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Zhang Q, Xia K, Jiang M, Li Q, Chen W, Han M, Li W, Ke R, Wang F, Zhao Y, Liu Y, Fan C, Gu H. Catalytic DNA-Assisted Mass Production of Arbitrary Single-Stranded DNA. Angew Chem Int Ed Engl 2023; 62:e202212011. [PMID: 36347780 DOI: 10.1002/anie.202212011] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/25/2022] [Accepted: 11/08/2022] [Indexed: 11/11/2022]
Abstract
Synthetic single-stranded (ss) DNA is a cornerstone for life and materials science, yet the purity, quantity, length, and customizability of synthetic DNA are still limiting in various applications. Here, we present PECAN, paired-end cutting assisted by DNAzymes (DNA enzymes or deoxyribozymes), which enables mass production of ssDNA of arbitrary sequence (up to 7000 nucleotides, or nt) with single-base precision. At the core of PECAN technique are two newly identified classes of DNAzymes, each robustly self-hydrolyzing with minimal sequence requirement up- or down-stream of its cleavage site. Flanking the target ssDNA with a pair of such DNAzymes generates a precursor ssDNA amplifiable by pseudogene-recombinant bacteriophage, which subsequently releases the target ssDNA in large quantities after efficient auto-processing. PECAN produces ssDNA of virtually any terminal bases and compositions with >98.5 % purity at the milligram-to-gram scale. We demonstrate the feasibility of using PECAN ssDNA for RNA in situ detection, homology-directed genome editing, and DNA-based data storage.
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Affiliation(s)
- Qiao Zhang
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai, 200433, China
| | - Kai Xia
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai, 200433, China.,Department of Chemical Biology, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 201108, China.,Shanghai Frontier Innovation Research Institute, Shanghai, 201108, China
| | - Meng Jiang
- School of Medicine and School of Biomedical Science, Huaqiao University, Fujian, 362021, China
| | - Qingting Li
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai, 200433, China.,Department of Chemical Biology, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 201108, China
| | - Weigang Chen
- Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China
| | - Mingzhe Han
- Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China
| | - Wei Li
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai, 200433, China
| | - Rongqin Ke
- School of Medicine and School of Biomedical Science, Huaqiao University, Fujian, 362021, China
| | - Fei Wang
- Department of Chemical Biology, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 201108, China
| | - Yongxing Zhao
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, and Key Laboratory of Advanced Drug Preparation Technologies, Zhengzhou University, Henan, 450001, China
| | - Yuehua Liu
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai, 200433, China
| | - Chunhai Fan
- Department of Chemical Biology, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 201108, China
| | - Hongzhou Gu
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai, 200433, China.,Department of Chemical Biology, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 201108, China
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2
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Zhang Y, Ren Y, Liu Y, Wang F, Zhang H, Liu K. Preservation and Encryption in DNA Digital Data Storage. Chempluschem 2022; 87:e202200183. [PMID: 35856827 DOI: 10.1002/cplu.202200183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/01/2022] [Indexed: 11/08/2022]
Abstract
The exponential growth of the total amount of global data presents a huge challenge to mainstream storage media. The emergence of molecular digital storage inspires the development of the new-generation higher-density digital data storage. In particular, DNA with high storage density, reproducibility, and long recoverable lifetime behaves the ideal representative of molecular digital storage media. With the development of DNA synthesis and sequencing technologies and the reduction of cost, DNA digital storage has attracted more and more attention and achieved significant breakthroughs. Herein, this Review briefly describes the workflow of DNA storage, and highlights the storage step of DNA digital data storage. Then, according to different information storage forms, the current DNA information encryption methods are emphatically expounded. Finally, the brief perspectives on the current challenges and optimizing proposals in DNA information preservation and encryption are presented.
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Affiliation(s)
- Yi Zhang
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
| | - Yubin Ren
- Department of Chemistry, Tsinghua University, Beijing, 100084, P. R. China
| | - Yangyi Liu
- Department of Chemistry, Tsinghua University, Beijing, 100084, P. R. China
| | - Fan Wang
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
| | - Hongjie Zhang
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
- Department of Chemistry, Tsinghua University, Beijing, 100084, P. R. China
| | - Kai Liu
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
- Department of Chemistry, Tsinghua University, Beijing, 100084, P. R. China
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3
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Schaudy E, Somoza MM, Lietard J. l-DNA Duplex Formation as a Bioorthogonal Information Channel in Nucleic Acid-Based Surface Patterning. Chemistry 2020; 26:14310-14314. [PMID: 32515523 PMCID: PMC7702103 DOI: 10.1002/chem.202001871] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Indexed: 01/02/2023]
Abstract
Photolithographic in situ synthesis of nucleic acids enables extremely high oligonucleotide sequence density as well as complex surface patterning and combined spatial and molecular information encoding. No longer limited to DNA synthesis, the technique allows for total control of both chemical and Cartesian space organization on surfaces, suggesting that hybridization patterns can be used to encode, display or encrypt informative signals on multiple chemically orthogonal levels. Nevertheless, cross-hybridization reduces the available sequence space and limits information density. Here we introduce an additional, fully independent information channel in surface patterning with in situ l-DNA synthesis. The bioorthogonality of mirror-image DNA duplex formation prevents both cross-hybridization on chimeric l-/d-DNA microarrays and also results in enzymatic orthogonality, such as nuclease-proof DNA-based signatures on the surface. We show how chimeric l-/d-DNA hybridization can be used to create informative surface patterns including QR codes, highly counterfeiting resistant authenticity watermarks, and concealed messages within high-density d-DNA microarrays.
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Affiliation(s)
- Erika Schaudy
- Institute of Inorganic ChemistryFaculty of ChemistryUniversity of ViennaAlthanstraße 14, UZA II1090ViennaAustria
| | - Mark M. Somoza
- Institute of Inorganic ChemistryFaculty of ChemistryUniversity of ViennaAlthanstraße 14, UZA II1090ViennaAustria
- Chair of Food Chemistry and Molecular and Sensory ScienceTechnical University of MunichLise-Meitner-Straße 3485354FreisingGermany
- Leibniz-Institute for Food Systems BiologyTechnical University of MunichLise-Meitner-Straße 3485354FreisingGermany
| | - Jory Lietard
- Institute of Inorganic ChemistryFaculty of ChemistryUniversity of ViennaAlthanstraße 14, UZA II1090ViennaAustria
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4
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Grass RN, Heckel R, Dessimoz C, Stark WJ. Genomic Encryption of Digital Data Stored in Synthetic DNA. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202001162] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Robert N. Grass
- Department of Chemistry and Applied Biosciences ETH Zurich Vladimir-Prelog-Weg 1 8093 Zurich Switzerland
| | - Reinhard Heckel
- Department of Electrical and Computer Engineering Rice University 6100 Main Street Houston TX 77005 USA
- Department of Electrical and Computer Engineering Technical University of Munich Munich Germany
| | - Christophe Dessimoz
- Department of Computational Biology and Center for Integrative Genomics University of Lausanne Lausanne Switzerland
- Swiss Institute of Bioinformatics Lausanne Switzerland
- Department of Genetics, Evolution & Environment and Department of Computer Science University College London UK
| | - Wendelin J. Stark
- Department of Chemistry and Applied Biosciences ETH Zurich Vladimir-Prelog-Weg 1 8093 Zurich Switzerland
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5
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Grass RN, Heckel R, Dessimoz C, Stark WJ. Genomic Encryption of Digital Data Stored in Synthetic DNA. Angew Chem Int Ed Engl 2020; 59:8476-8480. [PMID: 32083389 DOI: 10.1002/anie.202001162] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Indexed: 01/17/2023]
Abstract
Today, we can read human genomes and store digital data robustly in synthetic DNA. Herein, we report a strategy to intertwine these two technologies to enable the secure storage of valuable information in synthetic DNA, protected with personalized keys. We show that genetic short tandem repeats (STRs) contain sufficient entropy to generate strong encryption keys, and that only one technology, DNA sequencing, is required to simultaneously read the key and the data. Using this approach, we experimentally generated 80 bit strong keys from human DNA, and used such a key to encrypt 17 kB of digital information stored in synthetic DNA. Finally, the decrypted information was recovered perfectly from a single massively parallel sequencing run.
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Affiliation(s)
- Robert N Grass
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1, 8093, Zurich, Switzerland
| | - Reinhard Heckel
- Department of Electrical and Computer Engineering, Rice University, 6100 Main Street, Houston, TX, 77005, USA.,Department of Electrical and Computer Engineering, Technical University of Munich, Munich, Germany
| | - Christophe Dessimoz
- Department of Computational Biology and Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Department of Genetics, Evolution & Environment and Department of Computer Science, University College, London, UK
| | - Wendelin J Stark
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1, 8093, Zurich, Switzerland
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6
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From Designing the Molecules of Life to Designing Life: Future Applications Derived from Advances in DNA Technologies. Angew Chem Int Ed Engl 2018; 57:4313-4328. [DOI: 10.1002/anie.201707976] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 11/14/2017] [Indexed: 12/20/2022]
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7
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Kohman RE, Kunjapur AM, Hysolli E, Wang Y, Church GM. Vom Design der Moleküle des Lebens zum Design von Leben: Zukünftige Anwendungen von DNA-Technologien. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201707976] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Richie E. Kohman
- Wyss Institute for Biologically Inspired Engineering; Harvard University; Boston MA 02115 USA
| | | | - Eriona Hysolli
- Department of Genetics; Harvard Medical School; Boston MA 02115 USA
| | - Yu Wang
- Department of Genetics; Harvard Medical School; Boston MA 02115 USA
- Wyss Institute for Biologically Inspired Engineering; Harvard University; Boston MA 02115 USA
| | - George M. Church
- Department of Genetics; Harvard Medical School; Boston MA 02115 USA
- Wyss Institute for Biologically Inspired Engineering; Harvard University; Boston MA 02115 USA
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8
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Vybornyi M, Vyborna Y, Häner R. Silica Mineralization of DNA-Inspired 1D and 2D Supramolecular Polymers. ChemistryOpen 2017; 6:488-491. [PMID: 28794941 PMCID: PMC5542747 DOI: 10.1002/open.201700080] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Indexed: 01/17/2023] Open
Abstract
The preparation of hybrid materials from supramolecular polymers through the sol‐gel process is presented. Supramolecular polymers are assembled from phosphodiester‐linked pyrene oligomers and act as water‐soluble one‐ or two‐dimensional templates for silicification. The fibrillary and planar morphologies of the assemblies, as well as the excitonic interactions between the chromophores, remain unaffected by the silicification process.
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Affiliation(s)
- Mykhailo Vybornyi
- Department of Chemistry and Biochemistry University of Bern Freiestrasse 33012 Bern Switzerland.,Current address: The Department of Chemical Engineering and Chemistry Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands
| | - Yuliia Vyborna
- Department of Chemistry and Biochemistry University of Bern Freiestrasse 33012 Bern Switzerland
| | - Robert Häner
- Department of Chemistry and Biochemistry University of Bern Freiestrasse 33012 Bern Switzerland
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9
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König NF, Al Ouahabi A, Poyer S, Charles L, Lutz JF. A Simple Post-Polymerization Modification Method for Controlling Side-Chain Information in Digital Polymers. Angew Chem Int Ed Engl 2017; 56:7297-7301. [DOI: 10.1002/anie.201702384] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Indexed: 11/12/2022]
Affiliation(s)
- Niklas Felix König
- 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
| | - Salomé Poyer
- Aix Marseille Univ, CNRS; ICR UMR7273; 13397 Marseille France
| | | | - Jean-François Lutz
- Université de Strasbourg, CNRS; Institut Charles Sadron UPR22; 23 rue du Loess 67034 Strasbourg Cedex 2 France
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10
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König NF, Al Ouahabi A, Poyer S, Charles L, Lutz JF. Eine einfache Methode der nachträglichen Modifizierung zur Kontrolle der Seitenketteninformation digitaler Polymere. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702384] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Niklas Felix König
- Université de Strasbourg, CNRS; Institut Charles Sadron UPR22; 23 rue du Loess 67034 Strasbourg Cedex 2 Frankreich
| | - Abdelaziz Al Ouahabi
- Université de Strasbourg, CNRS; Institut Charles Sadron UPR22; 23 rue du Loess 67034 Strasbourg Cedex 2 Frankreich
| | - Salomé Poyer
- Aix Marseille Univ, CNRS; ICR UMR7273; 13397 Marseille Frankreich
| | - Laurence Charles
- Aix Marseille Univ, CNRS; ICR UMR7273; 13397 Marseille Frankreich
| | - Jean-François Lutz
- Université de Strasbourg, CNRS; Institut Charles Sadron UPR22; 23 rue du Loess 67034 Strasbourg Cedex 2 Frankreich
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11
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Mayer C, McInroy GR, Murat P, Van Delft P, Balasubramanian S. An Epigenetics-Inspired DNA-Based Data Storage System. Angew Chem Int Ed Engl 2016; 55:11144-8. [PMID: 27440712 PMCID: PMC5113786 DOI: 10.1002/anie.201605531] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Indexed: 12/22/2022]
Abstract
Biopolymers are an attractive alternative to store and circulate information. DNA, for example, combines remarkable longevity with high data storage densities and has been demonstrated as a means for preserving digital information. Inspired by the dynamic, biological regulation of (epi)genetic information, we herein present how binary data can undergo controlled changes when encoded in synthetic DNA strands. By exploiting differential kinetics of hydrolytic deamination reactions of cytosine and its naturally occurring derivatives, we demonstrate how multiple layers of information can be stored in a single DNA template. Moreover, we show that controlled redox reactions allow for interconversion of these DNA-encoded layers of information. Overall, such interlacing of multiple messages on synthetic DNA libraries showcases the potential of chemical reactions to manipulate digital information on (bio)polymers.
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Affiliation(s)
- Clemens Mayer
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Gordon R McInroy
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Pierre Murat
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Pieter Van Delft
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Shankar Balasubramanian
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
- Cancer Research, UK, Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK.
- School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0SP, UK.
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12
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Mayer C, McInroy GR, Murat P, Van Delft P, Balasubramanian S. An Epigenetics‐Inspired DNA‐Based Data Storage System. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605531] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Clemens Mayer
- Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Gordon R. McInroy
- Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Pierre Murat
- Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Pieter Van Delft
- Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Shankar Balasubramanian
- Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
- Cancer Research, UK, Cambridge Institute, Li Ka Shing Centre University of Cambridge Robinson Way Cambridge CB2 0RE UK
- School of Clinical Medicine University of Cambridge Cambridge CB2 0SP UK
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