1
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Huang X, Yang Z, Yang X, Liang Z, Zhong Q, Hu L, Huang Z, Zhang Z. New Wine in Old Bottle: Crown Ether-Functionalized Digital Polymer toward Efficient MALDI-TOF MS/MS Decoding via a Classical Supramolecular Interaction. ACS Macro Lett 2024; 13:979-986. [PMID: 39042378 DOI: 10.1021/acsmacrolett.4c00360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Digital polymers (DPs), which serve as promising molecular-level storage media, have increasingly garnered interest. Their application significantly depends on the efficiency of the information writing (synthesis) and reading processes (sequencing). For reading, rational incorporation of weak bonds in the main chain was applied in most cases in order to improve readability of the tandem mass spectra (MS/MS), which would limit the chain length of DPs, thus reducing the information storage capacity. In this study, the introduction of commercially available crown ether (CE) at the terminus of digital oligo(γ-butyrolactone)s (DOBLs) significantly enhances the predictability and fidelity of matrix-assisted laser desorption/ionization time-of-flight tandem mass spectra (MALDI-TOF MS/MS), thus improving the decoding process. The use of crown ether, leveraging a well-established supramolecular interaction with alkali cations known since 1967, offers a strong affinity between ionization agents and CE motifs, to form a selective effect of the desired fragments during the tandem MS. This method is particularly effective for long-chain DPs, extending up to 32-mer, and allows for customizable fragmentation patterns. The incorporation of CE at the DP chain end presents a novel and efficient strategy for enhancing MS/MS readability and amplifying the information storage capacity of polymers.
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Affiliation(s)
- Xiaoman Huang
- College of Chemistry, Chemical Engineering, and Materials Science, Soochow University, Suzhou 215123, China
| | - Zhilin Yang
- College of Chemistry, Chemical Engineering, and Materials Science, Soochow University, Suzhou 215123, China
- Jiangsu Yangnong Chemical Group Co., Ltd., Yangzhou 225009, China
| | - Xiaojie Yang
- College of Chemistry, Chemical Engineering, and Materials Science, Soochow University, Suzhou 215123, China
| | - Zhishan Liang
- College of Chemistry, Chemical Engineering, and Materials Science, Soochow University, Suzhou 215123, China
| | - Qinmeng Zhong
- College of Chemistry, Chemical Engineering, and Materials Science, Soochow University, Suzhou 215123, China
| | - Lihua Hu
- Analysis and Testing Center, Soochow University, Suzhou 215123, China
| | - Zhihao Huang
- College of Chemistry, Chemical Engineering, and Materials Science, Soochow University, Suzhou 215123, China
- Suzhou Key Laboratory of Macromolecular Design and Precision Synthesis, Suzhou 215123, China
| | - Zhengbiao Zhang
- College of Chemistry, Chemical Engineering, and Materials Science, Soochow University, Suzhou 215123, China
- State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou 215123, China
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2
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Shi Q, Zhang Z, Liu S. Precision Sequence-Defined Polymers: From Sequencing to Biological Functions. Angew Chem Int Ed Engl 2024; 63:e202313370. [PMID: 37875462 DOI: 10.1002/anie.202313370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/20/2023] [Accepted: 10/24/2023] [Indexed: 10/26/2023]
Abstract
Precise sequence-defined polymers (SDPs) with uniform chain-to-chain structure including chain length, unit sequence, and end functionalities represent the pinnacle of sophistication in the realm of polymer science. For example, the absolute control over the unit sequence of SDPs allows for the bottom-up design of polymers with hierarchical microstructures and functions. Accompanied with the development of synthetic techniques towards precision SDPs, the decoding of SDP sequences and construction of advanced functions irreplaceable by other synthetic materials is of central importance. In this Minireview, we focus on recent advances in SDP sequencing techniques including tandem mass spectrometry (MS), chemically assisted primary MS, as well as other non-destructive sequencing methods such as nuclear magnetic resonance (NMR) spectroscopy, circular dichroism (CD), and nanopore sequencing. Additionally, we delve into the promising prospects of SDP functions in the area of cutting-edge biological research. Topics of exploration include gene delivery systems, the development of hybrid materials combining SDPs and nucleic acids, protein recognition and regulation, as well as the interplay between chirality and biological functions. A brief outlook towards the future directions of SDPs is also presented.
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Affiliation(s)
- Qiangqiang Shi
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, and Key Laboratory of Precision and Intelligent Chemistry, Department of Polymer Science and Engineering, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
| | - Zhengbiao Zhang
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, College of Chemistry, Chemical Engineering and Materials Science, State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, 215123, China
| | - Shiyong Liu
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, and Key Laboratory of Precision and Intelligent Chemistry, Department of Polymer Science and Engineering, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
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3
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Schutz T, Sergent I, Obeid G, Oswald L, Al Ouahabi A, Baxter PNW, Clément JL, Gigmes D, Charles L, Lutz JF. Conception and Evaluation of a Library of Cleavable Mass Tags for Digital Polymers Sequencing. Angew Chem Int Ed Engl 2023; 62:e202310801. [PMID: 37738223 DOI: 10.1002/anie.202310801] [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: 07/27/2023] [Revised: 09/22/2023] [Accepted: 09/22/2023] [Indexed: 09/24/2023]
Abstract
A library of phosphoramidite monomers containing a main-chain cleavable alkoxyamine and a side-chain substituent of variable molar mass (i.e. mass tag) was prepared in this work. These monomers can be used in automated solid-phase phosphoramidite chemistry and therefore incorporated periodically as spacers inside digitally-encoded poly(phosphodiester) chains. Consequently, the formed polymers contain tagged cleavable sites that guide their fragmentation in mass spectrometry sequencing and enhance their digital readability. The spacers were all prepared via a seven steps synthetic procedure. They were afterwards tested for the synthesis and sequencing of model digital polymers. Uniform digitally-encoded polymers were obtained as major species in all cases, even though some minor defects were sometimes detected. Furthermore, the polymers were decoded in pseudo-MS3 conditions, thus confirming the reliability and versatility of the spacers library.
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Affiliation(s)
- Thibault Schutz
- Université de Strasbourg, CNRS, ISIS, 8 allée Gaspard Monge, 67000, Strasbourg, France
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR22, 23 rue du Loess, 67034, Strasbourg Cedex 2, France
| | - Isaure Sergent
- Aix Marseille Université, CNRS, UMR 7273, Institute of Radical Chemistry, 13397, Marseille Cedex 20, France
| | - Georgette Obeid
- Université de Strasbourg, CNRS, ISIS, 8 allée Gaspard Monge, 67000, Strasbourg, France
| | - Laurence Oswald
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR22, 23 rue du Loess, 67034, Strasbourg Cedex 2, France
| | - Abdelaziz Al Ouahabi
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR22, 23 rue du Loess, 67034, Strasbourg Cedex 2, France
| | - Paul N W Baxter
- Université de Strasbourg, CNRS, ISIS, 8 allée Gaspard Monge, 67000, Strasbourg, France
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR22, 23 rue du Loess, 67034, Strasbourg Cedex 2, France
| | - Jean-Louis Clément
- Aix Marseille Université, CNRS, UMR 7273, Institute of Radical Chemistry, 13397, Marseille Cedex 20, France
| | - Didier Gigmes
- Aix Marseille Université, CNRS, UMR 7273, Institute of Radical Chemistry, 13397, Marseille Cedex 20, France
| | - Laurence Charles
- Aix Marseille Université, CNRS, UMR 7273, Institute of Radical Chemistry, 13397, Marseille Cedex 20, France
| | - Jean-François Lutz
- Université de Strasbourg, CNRS, ISIS, 8 allée Gaspard Monge, 67000, Strasbourg, France
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR22, 23 rue du Loess, 67034, Strasbourg Cedex 2, France
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4
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Pardi-Tóth V, Kuki Á, Kordován MÁ, Róth G, Nagy L, Zsuga M, Nagy T, Kéki S. Molecular data storage using direct analysis in real time (DART) ionization mass spectrometry for decoding. Sci Rep 2023; 13:16576. [PMID: 37789061 PMCID: PMC10547761 DOI: 10.1038/s41598-023-43658-x] [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: 06/09/2023] [Accepted: 09/26/2023] [Indexed: 10/05/2023] Open
Abstract
Molecular data storage is becoming a viable alternative to traditional information storage systems. Here, we propose a method where the presence or absence of a given molecule in a mixture of compounds represents a bit of information. As a novel approach, direct analysis in real time (DART) ionization mass spectrometry is used to recover and decode the information stored at the molecular level. Nicotinic acid derivatives were synthesized and used as the 'bit compounds'. Their volatility and ease of ionization make these molecules especially suitable for DART-MS detection. The application of DART-MS as a method with an ambient ionization technique, enables the re-reading of digital chemical codes embedded in the material of ordinary objects. Our method is designed to store and read back short pieces of digital information, up to several hundred bits. These codes can have the function of barcodes or QR codes, as shown in our proof-of-principle applications. First, modelling a QR code as a link to our university's website, three solutions were prepared, each representing 22 bits. Proceeding further, the bit compounds were incorporated into a polymer matrix that is suitable for 3D printing, and a toy ship was created with a hidden barcode. In addition, decoding software was developed to process the DART-MS spectra. The nicotinic acid components representing the bits dominated the DART-MS spectra and error-free decoding was achieved.
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Grants
- TKP2021-NKTA-34 National Research, Development and Innovation Fund of Hungary
- TKP2021-NKTA-34 National Research, Development and Innovation Fund of Hungary
- TKP2021-NKTA-34 National Research, Development and Innovation Fund of Hungary
- TKP2021-NKTA-34 National Research, Development and Innovation Fund of Hungary
- TKP2021-NKTA-34 National Research, Development and Innovation Fund of Hungary
- TKP2021-NKTA-34 National Research, Development and Innovation Fund of Hungary
- TKP2021-NKTA-34 National Research, Development and Innovation Fund of Hungary
- TKP2021-NKTA-34 National Research, Development and Innovation Fund of Hungary
- FK-132385 National Research, Development and Innovation Office
- FK-132385 National Research, Development and Innovation Office
- FK-132385 National Research, Development and Innovation Office
- FK-132385 National Research, Development and Innovation Office
- FK-132385 National Research, Development and Innovation Office
- FK-132385 National Research, Development and Innovation Office
- FK-132385 National Research, Development and Innovation Office
- FK-132385 National Research, Development and Innovation Office
- GINOP-2.3.3-15-2016-00021 European Union and the European Regional Development Fund
- GINOP-2.3.3-15-2016-00021 European Union and the European Regional Development Fund
- GINOP-2.3.3-15-2016-00021 European Union and the European Regional Development Fund
- GINOP-2.3.3-15-2016-00021 European Union and the European Regional Development Fund
- GINOP-2.3.3-15-2016-00021 European Union and the European Regional Development Fund
- GINOP-2.3.3-15-2016-00021 European Union and the European Regional Development Fund
- GINOP-2.3.3-15-2016-00021 European Union and the European Regional Development Fund
- GINOP-2.3.3-15-2016-00021 European Union and the European Regional Development Fund
- BO/00212/20/7 Hungarian Academy of Sciences
- ÚNKP-22-05-DE-426 National Research, Development and Innovation Fund
- University of Debrecen
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Affiliation(s)
- Veronika Pardi-Tóth
- Department of Applied Chemistry, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, Debrecen, 4032, Hungary
- Doctoral School of Chemistry, University of Debrecen, Egyetem tér 1, Debrecen, 4032, Hungary
| | - Ákos Kuki
- Department of Applied Chemistry, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, Debrecen, 4032, Hungary
| | - Marcell Árpád Kordován
- Department of Applied Chemistry, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, Debrecen, 4032, Hungary
- Doctoral School of Chemistry, University of Debrecen, Egyetem tér 1, Debrecen, 4032, Hungary
| | - Gergő Róth
- Department of Applied Chemistry, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, Debrecen, 4032, Hungary
- Doctoral School of Chemistry, University of Debrecen, Egyetem tér 1, Debrecen, 4032, Hungary
| | - Lajos Nagy
- Department of Applied Chemistry, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, Debrecen, 4032, Hungary
| | - Miklós Zsuga
- Department of Applied Chemistry, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, Debrecen, 4032, Hungary
| | - Tibor Nagy
- Department of Applied Chemistry, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, Debrecen, 4032, Hungary.
| | - Sándor Kéki
- Department of Applied Chemistry, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, Debrecen, 4032, Hungary
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5
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Yu L, Chen B, Li Z, Huang Q, He K, Su Y, Han Z, Zhou Y, Zhu X, Yan D, Dong R. Digital synthetic polymers for information storage. Chem Soc Rev 2023; 52:1529-1548. [PMID: 36786068 DOI: 10.1039/d2cs01022d] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Digital synthetic polymers with uniform chain lengths and defined monomer sequences have recently become intriguing alternatives to traditional silicon-based information devices or natural biomacromolecules for data storage. The structural diversity of information-containing macromolecules endows the digital synthetic polymers with higher stability and storage density but less occupied space. Through subtly designing each unit of coded structure, the information can be readily encoded into digital synthetic polymers in a more economical scheme and more decodable, opening up new avenues for molecular digital data storage with high-level security. This tutorial review summarizes recent advances in salient features of digital synthetic polymers for data storage, including encoding, decoding, editing, erasing, encrypting, and repairing. The current challenges and outlook are finally discussed to offer potential solution guidance and new perspectives for the creation of next-generation digital synthetic polymers and broaden the scope of their applicability.
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Affiliation(s)
- Li Yu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
| | - Baiyang Chen
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
| | - Ziying Li
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
| | - Qijing Huang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
| | - Kaiyuan He
- School of Chemistry and Chemical Engineering, Frontiers Science Centre for Transformative Molecules, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
| | - Yue Su
- School of Chemistry and Chemical Engineering, Frontiers Science Centre for Transformative Molecules, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
| | - Zeguang Han
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
| | - Yongfeng Zhou
- School of Chemistry and Chemical Engineering, Frontiers Science Centre for Transformative Molecules, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
| | - Xinyuan Zhu
- School of Chemistry and Chemical Engineering, Frontiers Science Centre for Transformative Molecules, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
| | - Deyue Yan
- School of Chemistry and Chemical Engineering, Frontiers Science Centre for Transformative Molecules, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
| | - Ruijiao Dong
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
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6
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Soete M, Mertens C, Badi N, Du Prez FE. Reading Information Stored in Synthetic Macromolecules. J Am Chem Soc 2022; 144:22378-22390. [PMID: 36454647 DOI: 10.1021/jacs.2c10316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
The storage of information in synthetic (macro)molecules provides an attractive alternative for current archival storage media, and the advancements made within this area have prompted the investigation of such molecules for numerous other applications (e.g., anti-counterfeiting tags, steganography). While different strategies have been described for storing information at the molecular level, this Perspective aims to provide a critical overview of the most prominent approaches that can be utilized for retrieving the encoded information. The major part will focus on the sequence determination of synthetic macromolecules, wherein information is stored by the precise arrangement of constituting monomers, with an emphasis on chemically aided strategies, (tandem) mass spectrometry, and nanopore sensing. In addition, recent progress in utilizing (mixtures of) small molecules for information storage will be discussed. Finally, the closing remarks aim to highlight which strategy we believe is the most suitable for a series of specific applications, and will also touch upon the future research avenues that can be pursued for reading (macro)molecular information.
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Affiliation(s)
- Matthieu Soete
- Polymer Chemistry Research Group, Centre of Macromolecular Chemistry (CMaC), Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University, B-9000 Ghent, Belgium
| | - Chiel Mertens
- Polymer Chemistry Research Group, Centre of Macromolecular Chemistry (CMaC), Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University, B-9000 Ghent, Belgium
| | - Nezha Badi
- Polymer Chemistry Research Group, Centre of Macromolecular Chemistry (CMaC), Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University, B-9000 Ghent, Belgium
| | - Filip E Du Prez
- Polymer Chemistry Research Group, Centre of Macromolecular Chemistry (CMaC), Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University, B-9000 Ghent, Belgium
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7
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Guo Z, He J. Synthesis of Linear and Cyclic Discrete Oligomers with Defined Sequences via Efficient Anionic Coupling Reaction. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c01588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zhenhao Guo
- The State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
| | - Junpo He
- The State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
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8
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Dahlhauser S, Wight CD, Moor SR, Scanga RA, Ngo P, York JT, Vera MS, Blake KJ, Riddington IM, Reuther JF, Anslyn EV. Molecular Encryption and Steganography Using Mixtures of Simultaneously Sequenced, Sequence-Defined Oligourethanes. ACS CENTRAL SCIENCE 2022; 8:1125-1133. [PMID: 36032764 PMCID: PMC9413831 DOI: 10.1021/acscentsci.2c00460] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Molecular encoding in abiotic sequence-defined polymers (SDPs) has recently emerged as a versatile platform for information and data storage. However, the storage capacity of these sequence-defined polymers remains underwhelming compared to that of the information storing biopolymer DNA. In an effort to increase their information storage capacity, herein we describe the synthesis and simultaneous sequencing of eight sequence-defined 10-mer oligourethanes. Importantly, we demonstrate the use of different isotope labels, such as halogen tags, as a tool to deconvolute the complex sequence information found within a heterogeneous mixture of at least 96 unique molecules, with as little as four micromoles of total material. In doing so, relatively high-capacity data storage was achieved: 256 bits in this example, the most information stored in a single sample of abiotic SDPs without the use of long strands. Within the sequence information, a 256-bit cipher key was stored and retrieved. The key was used to encrypt and decrypt a plain text document containing The Wonderful Wizard of Oz. To validate this platform as a medium of molecular steganography and cryptography, the cipher key was hidden in the ink of a personal letter, mailed to a third party, extracted, sequenced, and deciphered successfully in the first try, thereby revealing the encrypted document.
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Affiliation(s)
- Samuel
D. Dahlhauser
- Department
of Chemistry, The University of Texas at
Austin, Austin, Texas 78712, United States
| | - Christopher D. Wight
- Department
of Chemistry, The University of Texas at
Austin, Austin, Texas 78712, United States
| | - Sarah R. Moor
- Department
of Chemistry, The University of Texas at
Austin, Austin, Texas 78712, United States
| | - Randall A. Scanga
- Department
of Chemistry, University of Massachusetts
Lowell, Lowell, Massachusetts 01854, United States
| | - Phuoc Ngo
- Department
of Chemistry, The University of Texas at
Austin, Austin, Texas 78712, United States
| | - Jordan T. York
- Department
of Chemistry, The University of Texas at
Austin, Austin, Texas 78712, United States
| | - Marissa S. Vera
- Department
of Chemistry, The University of Texas at
Austin, Austin, Texas 78712, United States
| | - Kristin J. Blake
- Department
of Chemistry, The University of Texas at
Austin, Austin, Texas 78712, United States
| | - Ian M. Riddington
- Department
of Chemistry, The University of Texas at
Austin, Austin, Texas 78712, United States
| | - James F. Reuther
- Department
of Chemistry, University of Massachusetts
Lowell, Lowell, Massachusetts 01854, United States
| | - Eric V. Anslyn
- Department
of Chemistry, The University of Texas at
Austin, Austin, Texas 78712, United States
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9
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Bohn P, Weisel MP, Wolfs J, Meier MAR. Molecular data storage with zero synthetic effort and simple read-out. Sci Rep 2022; 12:13878. [PMID: 35974033 PMCID: PMC9381582 DOI: 10.1038/s41598-022-18108-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/05/2022] [Indexed: 11/21/2022] Open
Abstract
Compound mixtures represent an alternative, additional approach to DNA and synthetic sequence-defined macromolecules in the field of non-conventional molecular data storage, which may be useful depending on the target application. Here, we report a fast and efficient method for information storage in molecular mixtures by the direct use of commercially available chemicals and thus, zero synthetic steps need to be performed. As a proof of principle, a binary coding language is used for encoding words in ASCII or black and white pixels of a bitmap. This way, we stored a 25 × 25-pixel QR code (625 bits) and a picture of the same size. Decoding of the written information is achieved via spectroscopic (1H NMR) or chromatographic (gas chromatography) analysis. In addition, for a faster and automated read-out of the data, we developed a decoding software, which also orders the data sets according to an internal "ordering" standard. Molecular keys or anticounterfeiting are possible areas of application for information-containing compound mixtures.
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Affiliation(s)
- Philipp Bohn
- Laboratory of Applied Chemistry, Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), Straße am Forum 7, 76131, Karlsruhe, Germany
| | - Maximilian P Weisel
- Laboratory of Applied Chemistry, Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), Straße am Forum 7, 76131, Karlsruhe, Germany
| | - Jonas Wolfs
- Laboratory of Applied Chemistry, Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), Straße am Forum 7, 76131, Karlsruhe, Germany
| | - Michael A R Meier
- Laboratory of Applied Chemistry, Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), Straße am Forum 7, 76131, Karlsruhe, Germany.
- Institute of Biological and Chemical Systems - Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany.
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10
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Shi Q, Miao T, Liu Y, Hu L, Yang H, Shen H, Piao M, Huang Z, Zhang Z. Fabrication and Decryption of a Microarray of Digital Dithiosuccinimide Oligomers. Macromol Rapid Commun 2022; 43:e2200029. [PMID: 35322486 DOI: 10.1002/marc.202200029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 03/11/2022] [Indexed: 11/11/2022]
Abstract
Digital polymer with precisely arranged binary units provides an important option for information storage. This is especially true if the digital polymers are assembled in a device, as it would be of great benefit to data writing and reading in practice. Herein, inspired by DNA microarray technique, the programmable information storing and reading on a mass spectrometry target plate is proposed. First, an array of 4-bit sequence-coded dithiosuccinimide oligomers was efficiently built through sequential thiol-maleimide Michael couplings with good sequence readability by tandem mass spectrometry (MS/MS). Then, toward engineering microarray for information storage, a programmed robotic arm was specifically designed for precisely loading sequence-coded oligomers onto the target plate, and a decoding software was developed for efficient readout of the data from MS/MS sequencing. Notably, short sequence-coded oligomers chains can be used to write long strings of information, and extra error-correction codes are not required as usual due to the inherent concomitant fragmentation signals. Not only text but also bitimages can be automatically stored and decoded with excellent accuracy. This work provides a promising platform of digital polymers for programmable information storing and reading. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Qiunan Shi
- Q. Shi, T. Miao, Y. Liu, Prof. H. Shen, Prof. Z. Huang, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, 215123, China
| | - Tengfei Miao
- Q. Shi, T. Miao, Y. Liu, Prof. H. Shen, Prof. Z. Huang, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, 215123, China
| | - Yuxin Liu
- Q. Shi, T. Miao, Y. Liu, Prof. H. Shen, Prof. Z. Huang, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, 215123, China
| | - Lihua Hu
- Dr. L. Hu, Analysis and Testing Center, Soochow University, Suzhou, 215123, China
| | - Hai Yang
- H. Yang, Eurosmart Intelligent Technology Research Institute, Nanjing, 211106, China
| | - Hang Shen
- Q. Shi, T. Miao, Y. Liu, Prof. H. Shen, Prof. Z. Huang, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, 215123, China
| | - Minghao Piao
- Prof. M. Piao, Collaborative Innovation Center of Novel Software Technology and Industrialization, School of Computer Science and Technology, Soochow University, Suzhou, 215123, China
| | - Zhihao Huang
- Q. Shi, T. Miao, Y. Liu, Prof. H. Shen, Prof. Z. Huang, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, 215123, China
| | - Zhengbiao Zhang
- Prof. Z. Zhang, College of Chemistry, Chemical Engineering and Materials Science, State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, 215123, China
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11
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Leguizamon SC, Scott TF. Mimicking DNA Functions with Abiotic, Sequence-Defined Polymers. POLYM REV 2021. [DOI: 10.1080/15583724.2021.2014519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Samuel C. Leguizamon
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Timothy F. Scott
- Department of Chemical Engineering, Monash University, Clayton, VIC, Australia
- Department of Materials Science and Engineering, Monash University, Clayton, VIC, Australia
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12
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Dahlhauser SD, Moor SR, Vera MS, York JT, Ngo P, Boley AJ, Coronado JN, Simpson ZB, Anslyn EV. Efficient molecular encoding in multifunctional self-immolative urethanes. CELL REPORTS. PHYSICAL SCIENCE 2021; 2:100393. [PMID: 34755143 PMCID: PMC8573738 DOI: 10.1016/j.xcrp.2021.100393] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Molecular encoding in sequence-defined polymers shows promise as a new paradigm for data storage. Here, we report what is, to our knowledge, the first use of self-immolative oligourethanes for storing and reading encoded information. As a proof of principle, we describe how a text passage from Jane Austen's Mansfield Park was encoded in sequence-defined oligourethanes and reconstructed via self-immolative sequencing. We develop Mol.E-coder, a software tool that uses a Huffman encoding scheme to convert the character table to hexadecimal. The oligourethanes are then generated by a high-throughput parallel synthesis. Sequencing of the oligourethanes by self-immolation is done concurrently in a parallel fashion, and the liquid chromatography-mass spectrometry (LC-MS) information decoded by our Mol.E-decoder software. The passage is capable of being reproduced wholly intact by a third-party, without any purifications or the use of tandem MS (MS/MS), despite multiple rounds of compression, encoding, and synthesis.
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Affiliation(s)
| | - Sarah R. Moor
- University of Texas at Austin, Austin, TX 78712, USA
| | | | | | - Phuoc Ngo
- University of Texas at Austin, Austin, TX 78712, USA
| | | | | | | | - Eric V. Anslyn
- University of Texas at Austin, Austin, TX 78712, USA
- Lead contact
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13
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Aksakal R, Mertens C, Soete M, Badi N, Du Prez F. Applications of Discrete Synthetic Macromolecules in Life and Materials Science: Recent and Future Trends. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2004038. [PMID: 33747749 PMCID: PMC7967060 DOI: 10.1002/advs.202004038] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/22/2020] [Indexed: 05/19/2023]
Abstract
In the last decade, the field of sequence-defined polymers and related ultraprecise, monodisperse synthetic macromolecules has grown exponentially. In the early stage, mainly articles or reviews dedicated to the development of synthetic routes toward their preparation have been published. Nowadays, those synthetic methodologies, combined with the elucidation of the structure-property relationships, allow envisioning many promising applications. Consequently, in the past 3 years, application-oriented papers based on discrete synthetic macromolecules emerged. Hence, material science applications such as macromolecular data storage and encryption, self-assembly of discrete structures and foldamers have been the object of many fascinating studies. Moreover, in the area of life sciences, such structures have also been the focus of numerous research studies. Here, it is aimed to highlight these recent applications and to give the reader a critical overview of the future trends in this area of research.
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Affiliation(s)
- Resat Aksakal
- Polymer Chemistry Research GroupCentre of Macromolecular Chemistry (CMaC)Department of Organic and Macromolecular ChemistryGhent UniversityKrijgslaan 281 S4‐bisGhentB‐9000Belgium
| | - Chiel Mertens
- Polymer Chemistry Research GroupCentre of Macromolecular Chemistry (CMaC)Department of Organic and Macromolecular ChemistryGhent UniversityKrijgslaan 281 S4‐bisGhentB‐9000Belgium
| | - Matthieu Soete
- Polymer Chemistry Research GroupCentre of Macromolecular Chemistry (CMaC)Department of Organic and Macromolecular ChemistryGhent UniversityKrijgslaan 281 S4‐bisGhentB‐9000Belgium
| | - Nezha Badi
- Polymer Chemistry Research GroupCentre of Macromolecular Chemistry (CMaC)Department of Organic and Macromolecular ChemistryGhent UniversityKrijgslaan 281 S4‐bisGhentB‐9000Belgium
| | - Filip Du Prez
- Polymer Chemistry Research GroupCentre of Macromolecular Chemistry (CMaC)Department of Organic and Macromolecular ChemistryGhent UniversityKrijgslaan 281 S4‐bisGhentB‐9000Belgium
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14
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Mondal T, Charles L, Lutz J. Damage and Repair in Informational Poly(
N
‐substituted urethane)s. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202008864] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Tathagata Mondal
- Precision Macromolecular Chemistry Université de Strasbourg CNRS Institut Charles Sadron UPR22 23 rue du Loess 67034 Strasbourg Cedex 2 France
| | - Laurence Charles
- Aix Marseille Université CNRS UMR 7273, Institut of Radical Chemistry 13397 Marseille Cedex 20 France
| | - Jean‐François Lutz
- Precision Macromolecular Chemistry Université de Strasbourg CNRS Institut Charles Sadron UPR22 23 rue du Loess 67034 Strasbourg Cedex 2 France
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15
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Mondal T, Charles L, Lutz JF. Damage and Repair in Informational Poly(N-substituted urethane)s. Angew Chem Int Ed Engl 2020; 59:20390-20393. [PMID: 32779792 DOI: 10.1002/anie.202008864] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/23/2020] [Indexed: 11/07/2022]
Abstract
The degradation and repair of uniform sequence-defined poly(N-substituted urethane)s was studied. Polymers containing an ω-OH end-group and only ethyl carbamate main-chain repeat units rapidly degrade in NaOH solution through an ω→α depolymerization mechanism with no apparent sign of random chain cleavage. The degradation mechanism is not notably affected by the nature of the side-chain N-substituents and took place for all studied sequences. On the other hand, depolymerization is significantly influenced by the molecular structure of the main-chain repeat units. For instance, hexyl carbamate main-chain motifs block unzipping and can therefore be used to control the degradation of specific sequence sections. Interestingly, the partially degraded polymers can also be repaired; for example by using a combination of N,N'-disuccinimidyl carbonate with a secondary amine building-block. Overall, these findings open up interesting new avenues for chain-healing and sequence editing.
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Affiliation(s)
- Tathagata Mondal
- Precision Macromolecular Chemistry, Université de Strasbourg, CNRS, Institut Charles Sadron UPR22, 23 rue du Loess, 67034, Strasbourg Cedex 2, France
| | - Laurence Charles
- Aix Marseille Université, CNRS, UMR 7273, Institut of Radical Chemistry, 13397, Marseille Cedex 20, France
| | - Jean-François Lutz
- Precision Macromolecular Chemistry, Université de Strasbourg, CNRS, Institut Charles Sadron UPR22, 23 rue du Loess, 67034, Strasbourg Cedex 2, France
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16
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Charles L, Mondal T, Greff V, Razzini M, Monnier V, Burel A, Carapito C, Lutz JF. Optimal conditions for tandem mass spectrometric sequencing of information-containing nitrogen-substituted polyurethanes. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8815. [PMID: 32311797 DOI: 10.1002/rcm.8815] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/13/2020] [Accepted: 04/16/2020] [Indexed: 06/11/2023]
Abstract
RATIONALE To prevent solubility issues faced with sequence-defined polyurethanes, a new family of digital polyurethanes was conceived with the alkyl coding chain held by the carbamate nitrogen (N) atom and CH3 instead of OH as the ϖ termination. This led to different dissociation mechanisms that were explored prior to optimizing tandem mass spectrometric (MS/MS) sequencing. METHODS N-Substituted polyurethanes (N-R PUs) were dissolved in methanol and subjected to collision-induced dissociation (CID) as deprotonated chains in the negative ion mode, and as ammonium and sodium adducts in the positive ion mode, using electrospray ionization (ESI) as the ionization technique. Their dissociation behavior was thoroughly investigated using a quadrupole time-of-flight (QTOF) instrument in order to provide accurate mass measurements to support proposed fragmentation mechanisms. RESULTS While O-(CO) bonds were broken in N-H PUs, the CH2 -O linkage between repeating units was cleaved upon CID of N-R PUs. This main process occurred either from deprotonated molecules or from cationized chains but was followed by different rearrangements, producing up to four product ion series. Yet, MS/MS spectra could be drastically simplified for precursor ions having their acidic α group methylated, as was found to spontaneously occur upon storage in methanol. CONCLUSIONS Using experimental conditions aimed at avoiding any reactive proton in precursor ions (no acidic end-groups and alkali adduction), full coverage sequence of N-R PUs was successfully achieved with the single ion series observed in MS/MS, opening a promising perspective for reading large amounts of information stored in these dyad-encoded polymers.
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Affiliation(s)
- Laurence Charles
- Aix Marseille Univ, CNRS, ICR, Institut de Chimie Radicalaire, Marseille, France
| | - Tathagata Mondal
- University de Strasbourg, CNRS, Institut Charles Sadron UPR22, Strasbourg, France
| | - Vincent Greff
- University de Strasbourg, CNRS, Institut Charles Sadron UPR22, Strasbourg, France
| | - Mattia Razzini
- University de Strasbourg, CNRS, Institut Charles Sadron UPR22, Strasbourg, France
| | - Valérie Monnier
- Aix Marseille Univ, CNRS, Fédération des Sciences Chimiques de Marseille, Marseille, France
| | - Alexandre Burel
- CNRS, Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, Strasbourg, France
| | - Christine Carapito
- CNRS, Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, Strasbourg, France
| | - Jean-François Lutz
- University de Strasbourg, CNRS, Institut Charles Sadron UPR22, Strasbourg, France
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17
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Laurent E, Amalian JA, Parmentier M, Oswald L, Al Ouahabi A, Dufour F, Launay K, Clément JL, Gigmes D, Delsuc MA, Charles L, Lutz JF. High-Capacity Digital Polymers: Storing Images in Single Molecules. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c00666] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Eline Laurent
- CNRS, Institut Charles Sadron UPR22, Université de Strasbourg, 23 rue du Loess, 67034 Cedex 2 Strasbourg, France
| | - Jean-Arthur Amalian
- CNRS, UMR 7273, Institute of Radical Chemistry, Aix Marseille Université, 13397 Cedex 20 Marseille, France
| | - Marie Parmentier
- CNRS, Institut Charles Sadron UPR22, Université de Strasbourg, 23 rue du Loess, 67034 Cedex 2 Strasbourg, France
| | - Laurence Oswald
- CNRS, Institut Charles Sadron UPR22, Université de Strasbourg, 23 rue du Loess, 67034 Cedex 2 Strasbourg, France
| | - Abdelaziz Al Ouahabi
- CNRS, Institut Charles Sadron UPR22, Université de Strasbourg, 23 rue du Loess, 67034 Cedex 2 Strasbourg, France
| | - Florent Dufour
- CNRS, Institut Charles Sadron UPR22, Université de Strasbourg, 23 rue du Loess, 67034 Cedex 2 Strasbourg, France
| | - Kevin Launay
- CNRS, UMR 7273, Institute of Radical Chemistry, Aix Marseille Université, 13397 Cedex 20 Marseille, France
| | - Jean-Louis Clément
- CNRS, UMR 7273, Institute of Radical Chemistry, Aix Marseille Université, 13397 Cedex 20 Marseille, France
| | - Didier Gigmes
- CNRS, UMR 7273, Institute of Radical Chemistry, Aix Marseille Université, 13397 Cedex 20 Marseille, France
| | - Marc-André Delsuc
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM, U596, CNRS, UMR7104, Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch-Graffenstaden, France
| | - Laurence Charles
- CNRS, UMR 7273, Institute of Radical Chemistry, Aix Marseille Université, 13397 Cedex 20 Marseille, France
| | - Jean-François Lutz
- CNRS, Institut Charles Sadron UPR22, Université de Strasbourg, 23 rue du Loess, 67034 Cedex 2 Strasbourg, France
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18
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Shi Q, Cao X, Zhang Y, Duan S, Hu L, Xu Y, Lu J, Huang Z, Zhang Z, Zhu X. Easily readable palindromic sequence-defined polymers built by cascade thiol-maleimide Michael couplings. Polym Chem 2020. [DOI: 10.1039/d0py01088j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The rational combination of cascade thiol-maleimide Michael couplings (CTMMC) with iterative exponential chain growth was demonstrated as an efficient way to synthesize palindromic sequence-defined polymers.
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