1
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Gumus S, Biechele-Speziale D, Manz KE, Pennell KD, Rubenstein BM, Rosenstein JK. Repurposing Waste Chemicals for Sustainable and Durable Molecular Data Storage. ACS OMEGA 2024; 9:19904-19910. [PMID: 38737050 PMCID: PMC11079871 DOI: 10.1021/acsomega.3c09234] [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: 11/19/2023] [Revised: 03/31/2024] [Accepted: 04/15/2024] [Indexed: 05/14/2024]
Abstract
Molecular data storage offers the intriguing possibility of higher theoretical density and longer lifetimes than today's electronic memory devices. Some demonstrations have used deoxyribonucleic acid (DNA), but bottlenecks in nucleic acid synthesis continue to make DNA data storage orders of magnitude more expensive than electronic storage media. Additionally, despite its potential for long-term storage, DNA faces durability challenges from environmental degradation. In this work, we demonstrate nongenomic molecular data storage using molecular libraries redirected from chemical waste streams. This approach requires no synthetic effort and can be implemented by using molecules that have a minimal associated cost. While the technique is agnostic about the exact molecular content of its inputs, we confirmed that some sources contained poly fluoroalkyl substances (PFAS), which persist for long periods in the natural environment and could offer extremely durable information storage as well as environmental benefits. These demonstrations provide a perspective on some of the valuable possibilities for nongenomic molecular information systems.
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Affiliation(s)
| | | | - Katherine E. Manz
- Brown
University, Providence, Rhode Island 02912, United States
- University
of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kurt D. Pennell
- Brown
University, Providence, Rhode Island 02912, United States
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2
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Liu S, Liu X, Zhu X, Yin J, Bao J. Multiple-Channel Information Encryption Based on Quantum Dot Absorption Spectra. ACS NANO 2023; 17:21349-21359. [PMID: 37883096 DOI: 10.1021/acsnano.3c06050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2023]
Abstract
Large-capacity information encryption has attracted significant interest in the information age. The diversity and controllability of spectra have positioned them to be widely applied for information encryption. Current spectra-based information encryption methods commonly rely on either spectral alteration induced by external stimuli or the utilization of narrowband channels within spectra. However, these methods encounter a common challenge in attaining both high security and large capacity simultaneously. To address these issues, we propose a multiple-channel information encryption system based on quantum dot (QD) absorption spectra. The diversity of QD absorption spectra and their broadband features ensure that the encrypted spectra can hardly be decrypted without knowing the correct channel matrix. Meanwhile, the large capacity is realized through the combination of multiple QD spectral channels with a theoretical maximum capacity of 24.0 bits in a single spectrum. In order to optimize the performance of our proposed system, the selection principle of the channel matrix is established to achieve the rapid identification of the optimal channel matrix in several milliseconds. The additivity of QD spectral channels and the consistency of QD spectra are also explored to minimize the impact of errors on information decryption. Furthermore, two spectral encryption scenarios of spatial pattern and spectral pattern are applied to demonstrate the feasibility, showcasing their ability to achieve both a high level of security and large capacity. Owing to the advantages offered by QD spectra, the QD spectra-based information system exhibits excellent potential for broader applications in information storage, authentication, and computing.
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Affiliation(s)
- Senyang Liu
- Department of Electronic Engineering, Tsinghua University, Beijing 100084, China
| | - Xiaohu Liu
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Xueyu Zhu
- Department of Mathematics, University of Iowa, Iowa City 52242, Iowa, United States
| | - Jinhua Yin
- Department of Electronic Engineering, Tsinghua University, Beijing 100084, China
| | - Jie Bao
- Department of Electronic Engineering, Tsinghua University, Beijing 100084, China
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3
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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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4
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Bögels BWA, Nguyen BH, Ward D, Gascoigne L, Schrijver DP, Makri Pistikou AM, Joesaar A, Yang S, Voets IK, Mulder WJM, Phillips A, Mann S, Seelig G, Strauss K, Chen YJ, de Greef TFA. DNA storage in thermoresponsive microcapsules for repeated random multiplexed data access. NATURE NANOTECHNOLOGY 2023; 18:912-921. [PMID: 37142708 PMCID: PMC10427423 DOI: 10.1038/s41565-023-01377-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 03/19/2023] [Indexed: 05/06/2023]
Abstract
DNA has emerged as an attractive medium for archival data storage due to its durability and high information density. Scalable parallel random access to information is a desirable property of any storage system. For DNA-based storage systems, however, this still needs to be robustly established. Here we report on a thermoconfined polymerase chain reaction, which enables multiplexed, repeated random access to compartmentalized DNA files. The strategy is based on localizing biotin-functionalized oligonucleotides inside thermoresponsive, semipermeable microcapsules. At low temperatures, microcapsules are permeable to enzymes, primers and amplified products, whereas at high temperatures, membrane collapse prevents molecular crosstalk during amplification. Our data show that the platform outperforms non-compartmentalized DNA storage compared with repeated random access and reduces amplification bias tenfold during multiplex polymerase chain reaction. Using fluorescent sorting, we also demonstrate sample pooling and data retrieval by microcapsule barcoding. Therefore, the thermoresponsive microcapsule technology offers a scalable, sequence-agnostic approach for repeated random access to archival DNA files.
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Affiliation(s)
- 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
| | - Bichlien H Nguyen
- Microsoft, Redmond, WA, USA
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - David Ward
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - Levena Gascoigne
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, The Netherlands
- Laboratory of Self-Organizing Soft Matter, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - David P Schrijver
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Anna-Maria Makri Pistikou
- 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
| | - Alex Joesaar
- 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
| | - Shuo Yang
- 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
| | - Ilja K Voets
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, The Netherlands
- Laboratory of Self-Organizing Soft Matter, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Willem J M Mulder
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | | | - Stephen Mann
- Centre for Protolife Research and Centre for Organized Matter Chemistry, School of Chemistry, University of Bristol, Bristol, UK
- School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Georg Seelig
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
- Department of Electrical Engineering, University of Washington, Seattle, WA, USA
| | - Karin Strauss
- Microsoft, Redmond, WA, USA
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - Yuan-Jyue Chen
- Microsoft, Redmond, WA, USA.
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA.
| | - 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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5
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Krasecki V, Sharma A, Cavell AC, Forman C, Guo SY, Jensen ET, Smith MA, Czerwinski R, Friederich P, Hickman RJ, Gianneschi N, Aspuru-Guzik A, Cronin L, Goldsmith RH. The Role of Experimental Noise in a Hybrid Classical-Molecular Computer to Solve Combinatorial Optimization Problems. ACS CENTRAL SCIENCE 2023; 9:1453-1465. [PMID: 37521801 PMCID: PMC10375572 DOI: 10.1021/acscentsci.3c00515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Indexed: 08/01/2023]
Abstract
Chemical and molecular-based computers may be promising alternatives to modern silicon-based computers. In particular, hybrid systems, where tasks are split between a chemical medium and traditional silicon components, may provide access and demonstration of chemical advantages such as scalability, low power dissipation, and genuine randomness. This work describes the development of a hybrid classical-molecular computer (HCMC) featuring an electrochemical reaction on top of an array of discrete electrodes with a fluorescent readout. The chemical medium, optical readout, and electrode interface combined with a classical computer generate a feedback loop to solve several canonical optimization problems in computer science such as number partitioning and prime factorization. Importantly, the HCMC makes constructive use of experimental noise in the optical readout, a milestone for molecular systems, to solve these optimization problems, as opposed to in silico random number generation. Specifically, we show calculations stranded in local minima can consistently converge on a global minimum in the presence of experimental noise. Scalability of the hybrid computer is demonstrated by expanding the number of variables from 4 to 7, increasing the number of possible solutions by 1 order of magnitude. This work provides a stepping stone to fully molecular approaches to solving complex computational problems using chemistry.
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Affiliation(s)
- Veronica
K. Krasecki
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Abhishek Sharma
- Department
of Chemistry, University of Glasgow, Glasgow, G12 8QQ, United Kingdom
| | - Andrew C. Cavell
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Christopher Forman
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Si Yue Guo
- Department
of Chemistry, University of Toronto, Toronto, Ontario MS5 3H6, Canada
| | - Evan Thomas Jensen
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Mackinsey A. Smith
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Rachel Czerwinski
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Pascal Friederich
- Department
of Chemistry, University of Toronto, Toronto, Ontario MS5 3H6, Canada
| | - Riley J. Hickman
- Department
of Chemistry, University of Toronto, Toronto, Ontario MS5 3H6, Canada
| | - Nathan Gianneschi
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Alán Aspuru-Guzik
- Department
of Chemistry, University of Toronto, Toronto, Ontario MS5 3H6, Canada
| | - Leroy Cronin
- Department
of Chemistry, University of Glasgow, Glasgow, G12 8QQ, United Kingdom
| | - Randall H. Goldsmith
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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6
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Sheng Y, Zhang Y, Xing F, Liu C, Di Y, Yang X, Wei S, Zhang X, Liu Y, Gan Z. Co-multiplexing spectral and temporal dimensions based on luminescent materials. OPTICS EXPRESS 2023; 31:24667-24677. [PMID: 37475287 DOI: 10.1364/oe.495972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 06/30/2023] [Indexed: 07/22/2023]
Abstract
Optical multiplexing is a pivotal technique for augmenting the capacity of optical data storage (ODS) and increasing the security of anti-counterfeiting. However, due to the dearth of appropriate storage media, optical multiplexing is generally restricted to a single dimension, thus curtailing the encoding capacity. Herein, the co-multiplexing spectral and temporal dimensions are proposed for optical encoding based on photoluminescence (PL) and persistent-luminescence (PersL) at four different wavelengths. Each emission color comprises four luminescence modes. The further multiplexing of four wavelengths leads to the maximum encoding capacity of 8 bits at each pixel. The wavelength difference between adjacent peaks is larger than 50 nm. The well-separated emission wavelengths significantly lower the requirements for high-resolution spectrometers. Moreover, the information is unable to be decoded until both PL and PersL spectra are collected, suggesting a substantial improvement in information security and the security level of anti-counterfeiting.
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7
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Trifoi LA, Dogantzis NP, Hodgson GK, Ortiz PD, Soha SA, Antonescu CN, Botelho RJ, Wylie RS, Impellizzeri S. Single-colour, visible light activation and excitation of the luminescence of a ‘switch-on’ dye and enhancement by silver nanoparticles. J Photochem Photobiol A Chem 2023. [DOI: 10.1016/j.jphotochem.2022.114369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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8
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Shinozaki Y, Popov S, Plenio H. Fluorescent organometallic dyads and triads: establishing spatial relationships. Chem Sci 2023; 14:350-361. [PMID: 36687348 PMCID: PMC9811503 DOI: 10.1039/d2sc04869h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 12/04/2022] [Indexed: 12/12/2022] Open
Abstract
FRET pairs involving up to three different Bodipy dyes are utilized to provide information on the assembly/disassembly of organometallic complexes. Azolium salts tagged with chemically robust and photostable blue or green or red fluorescent Bodipy, respectively, were synthesized and the azolium salts used to prepare metal complexes [(NHC_blue)ML], [(NHC_green)ML] and [(NHC_red)ML] (ML = Pd(allyl)Cl, IrCl(cod), RhCl(cod), AuCl, Au(NTf2), CuBr). The blue and the green Bodipy and the green and the red Bodipy, respectively, were designed to allow the formation of efficient FRET pairs with minimal cross-talk. Organometallic dyads formed from two subunits enable the transfer of excitation energy from the donor dye to the acceptor dye. The blue, green and red emission provide three information channels on the formation of complexes, which is demonstrated for alkyne or sulfur bridged digold species and for ion pairing of a red fluorescent cation and a green fluorescent anion. This approach is extended to probe an assembly of three different subunits. In such a triad, each component is tagged with either a blue, a green or a red Bodipy and the energy transfer blue →green → red proves the formation of the triad. The tagging of molecular components with robust fluorophores can be a general strategy in (organometallic) chemistry to establish connectivities for binuclear catalyst resting states and binuclear catalyst decomposition products in homogeneous catalysis.
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Affiliation(s)
- Yoshinao Shinozaki
- Organometallic Chemistry, Technical University of DarmstadtAlarich-Weiss-Str. 1264287 DarmstadtGermany
| | - Stepan Popov
- Organometallic Chemistry, Technical University of DarmstadtAlarich-Weiss-Str. 1264287 DarmstadtGermany
| | - Herbert Plenio
- Organometallic Chemistry, Technical University of DarmstadtAlarich-Weiss-Str. 1264287 DarmstadtGermany
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9
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Ye S, Meftahi N, Lyskov I, Tian T, Whitfield R, Kumar S, Christofferson AJ, Winkler DA, Shih CJ, Russo S, Leroux JC, Bao Y. Machine learning-assisted exploration of a versatile polymer platform with charge transfer-dependent full-color emission. Chem 2023. [DOI: 10.1016/j.chempr.2022.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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10
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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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11
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Gao J, He Y, Cong X, Yi H, Guo J. Reconfigurable Fluorescent Liquid Crystal Elastomers for Integrated Visual and Haptic Information Storage. ACS APPLIED MATERIALS & INTERFACES 2022; 14:53348-53358. [PMID: 36395006 DOI: 10.1021/acsami.2c17494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The rapid advancements in information technology require new information storage and display materials. However, the development of on-demand information storage systems with multiple modes remains a significant challenge. As a pioneering approach, this study designed an integrated visual and haptic information storage and display using a reconfigurable fluorescent liquid crystal elastomer (FLCE) with dynamic covalent bonds. The FLCEs were fabricated in two steps of amine-acrylate aza-Michael addition and photopolymerization, and they simultaneously exhibited phototunable fluorescence caused by the reversible Z/E photoisomerization of the chromophores and a reprogrammable shape owing to the catalyst-free transesterification. In addition, we established various information storage and display modes featuring the characteristics of reversibly photoswitchable fluorescence, shape memory, and thermally reconfigurable shape with a reconfigurable FLCE system. Moreover, a strategy to display the information by incorporating both visual and haptic feedback is implemented for fulfilling the needs of the visually impaired and related users. Such reconfigurable FLCE systems will aid in the development of on-demand information storage, display, and protection devices.
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Affiliation(s)
- Jingjing Gao
- Key Laboratory of Carbon Fibers and Functional Polymers, Ministry of Education, and College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing100029, China
| | - Yanrong He
- Key Laboratory of Carbon Fibers and Functional Polymers, Ministry of Education, and College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing100029, China
| | - Xiaoyang Cong
- Key Laboratory of Carbon Fibers and Functional Polymers, Ministry of Education, and College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing100029, China
| | - Huijie Yi
- Key Laboratory of Carbon Fibers and Functional Polymers, Ministry of Education, and College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing100029, China
| | - Jinbao Guo
- Key Laboratory of Carbon Fibers and Functional Polymers, Ministry of Education, and College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing100029, China
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12
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Zwillinger M, Fischer L, Sályi G, Szabó S, Csékei M, Huc I, Kotschy A. Isotope Ratio Encoding of Sequence-Defined Oligomers. J Am Chem Soc 2022; 144:19078-19088. [PMID: 36206533 DOI: 10.1021/jacs.2c08135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Information storage at the molecular level commonly entails encoding in the form of ordered sequences of different monomers and subsequent fragmentation and tandem mass spectrometry analysis to read this information. Recent approaches also include the use of mixtures of distinct molecules noncovalently bonded to one another. Here, we present an alternate isotope ratio encoding approach utilizing deuterium-labeled monomers to produce hundreds of oligomers endowed with unique isotope distribution patterns. Mass spectrometric recognition of these patterns then allowed us to directly readout encoded information with high fidelity. Specifically, we show that all 256 tetramers composed of four different monomers of identical constitution can be distinguished by their mass fingerprint using mono-, di-, tri-, and tetradeuterated building blocks. The method is robust to experimental errors and does not require the most sophisticated mass spectrometry instrumentation. Such isotope ratio-encoded oligomers may serve as tags that carry information, but the method mainly opens up the capability to write information, for example, about molecular identity, directly into a pure compound via its isotopologue distribution obviating the need for additional tagging and avoiding the use of mixtures of different molecules.
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Affiliation(s)
- Márton Zwillinger
- Servier Research Institute of Medicinal Chemistry, H-1031 Budapest, Hungary.,Hevesy György PhD School of Chemistry, Eötvös Loránd University, H-1053 Budapest, Hungary
| | - Lucile Fischer
- CBMN UMR5248, University of Bordeaux-CNRS-IPB, F-33600 Pessac, France
| | - Gergő Sályi
- Servier Research Institute of Medicinal Chemistry, H-1031 Budapest, Hungary
| | - Soma Szabó
- Servier Research Institute of Medicinal Chemistry, H-1031 Budapest, Hungary
| | - Márton Csékei
- Servier Research Institute of Medicinal Chemistry, H-1031 Budapest, Hungary
| | - Ivan Huc
- Department of Pharmacy and Center for Integrated Protein Science, Ludwig-Maximilians-University, D-81377 Munich, Germany
| | - András Kotschy
- Servier Research Institute of Medicinal Chemistry, H-1031 Budapest, Hungary
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13
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Lee J, Jang H, Lee SW, Kim KT. Nondestructive Sequencing of Enantiopure Oligoesters by Nuclear Magnetic Resonance Spectroscopy. JACS AU 2022; 2:2108-2118. [PMID: 36186555 PMCID: PMC9516704 DOI: 10.1021/jacsau.2c00388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/04/2022] [Accepted: 08/04/2022] [Indexed: 06/16/2023]
Abstract
Sequence-defined synthetic oligomers and polymers are promising molecular media for permanently storing digital information. However, the information decoding process relies on degradative sequencing methods such as mass spectrometry, which consumes the information-storing polymers upon decoding. Here, we demonstrate the nondestructive decoding of sequence-defined oligomers of enantiopure α-hydroxy acids, oligo(l-mandelic-co-d-phenyl lactic acid)s (oMPs), and oligo(l-lactic-co-glycolic acid)s (oLGs) by 13C nuclear magnetic resonance spectroscopy. We were able to nondestructively decode a bitmap image (192 bits) encoded using a library of 12 equimolar mixtures of an 8-bit-storing oMP and oLG, synthesized through semiautomated flow chemistry in less than 1% of the reaction time required for the repetition of conventional batch reactions. Our results highlight the potential of bundles of sequence-defined oligomers as efficient media for encoding and decoding large-scale information based on the automation of their synthesis and nondestructive sequencing processes.
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14
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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] [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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15
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Kretschmer J, David T, Dračínský M, Socha O, Jirak D, Vít M, Jurok R, Kuchař M, Císařová I, Polasek M. Paramagnetic encoding of molecules. Nat Commun 2022; 13:3179. [PMID: 35676253 PMCID: PMC9177614 DOI: 10.1038/s41467-022-30811-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 05/10/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractContactless digital tags are increasingly penetrating into many areas of human activities. Digitalization of our environment requires an ever growing number of objects to be identified and tracked with machine-readable labels. Molecules offer immense potential to serve for this purpose, but our ability to write, read, and communicate molecular code with current technology remains limited. Here we show that magnetic patterns can be synthetically encoded into stable molecular scaffolds with paramagnetic lanthanide ions to write digital code into molecules and their mixtures. Owing to the directional character of magnetic susceptibility tensors, each sequence of lanthanides built into one molecule produces a unique magnetic outcome. Multiplexing of the encoded molecules provides a high number of codes that grows double-exponentially with the number of available paramagnetic ions. The codes are readable by nuclear magnetic resonance in the radiofrequency (RF) spectrum, analogously to the macroscopic technology of RF identification. A prototype molecular system capable of 16-bit (65,535 codes) encoding is presented. Future optimized systems can conceivably provide 64-bit (~10^19 codes) or higher encoding to cover the labelling needs in drug discovery, anti-counterfeiting and other areas.
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16
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Paris G, Heidepriem J, Tsouka A, Liu Y, Mattes DS, Pinzón Martín S, Dallabernardina P, Mende M, Lindner C, Wawrzinek R, Rademacher C, Seeberger PH, Breitling F, Bischoff FR, Wolf T, Loeffler FF. Automated Laser-Transfer Synthesis of High-Density Microarrays for Infectious Disease Screening. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2200359. [PMID: 35429012 DOI: 10.1002/adma.202200359] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/23/2022] [Indexed: 06/14/2023]
Abstract
Laser-induced forward transfer (LIFT) is a rapid laser-patterning technique for high-throughput combinatorial synthesis directly on glass slides. A lack of automation and precision limits LIFT applications to simple proof-of-concept syntheses of fewer than 100 compounds. Here, an automated synthesis instrument is reported that combines laser transfer and robotics for parallel synthesis in a microarray format with up to 10 000 individual reactions cm- 2 . An optimized pipeline for amide bond formation is the basis for preparing complex peptide microarrays with thousands of different sequences in high yield with high reproducibility. The resulting peptide arrays are of higher quality than commercial peptide arrays. More than 4800 15-residue peptides resembling the entire Ebola virus proteome on a microarray are synthesized to study the antibody response of an Ebola virus infection survivor. Known and unknown epitopes that serve now as a basis for Ebola diagnostic development are identified. The versatility and precision of the synthesizer is demonstrated by in situ synthesis of fluorescent molecules via Schiff base reaction and multi-step patterning of precisely definable amounts of fluorophores. This automated laser transfer synthesis approach opens new avenues for high-throughput chemical synthesis and biological screening.
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Affiliation(s)
- Grigori Paris
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476, Potsdam, Germany
- Department of System Dynamics and Friction Physics, Institute of Mechanics, Technical University of Berlin, Str. des 17. Juni 135, 10623, Berlin, Germany
| | - Jasmin Heidepriem
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476, Potsdam, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Alexandra Tsouka
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476, Potsdam, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Yuxin Liu
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476, Potsdam, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Daniela S Mattes
- Institute of Microstructure Technology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafe, Germany
| | - Sandra Pinzón Martín
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476, Potsdam, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Pietro Dallabernardina
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Marco Mende
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Celina Lindner
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Robert Wawrzinek
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Christoph Rademacher
- Department of Pharmaceutical Sciences, University of Vienna, Althanstr. 14, Vienna, 1090, Austria
- Department of Microbiology and Immunobiology, Max F. Perutz Laboratories GmbH, Dr.-Bohr-Gasse 9, Vienna, 1030, Austria
| | - Peter H Seeberger
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476, Potsdam, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Frank Breitling
- Institute of Microstructure Technology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafe, Germany
| | - Frank Ralf Bischoff
- Department of Functional Genome Analysis, German Cancer Research Center, Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Timo Wolf
- Infectious Diseases Unit, Department of Medicine, Goethe University Hospital, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Felix F Loeffler
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476, Potsdam, Germany
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17
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Rodrigues EM, Calvert ND, Crawford JC, Liu N, Shuhendler AJ, Hemmer E. Phytoglycogen Encapsulation of Lanthanide-Based Nanoparticles as an Optical Imaging Platform with Therapeutic Potential. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2107130. [PMID: 35560500 DOI: 10.1002/smll.202107130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 04/23/2022] [Indexed: 06/15/2023]
Abstract
Lanthanide-based upconverting nanoparticles (UCNPs) are largely sought-after for biomedical applications ranging from bioimaging to therapy. A straightforward strategy is proposed here using the naturally sourced polymer phytoglycogen to coencapsulate UCNPs with hydrophobic photosensitizers as an optical imaging platform and light-induced therapeutic agents. The resulting multifunctional sub-micrometer-sized luminescent beads are shown to be cytocompatible as carrier materials, which encourages the assessment of their potential in biomedical applications. The loading of UCNPs of various elemental compositions enables multicolor hyperspectral imaging of the UCNP-loaded beads, endowing these materials with the potential to serve as luminescent tags for multiplexed imaging or simultaneous detection of different moieties under near-infrared (NIR) excitation. Coencapsulation of UCNPs and Rose Bengal opens the door for potential application of these microcarriers for collagen crosslinking. Alternatively, coloading UCNPs with Chlorin e6 enables NIR-light triggered generation of reactive oxygen species. Overall, the developed encapsulation methodology offers a straightforward and noncytotoxic strategy yielding water-dispersible UCNPs while preserving their bright and color-tunable upconversion emission that would allow them to fulfill their potential as multifunctional platforms for biomedical applications.
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Affiliation(s)
- Emille M Rodrigues
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie Private, Ottawa, Ontario, K1N 6N5, Canada
| | - Nicholas D Calvert
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie Private, Ottawa, Ontario, K1N 6N5, Canada
- University of Ottawa Heart Institute, University of Ottawa, 501 Smyth Road, Ottawa, Ontario, K1Y 4W7, Canada
| | - Justin C Crawford
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie Private, Ottawa, Ontario, K1N 6N5, Canada
| | - Nan Liu
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie Private, Ottawa, Ontario, K1N 6N5, Canada
| | - Adam J Shuhendler
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie Private, Ottawa, Ontario, K1N 6N5, Canada
- University of Ottawa Heart Institute, University of Ottawa, 501 Smyth Road, Ottawa, Ontario, K1Y 4W7, Canada
- Centre for Advanced Materials Research (CAMaR), University of Ottawa, 25 Templeton, Ottawa, Ontario, K1N 6X1, Canada
| | - Eva Hemmer
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie Private, Ottawa, Ontario, K1N 6N5, Canada
- Centre for Advanced Materials Research (CAMaR), University of Ottawa, 25 Templeton, Ottawa, Ontario, K1N 6X1, Canada
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