1
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Catalytic Antibodies: Design, Expression, and Their Applications in Medicine. Appl Biochem Biotechnol 2023; 195:1514-1540. [PMID: 36222989 PMCID: PMC9554387 DOI: 10.1007/s12010-022-04183-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2022] [Indexed: 01/24/2023]
Abstract
Catalytic antibodies made it feasible to develop new catalysts, which had previously been the subject of research. Scientists have discovered natural antibodies that can hydrolyze substrates such as nucleic acids, proteins, and polysaccharides during decades of research, as well as several ways of producing antibodies with specialized characteristics and catalytic functions. These antibodies are widely used in chemistry, biology, and medicine. Catalytic antibodies can continue to play a role and even fully prevent the emergence of autoimmune disorders, especially in the field of infection and immunity, where the process of its occurrence and development often takes a long time. In this work, the development, design and evolution methodologies, and the expression systems and applications of catalytic antibodies, are discussed. Trial registration: not applicable.
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2
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Ouyang Y, O'Hagan MP, Willner I. Functional catalytic nanoparticles (nanozymes) for sensing. Biosens Bioelectron 2022; 218:114768. [DOI: 10.1016/j.bios.2022.114768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/25/2022] [Accepted: 09/27/2022] [Indexed: 11/29/2022]
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3
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Ermakov EA, Nevinsky GA, Buneva VN. Immunoglobulins with Non-Canonical Functions in Inflammatory and Autoimmune Disease States. Int J Mol Sci 2020; 21:ijms21155392. [PMID: 32751323 PMCID: PMC7432551 DOI: 10.3390/ijms21155392] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/28/2020] [Accepted: 07/28/2020] [Indexed: 12/16/2022] Open
Abstract
Immunoglobulins are known to combine various effector mechanisms of the adaptive and the innate immune system. Classical immunoglobulin functions are associated with antigen recognition and the initiation of innate immune responses. However, in addition to classical functions, antibodies exhibit a variety of non-canonical functions related to the destruction of various pathogens due to catalytic activity and cofactor effects, the action of antibodies as agonists/antagonists of various receptors, the control of bacterial diversity of the intestine, etc. Canonical and non-canonical functions reflect the extreme human antibody repertoire and the variety of antibody types generated in the organism: antigen-specific, natural, polyreactive, broadly neutralizing, homophilic, bispecific and catalytic. The therapeutic effects of intravenous immunoglobulins (IVIg) are associated with both the canonical and non-canonical functions of antibodies. In this review, catalytic antibodies will be considered in more detail, since their formation is associated with inflammatory and autoimmune diseases. We will systematically summarize the diversity of catalytic antibodies in normal and pathological conditions. Translational perspectives of knowledge about natural antibodies for IVIg therapy will be also discussed.
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MESH Headings
- Adaptive Immunity
- Antibodies, Bispecific/chemistry
- Antibodies, Bispecific/genetics
- Antibodies, Bispecific/metabolism
- Antibodies, Catalytic/chemistry
- Antibodies, Catalytic/genetics
- Antibodies, Catalytic/metabolism
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/genetics
- Antibodies, Neutralizing/metabolism
- Autoimmune Diseases/genetics
- Autoimmune Diseases/immunology
- Autoimmune Diseases/pathology
- Autoimmune Diseases/therapy
- Humans
- Immunity, Innate
- Immunoglobulin Fab Fragments/chemistry
- Immunoglobulin Fab Fragments/genetics
- Immunoglobulin Fab Fragments/metabolism
- Immunoglobulin Fc Fragments/chemistry
- Immunoglobulin Fc Fragments/genetics
- Immunoglobulin Fc Fragments/metabolism
- Immunoglobulin Isotypes/chemistry
- Immunoglobulin Isotypes/classification
- Immunoglobulin Isotypes/genetics
- Immunoglobulin Isotypes/metabolism
- Immunoglobulins, Intravenous/therapeutic use
- Immunologic Tests
- Neurodegenerative Diseases/genetics
- Neurodegenerative Diseases/immunology
- Neurodegenerative Diseases/pathology
- Neurodegenerative Diseases/therapy
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Affiliation(s)
- Evgeny A. Ermakov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.A.E.); (G.A.N.)
- Novosibirsk State University, Department of Natural Sciences, 630090 Novosibirsk, Russia
| | - Georgy A. Nevinsky
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.A.E.); (G.A.N.)
- Novosibirsk State University, Department of Natural Sciences, 630090 Novosibirsk, Russia
| | - Valentina N. Buneva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.A.E.); (G.A.N.)
- Novosibirsk State University, Department of Natural Sciences, 630090 Novosibirsk, Russia
- Correspondence: ; Tel.: +7-(383)-363-51-27; Fax: +7-(383)-363-51-53
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4
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Chaaya N, Shahsavarian MA, Maffucci I, Friboulet A, Offmann B, Léger JB, Rousseau S, Avalle B, Padiolleau-Lefèvre S. Genetic background and immunological status influence B cell repertoire diversity in mice. Sci Rep 2019; 9:14261. [PMID: 31582818 PMCID: PMC6776527 DOI: 10.1038/s41598-019-50714-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 09/16/2019] [Indexed: 01/08/2023] Open
Abstract
The relationship between the immune repertoire and the physiopathological status of individuals is essential to apprehend the genesis and the evolution of numerous pathologies. Nevertheless, the methodological approaches to understand these complex interactions are challenging. We performed a study evaluating the diversity harbored by different immune repertoires as a function of their physiopathological status. In this study, we base our analysis on a murine scFv library previously described and representing four different immune repertoires: i) healthy and naïve, ii) healthy and immunized, iii) autoimmune prone and naïve, and iv) autoimmune prone and immunized. This library, 2.6 × 109 in size, is submitted to high throughput sequencing (Next Generation Sequencing, NGS) in order to analyze the gene subgroups encoding for immunoglobulins. A comparative study of the distribution of immunoglobulin gene subgroups present in the four libraries has revealed shifts in the B cell repertoire originating from differences in genetic background and immunological status of mice.
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Affiliation(s)
- Nancy Chaaya
- CNRS UMR 7025, Génie Enzymatique et Cellulaire. Centre de Recherche de Royallieu. CS 60319, 60203, Compiègne Cedex, France.,Sorbonne Universités, Université de Technologie de Compiègne, Génie Enzymatique et Cellulaire. Centre de Recherche de Royallieu. CS 60319, 60203, Compiègne Cedex, France
| | - Melody A Shahsavarian
- CNRS UMR 7025, Génie Enzymatique et Cellulaire. Centre de Recherche de Royallieu. CS 60319, 60203, Compiègne Cedex, France.,Sorbonne Universités, Université de Technologie de Compiègne, Génie Enzymatique et Cellulaire. Centre de Recherche de Royallieu. CS 60319, 60203, Compiègne Cedex, France
| | - Irene Maffucci
- CNRS UMR 7025, Génie Enzymatique et Cellulaire. Centre de Recherche de Royallieu. CS 60319, 60203, Compiègne Cedex, France.,Sorbonne Universités, Université de Technologie de Compiègne, Génie Enzymatique et Cellulaire. Centre de Recherche de Royallieu. CS 60319, 60203, Compiègne Cedex, France
| | - Alain Friboulet
- CNRS UMR 7025, Génie Enzymatique et Cellulaire. Centre de Recherche de Royallieu. CS 60319, 60203, Compiègne Cedex, France.,Sorbonne Universités, Université de Technologie de Compiègne, Génie Enzymatique et Cellulaire. Centre de Recherche de Royallieu. CS 60319, 60203, Compiègne Cedex, France
| | - Bernard Offmann
- Université de Nantes, Unité Fonctionnalité et Ingénierie des Protéines (UFIP), UMR 6286 CNRS, UFR Sciences et Techniques, 2, chemin de la Houssinière, 44322, Nantes, France
| | - Jean-Benoist Léger
- CNRS UMR 7253, Heudiasyc; Université de Technologie de Compiègne. Centre de Recherche de Royallieu. CS 60319, 60203, Compiègne Cedex, France.,Sorbonne Universités, Université de Technologie de Compiègne, Heudiasyc. Centre de Recherche de Royallieu. CS 60319, 60203, Compiègne Cedex, France
| | - Sylvain Rousseau
- CNRS UMR 7253, Heudiasyc; Université de Technologie de Compiègne. Centre de Recherche de Royallieu. CS 60319, 60203, Compiègne Cedex, France.,Sorbonne Universités, Université de Technologie de Compiègne, Heudiasyc. Centre de Recherche de Royallieu. CS 60319, 60203, Compiègne Cedex, France
| | - Bérangère Avalle
- CNRS UMR 7025, Génie Enzymatique et Cellulaire. Centre de Recherche de Royallieu. CS 60319, 60203, Compiègne Cedex, France.,Sorbonne Universités, Université de Technologie de Compiègne, Génie Enzymatique et Cellulaire. Centre de Recherche de Royallieu. CS 60319, 60203, Compiègne Cedex, France
| | - Séverine Padiolleau-Lefèvre
- CNRS UMR 7025, Génie Enzymatique et Cellulaire. Centre de Recherche de Royallieu. CS 60319, 60203, Compiègne Cedex, France. .,Sorbonne Universités, Université de Technologie de Compiègne, Génie Enzymatique et Cellulaire. Centre de Recherche de Royallieu. CS 60319, 60203, Compiègne Cedex, France.
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5
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Pressman AD, Liu Z, Janzen E, Blanco C, Müller UF, Joyce GF, Pascal R, Chen IA. Mapping a Systematic Ribozyme Fitness Landscape Reveals a Frustrated Evolutionary Network for Self-Aminoacylating RNA. J Am Chem Soc 2019; 141:6213-6223. [PMID: 30912655 PMCID: PMC6548421 DOI: 10.1021/jacs.8b13298] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Molecular
evolution can be conceptualized as a walk over a “fitness
landscape”, or the function of fitness (e.g., catalytic activity)
over the space of all possible sequences. Understanding evolution
requires knowing the structure of the fitness landscape and identifying
the viable evolutionary pathways through the landscape. However, the
fitness landscape for any catalytic biomolecule is largely unknown.
The evolution of catalytic RNA is of special interest because RNA
is believed to have been foundational to early life. In particular,
an essential activity leading to the genetic code would be the reaction
of ribozymes with activated amino acids, such as 5(4H)-oxazolones, to form aminoacyl-RNA. Here we combine in vitro selection
with a massively parallel kinetic assay to map a fitness landscape
for self-aminoacylating RNA, with nearly complete coverage of sequence
space in a central 21-nucleotide region. The method (SCAPE: sequencing
to measure catalytic activity paired with in vitro evolution) shows
that the landscape contains three major ribozyme families (landscape
peaks). An analysis of evolutionary pathways shows that, while local
optimization within a ribozyme family would be possible, optimization
of activity over the entire landscape would be frustrated by large
valleys of low activity. The sequence motifs associated with each
peak represent different solutions to the problem of catalysis, so
the inability to traverse the landscape globally corresponds to an
inability to restructure the ribozyme without losing activity. The
frustrated nature of the evolutionary network suggests that chance
emergence of a ribozyme motif would be more important than optimization
by natural selection.
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Affiliation(s)
- Abe D Pressman
- Department of Chemistry and Biochemistry 9510 , University of California , Santa Barbara , California 93106 , United States.,Program in Chemical Engineering , University of California , Santa Barbara , California 93106 , United States
| | - Ziwei Liu
- MRC Laboratory of Molecular Biology , Cambridge Biomedical Campus , Cambridge CB2 0QH , U.K.,IBMM, CNRS, University of Montpellier, ENSCM , 34090 Montpellier , France
| | - Evan Janzen
- Department of Chemistry and Biochemistry 9510 , University of California , Santa Barbara , California 93106 , United States.,Program in Biomolecular Sciences and Engineering , University of California , Santa Barbara , California 93106 , United States
| | - Celia Blanco
- Department of Chemistry and Biochemistry 9510 , University of California , Santa Barbara , California 93106 , United States
| | - Ulrich F Müller
- Department of Chemistry and Biochemistry , University of California , San Diego , California 92093 , United States
| | - Gerald F Joyce
- Salk Institute for Biological Studies , La Jolla , California 92037 , United States
| | - Robert Pascal
- IBMM, CNRS, University of Montpellier, ENSCM , 34090 Montpellier , France
| | - Irene A Chen
- Department of Chemistry and Biochemistry 9510 , University of California , Santa Barbara , California 93106 , United States.,Program in Biomolecular Sciences and Engineering , University of California , Santa Barbara , California 93106 , United States
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6
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Lee J, Kim M, Seo Y, Lee Y, Park H, Byun SJ, Kwon MH. The catalytic activity of a recombinant single chain variable fragment nucleic acid-hydrolysing antibody varies with fusion tag and expression host. Arch Biochem Biophys 2017; 633:110-117. [PMID: 28888872 DOI: 10.1016/j.abb.2017.09.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 08/31/2017] [Accepted: 09/05/2017] [Indexed: 12/12/2022]
Abstract
The antigen-binding properties of single chain Fv antibodies (scFvs) can vary depending on the position and type of fusion tag used, as well as the host cells used for expression. The issue is even more complicated with a catalytic scFv antibody that binds and hydrolyses a specific antigen. Herein, we investigated the antigen-binding and -hydrolysing activities of the catalytic anti-nucleic acid antibody 3D8 scFv expressed in Escherichia coli or HEK293f cells with or without additional amino acid residues at the N- and C-termini. DNA-binding activity was retained in all recombinant forms. However, the DNA-hydrolysing activity varied drastically between forms. The DNA-hydrolysing activity of E. coli-derived 3D8 scFvs was not affected by the presence of a C-terminal human influenza haemagglutinin (HA) or His tag. By contrast, the activity of HEK293f-derived 3D8 scFvs was completely lost when additional residues were included at the N-terminus and/or when a His tag was incorporated at the C-terminus, whereas a HA tag at the C-terminus did not diminish activity. Thus, we demonstrate that the antigen-binding and catalytic activities of a catalytic antibody can be separately affected by the presence of additional residues at the N- and C-termini, and by the host cell type.
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Affiliation(s)
- Joungmin Lee
- Department of Biomedical Sciences, Graduate School, Ajou University, 206 World Cup-ro, Yeongtong-gu, Suwon 16499, South Korea
| | - Minjae Kim
- Department of Biomedical Sciences, Graduate School, Ajou University, 206 World Cup-ro, Yeongtong-gu, Suwon 16499, South Korea
| | - Youngsil Seo
- Department of Biomedical Sciences, Graduate School, Ajou University, 206 World Cup-ro, Yeongtong-gu, Suwon 16499, South Korea
| | - Yeonjin Lee
- Department of Biomedical Sciences, Graduate School, Ajou University, 206 World Cup-ro, Yeongtong-gu, Suwon 16499, South Korea
| | - Hyunjoon Park
- Department of Biomedical Sciences, Graduate School, Ajou University, 206 World Cup-ro, Yeongtong-gu, Suwon 16499, South Korea
| | - Sung June Byun
- Animal Biotechnology Division, National Institute of Animal Science, Rural Development Administration, 1500, Kongjwipatjwi-ro, Iseo-myeon, Wanju-gun, Jeollabuk-do, 55365, South Korea
| | - Myung-Hee Kwon
- Department of Biomedical Sciences, Graduate School, Ajou University, 206 World Cup-ro, Yeongtong-gu, Suwon 16499, South Korea; Department of Microbiology, Ajou University School of Medicine, 206 World Cup-ro, Yeongtong-gu, Suwon 16499, South Korea.
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7
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Rahbarnia L, Farajnia S, Babaei H, Majidi J, Veisi K, Ahmadzadeh V, Akbari B. Evolution of phage display technology: from discovery to application. J Drug Target 2016; 25:216-224. [DOI: 10.1080/1061186x.2016.1258570] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Leila Rahbarnia
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Safar Farajnia
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Babaei
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jafar Majidi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Kamal Veisi
- Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tabriz, Iran
| | - Vahideh Ahmadzadeh
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Bahman Akbari
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, University Of Medical Sciences Tabriz, Tabriz, Iran
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8
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Oda M, Tsumuraya T, Fujii I. Effects of substrate conformational strain on binding kinetics of catalytic antibodies. Biophys Physicobiol 2016; 13:135-138. [PMID: 27924267 PMCID: PMC5042168 DOI: 10.2142/biophysico.13.0_135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 01/18/2016] [Indexed: 01/12/2023] Open
Abstract
We analyzed the correlation between the conformational strain and the binding kinetics in antigen-antibody interactions. The catalytic antibodies 6D9, 9C10, and 7C8 catalyze the hydrolysis of a nonbioactive chloramphenicol monoester derivative to generate a bioactive chloramphenicol. The crystal structure of 6D9 complexed with a transition-state analog (TSA) suggests that 6D9 binds the substrate to change the conformation of the ester moiety to a thermodynamically unstable twisted conformation, enabling the substrate to reach the transition state during catalysis. The present binding kinetic analysis showed that the association rate for 6D9 binding to the substrate was much lower than that to TSA, whereas those for 9C10 and 7C8 binding were similar to those to TSA. Considering that 7C8 binds to the substrate with little conformational change in the substrate, the slow association rate observed in 6D9 could be attributed to the conformational strain in the substrate.
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Affiliation(s)
- Masayuki Oda
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto 606-8522, Japan
| | - Takeshi Tsumuraya
- Graduate School of Science, Osaka Prefecture University, Sakai, Osaka 599-8570, Japan
| | - Ikuo Fujii
- Graduate School of Science, Osaka Prefecture University, Sakai, Osaka 599-8570, Japan
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9
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Kuah E, Toh S, Yee J, Ma Q, Gao Z. Enzyme Mimics: Advances and Applications. Chemistry 2016; 22:8404-30. [PMID: 27062126 DOI: 10.1002/chem.201504394] [Citation(s) in RCA: 179] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Indexed: 12/29/2022]
Abstract
Enzyme mimics or artificial enzymes are a class of catalysts that have been actively pursued for decades and have heralded much interest as potentially viable alternatives to natural enzymes. Aside from having catalytic activities similar to their natural counterparts, enzyme mimics have the desired advantages of tunable structures and catalytic efficiencies, excellent tolerance to experimental conditions, lower cost, and purely synthetic routes to their preparation. Although still in the midst of development, impressive advances have already been made. Enzyme mimics have shown immense potential in the catalysis of a wide range of chemical and biological reactions, the development of chemical and biological sensing and anti-biofouling systems, and the production of pharmaceuticals and clean fuels. This Review concerns the development of various types of enzyme mimics, namely polymeric and dendrimeric, supramolecular, nanoparticulate and proteinic enzyme mimics, with an emphasis on their synthesis, catalytic properties and technical applications. It provides an introduction to enzyme mimics and a comprehensive summary of the advances and current standings of their applications, and seeks to inspire researchers to perfect the design and synthesis of enzyme mimics and to tailor their functionality for a much wider range of applications.
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Affiliation(s)
- Evelyn Kuah
- Department of Chemistry, National University of Singapore, Singapore, 117543, Fax
| | - Seraphina Toh
- Department of Chemistry, National University of Singapore, Singapore, 117543, Fax
| | - Jessica Yee
- Department of Chemistry, National University of Singapore, Singapore, 117543, Fax
| | - Qian Ma
- Department of Chemistry, National University of Singapore, Singapore, 117543, Fax
| | - Zhiqiang Gao
- Department of Chemistry, National University of Singapore, Singapore, 117543, Fax.
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10
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Affiliation(s)
- Kenneth M. Nicholas
- Department of Chemistry and
Biochemistry Stephenson Life Sciences Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
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11
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