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Dolz M, Monterrey DT, Beltrán-Nogal A, Menés-Rubio A, Keser M, González-Pérez D, de Santos PG, Viña-González J, Alcalde M. The colors of peroxygenase activity: Colorimetric high-throughput screening assays for directed evolution. Methods Enzymol 2023; 693:73-109. [PMID: 37977739 DOI: 10.1016/bs.mie.2023.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Fungal unspecific peroxygenases (UPOs) are arising as versatile biocatalysts for C-H oxyfunctionalization reactions. In recent years, several directed evolution studies have been conducted to design improved UPO variants. An essential part of this protein engineering strategy is the design of reliable colorimetric high-throughput screening (HTS) assays for mutant library exploration. Here, we present a palette of 12 colorimetric HTS assays along with their step-by-step protocols, which have been validated for directed UPO evolution campaigns. This array of colorimetric assays will pave the way for the discovery and design of new UPO variants.
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Affiliation(s)
- Mikel Dolz
- Department of Biocatalysis, Institute of Catalysis, CSIC, C/ Marie Curie 2, Cantoblanco, Madrid, Spain
| | - Dianelis T Monterrey
- Department of Biocatalysis, Institute of Catalysis, CSIC, C/ Marie Curie 2, Cantoblanco, Madrid, Spain
| | - Alejandro Beltrán-Nogal
- Department of Biocatalysis, Institute of Catalysis, CSIC, C/ Marie Curie 2, Cantoblanco, Madrid, Spain
| | - Andrea Menés-Rubio
- Department of Biocatalysis, Institute of Catalysis, CSIC, C/ Marie Curie 2, Cantoblanco, Madrid, Spain
| | - Merve Keser
- Department of Biocatalysis, Institute of Catalysis, CSIC, C/ Marie Curie 2, Cantoblanco, Madrid, Spain
| | - David González-Pérez
- Department of Biocatalysis, Institute of Catalysis, CSIC, C/ Marie Curie 2, Cantoblanco, Madrid, Spain
| | | | - Javier Viña-González
- EvoEnzyme S.L., C/ Faraday 7. Parque Científico de Madrid, Cantoblanco, Madrid, Spain
| | - Miguel Alcalde
- Department of Biocatalysis, Institute of Catalysis, CSIC, C/ Marie Curie 2, Cantoblanco, Madrid, Spain.
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2
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Mihajlovic M, Rikkers M, Mihajlovic M, Viola M, Schuiringa G, Ilochonwu BC, Masereeuw R, Vonk L, Malda J, Ito K, Vermonden T. Viscoelastic Chondroitin Sulfate and Hyaluronic Acid Double-Network Hydrogels with Reversible Cross-Links. Biomacromolecules 2022; 23:1350-1365. [PMID: 35195399 PMCID: PMC8924925 DOI: 10.1021/acs.biomac.1c01583] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 02/11/2022] [Indexed: 12/13/2022]
Abstract
Viscoelastic hydrogels are gaining interest as they possess necessary requirements for bioprinting and injectability. By means of reversible, dynamic covalent bonds, it is possible to achieve features that recapitulate the dynamic character of the extracellular matrix. Dually cross-linked and double-network (DN) hydrogels seem to be ideal for the design of novel biomaterials and bioinks, as a wide range of properties required for mimicking advanced and complex tissues can be achieved. In this study, we investigated the fabrication of chondroitin sulfate/hyaluronic acid (CS/HA)-based DN hydrogels, in which two networks are interpenetrated and cross-linked with the dynamic covalent bonds of very different lifetimes. Namely, Diels-Alder adducts (between methylfuran and maleimide) and hydrazone bonds (between aldehyde and hydrazide) were chosen as cross-links, leading to viscoelastic hydrogels. Furthermore, we show that viscoelasticity and the dynamic character of the resulting hydrogels could be tuned by changing the composition, that is, the ratio between the two types of cross-links. Also, due to a very dynamic nature and short lifetime of hydrazone cross-links (∼800 s), the DN hydrogel is easily processable (e.g., injectable) in the first stages of gelation, allowing the material to be used in extrusion-based 3D printing. The more long-lasting and robust Diels-Alder cross-links are responsible for giving the network enhanced mechanical strength and structural stability. Being highly charged and hydrophilic, the cross-linked CS and HA enable a high swelling capacity (maximum swelling ratio ranging from 6 to 12), which upon confinement results in osmotically stiffened constructs, able to mimic the mechanical properties of cartilage tissue, with the equilibrium moduli ranging from 0.3 to 0.5 MPa. Moreover, the mesenchymal stromal cells were viable in the presence of the hydrogels, and the effect of the degradation products on the macrophages suggests their safe use for further translational applications. The DN hydrogels with dynamic covalent cross-links hold great potential for the development of novel smart and tunable viscoelastic materials to be used as biomaterial inks or bioinks in bioprinting and regenerative medicine.
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Affiliation(s)
- Marko Mihajlovic
- Department
of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, 3584 CG Utrecht, The Netherlands
- Department
of Biomedical Engineering, Eindhoven University
of Technology, 5612 AZ Eindhoven, The Netherlands
| | - Margot Rikkers
- Department
of Orthopaedics, University Medical Center Utrecht, Utrecht University, 3508
GA Utrecht, The Netherlands
| | - Milos Mihajlovic
- Department
of Pharmacology, Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Martina Viola
- Department
of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, 3584 CG Utrecht, The Netherlands
- Department
of Orthopaedics, University Medical Center Utrecht, Utrecht University, 3508
GA Utrecht, The Netherlands
| | - Gerke Schuiringa
- Department
of Biomedical Engineering, Eindhoven University
of Technology, 5612 AZ Eindhoven, The Netherlands
| | - Blessing C. Ilochonwu
- Department
of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Rosalinde Masereeuw
- Department
of Pharmacology, Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Lucienne Vonk
- Department
of Orthopaedics, University Medical Center Utrecht, Utrecht University, 3508
GA Utrecht, The Netherlands
| | - Jos Malda
- Department
of Orthopaedics, University Medical Center Utrecht, Utrecht University, 3508
GA Utrecht, The Netherlands
- Department
of Equine Sciences, Faculty of Veterinary Medicine, Utrecht University, 3508
GA Utrecht, the Netherlands
| | - Keita Ito
- Department
of Biomedical Engineering, Eindhoven University
of Technology, 5612 AZ Eindhoven, The Netherlands
- Department
of Orthopaedics, University Medical Center Utrecht, Utrecht University, 3508
GA Utrecht, The Netherlands
| | - Tina Vermonden
- Department
of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, 3584 CG Utrecht, The Netherlands
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3
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Svenssen DK, Mirsharghi S, Boas U. Solid-phase synthesis of polyfunctional polylysine dendrons using aldehyde linkers. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.04.127] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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4
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Two-Step Enzymatic Modification of Solid-Supported Bergenin in Aqueous and Organic Media. Tetrahedron Lett 2010; 51:1220. [PMID: 20174610 DOI: 10.1016/j.tetlet.2009.12.119] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The natural flavonoid bergenin was directly immobilized onto carboxylic acid functionalized controlled pore glass (carboxy-CPG) at 95% yield. Immobilized bergenin was brominated via chloroperoxidase in aqueous solution and then transesterified with vinyl butyrate in diisopropyl ether by subtilisin carslberg (SC) extracted into the organic solvent via ion pairing. Enzymatic cleavage of 7-bromo-4-butyrylbergenin from carboxy-CPG (9.6% final yield) was accomplished using lipase B (LipB) in an aqueous/organic mixture (90/10 v/v of water/acetonitrile), demonstrating the feasibility of solid phase biocatalysis of a natural product in aqueous and non-aqueous media.
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Iliashevsky O, Amir L, Glaser R, Marks RS, Lemcoff NG. Synthesis, characterization and protein binding properties of supported dendrons. ACTA ACUST UNITED AC 2009. [DOI: 10.1039/b908014g] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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6
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Fabrication of silver nanoparticles via self-regulated reduction by 1-(2-hydroxyethyl)-3-methylimidazolium tetrafluoroborate. KOREAN J CHEM ENG 2007. [DOI: 10.1007/s11814-007-0054-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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7
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Ghasemi M, Minier M, Tatoulian M, Arefi-Khonsari F. Determination of amine and aldehyde surface densities: application to the study of aged plasma treated polyethylene films. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2007; 23:11554-61. [PMID: 17915893 DOI: 10.1021/la701126t] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The aim of this work was to test and to compare different methods reported in the literature to quantify amine and aldehyde functions on the surface of polyethylene (PE) films treated by ammonia plasma and to specify their stability against time. A low pressure ammonia plasma reactor was used to functionalize PE films with amine groups, which could be subsequently used for further immobilization of biomolecules. In order to determine the density of amine groups on the surface of treated films, various molecule probes and spectrophotometric analytical methods have been investigated. Two methods using (i) sulfosuccinimidyl 6-[3'-(2-pyridyldithio)-propionamido] hexanoate (sulfo-LC-SPDP) and (ii) 2-iminothiolane (ITL) associated with bicinchoninic acid (BCA) have been proved to be reliable and sensitive enough to estimate the surface concentration of primary amine functions. The amount of primary amino groups on the functionalized polyethylene films was found to be between 1.2 and 1.4 molecules/nm2. In a second step, the surface concentration of glutaraldehyde (GA), which is currently used as a spacer arm before immobilization of biomolecules, has been assessed: two methods were used to determine the surface density of available aldehyde functions, after the reaction of GA with the aminated polyethylene film. The concentration of GA was found to be in the same range as primary amine concentration. The influence of aging time on the density of available amino and aldehyde groups on the surfaces were evaluated under different storage conditions. The results showed that 50% of the initial density of primary amine functions remained available after storage during 6 days of the PE samples in PBS (pH 7.6) at 4 degrees C. In the case of aldehyde groups, the same percentage of the initial density (50%) remained active after storage in air at RT over a longer period, i.e., 15 days.
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Affiliation(s)
- Mahsa Ghasemi
- Ecole Nationale Supérieure de Chimie de Paris, Laboratoire de Génie des Procédés Plasma et Traitements de Surface, 11 rue Pierre et Marie Curie, 75231 Paris Cedex France.
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8
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Putt KS, Hergenrother PJ. A nonradiometric, high-throughput assay for poly(ADP-ribose) glycohydrolase (PARG): application to inhibitor identification and evaluation. Anal Biochem 2005; 333:256-64. [PMID: 15450800 DOI: 10.1016/j.ab.2004.04.032] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2004] [Indexed: 10/26/2022]
Abstract
The enzyme poly(ADP-ribose) glycohydrolase (PARG) catalyzes the hydrolysis of glycosidic bonds of ADP-ribose polymers, producing monomeric ADP-ribose units. Thus, in conjunction with poly(ADP-ribose) polymerase (PARP), PARG activity regulates the extent of in vivo poly(ADP-ribosyl)ation. Small molecule inhibitors of PARP and PARG have shown considerable promise in cellular models of ischemia-reperfusion injury and oxidative neuronal cell death. However, currently available PARG inhibitors are not ideal due to cell permeability, size, and/or toxicity concerns; therefore, new small molecule inhibitors of this important enzyme are sorely needed. Existing methodologies for in vitro assessment of PARG enzymatic activity do not lend themselves to high-throughput screening applications, as they typically use a radiolabeled substrate and determine product quantities through TLC analysis. This article describes a method whereby the ADP-ribose product of the PARG-catalyzed reaction is converted into a fluorescent dye. This highly sensitive and reproducible method is demonstrated by identifying two known PARG inhibitors in a 384-well plate assay and by subsequently determining IC(50) values for these compounds. Thus, this high-throughput, nonradioactive PARG assay should find widespread use in experiments directed toward identification of novel PARG inhibitors.
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Affiliation(s)
- Karson S Putt
- Department of Biochemistry, University of Illinois, Urbana, IL 61801, USA
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Heidler P, Link A. N-Acyl-N-alkyl-sulfonamide anchors derived from Kenner’s safety-catch linker: powerful tools in bioorganic and medicinal chemistry. Bioorg Med Chem 2005; 13:585-99. [PMID: 15653327 DOI: 10.1016/j.bmc.2004.10.045] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2004] [Accepted: 10/18/2004] [Indexed: 11/16/2022]
Abstract
In 1971 Kenner et al. introduced the safety-catch principle into solid phase peptide synthesis. Thus two contradicting needs were addressed. On the one hand, sufficient stability of the linker substrate bond to impede hydrolysis or similar side reactions, on the other hand mild chemical conditions allowing for unscathed liberation of the precious products. Over the years this linker type emerged in several different chemical disciplines and nowadays it presents a useful and broadly applicable tool. Recent advancements and applications based on Kenner's safety-catch linker are reviewed.
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Affiliation(s)
- Philipp Heidler
- Faculty of Pharmacy, Philipps-University Marburg, Marbacher Weg 6, D-35032, Germany
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11
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Abstract
The attachment of linker molecules to polymer beads used as insoluble supports for organic synthesis is a frequent requirement. Defined immobilization of these linker molecules before loading selected building blocks is crucial for subsequent transformations. Therefore, the control of the linker attachment is a central task. Because the molecular bodies of linkers are not incorporated in the final molecules, they can often be replaced or modified without affecting the structure of the products that are finally released. Consequently, it seems straightforward to look for coloured substitutes to established linker molecules. By using coloured linkers, visual inspection of the beads enables fast property estimation after attachment and monitoring of losses during synthesis. This very simple estimation does not have a validated loading determination, but is a useful element of straightforward and non-destructive reaction control that has general applicability. Here we present a red azo dye as an alternative to the Kenner safety-catch linker.
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Gaggini F, Porcheddu A, Reginato G, Rodriquez M, Taddei M. Colorimetric Tools for Solid-Phase Organic Synthesis. ACTA ACUST UNITED AC 2004; 6:805-10. [PMID: 15360217 DOI: 10.1021/cc049963a] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
One of the unresolved problems of solid-phase organic synthesis (SPOS) is the availability of general and rapid methods to monitor the transformation of functional groups present in molecules supported on insoluble supports. Color tests, far from providing the ultimate solution, may help in detection (and sometimes in quantification) of different functional groups. In this short review, we have collected most of the methods available and applied in SPOS with an Experimental Section that describes the procedure we have successfully applied to bead analyses in our laboratories.
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Affiliation(s)
- Francesca Gaggini
- CNR, Istituto di Chimica dei Composti Organo Metallici, c/o Dipartimento di Chimica Organica "Ugo Schiff", Polo Scientifico, Università degli Studi di Firenze, Via della Lastruccia, 13, 50019 Sesto Fiorentino, Italy
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Shannon SK, Barany G. 4-(9-Fluorenylmethyloxycarbonyl)phenylhydrazine (FmPH): A New Chromophoric Reagent for Quantitative Monitoring of Solid-Phase Aldehydes1-3. J Org Chem 2004; 69:4586-94. [PMID: 15230579 DOI: 10.1021/jo049830b] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A direct method for quantifying solid-phase aldehydes has been developed, using a new reagent, 4-(9-fluorenylmethyloxycarbonyl)phenylhydrazine (FmPH). The FmPH reagent was synthesized in three steps (24% overall yield) from commercially available p-hydrazinobenzoic acid. Resin-bound aldehydes reacted quantitatively with FmPH, in the presence of trimethylorthoformate (TMOF) as a dehydrating agent, to form a highly conjugated, immobilized FmPH-hydrazone. Next, mild treatment of the hydrazone with an excess of piperidine-N,N-dimethylformamide (1:1) released the piperidine-dibenzofulvene adduct chromophore (epsilon(301nm) = 7800 M(-1) cm(-1)) from the support. FmPH quantitation of aldehydes proved to be a straightforward, sensitive, and reproducible technique for monitoring resin-bound aldehydes [albeit insufficiently reactive to allow reliable quantification of ketones]. The FmPH aldehyde assay is applicable to a range of solid supports, as demonstrated specifically for poly(ethylene glycol)-polystyrene (PEG-PS), aminomethylpolystyrene (AMP), and cross-linked ethoxylate acrylate resin (CLEAR).
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Affiliation(s)
- Simon K Shannon
- Department of Chemistry, University of Minnesota, 207 Pleasant Street S E, Minneapolis, Minnesota 55455, USA
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Shannon SK, Barany G. Colorimetric Monitoring of Solid-Phase Aldehydes Using 2,4-Dinitrophenylhydrazine. ACTA ACUST UNITED AC 2004; 6:165-70. [PMID: 15002963 DOI: 10.1021/cc034033x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A simple and rapid method to achieve colorimetric monitoring of resin-bound aldehydes, based on ambient temperature reaction with 2,4-dinitrophenylhydrazine (DNPH) in the presence of dilute acid, has been developed as an adjunct to solid-phase organic synthesis and combinatorial chemistry. By this test, the presence of aldehydes is indicated by a red to dark-orange appearance, within a minute. Alternatively, resins that are free of aldehydes or in which aldehyde functions have reacted completely retain their original color. The DNPH test was demonstrated for poly(ethylene glycol)-polystyrene (PEG-PS), aminomethyl polystyrene (AMP), cross-linked ethoxylate acrylate resin (CLEAR), and acryloylated O,O'-bis(2-aminopropyl)poly(ethylene glycol) (PEGA) supports and gave results visible to the naked eye at levels as low as 18 micromol of aldehyde per gram of resin.
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Affiliation(s)
- Simon K Shannon
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455, USA
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Synthesis of an olefin-containing cyclic peptide using the solid-phase Horner–Emmons reaction. Tetrahedron Lett 2004. [DOI: 10.1016/j.tetlet.2003.10.093] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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16
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Suenaga T, Schutz C, Nakata T. A real time reaction monitoring using fluorescent dansyl group as a solid-phase leaving group. Tetrahedron Lett 2003. [DOI: 10.1016/s0040-4039(03)01406-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Abstract
Results obtained in the application of these tests are summarized in Table II. We have encountered some variations in the reproducibility and accuracy of some tests. Due to the numerous factors that can influence colorimetric test results (e.g., test reagent stability, resin type, functional group interference, and lability of protecting group) we highly recommend performing a positive and a negative control for any test applied to a new synthesis. We also emphasize the importance of reagent solution purity on the outcome of test results, hence we strongly encourage the use of correctly prepared and carefully stored reactants. To minimize false results due to lability of the resin-product bond or the product itself (such as Fmoc-protected amino acids), colorimetric tests should be performed with the utmost immediacy in regards to completion of the step to be monitored. Hence the storage of resin over long periods of time (more than 24 h) before testing is not advisable. When the result of a colorimetric test is in doubt we advise repeating the test a few times until a reproducible result is obtained. The use of multiple tests for the same functional group may elucidate ambiguous or otherwise challenging cases.
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Affiliation(s)
- Jesús Vázquez
- University of Barcelona, Barcelona Biomedical Research Institute, Barcelona Science Park, Josep Samitier 1, Barcelona, 08028, Spain
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