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Day EC, Chittari SS, Bogen MP, Knight AS. Navigating the Expansive Landscapes of Soft Materials: A User Guide for High-Throughput Workflows. ACS POLYMERS AU 2023; 3:406-427. [PMID: 38107416 PMCID: PMC10722570 DOI: 10.1021/acspolymersau.3c00025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 12/19/2023]
Abstract
Synthetic polymers are highly customizable with tailored structures and functionality, yet this versatility generates challenges in the design of advanced materials due to the size and complexity of the design space. Thus, exploration and optimization of polymer properties using combinatorial libraries has become increasingly common, which requires careful selection of synthetic strategies, characterization techniques, and rapid processing workflows to obtain fundamental principles from these large data sets. Herein, we provide guidelines for strategic design of macromolecule libraries and workflows to efficiently navigate these high-dimensional design spaces. We describe synthetic methods for multiple library sizes and structures as well as characterization methods to rapidly generate data sets, including tools that can be adapted from biological workflows. We further highlight relevant insights from statistics and machine learning to aid in data featurization, representation, and analysis. This Perspective acts as a "user guide" for researchers interested in leveraging high-throughput screening toward the design of multifunctional polymers and predictive modeling of structure-property relationships in soft materials.
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Affiliation(s)
| | | | - Matthew P. Bogen
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Abigail S. Knight
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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2
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Bracchi ME, Dura G, Fulton DA. The synthesis of poly(arylthiols) and their utilization in the preparation of cross-linked dynamic covalent polymer nanoparticles and hydrogels. Polym Chem 2019. [DOI: 10.1039/c9py00057g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Poly(arylthiols) can reversibly cross-link to form nanoparticles and hydrogels.
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Affiliation(s)
- Michael E. Bracchi
- Chemical Nanoscience Laboratory
- Chemistry-School of Natural and Environmental Sciences
- Newcastle University
- Newcastle Upon Tyne
- UK
| | - Gema Dura
- Chemical Nanoscience Laboratory
- Chemistry-School of Natural and Environmental Sciences
- Newcastle University
- Newcastle Upon Tyne
- UK
| | - David A. Fulton
- Chemical Nanoscience Laboratory
- Chemistry-School of Natural and Environmental Sciences
- Newcastle University
- Newcastle Upon Tyne
- UK
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3
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Higgs PL, Ruiz-Sanchez AJ, Dalmina M, Horrocks BR, Leach AG, Fulton DA. Enhancing the kinetics of hydrazone exchange processes: an experimental and computational study. Org Biomol Chem 2019; 17:3218-3224. [DOI: 10.1039/c9ob00058e] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Hydrogen-bond acceptors (A) stabilize the transition state, lowering the energy barrier to rapid hydrazone exchange, without need for exogenous catalyst.
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Affiliation(s)
- Patrick L. Higgs
- Chemical Nanoscience Laboratory
- Chemistry-School of Natural and Environmental Sciences
- Bedson Building
- Newcastle University
- Newcastle upon Tyne
| | - Antonio J. Ruiz-Sanchez
- Chemical Nanoscience Laboratory
- Chemistry-School of Natural and Environmental Sciences
- Bedson Building
- Newcastle University
- Newcastle upon Tyne
| | - Milene Dalmina
- Chemical Nanoscience Laboratory
- Chemistry-School of Natural and Environmental Sciences
- Bedson Building
- Newcastle University
- Newcastle upon Tyne
| | - Benjamin R. Horrocks
- Chemical Nanoscience Laboratory
- Chemistry-School of Natural and Environmental Sciences
- Bedson Building
- Newcastle University
- Newcastle upon Tyne
| | - Andrew G. Leach
- School of Pharmacy and Biomolecular Sciences
- James Parsons Building
- Liverpool John Moores University
- Liverpool
- UK
| | - David A. Fulton
- Chemical Nanoscience Laboratory
- Chemistry-School of Natural and Environmental Sciences
- Bedson Building
- Newcastle University
- Newcastle upon Tyne
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4
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Culver HR, Wechsler ME, Peppas NA. Label-Free Detection of Tear Biomarkers Using Hydrogel-Coated Gold Nanoshells in a Localized Surface Plasmon Resonance-Based Biosensor. ACS NANO 2018; 12:9342-9354. [PMID: 30204412 PMCID: PMC6156935 DOI: 10.1021/acsnano.8b04348] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The dependence of the localized surface plasmon resonance (LSPR) of noble-metal nanomaterials on refractive index makes LSPR a useful, label-free signal transduction strategy for biosensing. In particular, by decorating gold nanomaterials with molecular recognition agents, analytes of interest can be trapped near the surface, resulting in an increased refractive index surrounding the nanomaterial, and, consequently, a red shift in the LSPR wavelength. Ionic poly( N-isopropylacrylamide- co-methacrylic acid) (PNM) hydrogels were used as protein receptors because PNM nanogels exhibit a large increase in refractive index upon protein binding. Specifically, PNM hydrogels were synthesized on the surface of silica gold nanoshells (AuNSs). This composite material (AuNS@PNM) was used to detect changes in the concentration of two protein biomarkers of chronic dry eye: lysozyme and lactoferrin. Both of these proteins have high isoelectric points, resulting in electrostatic attraction between the negatively charged PNM hydrogels and positively charged proteins. Upon binding lysozyme or lactoferrin, AuNS@PNM exhibits large, concentration-dependent red shifts in LSPR wavelength, which enabled the detection of clinically relevant concentration changes of both biomarkers in human tears. The LSPR-based biosensor described herein has potential utility as an affordable screening tool for chronic dry eye and associated conditions.
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Affiliation(s)
- Heidi R. Culver
- Institute for Biomaterials, Drug Delivery, and Regenerative Medicine
- Department of Biomedical Engineering
| | - Marissa E. Wechsler
- Institute for Biomaterials, Drug Delivery, and Regenerative Medicine
- Department of Biomedical Engineering
| | - Nicholas A. Peppas
- Institute for Biomaterials, Drug Delivery, and Regenerative Medicine
- Department of Biomedical Engineering
- McKetta Department of Chemical Engineering
- Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy
- Department of Surgery and Perioperative Care, Dell Medical School, The University of Texas at Austin, Austin, TX, 78712, United States
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5
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Ruiz-Sanchez AJ, Higgs PL, Peters DT, Turley AT, Dobson MA, North AJ, Fulton DA. Probing the Surfaces of Biomacromolecules with Polymer-Scaffolded Dynamic Combinatorial Libraries. ACS Macro Lett 2017; 6:903-907. [PMID: 35650888 DOI: 10.1021/acsmacrolett.7b00561] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Methods to analyze and compare biomacromolecular surfaces are still in their relative infancy on account of the challenges involved in comparing surfaces computationally. We describe a systems chemistry approach that utilizes polymer-scaffolded dynamic combinatorial libraries to experimentally probe biomacromolecular surfaces in aqueous solution which provides feedback as to the nature of the surfaces, allowing the comparison of three globular proteins and a nucleic acid.
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Affiliation(s)
- Antonio J. Ruiz-Sanchez
- Chemical
Nanoscience Laboratory, School of Chemistry, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
| | - Patrick L. Higgs
- Chemical
Nanoscience Laboratory, School of Chemistry, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
| | - Daniel T. Peters
- Institute
for Cell and Molecular Biosciences, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, U.K
| | - Andrew T. Turley
- Chemical
Nanoscience Laboratory, School of Chemistry, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
| | - Matthew A. Dobson
- Chemical
Nanoscience Laboratory, School of Chemistry, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
| | - Adam J. North
- Chemical
Nanoscience Laboratory, School of Chemistry, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
| | - David A. Fulton
- Chemical
Nanoscience Laboratory, School of Chemistry, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
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6
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Beierle JM, Ura Y, Ghadiri MR, Leman LJ. Templated Self-Assembly of Dynamic Peptide Nucleic Acids. Biochemistry 2017; 57:160-172. [PMID: 28832127 DOI: 10.1021/acs.biochem.7b00656] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Template-directed macromolecule synthesis is a hallmark of living systems. Inspired by this natural process, several fundamentally novel mechanisms for template-directed assembly of nucleic acid analogues have been developed. Although these approaches have broad significance, including potential applications in biotechnology and implications for the origins of life, there are unresolved challenges in how to characterize in detail the complex assembly equilibria associated with dynamic templated reactions. Here we describe mechanistic studies of template-directed dynamic assembly for thioester peptide nucleic acid (tPNA), an informational polymer that responds to selection pressures under enzyme-free conditions. To overcome some of the inherent challenges of mechanistic studies of dynamic oligomers, we designed, synthesized, and implemented tPNA-DNA conjugates. The DNA primer region affords a high level of control over the location and register of the tPNA backbone in relation to the template strand. We characterized the degree and kinetics of dynamic nucleobase mismatch correction at defined backbone positions. Furthermore, we report the fidelity of dynamic assembly in tPNA as a function of position along the peptide backbone. Finally, we present theoretical studies that explore the level of fidelity that can be expected for an oligomer having a given hybridization affinity in dynamic templated reactions and provide guidance for the future development of sequence self-editing polymers and materials. As our results demonstrate, the use of molecular conjugates of constitutionally static and dynamic polymers establishes a new methodology for expediting the characterization of the complex chemical equilibria that underlie the assembly of dynamic informational polymers.
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Affiliation(s)
- John M Beierle
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Yasuyuki Ura
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - M Reza Ghadiri
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Luke J Leman
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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7
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Culver HR, Steichen SD, Peppas NA. A Closer Look at the Impact of Molecular Imprinting on Adsorption Capacity and Selectivity for Protein Templates. Biomacromolecules 2016; 17:4045-4053. [PMID: 27936715 DOI: 10.1021/acs.biomac.6b01482] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Molecularly imprinted polymers (MIPs) are often investigated as lower cost, more environmentally robust alternatives to natural recognitive biomolecules, such as antibodies. When synthesized on the surface of nanomaterial supports, MIPs are capable of quick and effective binding of macromolecular templates when compared to traditional bulk-imprinted polymers. We have developed a method for imprinting proteins on biodegradable nanoparticle supports and have used these materials to investigate the impact of molecular imprinting on adsorption capacity and selectivity for lysozyme, the template protein. The imprinting process increased the adsorption capacity of the polymer for the template, lysozyme, with the MIPs being able to bind up to 83.5% of their dry weight as compared to 55.7% for nonimprinted polymers (NIPs). In noncompetitive binding experiments, where proteins were independently incubated with MIPs, the difference between adsorption capacity for lysozyme and proteins with much lower isoelectric points (pI < 8.0) was statistically significant. However, there was no statistical difference between adsorption capacity for lysozyme and other high-isoelectric point proteins, suggesting that MIPs are semiselective for this class of proteins. In competitive binding experiments, both MIPs and NIPs preferentially bound lysozyme over other high-isoelectric point proteins. This result demonstrated that imprinting alone could not account for the observed selectivity for lysozyme. Analysis of the solvent accessible surface area of lysozyme and its high-isoelectric point competitors revealed why lysozyme is an exceptional binder to the polymer system used in this work, with or without imprinting.
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Affiliation(s)
- Heidi R Culver
- Institute for Biomaterials, Drug Delivery, and Regenerative Medicine, C0800, ‡Department of Biomedical Engineering, C0800, §McKetta Department of Chemical Engineering, C0400, ∥Department of Surgery and Perioperative Care, Dell Medical School, and ⊥College of Pharmacy, A1900, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Stephanie D Steichen
- Institute for Biomaterials, Drug Delivery, and Regenerative Medicine, C0800, ‡Department of Biomedical Engineering, C0800, §McKetta Department of Chemical Engineering, C0400, ∥Department of Surgery and Perioperative Care, Dell Medical School, and ⊥College of Pharmacy, A1900, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Nicholas A Peppas
- Institute for Biomaterials, Drug Delivery, and Regenerative Medicine, C0800, ‡Department of Biomedical Engineering, C0800, §McKetta Department of Chemical Engineering, C0400, ∥Department of Surgery and Perioperative Care, Dell Medical School, and ⊥College of Pharmacy, A1900, The University of Texas at Austin , Austin, Texas 78712, United States
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8
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Deng J, Liu X, Ma L, Cheng C, Sun S, Zhao C. Switching biological functionalities of biointerfaces via dynamic covalent bonds. J Mater Chem B 2016; 4:694-703. [DOI: 10.1039/c5tb02072g] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We construct a stimuli responsive biointerface via a dynamic covalent bond that could switch its surface biofunctionalities on demand. The switchability is achieved via reversible attaching/detaching of aldehyde end-functionalized biomacromolecules.
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Affiliation(s)
- Jie Deng
- College of Polymer Science and Engineering
- State Key Laboratory of Polymer Materials and Engineering
- Sichuan University
- Chengdu 610065
- China
| | - Xinyue Liu
- College of Polymer Science and Engineering
- State Key Laboratory of Polymer Materials and Engineering
- Sichuan University
- Chengdu 610065
- China
| | - Lang Ma
- College of Polymer Science and Engineering
- State Key Laboratory of Polymer Materials and Engineering
- Sichuan University
- Chengdu 610065
- China
| | - Chong Cheng
- College of Polymer Science and Engineering
- State Key Laboratory of Polymer Materials and Engineering
- Sichuan University
- Chengdu 610065
- China
| | - Shudong Sun
- College of Polymer Science and Engineering
- State Key Laboratory of Polymer Materials and Engineering
- Sichuan University
- Chengdu 610065
- China
| | - Changsheng Zhao
- College of Polymer Science and Engineering
- State Key Laboratory of Polymer Materials and Engineering
- Sichuan University
- Chengdu 610065
- China
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9
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Mahon CS, Fascione MA, Sakonsinsiri C, McAllister TE, Bruce Turnbull W, Fulton DA. Templating carbohydrate-functionalised polymer-scaffolded dynamic combinatorial libraries with lectins. Org Biomol Chem 2015; 13:2756-61. [DOI: 10.1039/c4ob02587c] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The templation of carbohydrate-functionalised Polymer-Scaffolded Dynamic Combinatorial Libraries affords polymers possessing significantly enhanced affinities for the template, with enhancements in free energy of binding in the range of 5.2–8.8 kJ mol−1 observed.
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Affiliation(s)
- Clare S. Mahon
- Chemical Nanoscience Laboratory
- School of Chemistry
- Newcastle University
- Newcastle-upon-Tyne
- UK
| | - Martin A. Fascione
- School of Chemistry and Astbury Centre for Structural Molecular Biology
- University of Leeds
- Leeds
- UK
- Department of Chemistry
| | - Chadamas Sakonsinsiri
- School of Chemistry and Astbury Centre for Structural Molecular Biology
- University of Leeds
- Leeds
- UK
| | - Tom E. McAllister
- School of Chemistry and Astbury Centre for Structural Molecular Biology
- University of Leeds
- Leeds
- UK
| | - W. Bruce Turnbull
- School of Chemistry and Astbury Centre for Structural Molecular Biology
- University of Leeds
- Leeds
- UK
| | - David A. Fulton
- Chemical Nanoscience Laboratory
- School of Chemistry
- Newcastle University
- Newcastle-upon-Tyne
- UK
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10
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Herrmann A. Dynamic combinatorial/covalent chemistry: a tool to read, generate and modulate the bioactivity of compounds and compound mixtures. Chem Soc Rev 2014; 43:1899-933. [PMID: 24296754 DOI: 10.1039/c3cs60336a] [Citation(s) in RCA: 281] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Reversible covalent bond formation under thermodynamic control adds reactivity to self-assembled supramolecular systems, and is therefore an ideal tool to assess complexity of chemical and biological systems. Dynamic combinatorial/covalent chemistry (DCC) has been used to read structural information by selectively assembling receptors with the optimum molecular fit around a given template from a mixture of reversibly reacting building blocks. This technique allows access to efficient sensing devices and the generation of new biomolecules, such as small molecule receptor binders for drug discovery, but also larger biomimetic polymers and macromolecules with particular three-dimensional structural architectures. Adding a kinetic factor to a thermodynamically controlled equilibrium results in dynamic resolution and in self-sorting and self-replicating systems, all of which are of major importance in biological systems. Furthermore, the temporary modification of bioactive compounds by reversible combinatorial/covalent derivatisation allows control of their release and facilitates their transport across amphiphilic self-assembled systems such as artificial membranes or cell walls. The goal of this review is to give a conceptual overview of how the impact of DCC on supramolecular assemblies at different levels can allow us to understand, predict and modulate the complexity of biological systems.
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Affiliation(s)
- Andreas Herrmann
- Firmenich SA, Division Recherche et Développement, Route des Jeunes 1, B. P. 239, CH-1211 Genève 8, Switzerland.
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11
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Mahon CS, Fulton DA. Mimicking nature with synthetic macromolecules capable of recognition. Nat Chem 2014; 6:665-72. [PMID: 25054935 DOI: 10.1038/nchem.1994] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 05/30/2014] [Indexed: 02/06/2023]
Abstract
Nature has, through billions of years of evolution, assembled a multitude of polymeric macromolecules capable of exquisite molecular recognition. This functionality arises from the precise control exerted over their biosynthesis that results in key residues being anchored in the appropriate positions to interact with target substrates. Developing 'wholly synthetic' macromolecular analogues that can mimic this behaviour presents a considerable challenge to chemists, who lack the 'biological machinery' used in nature to assemble polymers with such precision. In addressing this challenge, familiar chemical concepts, such as combinatorial methods and supramolecular interactions, have been adapted for application in the macromolecular arena. Working from a limited set of residues, synthetic macromolecules have been produced that display surprisingly high binding affinities towards target proteins, even possessing useful in vivo activities. These observations are all the more surprising when one considers the heterogeneity inherent within these synthetic macromolecular receptors, and provoke intriguing questions regarding our assumptions about the design of receptors.
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Affiliation(s)
- Clare S Mahon
- Chemical Nanoscience Laboratory, School of Chemistry, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - David A Fulton
- Chemical Nanoscience Laboratory, School of Chemistry, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
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12
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Wang S, Shen Q, Nawaz MH, Zhang W. Photocontrolled reversible supramolecular assemblies of a diblock azo-copolymer based on β-cyclodextrin–Azo host–guest inclusion complexation. Polym Chem 2013. [DOI: 10.1039/c3py21148g] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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13
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Mahon CS, Fulton DA. Templation-induced re-equilibration in polymer-scaffolded dynamic combinatorial libraries leads to enhancements in binding affinities. Chem Sci 2013. [DOI: 10.1039/c3sc51413g] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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