to a broad range of sulfur-containing isocytosine derivatives.
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Affiliation(s)
- Faheem Fayaz
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
- Natural Product & Medicinal Chemistry, CSIR-Indian Institute of Integrative Medicine, Jammu-180001, India.
| | - Majid Ahmad Ganie
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
- Natural Product & Medicinal Chemistry, CSIR-Indian Institute of Integrative Medicine, Jammu-180001, India.
| | - Sourav Kumar
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
- Natural Product & Medicinal Chemistry, CSIR-Indian Institute of Integrative Medicine, Jammu-180001, India.
| | - Shabnam Raheem
- Department of Chemistry, University of Kashmir, Srinagar, 190006, India
| | | | - Bhahwal Ali Shah
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
- Natural Product & Medicinal Chemistry, CSIR-Indian Institute of Integrative Medicine, Jammu-180001, India.
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31
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Dou C, Yang Y, Zhu F, Li B, Duan Y. Explorer: efficient DNA coding by De Bruijn graph toward arbitrary local and global biochemical constraints. Brief Bioinform 2024; 25:bbae363. [PMID: 39073829 DOI: 10.1093/bib/bbae363] [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: 01/30/2024] [Revised: 06/25/2024] [Accepted: 07/13/2024] [Indexed: 07/30/2024] Open
Abstract
With the exponential growth of digital data, there is a pressing need for innovative storage media and techniques. DNA molecules, due to their stability, storage capacity, and density, offer a promising solution for information storage. However, DNA storage also faces numerous challenges, such as complex biochemical constraints and encoding efficiency. This paper presents Explorer, a high-efficiency DNA coding algorithm based on the De Bruijn graph, which leverages its capability to characterize local sequences. Explorer enables coding under various biochemical constraints, such as homopolymers, GC content, and undesired motifs. This paper also introduces Codeformer, a fast decoding algorithm based on the transformer architecture, to further enhance decoding efficiency. Numerical experiments indicate that, compared with other advanced algorithms, Explorer not only achieves stable encoding and decoding under various biochemical constraints but also increases the encoding efficiency and bit rate by ¿10%. Additionally, Codeformer demonstrates the ability to efficiently decode large quantities of DNA sequences. Under different parameter settings, its decoding efficiency exceeds that of traditional algorithms by more than two-fold. When Codeformer is combined with Reed-Solomon code, its decoding accuracy exceeds 99%, making it a good choice for high-speed decoding applications. These advancements are expected to contribute to the development of DNA-based data storage systems and the broader exploration of DNA as a novel information storage medium.
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Affiliation(s)
- Chang Dou
- Center for Applied Mathematics, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin 300072, China
| | - Yijie Yang
- Center for Applied Mathematics, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin 300072, China
| | - Fei Zhu
- Center for Applied Mathematics, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin 300072, China
| | - BingZhi Li
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin 300072, China
- School of Chemical Engineering and Technology, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin 300072, China
| | - Yuping Duan
- Center for Applied Mathematics, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin 300072, China
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32
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Smith D, Thomas C, Craig J, Brinkerhoff H, Abell S, Franzi M, Carrasco J, Hoshika S, Benner S, Gundlach J, Laszlo A. Nanopores map the acid-base properties of a single site in a single DNA molecule. Nucleic Acids Res 2024; 52:7429-7436. [PMID: 38884270 PMCID: PMC11260478 DOI: 10.1093/nar/gkae518] [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: 04/23/2024] [Revised: 05/31/2024] [Accepted: 06/04/2024] [Indexed: 06/18/2024] Open
Abstract
Nanopores are increasingly powerful tools for single molecule sensing, in particular, for sequencing DNA, RNA and peptides. This success has spurred efforts to sequence non-canonical nucleic acid bases and amino acids. While canonical DNA and RNA bases have pKas far from neutral, certain non-canonical bases, natural RNA modifications, and amino acids are known to have pKas near neutral pHs at which nanopore sequencing is typically performed. Previous reports have suggested that the nanopore signal may be sensitive to the protonation state of an individual moiety. We sequenced ion currents with the MspA nanopore using a single stranded DNA containing a single non-canonical DNA base (Z) at various pH conditions. The Z-base has a near-neutral pKa ∼ 7.8. We find that the measured ion current is remarkably sensitive to the protonation state of the Z-base. We demonstrate how nanopores can be used to localize and determine the pKa of individual moieties along a polymer. More broadly, these experiments provide a path to mapping different protonation sites along polymers and give insight in how to optimize sequencing of polymers that contain moieties with near-neutral pKas.
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Affiliation(s)
- Drew C Smith
- Department of Physics, University of Washington, Seattle, WA 98195, USA
| | | | - Jonathan M Craig
- Department of Physics, University of Washington, Seattle, WA 98195, USA
| | - Henry Brinkerhoff
- Department of Physics, University of Washington, Seattle, WA 98195, USA
| | - Sarah J Abell
- Department of Physics, University of Washington, Seattle, WA 98195, USA
| | - Michaela C Franzi
- Department of Physics, University of Washington, Seattle, WA 98195, USA
| | | | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution, Alachua, FL 32615, USA
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, Alachua, FL 32615, USA
| | - Jens H Gundlach
- Department of Physics, University of Washington, Seattle, WA 98195, USA
| | - Andrew H Laszlo
- Department of Physics, University of Washington, Seattle, WA 98195, USA
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33
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Cui X, Yuan H, Chen X, Meng Q, Zhang C. Newly Designed Quasi-intrinsic Photosensitizers for Fluorescence Image-Guided Two-Photon Photodynamic Therapy with Type I/II Photoreactions. J Med Chem 2024; 67:8902-8912. [PMID: 38815214 DOI: 10.1021/acs.jmedchem.4c00191] [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: 06/01/2024]
Abstract
In this work, a set of quasi-intrinsic photosensitizers are theoretically proposed based on the 2-amino-8-(1'-β-d-2'-deoxyribofuranosyl)-imidazo[1,2-α]-1,3,5-triazin-4(8H)-one (P), which could pair with the 6-amino-5-nitro-3-(1'-β-d-2'-deoxyribofuranosyl)-2(1H)-pyridone (Z) and keep the essential structural characters of nucleic acid. It is revealed that the ring expansion and electron-donating/electron-withdrawing substitution bring enhanced two-photon absorption and bright photoluminescence of these monomers, thereby facilitating the selective excitation and tumor localization through fluorescence imaging. However, instead of undergoing radiative transition (S1 → S0), the base pairing induced fluorescence quenching and rapid intersystem crossing (S1 → Tn) are observed and characterized by the reduced singlet-triplet energy gaps and large spin-orbit coupling values. To ensure the phototherapeutic properties of the considered base pairs in long-lived T1 state, we examined the vertical electron affinity as well as vertical ionization potential for production of superoxide anions via Type I photoreaction, and their required T1 energy (0.98 eV) to generate singlet oxygen 1O2 via Type II mechanism.
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Affiliation(s)
- Xixi Cui
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, P. R. China
| | - Hongxiu Yuan
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, P. R. China
| | - Xiaolin Chen
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, P. R. China
| | - Qingtian Meng
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, P. R. China
| | - Changzhe Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, P. R. China
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34
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Sigal M, Matsumoto S, Beattie A, Katoh T, Suga H. Engineering tRNAs for the Ribosomal Translation of Non-proteinogenic Monomers. Chem Rev 2024; 124:6444-6500. [PMID: 38688034 PMCID: PMC11122139 DOI: 10.1021/acs.chemrev.3c00894] [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: 12/01/2023] [Revised: 02/21/2024] [Accepted: 04/10/2024] [Indexed: 05/02/2024]
Abstract
Ribosome-dependent protein biosynthesis is an essential cellular process mediated by transfer RNAs (tRNAs). Generally, ribosomally synthesized proteins are limited to the 22 proteinogenic amino acids (pAAs: 20 l-α-amino acids present in the standard genetic code, selenocysteine, and pyrrolysine). However, engineering tRNAs for the ribosomal incorporation of non-proteinogenic monomers (npMs) as building blocks has led to the creation of unique polypeptides with broad applications in cellular biology, material science, spectroscopy, and pharmaceuticals. Ribosomal polymerization of these engineered polypeptides presents a variety of challenges for biochemists, as translation efficiency and fidelity is often insufficient when employing npMs. In this Review, we will focus on the methodologies for engineering tRNAs to overcome these issues and explore recent advances both in vitro and in vivo. These efforts include increasing orthogonality, recruiting essential translation factors, and creation of expanded genetic codes. After our review on the biochemical optimizations of tRNAs, we provide examples of their use in genetic code manipulation, with a focus on the in vitro discovery of bioactive macrocyclic peptides containing npMs. Finally, an analysis of the current state of tRNA engineering is presented, along with existing challenges and future perspectives for the field.
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Affiliation(s)
- Maxwell Sigal
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Satomi Matsumoto
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Adam Beattie
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takayuki Katoh
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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35
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Wang B, Bradley KM, Kim MJ, Laos R, Chen C, Gerloff DL, Manfio L, Yang Z, Benner SA. Enzyme-assisted high throughput sequencing of an expanded genetic alphabet at single base resolution. Nat Commun 2024; 15:4057. [PMID: 38744910 PMCID: PMC11094070 DOI: 10.1038/s41467-024-48408-9] [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: 12/11/2023] [Accepted: 04/29/2024] [Indexed: 05/16/2024] Open
Abstract
With just four building blocks, low sequence information density, few functional groups, poor control over folding, and difficulties in forming compact folds, natural DNA and RNA have been disappointing platforms from which to evolve receptors, ligands, and catalysts. Accordingly, synthetic biology has created "artificially expanded genetic information systems" (AEGIS) to add nucleotides, functionality, and information density. With the expected improvements seen in AegisBodies and AegisZymes, the task for synthetic biologists shifts to developing for expanded DNA the same analytical tools available to natural DNA. Here we report one of these, an enzyme-assisted sequencing of expanded genetic alphabet (ESEGA) method to sequence six-letter AEGIS DNA. We show how ESEGA analyses this DNA at single base resolution, and applies it to optimized conditions for six-nucleotide PCR, assessing the fidelity of various DNA polymerases, and extending this to AEGIS components with functional groups. This supports the renewed exploitation of expanded DNA alphabets in biotechnology.
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Affiliation(s)
- Bang Wang
- Foundation for Applied Molecular Evolution, Alachua, FL, USA
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | | | | | - Roberto Laos
- Foundation for Applied Molecular Evolution, Alachua, FL, USA
| | - Cen Chen
- Foundation for Applied Molecular Evolution, Alachua, FL, USA
| | | | - Luran Manfio
- Foundation for Applied Molecular Evolution, Alachua, FL, USA
| | - Zunyi Yang
- Foundation for Applied Molecular Evolution, Alachua, FL, USA.
- Firebird Biomolecular Sciences, LLC, Alachua, FL, USA.
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, Alachua, FL, USA.
- Firebird Biomolecular Sciences, LLC, Alachua, FL, USA.
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36
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Gómez-Márquez J. The Lithbea Domain. Adv Biol (Weinh) 2024; 8:e2300679. [PMID: 38386280 DOI: 10.1002/adbi.202300679] [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: 12/11/2023] [Revised: 02/09/2024] [Indexed: 02/23/2024]
Abstract
The tree of life is the evolutionary metaphor for the past and present connections of all cellular organisms. Today, to speak of biodiversity is not only to speak of archaea, bacteria, and eukaryotes, but they should also consider the "new biodiversity" that includes viruses and synthetic organisms, which represent the new forms of life created in laboratories. There is even a third group of artificial entities that, although not living systems, pretend to imitate the living. To embrace and organize all this new biodiversity, I propose the creation of a new domain, with the name Lithbea (from life-on-the-border entites) The criteria for inclusion as members of Lithbea are: i) the acellular nature of the living system, ii) its origin in laboratory manipulation, iii) showing new biological traits, iv) the presence of exogenous genetic elements, v) artificial or inorganic nature. Within Lithbea there are two subdomains: Virworld (from virus world) which includes all viruses, regarded as lifeless living systems, and classified according to the International Committee on Taxonomy of Viruses (ICTV), and ii) Humade (from human-made) which includes all synthetic organisms and artificial entities. The relationships of Lithbea members to the three classical woesian domains and their implications are briefly discussed.
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Affiliation(s)
- Jaime Gómez-Márquez
- Department of Biochemistry and Molecular Biology, University of Santiago de Compostela, Santiago de Compostela, Galicia, 15782, Spain
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37
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Babar V, Sharma S, Shaikh AR, Oliva R, Chawla M, Cavallo L. Detecting Hachimoji DNA: An Eight-Building-Block Genetic System with MoS 2 and Janus MoSSe Monolayers. ACS APPLIED MATERIALS & INTERFACES 2024; 16:21427-21437. [PMID: 38634539 PMCID: PMC11071042 DOI: 10.1021/acsami.3c18400] [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: 12/08/2023] [Revised: 04/03/2024] [Accepted: 04/09/2024] [Indexed: 04/19/2024]
Abstract
In the pursuit of personalized medicine, the development of efficient, cost-effective, and reliable DNA sequencing technology is crucial. Nanotechnology, particularly the exploration of two-dimensional materials, has opened different avenues for DNA nucleobase detection, owing to their impressive surface-to-volume ratio. This study employs density functional theory with van der Waals corrections to methodically scrutinize the adsorption behavior and electronic band structure properties of a DNA system composed of eight hachimoji nucleotide letters adsorbed on both MoS2 and MoSSe monolayers. Through a comprehensive conformational search, we pinpoint the most favorable adsorption sites, quantifying their adsorption energies and charge transfer properties. The analysis of electronic band structure unveils the emergence of flat bands in close proximity to the Fermi level post-adsorption, a departure from the pristine MoS2 and MoSSe monolayers. Furthermore, leveraging the nonequilibrium Green's function approach, we compute the current-voltage characteristics, providing valuable insights into the electronic transport properties of the system. All hachimoji bases exhibit physisorption with a horizontal orientation on both monolayers. Notably, base G demonstrates high sensitivity on both substrates. The obtained current-voltage (I-V) characteristics, both without and with base adsorption on MoS2 and the Se side of MoSSe, affirm excellent sensing performance. This research significantly advances our understanding of potential DNA sensing platforms and their electronic characteristics, thereby propelling the endeavor for personalized medicine through enhanced DNA sequencing technologies.
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Affiliation(s)
- Vasudeo Babar
- Physical
Sciences and Engineering Division, KAUST Catalysis Center, King Abdullah University of Science and Technology
(KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Sitansh Sharma
- Department
of Research and Innovation, STEMskills Research
and Education Lab Private Limited, Faridabad, Haryana 121002, India
| | - Abdul Rajjak Shaikh
- Department
of Research and Innovation, STEMskills Research
and Education Lab Private Limited, Faridabad, Haryana 121002, India
| | - Romina Oliva
- Department
of Sciences and Technologies, University
Parthenope of Naples, Centro Direzionale Isola C4, 80143 Naples, Italy
| | - Mohit Chawla
- Physical
Sciences and Engineering Division, KAUST Catalysis Center, King Abdullah University of Science and Technology
(KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Luigi Cavallo
- Physical
Sciences and Engineering Division, KAUST Catalysis Center, King Abdullah University of Science and Technology
(KAUST), Thuwal 23955-6900, Saudi Arabia
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38
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Sawant AA, Tripathi S, Galande S, Rajamani S. A Prebiotic Genetic Nucleotide as an Early Darwinian Ancestor for Pre-RNA Evolution. ACS OMEGA 2024; 9:18072-18082. [PMID: 38680342 PMCID: PMC11044211 DOI: 10.1021/acsomega.3c09949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/22/2024] [Accepted: 03/29/2024] [Indexed: 05/01/2024]
Abstract
Prebiotic genetic nucleotides (PGNs) often outcompete canonical alphabets in the formation of nucleotides and subsequent RNA oligomerization under early Earth conditions. This indicates that the early genetic code might have been dominated by pre-RNA that contained PGNs for information transfer and catalysis. Despite this, deciphering pre-RNAs' capacity to acquire function and delineating their evolutionary transition to a canonical RNA World has remained under-researched in the origins of life (OoL) field. We report the synthesis of a prebiotically relevant nucleotide (BaTP) containing the noncanonical nucleobase barbituric acid. We demonstrate the first instance of its enzymatic incorporation into an RNA, using a T7 RNA polymerase. BaTP's incorporation into baby spinach aptamer allowed it to retain its overall secondary structure and function. Finally, we also demonstrate faithful transfer of information from the pre-RNA-containing BaTP to DNA, using a high-fidelity RNA-dependent DNA polymerase, alluding to how selection pressures and complexities could have ensued during the molecular evolution of the early genetic code.
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Affiliation(s)
- Anupam A. Sawant
- Department
of Biology, Indian Institute of Science
Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune, Maharashtra 411008, India
| | - Sneha Tripathi
- Department
of Biology, Indian Institute of Science
Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune, Maharashtra 411008, India
| | - Sanjeev Galande
- Department
of Biology, Indian Institute of Science
Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune, Maharashtra 411008, India
- Center
of Excellence in Epigenetics, Department of Life Sciences, School
of Natural Sciences, Shiv Nadar Institution
of Eminence, Gautam Buddha
Nagar, Uttar Pradesh 201314, India
| | - Sudha Rajamani
- Department
of Biology, Indian Institute of Science
Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune, Maharashtra 411008, India
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39
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Rothschild LJ, Averesch NJH, Strychalski EA, Moser F, Glass JI, Cruz Perez R, Yekinni IO, Rothschild-Mancinelli B, Roberts Kingman GA, Wu F, Waeterschoot J, Ioannou IA, Jewett MC, Liu AP, Noireaux V, Sorenson C, Adamala KP. Building Synthetic Cells─From the Technology Infrastructure to Cellular Entities. ACS Synth Biol 2024; 13:974-997. [PMID: 38530077 PMCID: PMC11037263 DOI: 10.1021/acssynbio.3c00724] [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: 12/01/2023] [Revised: 02/01/2024] [Accepted: 02/06/2024] [Indexed: 03/27/2024]
Abstract
The de novo construction of a living organism is a compelling vision. Despite the astonishing technologies developed to modify living cells, building a functioning cell "from scratch" has yet to be accomplished. The pursuit of this goal alone has─and will─yield scientific insights affecting fields as diverse as cell biology, biotechnology, medicine, and astrobiology. Multiple approaches have aimed to create biochemical systems manifesting common characteristics of life, such as compartmentalization, metabolism, and replication and the derived features, evolution, responsiveness to stimuli, and directed movement. Significant achievements in synthesizing each of these criteria have been made, individually and in limited combinations. Here, we review these efforts, distinguish different approaches, and highlight bottlenecks in the current research. We look ahead at what work remains to be accomplished and propose a "roadmap" with key milestones to achieve the vision of building cells from molecular parts.
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Affiliation(s)
- Lynn J. Rothschild
- Space Science
& Astrobiology Division, NASA Ames Research
Center, Moffett
Field, California 94035-1000, United States
- Department
of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Nils J. H. Averesch
- Department
of Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
| | | | - Felix Moser
- Synlife, One Kendall Square, Cambridge, Massachusetts 02139-1661, United States
| | - John I. Glass
- J.
Craig
Venter Institute, La Jolla, California 92037, United States
| | - Rolando Cruz Perez
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States
- Blue
Marble
Space Institute of Science at NASA Ames Research Center, Moffett Field, California 94035-1000, United
States
| | - Ibrahim O. Yekinni
- Department
of Biomedical Engineering, University of
Minnesota, Minneapolis, Minnesota 55455, United States
| | - Brooke Rothschild-Mancinelli
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332-0150, United States
| | | | - Feilun Wu
- J. Craig
Venter Institute, Rockville, Maryland 20850, United States
| | - Jorik Waeterschoot
- Mechatronics,
Biostatistics and Sensors (MeBioS), KU Leuven, 3000 Leuven Belgium
| | - Ion A. Ioannou
- Department
of Chemistry, MSRH, Imperial College London, London W12 0BZ, U.K.
| | - Michael C. Jewett
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States
| | - Allen P. Liu
- Mechanical
Engineering & Biomedical Engineering, Cellular and Molecular Biology,
Biophysics, Applied Physics, University
of Michigan, Ann Arbor, Michigan 48109, United States
| | - Vincent Noireaux
- Physics
and Nanotechnology, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Carlise Sorenson
- Department
of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Katarzyna P. Adamala
- Department
of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455, United States
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40
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Tiwari G, Mishra VK, Khanna A, Tyagi R, Sagar R. Synthesis of Chirally Enriched Pyrazolylpyrimidinone-Based Glycohybrids via Annulation of Glycals with 2-Hydrazineylpyrimidin-4(3 H)-ones. J Org Chem 2024; 89:5000-5009. [PMID: 38471017 DOI: 10.1021/acs.joc.4c00211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
A new strategy for synthesizing chirally enriched pyrazolylpyrimidinone-based glycohybrids has been achieved, employing an annulation approach in ethanol without any additives or catalysts under microwave conditions. The designed compounds were obtained within a short reaction time (5 min). This method offers several advantages, including mild reaction conditions, a green solvent, and a metal-free approach. Furthermore, the protocol demonstrated a broad substrate scope, successfully incorporating various functional groups with stereochemical diversity and furnishing chirally enriched molecules.
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Affiliation(s)
- Ghanshyam Tiwari
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Vinay Kumar Mishra
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Ashish Khanna
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Rajdeep Tyagi
- Glycochemistry Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Ram Sagar
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi 221005, India
- Glycochemistry Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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41
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Tan HP, Kimoto M, Hirao I. Advancing Genetic Alphabet Expansion: Synthesis of 7-(2-Thienyl)-Imidazo[4,5-b]pyridine (Ds) and 4-(4-Pentyne-1,2-diol)-1-Propynyl-2-Nitropyrrole (Diol-Px) for Use in Replicable Unnatural Base Pairs for PCR Applications. Curr Protoc 2024; 4:e1009. [PMID: 38572677 DOI: 10.1002/cpz1.1009] [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: 04/05/2024]
Abstract
Expanding the genetic alphabet enhances DNA recombinant technologies by introducing unnatural base pairs (UBPs) beyond the standard A-T and G-C pairs, leading to biomaterials with novel and increased functionalities. Recent developments include UBPs that effectively function as a third base pair in replication, transcription, and/or translation processes. One such UBP, Ds-Px, demonstrates extremely high specificity in replication. Chemically synthesized DNA fragments containing Ds bases are amplified by PCR with the 5'-triphosphates of Ds and Px deoxyribonucleosides (dDsTP and dPxTP). The Ds-Px pair system has applications in enhanced DNA data storage, generation of high-affinity DNA aptamers, and incorporation of functional elements into RNA through transcription. This protocol describes the synthesis of the amidite derivative of Ds (dDs amidite), the triphosphate dDsTP, and the diol-modified dPxTP (Diol-dPxTP) for PCR amplifications involving the Ds-Px pair. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Synthesis of Ds deoxyribonucleoside (dDs) Basic Protocol 2: Synthesis of dDs amidite Basic Protocol 3: Synthesis of dDs triphosphate (dDsTP) Basic Protocol 4: Synthesis of Pn deoxyribonucleoside (4-iodo-dPn) Basic Protocol 5: Synthesis of acetyl-protected diol-modified Px deoxyribonucleoside (Diol-dPx) Basic Protocol 6: Synthesis of Diol-dPx triphosphate (Diol-dPxTP) Basic Protocol 7: Purification of triphosphates Support Protocol 1: Synthesis of Hoffer's chlorosugar Support Protocol 2: Preparation of 0.5 M pyrophosphate in DMF Support Protocol 3: Preparation of 2 M TEAB buffer.
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42
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Depmeier H, Kath-Schorr S. Expanding the Horizon of the Xeno Nucleic Acid Space: Threose Nucleic Acids with Increased Information Storage. J Am Chem Soc 2024; 146:7743-7751. [PMID: 38442021 DOI: 10.1021/jacs.3c14626] [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: 03/07/2024]
Abstract
Xeno nucleic acids (XNAs) constitute a class of synthetic nucleic acid analogues characterized by distinct, non-natural modifications within the tripartite structure of the nucleic acid polymers. While most of the described XNAs contain a modification in only one structural element of the nucleic acid scaffold, this work explores the XNA chemical space to create more divergent variants with modifications in multiple parts of the nucleosidic scaffold. Combining the enhanced nuclease resistance of α-l-threofuranosyl nucleic acid (TNA) and the almost natural-like replication efficiency and fidelity of the unnatural hydrophobic base pair (UBP) TPT3:NaM, novel modified nucleoside triphosphates with a dual modification pattern were synthesized. We investigated the enzymatic incorporation of these nucleotide building blocks by XNA-compatible polymerases and confirmed the successful enzymatic synthesis of TPT3-modified TNA, while the preparation of NaM-modified TNA presented greater challenges. This study marks the first enzymatic synthesis of TNA with an expanded genetic alphabet (exTNA), opening promising opportunities in nucleic acid therapeutics, particularly for the selection and evolution of nuclease-resistant, high-affinity aptamers with increased chemical diversity.
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Affiliation(s)
- Hannah Depmeier
- Institute of Organic Chemistry, Department of Chemistry, University of Cologne, Greinstrasse 4, Cologne 50939, Germany
| | - Stephanie Kath-Schorr
- Institute of Organic Chemistry, Department of Chemistry, University of Cologne, Greinstrasse 4, Cologne 50939, Germany
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43
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Crespo-Hernández CE. Special issue on nucleic acid photophysics. Photochem Photobiol 2024; 100:257-261. [PMID: 38501585 DOI: 10.1111/php.13923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/02/2024] [Accepted: 02/03/2024] [Indexed: 03/20/2024]
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44
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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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45
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Ma C, Xiong Q, Lin J, Wong AKW, Wang M, Kwok WM. Ultrafast excited state dynamics of isocytosine unveiled by femtosecond broadband time-resolved spectroscopy combined with density functional theoretical study. Photochem Photobiol 2024; 100:355-367. [PMID: 37688287 DOI: 10.1111/php.13849] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 08/12/2023] [Accepted: 08/14/2023] [Indexed: 09/10/2023]
Abstract
Isocytosine, having important applications in antivirus and drug development, is among the building blocks of Hachimoji nucleic acids. In this report, we present an investigation of the excited state dynamics of isocytosine in both protic and aprotic solvents, which was conducted by a combination of methods including steady-state spectroscopy, femtosecond broadband time-resolved fluorescence, and transient absorption. These methods were coupled with density functional and time-dependent density functional theory calculations. The results of our study provide the first direct evidence for a highly efficient nonradiative mechanism achieved through internal conversion from the ππ* state of the isocytosine keto-N(3)H form occurring within subpicoseconds and picoseconds following photo-excitation. Our study also unveils a crucial role of solvent, particularly solute-solvent hydrogen bonding, in determining the tautomeric composition and regulating the pathways and dynamics of the deactivation processes. The deactivation processes of isocytosine in the solvents examined are found to be distinct from those of cytosine and the case known for isocytosine in the gas phase mainly due to different tautomeric forms involved. Overall, our findings demonstrate the high photo-stability of isocytosine in the solution and showcase the remarkable effect of covalent modification in altering the spectral character and excited state dynamics of nucleobases.
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Affiliation(s)
- Chensheng Ma
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, China
| | - Qingwu Xiong
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China
| | - Jingdong Lin
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, China
| | - Allen Ka-Wa Wong
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China
| | - Mingliang Wang
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, China
| | - Wai-Ming Kwok
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China
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Grefenstette N, Chou L, Colón-Santos S, Fisher TM, Mierzejewski V, Nural C, Sinhadc P, Vidaurri M, Vincent L, Weng MM. Chapter 9: Life as We Don't Know It. ASTROBIOLOGY 2024; 24:S186-S201. [PMID: 38498819 DOI: 10.1089/ast.2021.0103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
While Earth contains the only known example of life in the universe, it is possible that life elsewhere is fundamentally different from what we are familiar with. There is an increased recognition in the astrobiology community that the search for life should steer away from terran-specific biosignatures to those that are more inclusive to all life-forms. To start exploring the space of possibilities that life could occupy, we can try to dissociate life from the chemistry that composes it on Earth by envisioning how different life elsewhere could be in composition, lifestyle, medium, and form, and by exploring how the general principles that govern living systems on Earth might be found in different forms and environments across the Solar System. Exotic life-forms could exist on Mars or Venus, or icy moons like Europa and Enceladus, or even as a shadow biosphere on Earth. New perspectives on agnostic biosignature detection have also begun to emerge, allowing for a broader and more inclusive approach to seeking exotic life with unknown chemistry that is distinct from life as we know it on Earth.
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Affiliation(s)
- Natalie Grefenstette
- Santa Fe Institute, Santa Fe, New Mexico, USA
- Blue Marble Space Institute of Science, Seattle, Washington, USA
| | - Luoth Chou
- NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
- Georgetown University, Washington, DC, USA
| | | | - Theresa M Fisher
- School of Earth and Space Exploration, Arizona State University, Arizona, USA
| | | | - Ceren Nural
- Istanbul Technical University, Istanbul, Turkey
| | - Pritvik Sinhadc
- BEYOND: Center For Fundamental Concepts in Science, Arizona State University, Arizona, USA
- Dubai College, Dubai, United Arab Emirates
| | - Monica Vidaurri
- NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
- Howard University, DC, USA
| | - Lena Vincent
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Wisconsin, USA
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Debnath T, Cisneros GA. Investigation of the stability of D5SIC-DNAM-incorporated DNA duplex in Taq polymerase binary system: a systematic classical MD approach. Phys Chem Chem Phys 2024; 26:7287-7295. [PMID: 38353000 PMCID: PMC11078294 DOI: 10.1039/d3cp05571j] [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] [Indexed: 02/29/2024]
Abstract
DNA polymerases are fundamental enzymes that play a crucial role in processing DNA with high fidelity and accuracy ensuring the faithful transmission of genetic information. The recognition of unnatural base pairs (UBPs) by polymerases, enabling their replication, represents a significant and groundbreaking discovery with profound implications for genetic expansion. Romesberg et al. examined the impact of DNA containing 2,6-dimethyl-2H-isoquiniline-1-thione: D5SIC (DS) and 2-methoxy-3-methylnaphthalene: DNAM (DN) UBPs bound to T. aquaticus DNA polymerase (Taq) through crystal structure analysis. Here, we have used polarizable and nonpolarizable classical molecular dynamics (MD) simulations to investigate the structural aspects and stability of Taq in complex with a DNA duplex including a DS-DN pair in the terminal 3' and 5' positions. Our results suggest that the flexibility of UBP-incorporated DNA in the terminal position is arrested by the polymerase, thus preventing fraying and mispairing. Our investigation also reveals that the UBP remains in an intercalated conformation inside the active site, exhibiting two distinct orientations in agreement with experimental findings. Our analysis pinpoints particular residues responsible for favorable interactions with the UBP, with some relying on van der Waals interactions while other on Coulombic forces.
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Affiliation(s)
- Tanay Debnath
- Department of Physics, University of Texas at Dallas, Richardson, Texas 75080, Dallas, USA.
| | - G Andrés Cisneros
- Department of Physics, University of Texas at Dallas, Richardson, Texas 75080, Dallas, USA.
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas 75080, Dallas, USA
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Debnath T, Cisneros GA. Investigation of dynamical flexibility of D5SIC-DNAM inside DNA duplex in aqueous solution: a systematic classical MD approach. Phys Chem Chem Phys 2024; 26:7435-7445. [PMID: 38353005 PMCID: PMC11080001 DOI: 10.1039/d3cp05572h] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Incorporation of artificial 3rd base pairs (unnatural base pairs, UBPs) has emerged as a fundamental technique in pursuit of expanding the genetic alphabet. 2,6-Dimethyl-2H-isoquiniline-1-thione: D5SIC (DS) and 2-methoxy-3-methylnaphthalene: DNAM (DN), a potential unnatural base pair (UBP) developed by Romesberg and colleagues, has been shown to have remarkable capability for replication within DNA. Crystal structures of a Taq polymerase/double-stranded DNA (ds-DNA) complex containing a DS-DN pair in the 3' terminus showed a parallelly stacked geometry for the pre-insertion, and an intercalated geometry for the post-insertion structure. Unconventional orientations of DS-DN inside a DNA duplex have inspired scientists to investigate the conformational orientations and structural properties of UBP-incorporated DNA. In recent years, computational simulations have been used to investigate the geometry of DS-DN within the DNA duplex; nevertheless, unresolved questions persist owing to inconclusive findings. In this work, we investigate the structural and dynamical properties of DS and DN inside a ds-DNA strand in aqueous solution considering both short and long DNA templates using polarizable, and non-polarizable classical MD simulations. Flexible conformational change of UBP with major populations of Watson-Crick-Franklin (WCF) and three distinct non-Watson-Crick-Franklin (nWCFP1, nWCFP2, nWCFO) conformations through intra and inter-strand flipping have been observed. Our results suggest that a dynamical conformational change leads to the production of diffierent conformational distribution for the systems. Simulations with a short ds-DNA duplex suggest nWCF (P1 and O) as the predominant structures, whereas long ds-DNA duplex simulations indicate almost equal populations of WCF, nWCFP1, nWCFO. DS-DN in the terminal position is found to be more flexible with occasional mispairing and fraying. Overall, these results suggest flexibility and dynamical conformational change of the UBP as well as indicate varied conformational distribution irrespective of starting orientation of the UBP and length og DNA strand.
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Affiliation(s)
- Tanay Debnath
- Department of Physics, University of Texas at Dallas, Richardson, Texas 75080, Dallas, USA.
| | - G Andrés Cisneros
- Department of Physics, University of Texas at Dallas, Richardson, Texas 75080, Dallas, USA.
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas 75080, Dallas, USA
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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: 21] [Impact Index Per Article: 21.0] [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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Ma C, Xiong Q, Lin J, Zeng X, Wang M, Kwok WM. Is 1-methylcytosine a faithful model compound for ultrafast deactivation dynamics of cytosine nucleosides in solution? Phys Chem Chem Phys 2024; 26:2963-2972. [PMID: 38214513 DOI: 10.1039/d3cp05509d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
1-Methylcytosine (1mCyt) is the base for nucleoside N1-methylpseudodeoxycytidine of Hachimoji nucleic acids and a frequently used model compound for theoretical studies on excited states of cytosine nucleosides. However, there is little experimental characterization of spectra and photo-dynamic properties of 1mCyt. Herein, we report a comprehensive investigation into excited state dynamics and effects of solvents on fluorescence dynamics of 1mCyt in both water and acetonitrile. The study employed femtosecond broadband time-resolved fluorescence, transient absorption, and steady-state spectroscopy, along with density functional theory and time-dependent density functional theory calculations. The results obtained provide the first experimental evidence for identifying a dark-natured ∼5.7 ps lifetime nπ* state in the ultrafast non-radiative deactivation with 1mCyt in aqueous solution. This study also demonstrates a significant effect of the solvent on 1mCyt's fluorescence emission, which highlights the crucial role of solute-solvent hydrogen bonding in altering structures and reshaping the radiative as well as nonradiative dynamics of the 1mCyt's ππ* state in the aprotic solvent compared to the protic solvent. The solvent effect exhibited by 1mCyt is distinctive from that known for deoxycytidine, indicating the need for caution in using 1mCyt for modelling the ultrafast dynamics of Cyt nucleosides in solvents with varying properties. Overall, our study unveils a deactivation mechanism that confers a high degree of photo-stability for 1mCyt in solution, shedding light on the molecular basis for solvent-induced effects on the excited state dynamics of nucleobases and derivatives.
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Affiliation(s)
- Chensheng Ma
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, 518071, P. R. China.
| | - Qingwu Xiong
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, 518071, P. R. China.
- College of Physics and optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, P. R. China
| | - Jingdong Lin
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, 518071, P. R. China.
| | - Xiaoyan Zeng
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, 518071, P. R. China.
| | - Mingliang Wang
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, 518071, P. R. China.
| | - Wai-Ming Kwok
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, 999077, P. R. China.
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