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Singhal A, Singh A, Shrivastava A, Khan R. Epitope imprinted polymeric materials: application in electrochemical detection of disease biomarkers. J Mater Chem B 2023; 11:936-954. [PMID: 36606445 DOI: 10.1039/d2tb02135h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Epitope imprinting is a promising method for creating specialized recognition sites that resemble natural biorecognition elements. Epitope-imprinted materials have gained a lot of attention recently in a variety of fields, including bioanalysis, drug delivery, and clinical therapy. The vast applications of epitope imprinted polymers are due to the flexibility in choosing monomers, the simplicity in obtaining templates, specificity toward targets, and resistance to harsh environments along with being cost effective in nature. The "epitope imprinting technique," which uses only a tiny subunit of the target as the template during imprinting, offers a way around various drawbacks inherent to biomacromolecule systems i.e., traditional molecular imprinting techniques with regards to the large size of proteins, such as the size, complexity, accessibility, and conformational flexibility of the template. Electrochemical based sensors are proven to be promising tool for the quick, real-time monitoring of biomarkers. This review unravels epitope imprinting techniques, approaches, and strategies and highlights the applicability of these techniques for the electrochemical quantification of biomarkers for timely disease monitoring. In addition, some challenges are discussed along with future prospective developments.
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Affiliation(s)
- Ayushi Singhal
- CSIR-Advanced Materials and Processes Research Institute (AMPRI), Hoshangabad Road, Bhopal - 462026, MP, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Amrita Singh
- Department of Biotechnology, Barkatullah University, Habibganj, Bhopal, Madhya Pradesh 462026, India
| | - Apoorva Shrivastava
- Dr D. Y. Patil Biotechnology and Bioinformatics Institute, Dr D. Y. Patil Vidyapeeth, Sr. No. 87-88, Mumbai-Bangalore Highway, Tathawade, Pune, Maharashtra, 411033, India
| | - Raju Khan
- CSIR-Advanced Materials and Processes Research Institute (AMPRI), Hoshangabad Road, Bhopal - 462026, MP, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
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Kanubaddi KR, Yang CL, Huang PY, Lin CY, Tai DF, Lee CH. Peptide conformational imprints enhanced the catalytic activity of papain for esterification. Front Bioeng Biotechnol 2022; 10:943751. [PMID: 36051592 PMCID: PMC9424681 DOI: 10.3389/fbioe.2022.943751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
Peptide conformational imprints (PCIs) offer a promising perspective to directly generate binding sites for preserving enzymes with high catalytic activity and stability. In this study, we synthesized a new chiral cross-linker cost-effectively for controlling the matrix morphology of PCIs on magnetic particles (PCIMPs) to stabilize their recognition capability. Meanwhile, based on the flank part of the sequences on papain (PAP), three epitope peptides were selected and synthesized. Molecularly imprinted polymers (MIPs) were then fabricated in the presence of the epitope peptide using our new cross-linker on magnetic particles (MPs) to generate PCIMPs. PCIMPs were formed with helical cavities that complement the PAP structure to adsorb specifically at the targeted position of PAP. PCIMPs65–79 were found to have the best binding parameters to the PAP with Kd = 0.087 μM and Bmax = 4.56 μM. Upon esterification of N-Boc-His-OH, proton nuclear magnetic resonance (1H-NMR) was used to monitor the yield of the reaction and evaluate the activity of PAP/PCIMPs. The kinetic parameters of PAP/PCIMPs65–79 were calculated as Vmax = 3.0 μM s−1, Km = 5 × 10−2 M, kcat = 1.1 × 10–1 s−1, and kcat/Km = 2.2 M−1 s−1. In addition, PAP is bound tightly to PCIMPs to sustain its activity after four consecutive cycles.
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Affiliation(s)
- Kiran Reddy Kanubaddi
- Department of Life Science and Institute of Biotechnology, National Dong Hwa University, Hualien, Taiwan
| | - Ching-Lun Yang
- Department of Chemistry, National Dong Hwa University, Hualien, Taiwan
| | - Pei-Yu Huang
- Department of Chemistry, National Dong Hwa University, Hualien, Taiwan
| | - Chung-Yin Lin
- Medical Imaging Research Center, Institute for Radiological Research, Chang Gung University, Taoyuan, Taiwan
- Department of Neurology, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- *Correspondence: Chung-Yin Lin, ; Dar-Fu Tai,
| | - Dar-Fu Tai
- Department of Chemistry, National Dong Hwa University, Hualien, Taiwan
- *Correspondence: Chung-Yin Lin, ; Dar-Fu Tai,
| | - Chia-Hung Lee
- Department of Life Science and Institute of Biotechnology, National Dong Hwa University, Hualien, Taiwan
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Integration of Adenylate Kinase 1 with Its Peptide Conformational Imprint. Int J Mol Sci 2022; 23:ijms23126521. [PMID: 35742970 PMCID: PMC9223553 DOI: 10.3390/ijms23126521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/09/2022] [Accepted: 06/09/2022] [Indexed: 02/01/2023] Open
Abstract
In the present study, molecularly imprinted polymers (MIPs) were used as a tool to grasp a targeted α-helix or β-sheet of protein. During the fabrication of the hinge-mediated MIPs, elegant cavities took shape in a special solvent on quartz crystal microbalance (QCM) chips. The cavities, which were complementary to the protein secondary structure, acted as a peptide conformational imprint (PCI) for adenylate kinase 1 (AK1). We established a promising strategy to examine the binding affinities of human AK1 in conformational dynamics using the peptide-imprinting method. Moreover, when bound to AK1, PCIs are able to gain stability and tend to maintain higher catalytic activities than free AK1. Such designed fixations not only act on hinges as accelerators; some are also inhibitors. One example of PCI inhibition of AK1 catalytic activity takes place when PCI integrates with an AK19-23 β-sheet. In addition, conformation ties, a general MIP method derived from random-coil AK1133-144 in buffer/acetonitrile, are also inhibitors. The inhibition may be due to the need for this peptide to execute conformational transition during catalysis.
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Mier A, Maffucci I, Merlier F, Prost E, Montagna V, Ruiz‐Esparza GU, Bonventre JV, Dhal PK, Tse Sum Bui B, Sakhaii P, Haupt K. Molecularly Imprinted Polymer Nanogels for Protein Recognition: Direct Proof of Specific Binding Sites by Solution STD and WaterLOGSY NMR Spectroscopies. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106507] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Alejandra Mier
- CNRS Enzyme and Cell Engineering Laboratory Université de Technologie de Compiègne Rue du Docteur Schweitzer, CS 60319 60203 Compiègne Cedex France
| | - Irene Maffucci
- CNRS Enzyme and Cell Engineering Laboratory Université de Technologie de Compiègne Rue du Docteur Schweitzer, CS 60319 60203 Compiègne Cedex France
| | - Franck Merlier
- CNRS Enzyme and Cell Engineering Laboratory Université de Technologie de Compiègne Rue du Docteur Schweitzer, CS 60319 60203 Compiègne Cedex France
| | - Elise Prost
- CNRS Enzyme and Cell Engineering Laboratory Université de Technologie de Compiègne Rue du Docteur Schweitzer, CS 60319 60203 Compiègne Cedex France
| | - Valentina Montagna
- CNRS Enzyme and Cell Engineering Laboratory Université de Technologie de Compiègne Rue du Docteur Schweitzer, CS 60319 60203 Compiègne Cedex France
| | - Guillermo U. Ruiz‐Esparza
- Divisions of Engineering in Medicine and Renal Medicine Department of Medicine Harvard Medical School, Brigham and Women's Hospital Boston MA 02115 USA
- Division of Health Science and Technology Harvard University—Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Joseph V. Bonventre
- Divisions of Engineering in Medicine and Renal Medicine Department of Medicine Harvard Medical School, Brigham and Women's Hospital Boston MA 02115 USA
- Division of Health Science and Technology Harvard University—Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Pradeep K. Dhal
- US Early Development Sanofi Global R&D 153 Second Avenue Waltham MA 02451 USA
| | - Bernadette Tse Sum Bui
- CNRS Enzyme and Cell Engineering Laboratory Université de Technologie de Compiègne Rue du Docteur Schweitzer, CS 60319 60203 Compiègne Cedex France
| | - Peyman Sakhaii
- R&D Global CMC Development—Synthetics—Early Development Frankfurt Sanofi-Aventis (Deutschland) GmbH Industriepark Hoechst Frankfurt am Main Germany
| | - Karsten Haupt
- CNRS Enzyme and Cell Engineering Laboratory Université de Technologie de Compiègne Rue du Docteur Schweitzer, CS 60319 60203 Compiègne Cedex France
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Mier A, Maffucci I, Merlier F, Prost E, Montagna V, Ruiz-Esparza GU, Bonventre JV, Dhal PK, Tse Sum Bui B, Sakhaii P, Haupt K. Molecularly Imprinted Polymer Nanogels for Protein Recognition: Direct Proof of Specific Binding Sites by Solution STD and WaterLOGSY NMR Spectroscopies. Angew Chem Int Ed Engl 2021; 60:20849-20857. [PMID: 34296498 PMCID: PMC8562893 DOI: 10.1002/anie.202106507] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/15/2021] [Indexed: 11/07/2022]
Abstract
Molecularly imprinted polymers (MIPs) are tailor-made synthetic antibodies possessing specific binding cavities designed for a target molecule. Currently, MIPs for protein targets are synthesized by imprinting a short surface-exposed fragment of the protein, called epitope or antigenic determinant. However, finding the epitope par excellence that will yield a peptide "synthetic antibody" cross-reacting exclusively with the protein from which it is derived, is not easy. We propose a computer-based rational approach to unambiguously identify the "best" epitope candidate. Then, using Saturation Transfer Difference (STD) and WaterLOGSY NMR spectroscopies, we prove the existence of specific binding sites created by the imprinting of this peptide epitope in the MIP nanogel. The optimized MIP nanogel could bind the epitope and cognate protein with a high affinity and selectivity. The study was performed on Hepatitis A Virus Cell Receptor-1 protein, also known as KIM-1 and TIM-1, for its ubiquitous implication in numerous pathologies.
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Affiliation(s)
- Alejandra Mier
- CNRS Enzyme and Cell Engineering Laboratory, Université de Technologie de Compiègne, Rue du Docteur Schweitzer, CS 60319, 60203, Compiègne Cedex, France
| | - Irene Maffucci
- CNRS Enzyme and Cell Engineering Laboratory, Université de Technologie de Compiègne, Rue du Docteur Schweitzer, CS 60319, 60203, Compiègne Cedex, France
| | - Franck Merlier
- CNRS Enzyme and Cell Engineering Laboratory, Université de Technologie de Compiègne, Rue du Docteur Schweitzer, CS 60319, 60203, Compiègne Cedex, France
| | - Elise Prost
- CNRS Enzyme and Cell Engineering Laboratory, Université de Technologie de Compiègne, Rue du Docteur Schweitzer, CS 60319, 60203, Compiègne Cedex, France
| | - Valentina Montagna
- CNRS Enzyme and Cell Engineering Laboratory, Université de Technologie de Compiègne, Rue du Docteur Schweitzer, CS 60319, 60203, Compiègne Cedex, France
| | - Guillermo U Ruiz-Esparza
- Divisions of Engineering in Medicine and Renal Medicine, Department of Medicine, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Division of Health Science and Technology, Harvard University-Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Joseph V Bonventre
- Divisions of Engineering in Medicine and Renal Medicine, Department of Medicine, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Division of Health Science and Technology, Harvard University-Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Pradeep K Dhal
- US Early Development, Sanofi Global R&D, 153 Second Avenue, Waltham, MA, 02451, USA
| | - Bernadette Tse Sum Bui
- CNRS Enzyme and Cell Engineering Laboratory, Université de Technologie de Compiègne, Rue du Docteur Schweitzer, CS 60319, 60203, Compiègne Cedex, France
| | - Peyman Sakhaii
- R&D Global CMC Development-Synthetics-Early Development Frankfurt, Sanofi-Aventis (Deutschland) GmbH, Industriepark Hoechst, Frankfurt am Main, Germany
| | - Karsten Haupt
- CNRS Enzyme and Cell Engineering Laboratory, Université de Technologie de Compiègne, Rue du Docteur Schweitzer, CS 60319, 60203, Compiègne Cedex, France
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Wang X, Chen G, Zhang P, Jia Q. Advances in epitope molecularly imprinted polymers for protein detection: a review. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:1660-1671. [PMID: 33861232 DOI: 10.1039/d1ay00067e] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Epitope molecularly imprinted polymers (EMIPs) are novel imprinted materials using short characteristic peptides as templates rather than entire proteins. To be specific, the amino acid sequence of the template peptide is the same as an exposed N- or C-terminus of a target protein, or its amino acid composition and sequence replicate a similar conformational arrangement as the same amino acid residues on the surface of the target protein. EMIPs have a good application prospect in protein research. Herein, we focus on classification of epitope imprinting techniques, methods of epitope immobilization on matrix materials including boronate affinity immobilization, covalent bonding immobilization, physical adsorption immobilization and metal ion chelation immobilization, and application of EMIPs in peptides, proteins, target imaging and target therapy fields. Finally, the main problems and future development are summarized.
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Affiliation(s)
- Xindi Wang
- College of Chemistry, Jilin University, Changchun, 130012, P. R. China.
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Kanubaddi KR, Huang PY, Chang YL, Wu CH, Li W, Kankala RK, Tai DF, Lee CH. Deviation of Trypsin Activity Using Peptide Conformational Imprints. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:334. [PMID: 33513990 PMCID: PMC7911952 DOI: 10.3390/nano11020334] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 12/02/2022]
Abstract
In this study, a methodology utilizing peptide conformational imprints (PCIs) as a tool to specifically immobilize porcine pancreatic alpha-trypsin (PPT) at a targeted position is demonstrated. Owing to the fabrication of segment-mediated PCIs on the magnetic particles (PCIMPs), elegant cavities complementary to the PPT structure are constructed. Based on the sequence on targeted PPT, the individual region of the enzyme is trapped with different template-derived PCIMPs to show certain types of inhibition. Upon hydrolysis, N-benzoyl-L-arginine ethyl ester (BAEE) is employed to assess the hydrolytic activity of PCIMPs bound to the trypsin using high-performance liquid chromatography (HPLC) analysis. Further, the kinetic data of four different PCIMPs are compared. As a result, the PCIMPs presented non-competitive inhibition toward trypsin, according to the Lineweaver-Burk plot. Further, the kinetic analysis confirmed that the best parameters of PPT/PCIMPs 233-245+G were Vmax = 1.47 × 10-3 mM s-1, Km = 0.42 mM, kcat = 1.16 s-1, and kcat/Km = 2.79 mM-1 s-1. As PPT is bound tightly to the correct position, its catalytic activities could be sustained. Additionally, our findings stated that the immobilized PPT could maintain stable activity even after four successive cycles.
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Affiliation(s)
- Kiran Reddy Kanubaddi
- Department of Life Science, National Dong Hwa University, Hualien 97401, Taiwan; (K.R.K.); (R.K.K.)
| | - Pei-Yu Huang
- Department of Chemistry, National Dong Hwa University, Hualien 97401, Taiwan; (P.-Y.H.); (Y.-L.C.); (C.H.W.); (W.L.)
| | - Ya-Lin Chang
- Department of Chemistry, National Dong Hwa University, Hualien 97401, Taiwan; (P.-Y.H.); (Y.-L.C.); (C.H.W.); (W.L.)
| | - Cheng Hsin Wu
- Department of Chemistry, National Dong Hwa University, Hualien 97401, Taiwan; (P.-Y.H.); (Y.-L.C.); (C.H.W.); (W.L.)
| | - Wei Li
- Department of Chemistry, National Dong Hwa University, Hualien 97401, Taiwan; (P.-Y.H.); (Y.-L.C.); (C.H.W.); (W.L.)
| | - Ranjith Kumar Kankala
- Department of Life Science, National Dong Hwa University, Hualien 97401, Taiwan; (K.R.K.); (R.K.K.)
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, China
| | - Dar-Fu Tai
- Department of Chemistry, National Dong Hwa University, Hualien 97401, Taiwan; (P.-Y.H.); (Y.-L.C.); (C.H.W.); (W.L.)
| | - Chia-Hung Lee
- Department of Life Science, National Dong Hwa University, Hualien 97401, Taiwan; (K.R.K.); (R.K.K.)
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Sensing HIV Protease and Its Inhibitor Using "Helical Epitope"-Imprinted Polymers. SENSORS 2020; 20:s20123592. [PMID: 32630459 PMCID: PMC7348739 DOI: 10.3390/s20123592] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/21/2020] [Accepted: 06/22/2020] [Indexed: 12/15/2022]
Abstract
A helical epitope-peptide (lle85-Gly94) was selected from the α-helix structure of the HIV protease (PR) as the template, which represents an intricate interplay between structure conformation and dimerization. The peptide template was mixed with water, trifluoroethanol (TFE), and acetonitrile (ACN) at a certain ratio to enlarge the helical conformation in the solution for the fabrication of helical epitope-mediated molecularly imprinted polymers (HEMIPs) on a quartz crystal microbalance (QCM) chip. The template molecules were then removed under equilibrium batch rebinding conditions involving 5% acetic acid/water. The resulting HEMIPs chip exhibited a high affinity toward template peptide HIV PR85-94, His-tagged HIV PR, and HIV PR, with dissociation constants (Kd) as 160, 43.3, and 78.5 pM, respectively. The detection limit of the developed HIV PR85-94 QCM sensor is 0.1 ng/mL. The HEMIPs chip exhibited a high affinity and selectivity to bind HIV PR and subsequently to an inhibitor of HIV PR (nelfinavir). The HIV PR binding site was properly oriented on the HEMIPs-chip to develop a HIV PR/HEMIPs chip, which can effectively bind nelfinavir to establish a sandwich assay. The nelfinavir then attached to the HIV PR/HEMIPs chip, which can be easily removed involving 0.8% acetic acid/water. Therefore, HIV PR/HEMIPs chip can be useful to screen for other HIV PR inhibitors. This technique may improve drug targeting for HIV therapy and also strengthen investigations into other virus assays.
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Lee MH, Thomas JL, Liao CL, Jurcevic S, Crnogorac-Jurcevic T, Lin HY. Polymers imprinted with three REG1B peptides for electrochemical determination of Regenerating Protein 1B, a urinary biomarker for pancreatic ductal adenocarcinoma. Mikrochim Acta 2017. [DOI: 10.1007/s00604-017-2169-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Molecularly imprinted polymers for separating and sensing of macromolecular compounds and microorganisms. Biotechnol Adv 2015; 34:30-46. [PMID: 26656748 DOI: 10.1016/j.biotechadv.2015.12.002] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 11/26/2015] [Accepted: 12/01/2015] [Indexed: 12/22/2022]
Abstract
The present review article focuses on gathering, summarizing, and critically evaluating the results of the last decade on separating and sensing macromolecular compounds and microorganisms with the use of molecularly imprinted polymer (MIP) synthetic receptors. Macromolecules play an important role in biology and are termed that way to contrast them from micromolecules. The former are large and complex molecules with relatively high molecular weights. The article mainly considers chemical sensing of deoxyribonucleic acids (DNAs), proteins and protein fragments as well as sugars and oligosaccharides. Moreover, it briefly discusses fabrication of chemosensors for determination of bacteria and viruses that can ultimately be considered as extremely large macromolecules.
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Liu Y, Huang S, Li Z, Zhao M. Molecularly Imprinted Polymers as Tools for Bioassays and Biotransformation. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2015; 150:207-26. [DOI: 10.1007/10_2015_315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Whitcombe MJ, Kirsch N, Nicholls IA. Molecular imprinting science and technology: a survey of the literature for the years 2004-2011. J Mol Recognit 2014; 27:297-401. [PMID: 24700625 DOI: 10.1002/jmr.2347] [Citation(s) in RCA: 275] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 10/28/2013] [Accepted: 12/01/2013] [Indexed: 12/11/2022]
Abstract
Herein, we present a survey of the literature covering the development of molecular imprinting science and technology over the years 2004-2011. In total, 3779 references to the original papers, reviews, edited volumes and monographs from this period are included, along with recently identified uncited materials from prior to 2004, which were omitted in the first instalment of this series covering the years 1930-2003. In the presentation of the assembled references, a section presenting reviews and monographs covering the area is followed by sections describing fundamental aspects of molecular imprinting including the development of novel polymer formats. Thereafter, literature describing efforts to apply these polymeric materials to a range of application areas is presented. Current trends and areas of rapid development are discussed.
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