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Practical Guidance for Developing Small-Molecule Optical Probes for In Vivo Imaging. Mol Imaging Biol 2023; 25:240-264. [PMID: 36745354 DOI: 10.1007/s11307-023-01800-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 12/31/2022] [Accepted: 01/05/2023] [Indexed: 02/07/2023]
Abstract
The WMIS Education Committee (2019-2022) reached a consensus that white papers on molecular imaging could be beneficial for practitioners of molecular imaging at their early career stages and other scientists who are interested in molecular imaging. With this consensus, the committee plans to publish a series of white papers on topics related to the daily practice of molecular imaging. In this white paper, we aim to provide practical guidance that could be helpful for optical molecular imaging, particularly for small molecule probe development and validation in vitro and in vivo. The focus of this paper is preclinical animal studies with small-molecule optical probes. Near-infrared fluorescence imaging, bioluminescence imaging, chemiluminescence imaging, image-guided surgery, and Cerenkov luminescence imaging are discussed in this white paper.
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2
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Intensification of Inclusion Body Processing via Temperature-Based Refolding. Methods Mol Biol 2023; 2617:189-200. [PMID: 36656525 DOI: 10.1007/978-1-0716-2930-7_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Inclusion bodies (IB) are dense insoluble aggregates of mostly misfolded polypeptides that usually result from recombinant protein overexpression. IB formation has been observed in protein expression systems such as E. coli, yeast, and higher eukaryotes. To recover soluble recombinant proteins in their native state, IB are commonly first solubilized with a high concentration of denaturant. This is followed by concurrent denaturant removal or reduction and a transition into a refolding-favorable chemical environment to facilitate the refolding of solubilized protein to its native state. Due to the high concentration of denaturant used, conventional refolding approaches can result in dilute products and are buffer inefficient. To circumvent the limitations of conventional refolding approaches, a temperature-based refolding approach which combines a low concentration of denaturant (0.5 M guanidine hydrochloride, GdnHCl) with a high temperature (95 °C) during solubilization was proposed. In this chapter, we describe a temperature-based refolding approach for the recovery of core streptavidin (cSAV) from IB. Through the temperature-based approach, intensification was achieved through the elimination of a concentration step which would be required by a dilution approach and through a reduction in buffer volumes required for dilution or denaturant removal. High-temperature treatment during solubilization may have also resulted in the denaturation and aggregation of undesired host-cell proteins, which could then be removed through a centrifugation step resulting in refolded cSAV of high purity without the need for column purification. Refolded cSAV was characterized by biotin-binding assay and SDS-PAGE, while purity was determined by RP-HPLC.
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3
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Ayan E, Yuksel B, Destan E, Ertem FB, Yildirim G, Eren M, Yefanov OM, Barty A, Tolstikova A, Ketawala GK, Botha S, Dao EH, Hayes B, Liang M, Seaberg MH, Hunter MS, Batyuk A, Mariani V, Su Z, Poitevin F, Yoon CH, Kupitz C, Cohen A, Doukov T, Sierra RG, Dağ Ç, DeMirci H. Cooperative allostery and structural dynamics of streptavidin at cryogenic- and ambient-temperature. Commun Biol 2022; 5:73. [PMID: 35058563 PMCID: PMC8776744 DOI: 10.1038/s42003-021-02903-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 10/28/2021] [Indexed: 11/11/2022] Open
Abstract
Multimeric protein assemblies are abundant in nature. Streptavidin is an attractive protein that provides a paradigm system to investigate the intra- and intermolecular interactions of multimeric protein complexes. Also, it offers a versatile tool for biotechnological applications. Here, we present two apo-streptavidin structures, the first one is an ambient temperature Serial Femtosecond X-ray crystal (Apo-SFX) structure at 1.7 Å resolution and the second one is a cryogenic crystal structure (Apo-Cryo) at 1.1 Å resolution. These structures are mostly in agreement with previous structural data. Combined with computational analysis, these structures provide invaluable information about structural dynamics of apo streptavidin. Collectively, these data further reveal a novel cooperative allostery of streptavidin which binds to substrate via water molecules that provide a polar interaction network and mimics the substrate biotin which displays one of the strongest affinities found in nature.
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Affiliation(s)
- Esra Ayan
- Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
| | - Busra Yuksel
- Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
| | - Ebru Destan
- Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
| | - Fatma Betul Ertem
- Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
| | - Gunseli Yildirim
- Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
| | - Meryem Eren
- Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
| | | | - Anton Barty
- Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | | | - Gihan K Ketawala
- Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA
| | - Sabine Botha
- Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA
| | - E Han Dao
- Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, CA, 94025, USA
| | - Brandon Hayes
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Mengning Liang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Matthew H Seaberg
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Alexander Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Valerio Mariani
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Zhen Su
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
- Department of Applied Physics, Stanford University, Stanford, CA, 94305, USA
| | - Frederic Poitevin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Chun Hong Yoon
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Christopher Kupitz
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Aina Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Tzanko Doukov
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Raymond G Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Çağdaş Dağ
- Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
- Nanofabrication and Nanocharacterization Center for Scientific and Technological Advanced Research, Koc University, 34450, Istanbul, Turkey
- Koc University Isbank Center for Infectious Diseases (KUISCID), 34010, Istanbul, Turkey
| | - Hasan DeMirci
- Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey.
- Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, CA, 94025, USA.
- Koc University Isbank Center for Infectious Diseases (KUISCID), 34010, Istanbul, Turkey.
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4
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Chemically stable fluorescent proteins for advanced microscopy. Nat Methods 2022; 19:1612-1621. [PMID: 36344833 PMCID: PMC9718679 DOI: 10.1038/s41592-022-01660-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 09/26/2022] [Indexed: 11/09/2022]
Abstract
We report the rational engineering of a remarkably stable yellow fluorescent protein (YFP), 'hyperfolder YFP' (hfYFP), that withstands chaotropic conditions that denature most biological structures within seconds, including superfolder green fluorescent protein (GFP). hfYFP contains no cysteines, is chloride insensitive and tolerates aldehyde and osmium tetroxide fixation better than common fluorescent proteins, enabling its use in expansion and electron microscopies. We solved crystal structures of hfYFP (to 1.7-Å resolution), a monomeric variant, monomeric hyperfolder YFP (1.6 Å) and an mGreenLantern mutant (1.2 Å), and then rationally engineered highly stable 405-nm-excitable GFPs, large Stokes shift (LSS) monomeric GFP (LSSmGFP) and LSSA12 from these structures. Lastly, we directly exploited the chemical stability of hfYFP and LSSmGFP by devising a fluorescence-assisted protein purification strategy enabling all steps of denaturing affinity chromatography to be visualized using ultraviolet or blue light. hfYFP and LSSmGFP represent a new generation of robustly stable fluorescent proteins developed for advanced biotechnological applications.
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5
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Oberbichler E, Wiesauer M, Schlögl E, Stangl J, Faschinger F, Knör G, Gruber HJ, Hytönen VP. Competitive binding assay for biotin and biotin derivatives, based on avidin and biotin-4-fluorescein. Methods Enzymol 2021; 633:1-20. [PMID: 32046840 DOI: 10.1016/bs.mie.2019.10.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Biotinylated molecules are extensively employed in bioanalytics and biotechnology. The currently available assays for quantification of biotin groups suffer from low sensitivity, low accuracy, or provide highly variable responses for different biotin derivatives. We developed a competitive binding assay in which avidin was pre-blocked to different extents by the biotinylated analyte and a constant amount of biotin-4-fluorescein (B4F) was added, resulting in strong quenching of the B4F. The assay was robust and the shape of the titration curve immediately revealed whether the data were reliable or perturbed by steric hindrance in case of large biotin derivatives. These advantages justified well the 10× higher sample consumption (~0.6nmol) compared to single point assays. The assay was applied to a representative set of small biotin derivatives and validated by cross-control with the well-established 2-anilinonaphthalene-6-sulfonic acid (2,6-ANS) binding assay. In comparison to the 2,6-ANS binding assay, the lower precision (±10%) was compensated by the 100-fold higher sensitivity and the deviations from the ANS assay were ≤5%. In comparison to the more sensitive biotin group assays, the new assay has the advantage of minimal bias for different biotin derivatives. In case of biotinylated DNA with 30 nucleotides, steric hindrance was found to reduce the accuracy of biotin group determination; this problem was overcome by partial digestion to n≤5 nucleotide residues with a 3'-exonuclease. The newly proposed biotin group assay offers a useful compromise in terms of sensitivity, precision, trueness, and robustness.
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Affiliation(s)
- Elke Oberbichler
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | - Maria Wiesauer
- Institute of Inorganic Chemistry, Johannes Kepler University, Linz, Austria
| | - Eva Schlögl
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | - Jessica Stangl
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | - Felix Faschinger
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | - Günther Knör
- Institute of Inorganic Chemistry, Johannes Kepler University, Linz, Austria
| | - Hermann J Gruber
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | - Vesa P Hytönen
- Faculty of Medicine and Health Technology and BioMediTech, Tampere University, Tampere, Finland; Fimlab Laboratories, Tampere, Finland.
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6
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Vornholt T, Christoffel F, Pellizzoni MM, Panke S, Ward TR, Jeschek M. Systematic engineering of artificial metalloenzymes for new-to-nature reactions. SCIENCE ADVANCES 2021; 7:eabe4208. [PMID: 33523952 DOI: 10.1126/sciadv.abe4208] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 12/04/2020] [Indexed: 06/12/2023]
Abstract
Artificial metalloenzymes (ArMs) catalyzing new-to-nature reactions could play an important role in transitioning toward a sustainable economy. While ArMs have been created for various transformations, attempts at their genetic optimization have been case specific and resulted mostly in modest improvements. To realize their full potential, methods to rapidly discover active ArM variants for ideally any reaction of interest are required. Here, we introduce a reaction-independent, automation-compatible platform, which relies on periplasmic compartmentalization in Escherichia coli to rapidly and reliably engineer ArMs based on the biotin-streptavidin technology. We systematically assess 400 ArM mutants for five bioorthogonal transformations involving different metals, reaction mechanisms, and reactants, which include novel ArMs for gold-catalyzed hydroamination and hydroarylation. Activity enhancements up to 15-fold highlight the potential of the systematic approach. Furthermore, we suggest smart screening strategies and build machine learning models that accurately predict ArM activity from sequence, which has crucial implications for future ArM development.
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Affiliation(s)
- Tobias Vornholt
- Department of Biosystems Science and Engineering, ETH Zurich, CH-4058 Basel, Switzerland
- National Centre of Competence in Research (NCCR) Molecular Systems Engineering, Basel, Switzerland
| | - Fadri Christoffel
- National Centre of Competence in Research (NCCR) Molecular Systems Engineering, Basel, Switzerland
- Department of Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, CH-4002 Basel, Switzerland
| | - Michela M Pellizzoni
- National Centre of Competence in Research (NCCR) Molecular Systems Engineering, Basel, Switzerland
- Department of Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, CH-4002 Basel, Switzerland
| | - Sven Panke
- Department of Biosystems Science and Engineering, ETH Zurich, CH-4058 Basel, Switzerland
- National Centre of Competence in Research (NCCR) Molecular Systems Engineering, Basel, Switzerland
| | - Thomas R Ward
- National Centre of Competence in Research (NCCR) Molecular Systems Engineering, Basel, Switzerland
- Department of Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, CH-4002 Basel, Switzerland
| | - Markus Jeschek
- Department of Biosystems Science and Engineering, ETH Zurich, CH-4058 Basel, Switzerland.
- National Centre of Competence in Research (NCCR) Molecular Systems Engineering, Basel, Switzerland
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7
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Błauż A, Rychlik B, Plazuk D, Peccati F, Jiménez-Osés G, Steinke U, Sierant M, Trzeciak K, Skorupska E, Miksa B. Biotin-phenosafranin as a new photosensitive conjugate for targeted therapy and imaging. NEW J CHEM 2021. [DOI: 10.1039/d0nj06170k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A biotinylated phenazine compound as a phenosafranin conjugate (Biot-PSF) was synthesized and reported for the first time.
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Affiliation(s)
- Andrzej Błauż
- Cytometry Laboratory
- Department of Molecular Biophysics
- Faculty of Biology & Environmental Protection
- University of Lodz
- 90-236 Lodz
| | - Błażej Rychlik
- Cytometry Laboratory
- Department of Molecular Biophysics
- Faculty of Biology & Environmental Protection
- University of Lodz
- 90-236 Lodz
| | - Damian Plazuk
- Department of Organic Chemistry
- Faculty of Chemistry
- University of Lodz
- 91-403 Lodz
- Poland
| | - Francesca Peccati
- CIC bioGUNE
- Center for Cooperative Research in Bioscience
- Bizkaia Science and Technology Park
- Computational Chemistry Lab
- 48160 Derio-Bizkaia
| | - Gonzalo Jiménez-Osés
- CIC bioGUNE
- Center for Cooperative Research in Bioscience
- Bizkaia Science and Technology Park
- Computational Chemistry Lab
- 48160 Derio-Bizkaia
| | - Urszula Steinke
- Centre of Molecular and Macromolecular Studies Polish Academy of Science
- 90-363 Lodz
- Poland
| | - Malgorzata Sierant
- Centre of Molecular and Macromolecular Studies Polish Academy of Science
- 90-363 Lodz
- Poland
| | - Katarzyna Trzeciak
- Centre of Molecular and Macromolecular Studies Polish Academy of Science
- 90-363 Lodz
- Poland
| | - Ewa Skorupska
- Centre of Molecular and Macromolecular Studies Polish Academy of Science
- 90-363 Lodz
- Poland
| | - Beata Miksa
- Centre of Molecular and Macromolecular Studies Polish Academy of Science
- 90-363 Lodz
- Poland
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8
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Berg Luecke L, Gundry RL. Assessment of Streptavidin Bead Binding Capacity to Improve Quality of Streptavidin-based Enrichment Studies. J Proteome Res 2020; 20:1153-1164. [PMID: 33270449 DOI: 10.1021/acs.jproteome.0c00772] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The streptavidin-based enrichment of biotin-tagged molecules is a common methodology that is routinely used across multiple disciplines in biomedical research. Numerous and varied formats of immobilized streptavidin and related proteins are available, but predicting which product is most apt for a given application is complicated by the fact that there are numerous technical considerations and no universal reporting standards for describing the binding capacity of the beads. Here, we define criteria that should be considered when performing a fit-for-purpose evaluation of streptavidin beads. We also describe a colorimetric competitive displacement assay, the streptAVIdin binDing capacITY (AVIDITY) assay, a fast, easy, and inexpensive absorbance-based method to measure the binding capacity of streptavidin beads, which can be used to compare different products and evaluate variation among many of the same product. We expect that the fit-for-purpose criteria and the AVIDITY assay will benefit users across disciplines to make informed decisions regarding the most apt streptavidin bead products for their own experiments.
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Affiliation(s)
- Linda Berg Luecke
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States.,CardiOmics Program, Center for Heart and Vascular Research; Division of Cardiovascular Medicine; and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Rebekah L Gundry
- CardiOmics Program, Center for Heart and Vascular Research; Division of Cardiovascular Medicine; and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
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9
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Denham EM, Barton MI, Black SM, Bridge MJ, de Wet B, Paterson RL, van der Merwe PA, Goyette J. A generic cell surface ligand system for studying cell-cell recognition. PLoS Biol 2019; 17:e3000549. [PMID: 31815943 PMCID: PMC6922461 DOI: 10.1371/journal.pbio.3000549] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 12/19/2019] [Accepted: 11/12/2019] [Indexed: 01/11/2023] Open
Abstract
Dose-response experiments are a mainstay of receptor biology studies and can reveal valuable insights into receptor function. Such studies of receptors that bind cell surface ligands are currently limited by the difficulty in manipulating the surface density of ligands at a cell–cell interface. Here, we describe a generic cell surface ligand system that allows precise manipulation of cell surface ligand densities over several orders of magnitude. These densities are robustly quantifiable, a major advance over previous studies. We validate the system for a range of immunoreceptors, including the T-cell receptor (TCR), and show that this generic ligand stimulates via the TCR at a similar surface density as its native ligand. We also extend our work to the activation of chimeric antigen receptors. This novel system allows the effect of varying the surface density, valency, dimensions, and affinity of the ligand to be investigated. It can be readily broadened to other receptor–cell surface ligand interactions and will facilitate investigation into the activation of, and signal integration between, cell surface receptors. This study describes a generic cell-surface ligand system that allows precise manipulation of ligand densities, valency, dimensions, and affinity. The system is validated for a range of immunoreceptors, including the T-cell receptor, and can be readily broadened to other cell-surface receptor-ligand interactions.
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Affiliation(s)
- Eleanor M. Denham
- Sir William Dunn School of Pathology, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Michael I. Barton
- Sir William Dunn School of Pathology, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Susannah M. Black
- Sir William Dunn School of Pathology, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Marcus J. Bridge
- Sir William Dunn School of Pathology, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Ben de Wet
- Sir William Dunn School of Pathology, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Rachel L. Paterson
- Sir William Dunn School of Pathology, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - P. Anton van der Merwe
- Sir William Dunn School of Pathology, University of Oxford, Oxford, Oxfordshire, United Kingdom
- * E-mail: (JG); (PAvdM)
| | - Jesse Goyette
- Sir William Dunn School of Pathology, University of Oxford, Oxford, Oxfordshire, United Kingdom
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, New South Wales, Australia
- * E-mail: (JG); (PAvdM)
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10
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11
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Delgadillo RF, Mueser TC, Zaleta-Rivera K, Carnes KA, González-Valdez J, Parkhurst LJ. Detailed characterization of the solution kinetics and thermodynamics of biotin, biocytin and HABA binding to avidin and streptavidin. PLoS One 2019; 14:e0204194. [PMID: 30818336 PMCID: PMC6394990 DOI: 10.1371/journal.pone.0204194] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 02/01/2019] [Indexed: 01/02/2023] Open
Abstract
The high affinity (KD ~ 10−15 M) of biotin for avidin and streptavidin is the essential component in a multitude of bioassays with many experiments using biotin modifications to invoke coupling. Equilibration times suggested for these assays assume that the association rate constant (kon) is approximately diffusion limited (109 M-1s-1) but recent single molecule and surface binding studies indicate that they are slower than expected (105 to 107 M-1s-1). In this study, we asked whether these reactions in solution are diffusion controlled, which reaction model and thermodynamic cycle describes the complex formation, and if there are any functional differences between avidin and streptavidin. We have studied the biotin association by two stopped-flow methodologies using labeled and unlabeled probes: I) fluorescent probes attached to biotin and biocytin; and II) unlabeled biotin and HABA, 2-(4’-hydroxyazobenzene)-benzoic acid. Both native avidin and streptavidin are homo-tetrameric and the association data show no cooperativity between the binding sites. The kon values of streptavidin are faster than avidin but slower than expected for a diffusion limited reaction in both complexes. Moreover, the Arrhenius plots of the kon values revealed strong temperature dependence with large activation energies (6–15 kcal/mol) that do not correspond to a diffusion limited process (3–4 kcal/mol). Accordingly, we propose a simple reaction model with a single transition state for non-immobilized reactants whose forward thermodynamic parameters complete the thermodynamic cycle, in agreement with previously reported studies. Our new understanding and description of the kinetics, thermodynamics, and spectroscopic parameters for these complexes will help to improve purification efficiencies, molecule detection, and drug screening assays or find new applications.
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Affiliation(s)
- Roberto F. Delgadillo
- Department of Chemistry, University of Nebraska—Lincoln, Lincoln, Nebraska, United States of America
- * E-mail: (RFD); (LJP)
| | - Timothy C. Mueser
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, Ohio, United States of America
| | - Kathia Zaleta-Rivera
- Department of Bioengineering, University of California San Diego, San Diego, California, United States of America
| | - Katie A. Carnes
- GlaxoSmithKline, Medicinal Science and Technology, R&D, King of Prussia, Pennsylvania, United States of America
| | - José González-Valdez
- Tecnologico de Monterrey, School of Engineering and Science, NL, Monterrey, Mexico
| | - Lawrence J. Parkhurst
- Department of Chemistry, University of Nebraska—Lincoln, Lincoln, Nebraska, United States of America
- * E-mail: (RFD); (LJP)
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12
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Andreoni A, Nardo L, Rigler R. Time-resolved homo-FRET studies of biotin-streptavidin complexes. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 162:656-662. [PMID: 27494295 DOI: 10.1016/j.jphotobiol.2016.07.042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 07/27/2016] [Indexed: 11/25/2022]
Abstract
Förster resonance energy transfer is a mechanism of fluorescence quenching that is notably useful for characterizing properties of biomolecules and/or their interactions. Here we study water-solutions of Biotin-Streptavidin complexes, in which Biotin is labeled with a rigidly-bound fluorophore that can interact by Förster resonance energy transfer with the fluorophores labeling the other, up to three, Biotins of the same complex. The fluorophore, Atto550, is a Rhodamine analogue. We detect the time-resolved fluorescence decay of the fluorophores with an apparatus endowed with single-photon sensitivity and temporal resolution of ~30ps. The decay profiles we observe for samples containing constant Biotin-Atto550 conjugates and varying Streptavidin concentrations are multi-exponential. Each decay component can be associated with the rate of quenching exerted on each donor by each of the acceptors that label the other Biotin molecules, depending on the binding site they occupy. The main features that lead to this result are that (i) the transition dipole moments of the up-to-four Atto550 fluorophores that label the complexes are fixed as to both relative positions and mutual orientations; (ii) the fluorophores are identical and the role of donor in each Biotin-Streptavidin complex is randomly attributed to the one that has absorbed the excitation light (homo-FRET). Obviously the high-temporal resolution of the excitation-detection apparatus is necessary to discriminate among the fluorescence decay components.
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Affiliation(s)
- Alessandra Andreoni
- Department of Science and High Technology, University of Insubria, Como 22100, Italy.
| | - Luca Nardo
- Department of Science and High Technology, University of Insubria, Como 22100, Italy.
| | - Rudolf Rigler
- Department of Medical Biophysics, Karolinska Institutet, 17 177 Stockholm, Sweden; Laboratory of Biomedical Optics, Swiss Federal Institute of Technology, 1015 Lausanne, Switzerland.
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13
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Phan JC, Nehilla BJ, Srinivasan S, Coombs RW, Woodrow KA, Lai JJ. Human Immunodeficiency Virus (HIV) Separation and Enrichment via the Combination of Antiviral Lectin Recognition and a Thermoresponsive Reagent System. Pharm Res 2016; 33:2411-20. [PMID: 27401412 DOI: 10.1007/s11095-016-1980-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Accepted: 06/21/2016] [Indexed: 11/28/2022]
Abstract
PURPOSE In order to improve the detection limit of existing HIV diagnostic assays, we explored the use of a temperature-responsive magnetic nanoparticle reagent system in conjunction with cyanovirin-N for HIV recognition to rapidly and efficiently concentrate viral particles from larger sample volumes, ~ 1 ml. METHODS Cyanovirin-N (CVN) mutant, Q62C, was expressed, biotinylated, and then complexed with a thermally responsive polymer-streptavidin conjugate. Confirmation of protein expression/activity was performed using matrix assisted laser desorption/ionization (MALDI) and a TZM-bl HIV inhibition assay. Biotinylated CVN mutant recognition with gp120 was characterized using surface plasmon resonance (SPR). Virus separation and enrichment using a thermoresponsive magnetic nanoparticle reagent system were measured using RT-PCR. RESULTS Biotinylated Q62C exhibited a KD of 0.6 nM to gp120. The temperature-responsive binary reagent system achieved a maximum viral capture of nearly 100% HIV, 1 × 10(5) virus copies in 100 μl, using pNIPAAm-Q62C within 30 minutes. Additionally, the same reagent system achieved nearly 9-fold enrichment by processing a 10-times larger sample of 1000 μl (Fig. 3). CONCLUSION This work demonstrated a temperature-responsive reagent system that provides enrichment of HIV using antiviral lectin CVN for recognition, which is potentially amenable for use in point-of-care settings.
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Affiliation(s)
- Joseph C Phan
- Department of Bioengineering, University of Washington, Box 355061, Seattle, Washington, 98195, USA
| | - Barrett J Nehilla
- Nexgenia, Inc., 4000 Mason Rd., Fluke Hall, Suite 312-1, Seattle, Washington, 98195, USA
| | - Selvi Srinivasan
- Department of Bioengineering, University of Washington, Box 355061, Seattle, Washington, 98195, USA
| | - Robert W Coombs
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, 98104, USA
| | - Kim A Woodrow
- Department of Bioengineering, University of Washington, Box 355061, Seattle, Washington, 98195, USA.
| | - James J Lai
- Department of Bioengineering, University of Washington, Box 355061, Seattle, Washington, 98195, USA.
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Müller JM, Bruhn S, Flaschel E, Friehs K, Risse JM. GAP promoter-based fed-batch production of highly bioactive core streptavidin byPichia pastoris. Biotechnol Prog 2016; 32:855-64. [DOI: 10.1002/btpr.2283] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 03/02/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Jakob Michael Müller
- Lehrstuhl Für Fermentationstechnik, Technische Fakultät, Universität Bielefeld; PF 10 01 31 Bielefeld D-33501 Germany
| | - Simon Bruhn
- Lehrstuhl Für Fermentationstechnik, Technische Fakultät, Universität Bielefeld; PF 10 01 31 Bielefeld D-33501 Germany
| | - Erwin Flaschel
- Lehrstuhl Für Fermentationstechnik, Technische Fakultät, Universität Bielefeld; PF 10 01 31 Bielefeld D-33501 Germany
| | - Karl Friehs
- Lehrstuhl Für Fermentationstechnik, Technische Fakultät, Universität Bielefeld; PF 10 01 31 Bielefeld D-33501 Germany
| | - Joe Max Risse
- Lehrstuhl Für Fermentationstechnik, Technische Fakultät, Universität Bielefeld; PF 10 01 31 Bielefeld D-33501 Germany
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15
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Wetzel D, Müller JM, Flaschel E, Friehs K, Risse JM. Fed-batch production and secretion of streptavidin by Hansenula polymorpha: Evaluation of genetic factors and bioprocess development. J Biotechnol 2016; 225:3-9. [DOI: 10.1016/j.jbiotec.2016.03.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 03/04/2016] [Accepted: 03/10/2016] [Indexed: 11/16/2022]
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16
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Library design and screening protocol for artificial metalloenzymes based on the biotin-streptavidin technology. Nat Protoc 2016; 11:835-52. [DOI: 10.1038/nprot.2016.019] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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17
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Constitutive production and efficient secretion of soluble full-length streptavidin by an Escherichia coli ‘leaky mutant’. J Biotechnol 2016; 221:91-100. [DOI: 10.1016/j.jbiotec.2016.01.032] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Revised: 01/18/2016] [Accepted: 01/22/2016] [Indexed: 11/22/2022]
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18
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Lippert LG, Hallock JT, Dadosh T, Diroll BT, Murray CB, Goldman YE. NeutrAvidin Functionalization of CdSe/CdS Quantum Nanorods and Quantification of Biotin Binding Sites using Biotin-4-Fluorescein Fluorescence Quenching. Bioconjug Chem 2016; 27:562-8. [PMID: 26722835 DOI: 10.1021/acs.bioconjchem.5b00577] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We developed methods to solubilize, coat, and functionalize with NeutrAvidin elongated semiconductor nanocrystals (quantum nanorods, QRs) for use in single molecule polarized fluorescence microscopy. Three different ligands were compared with regard to efficacy for attaching NeutrAvidin using the "zero-length cross-linker" 1-ethyl-3-[3-(dimethylamino)propyl]carbodiimide (EDC). Biotin-4-fluorescene (B4F), a fluorophore that is quenched when bound to avidin proteins, was used to quantify biotin binding activity of the NeutrAvidin coated QRs and biotin binding activity of commercially available streptavidin coated quantum dots (QDs). All three coating methods produced QRs with NeutrAvidin coating density comparable to the streptavidin coating density of the commercially available quantum dots (QDs) in the B4F assay. One type of QD available from the supplier (ITK QDs) exhibited ∼5-fold higher streptavidin surface density compared to our QRs, whereas the other type of QD (PEG QDs) had 5-fold lower density. The number of streptavidins per QD increased from ∼7 streptavidin tetramers for the smallest QDs emitting fluorescence at 525 nm (QD525) to ∼20 tetramers for larger, longer wavelength QDs (QD655, QD705, and QD800). QRs coated with NeutrAvidin using mercaptoundecanoicacid (MUA) and QDs coated with streptavidin bound to biotinylated cytoplasmic dynein in single molecule TIRF microscopy assays, whereas Poly(maleic anhydride-alt-1-ocatdecene) (PMAOD) or glutathione (GSH) QRs did not bind cytoplasmic dynein. The coating methods require optimization of conditions and concentrations to balance between substantial NeutrAvidin binding vs tendency of QRs to aggregate and degrade over time.
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Affiliation(s)
| | | | - Tali Dadosh
- Electron Microscopy Unit, Department of Chemical Research Support, Weizmann Institute of Science , Rehovot 7610001, Israel
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19
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Lo KKW. Luminescent Iridium(III) and Rhenium(I) Complexes as Biomolecular Probes and Imaging Reagents. ADVANCES IN INORGANIC CHEMISTRY 2016. [DOI: 10.1016/bs.adioch.2015.09.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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20
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Optimizing immobilization of avidin on surface-modified magnetic nanoparticles: characterization and application of protein-immobilized nanoparticles. Bioprocess Biosyst Eng 2015. [DOI: 10.1007/s00449-015-1443-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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21
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Müller JM, Risse JM, Friehs K, Flaschel E. Model-based development of an assay for the rapid detection of biotin-blocked binding sites of streptavidin. Eng Life Sci 2015. [DOI: 10.1002/elsc.201400227] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Jakob M. Müller
- Chair of Fermentation Engineering; Faculty of Technology; Bielefeld University; Bielefeld Germany
| | - Joe M. Risse
- Chair of Fermentation Engineering; Faculty of Technology; Bielefeld University; Bielefeld Germany
| | - Karl Friehs
- Chair of Fermentation Engineering; Faculty of Technology; Bielefeld University; Bielefeld Germany
| | - Erwin Flaschel
- Chair of Fermentation Engineering; Faculty of Technology; Bielefeld University; Bielefeld Germany
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22
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Swanepoel A, du Preez I, Mahlangu T, Chetty A, Klumperman B. Development of bioconjugated dye-doped poly(styrene-co-maleimide) nanoparticles as a new bioprobe. J Mater Chem B 2015; 3:2635-2640. [DOI: 10.1039/c4tb01520g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fluorescent dye-doped poly(styrene-co-maleimide) nanoparticles were synthesised and functionalized with amine groups and avidin and the dye-loading was varied.
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Affiliation(s)
- A. Swanepoel
- Polymers and Composites
- Materials Science and Manufacturing
- Council for Scientific and Industrial Research
- Pretoria
- South Africa
| | - I. du Preez
- Polymers and Composites
- Materials Science and Manufacturing
- Council for Scientific and Industrial Research
- Pretoria
- South Africa
| | - T. Mahlangu
- Polymers and Composites
- Materials Science and Manufacturing
- Council for Scientific and Industrial Research
- Pretoria
- South Africa
| | - A. Chetty
- Polymers and Composites
- Materials Science and Manufacturing
- Council for Scientific and Industrial Research
- Pretoria
- South Africa
| | - B. Klumperman
- Department of Chemistry and Polymer Science
- Stellenbosch University
- Stellenbosch
- South Africa
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23
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Sun Q, Qian J, Tian H, Duan L, Zhang W. Rational design of biotinylated probes: fluorescent turn-on detection of (strept)avidin and bioimaging in cancer cells. Chem Commun (Camb) 2014; 50:8518-21. [DOI: 10.1039/c4cc03315a] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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24
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Wilson YM, Dürrenberger M, Nogueira ES, Ward TR. Neutralizing the detrimental effect of glutathione on precious metal catalysts. J Am Chem Soc 2014; 136:8928-32. [PMID: 24918731 DOI: 10.1021/ja500613n] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We report our efforts to enable transition-metal catalysis in the presence of cellular debris, notably Escherichia coli cell free extracts and cell lysates. This challenging goal is hampered by the presence of thiols, mainly present in the form of glutathione (GSH), which poison precious metal catalysts. To overcome this, we evaluated a selection of oxidizing agents and electrophiles toward their potential to neutralize the detrimental effect of GSH on a Ir-based transfer hydrogenation catalyst. While the bare catalyst was severely inhibited by cellular debris, embedding the organometallic moiety within a host protein led to promising results in the presence of some neutralizing agents. In view of its complementary to natural enzymes, the asymmetric imine reductase based on the incorporation of a biotinylated iridium pianostool complex within streptavidin (Sav) isoforms was selected as a model reaction. Compared to purified protein samples, we show that pretreatment of cell free extracts and cell lysates containing Sav mutants with diamide affords up to >100 TON's and only a modest erosion of enantioselectivity.
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Affiliation(s)
- Yvonne M Wilson
- Department of Chemistry, University of Basel , Spitalstrasse 51, CH-4056 Basel, Switzerland
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25
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Fairhead M, Krndija D, Lowe ED, Howarth M. Plug-and-play pairing via defined divalent streptavidins. J Mol Biol 2014; 426:199-214. [PMID: 24056174 PMCID: PMC4047826 DOI: 10.1016/j.jmb.2013.09.016] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 09/07/2013] [Accepted: 09/12/2013] [Indexed: 11/29/2022]
Abstract
Streptavidin is one of the most important hubs for molecular biology, either multimerizing biomolecules, bridging one molecule to another, or anchoring to a biotinylated surface/nanoparticle. Streptavidin has the advantage of rapid ultra-stable binding to biotin. However, the ability of streptavidin to bind four biotinylated molecules in a heterogeneous manner is often limiting. Here, we present an efficient approach to isolate streptavidin tetramers with two biotin-binding sites in a precise arrangement, cis or trans. We genetically modified specific subunits with negatively charged tags, refolded a mixture of monomers, and used ion-exchange chromatography to resolve tetramers according to the number and orientation of tags. We solved the crystal structures of cis-divalent streptavidin to 1.4Å resolution and trans-divalent streptavidin to 1.6Å resolution, validating the isolation strategy and explaining the behavior of the Dead streptavidin variant. cis- and trans-divalent streptavidins retained tetravalent streptavidin's high thermostability and low off-rate. These defined divalent streptavidins enabled us to uncover how streptavidin binding depends on the nature of the biotin ligand. Biotinylated DNA showed strong negative cooperativity of binding to cis-divalent but not trans-divalent streptavidin. A small biotinylated protein bound readily to cis and trans binding sites. We also solved the structure of trans-divalent streptavidin bound to biotin-4-fluorescein, showing how one ligand obstructs binding to an adjacent biotin-binding site. Using a hexaglutamate tag proved a more powerful way to isolate monovalent streptavidin, for ultra-stable labeling without undesired clustering. These forms of streptavidin allow this key hub to be used with a new level of precision, for homogeneous molecular assembly.
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Affiliation(s)
- Michael Fairhead
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Denis Krndija
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Ed D Lowe
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Mark Howarth
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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26
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Lo KKW, Hui WK, Chung CK, Tsang KHK, Lee TKM, Ng DCM. Luminescent Transition Metal Polypyridine Biotin Complexes. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.200600007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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27
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Development of fed-batch strategies for the production of streptavidin by Streptomyces avidinii based on power input and oxygen supply studies. J Biotechnol 2013; 163:325-32. [DOI: 10.1016/j.jbiotec.2012.10.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 10/29/2012] [Accepted: 10/31/2012] [Indexed: 11/18/2022]
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28
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Yu M, Yu Q, Rutledge PJ, Todd MH. A fluorescent "allosteric scorpionand" complex visualizes a biological recognition event. Chembiochem 2013; 14:224-9. [PMID: 23303717 DOI: 10.1002/cbic.201200637] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Indexed: 12/31/2022]
Abstract
We describe a new class of fluorescent reporter and its employment to visualize the biotin/avidin binding interaction. Derivatives of the azamacrocycle cyclam that contain a pendant naphthalimide dye are inherently fluorescent when zinc(II) is coordinated. Introducing a second pendant group--biotin--affords an unsymmetrical bis-triazole-scorpionand ligand that interacts specifically with avidin. This ligand has been assembled by using a one-pot "double-click" strategy and complexed with copper(II) and zinc(II). The zinc(II) complex is fluorescent, and its fluorescence output changes in the presence of avidin. Upon avidin binding, the fluorescence output is diminished by interaction with the protein, at [complex]/[avidin] ratios of up to 4:1. The observed change might arise from a specific quenching effect in the biotin binding pocket or from a binding-induced change in the coordination geometry of the complex.
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Affiliation(s)
- Mingfeng Yu
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
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29
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Cai L, Chen ZZ, Chen MY, Tang HW, Pang DW. MUC-1 aptamer-conjugated dye-doped silica nanoparticles for MCF-7 cells detection. Biomaterials 2012; 34:371-81. [PMID: 23084552 DOI: 10.1016/j.biomaterials.2012.09.084] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 09/30/2012] [Indexed: 11/25/2022]
Abstract
In this work, we have prepared three types of aptamer-conjugated Rubpy-doped silica nanoparticles for Human breast carcinoma MCF-7 cells labeling. Probe A is prepared through covalent conjugation between amine-labeled MUC-1 aptamer and carboxyl-modified Rubpy-doped NPs (NPs-aptamer). Probe B is prepared based on the interaction between biotin-labeled MUC-1 aptamer and avidin-conjugated Rubpy-doped NPs (NPs-avidin-biotin-aptamer). For Probe C, there is a PEG with flexible long chain as the bridge between avidin and the NPs (NPs-PEG-avidin-biotin-aptamer). In addition, we further investigate the practical number of MUC-1 aptamers on an NP of each probe using hoechst33258 dye. The binding efficiency of MUC-1 aptamer on the three types of probes as follows: Probe A < Probe B < Probe C. In addition, microscopic fluorescence imaging shows that Probe C containing the PEG molecules can be effectively applied for the recognition of MUC-1 protein in human breast carcinoma MCF-7 cells thus demonstrates that the PEG with flexible long chain as the bridge between the aptamer and NP can greatly enhances the freedom of MUC-1 aptamer. Compared with common organic dyes, the dye-doped silica nanoparticles serve as a stable bioprobe because of their facile conjugation with the desirable biomolecules, and have exhibited great potential in bioanalysis.
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Affiliation(s)
- Li Cai
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, PR China
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Quiñones GA, Miller SC, Bhattacharyya S, Sobek D, Stephan JP. Ultrasensitive detection of cellular protein interactions using bioluminescence resonance energy transfer quantum dot-based nanoprobes. J Cell Biochem 2012; 113:2397-405. [DOI: 10.1002/jcb.24111] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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31
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Chen ZZ, Cai L, Dong XM, Tang HW, Pang DW. Covalent conjugation of avidin with dye-doped silica nanopaticles and preparation of high density avidin nanoparticles as photostable bioprobes. Biosens Bioelectron 2012; 37:75-81. [PMID: 22608767 DOI: 10.1016/j.bios.2012.04.041] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Revised: 04/27/2012] [Accepted: 04/27/2012] [Indexed: 10/28/2022]
Abstract
Progress in biomedical imaging depends on the development of bioprobes with a high sensitivity and stability. Fluorescent silica nanoparticles (NPs) covalent conjugation of avidin has been proposed for cancer cells imaging by fluorescence microscopy. Uniform silica NPs were prepared using water-in-oil (W/O) microemulsion methods and primary amine groups were introduced onto the surface of the NPs by condensation of tetraethyl orthosilicate (TEOS). Optically stable organic dyes, tris(2,2'-bipyridyl) dichlororuthenium(II) hexahydrate (Rubpy), were doped inside the silica NPs. The amine functions were transferred to carboxyl groups coupled with a linker elongation. Avidin was immobilized at the surface of the NPs by covalent binding to the carboxyl linkers. The binding capacity of the avidin-covered NPs for ligand biotin was quantified by titration with biotin(5-fluorescein) conjugate to 1.25 biotin binding sites/100 nm(2). We used biotinylated antibody and cell recognition by fluorescence microscopy imaging technique. The lung carcinoma cells were identified easily with high efficiency using these antibody-coated NPs. By comparison with fluorescein isothiocyanate (FITC), dye-doped silica NPs display dramatically increased stability of fluorescence as well as photostability, as compared to the common organic dye, when under continuous irradiation.
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Affiliation(s)
- Ze-Zhong Chen
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Research Center for Nanobiology and Nanomedicine (MOE 985 Innovative Platform), Wuhan Institute of Biotechnology, and State Key Laboratory of Virology, Wuhan University, Wuhan 430072, PR China
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Sun S, Huang X, Ma M, Qiu N, Cai Z, Luo Z, Alies NP. Systematic evaluation of avidin-biotin interaction by fluorescence spectrophotometry. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2012; 89:99-104. [PMID: 22261100 DOI: 10.1016/j.saa.2011.12.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2011] [Accepted: 12/04/2011] [Indexed: 05/31/2023]
Abstract
The avidin-biotin interaction was evaluated systematically by fluorescence spectroscopy under different conditions of temperature, pressure, pH, metal ions, incubation time and initial avidin concentration. The binding constant was calculated according to the modified Stern-Volmer equation, which deduced the existence of static quenching mechanism. The data obtained revealed that avidin-biotin interaction exhibited temperature, pH, metal ions, incubation time and initial avidin concentration sensitivity. The binding constants decreased with increase in temperature, while the binding sites were independent of temperature. The values of thermodynamic parameter ΔH (-149.85 kJ mol(-1)) and ΔS (-284.26 J mol(-1) K(-1)) suggested hydrogen bonds and van der Waals played a major role in the reaction. The binding constants between avidin and biotin increased firstly and then decreased gradually with the increase of pH values. Metal ions can also affected the binding constants between avidin and biotin. The association kinetics firstly acquired by the combination of the change in fluorescence per unit time and the modified Stern-Volmer equation indicated that the reaction time required to reach equilibrium was 2200 s, and the average reaction rate for the binding process was very high in the first 180 s. Reaction of the avidin in the first 180 s was more than 40% of the total avidin involved in the whole process.
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Affiliation(s)
- Shuguo Sun
- National Research and Development Center for Egg Processing, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
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Sun S, Ma M, Qiu N, Huang X, Cai Z, Huang Q, Hu X. Affinity adsorption and separation behaviors of avidin on biofunctional magnetic nanoparticles binding to iminobiotin. Colloids Surf B Biointerfaces 2011; 88:246-53. [DOI: 10.1016/j.colsurfb.2011.06.039] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Revised: 06/26/2011] [Accepted: 06/28/2011] [Indexed: 10/18/2022]
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Zhou D, Wu Y, Liu P, Bai H, Tang L, Yu R, Jiang J. Homogeneous label-free fluorescent assay of small molecule-protein interactions using protein binding-inhibited transcription nanomachine. Sci China Chem 2011. [DOI: 10.1007/s11426-011-4337-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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35
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A continuous fluorescence displacement assay for BioA: an enzyme involved in biotin biosynthesis. Anal Biochem 2011; 416:27-38. [PMID: 21621502 DOI: 10.1016/j.ab.2011.05.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Revised: 04/30/2011] [Accepted: 05/02/2011] [Indexed: 11/23/2022]
Abstract
Cofactor biosynthetic pathways represent a rich source of potential antibiotic targets. The second step in biotin biosynthesis is performed by BioA, a pyridoxal 5'-phosphate (PLP)-dependent enzyme. This enzyme has been confirmed as a candidate target in Mycobacterium tuberculosis; however, the current bioassay used to measure BioA activity is cumbersome and low throughput. Here we describe the design, development, and optimization of a continuous coupled fluorescence displacement assay to measure BioA activity. In this coupled assay, BioD converts the product of the BioA-catalyzed reaction into dethiobiotin, which is subsequently detected by displacement of a fluorescently labeled dethiobiotin probe from streptavidin. The assay was further adapted to a high-throughput screening format and validated against the LOPAC(1280) library.
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36
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Mittal R, Bruchez MP. Biotin-4-fluorescein based fluorescence quenching assay for determination of biotin binding capacity of streptavidin conjugated quantum dots. Bioconjug Chem 2011; 22:362-8. [PMID: 21314110 PMCID: PMC3059817 DOI: 10.1021/bc100321c] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The valency of quantum dot nanoparticles conjugated with biomolecules is closely related to their performance in cell tagging, tracking, and imaging experiments. Commercially available streptavidin conjugates (SAv QDs) are the most commonly used tool for preparing QD−biomolecule conjugates. The fluorescence quenching of biotin-4-fluorscein (B4F) provides a straightforward assay to quantify the number of biotin binding sites per SAv QD. The utility of this method was demonstrated by quantitatively characterizing the biotin binding capacity of commercially available amphiphilic poly(acrylic acid) Qdot ITK SAv conjugates and poly(ethylene glycol) modified Qdot PEG SAv conjugates with emission wavelengths of 525, 545, 565, 585, 605, 625, 655, 705, and 800 nm. Results showed that 5- to 30-fold more biotin binding sites are available on ITK SAv QDs compared to PEG SAv QDs of the same color with no systematic variation of biotin binding capacity with size.
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Affiliation(s)
- Rowena Mittal
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
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Wang C, Zhu Z, Song Y, Lin H, Yang CJ, Tan W. Caged molecular beacons: controlling nucleic acid hybridization with light. Chem Commun (Camb) 2011; 47:5708-10. [DOI: 10.1039/c1cc10481k] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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38
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Computational and mutagenesis studies of the streptavidin native dimer interface. J Mol Graph Model 2010; 29:295-308. [DOI: 10.1016/j.jmgm.2010.09.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2010] [Revised: 08/08/2010] [Accepted: 09/15/2010] [Indexed: 11/20/2022]
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39
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Plażuk D, Zakrzewski J, Salmain M. Biotin as acylating agent in the Friedel-Crafts reaction. Avidin affinity of biotinyl derivatives of ferrocene, ruthenocene and pyrene and fluorescence properties of 1-biotinylpyrene. Org Biomol Chem 2010; 9:408-17. [PMID: 20967359 DOI: 10.1039/c0ob00319k] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
(D)-Biotin was used for Friedel-Crafts acylation of electron-rich aromatic molecules--ferrocene, ruthenocene and pyrene. The reaction carried out in the presence of trifluoroacetic anhydride and trifluoromethanesulfonic acid afforded the corresponding biotinylarenes in moderate yields. These compounds, although lacking an amide bond, exhibited high affinity for avidin, with the ability to displace 2-(4'-hydroxyphenylazo)-benzoic acid (HABA) in its complex with avidin. Their affinity for avidin was determined by a solid-phase competitive enzymatic assay, which gave IC(50) values in the range of 33-58 nM (under the same conditions biotin showed IC(50) = 24 ± 7 nM). 1-Biotinylpyrene (1c) excited at 355 nm displayed fluorescence emission in aqueous solutions with λ(max) = 461 nm. The fluorescence maximum was shifted to 425 nm upon binding of 1c to avidin. Formation of the avidin-1c complex was also evidenced by quenching of the fluorescence from the protein tryptophan residues (342 nm) and appearance of the emission band of the avidin-bound 1c at 430 nm as a result of a Förster resonance energy transfer (FRET) phenomenon.
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Affiliation(s)
- Damian Plażuk
- Department of Organic Chemistry, University of Łódź, 91-403 Łódź, Tamka 12, Poland
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40
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Krauser JA, Joshi AL, Kady IO. Metal complexes of modified cyclen as catalysts for hydrolytic restriction of plasmid DNA. J Inorg Biochem 2010; 104:877-84. [DOI: 10.1016/j.jinorgbio.2010.04.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2009] [Revised: 04/15/2010] [Accepted: 04/16/2010] [Indexed: 11/30/2022]
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41
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Towards a fluorescent molecular switch for nucleic acid biosensing. Anal Bioanal Chem 2010; 398:1605-14. [DOI: 10.1007/s00216-010-3794-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2010] [Accepted: 04/26/2010] [Indexed: 10/19/2022]
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42
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Liem KP, Noble GT, Flitsch SL, Webb SJ. The effect of multivalent binding on the lateral phase separation of adhesive lipids. Faraday Discuss 2010. [DOI: 10.1039/b907114h] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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43
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Fürstenberg A, Kel O, Gradinaru J, Ward TR, Emery D, Bollot G, Mareda J, Vauthey E. Site-dependent excited-state dynamics of a fluorescent probe bound to avidin and streptavidin. Chemphyschem 2009; 10:1517-32. [PMID: 19565577 DOI: 10.1002/cphc.200900132] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The excited-state dynamics of biotin-spacer-Lucifer-Yellow (LY) constructs bound to avidin (Avi) and streptavidin (Sav) was investigated using femtosecond spectroscopy. Two different locations in the proteins, identified by molecular dynamics simulations of Sav, namely the entrance of the binding pocket and the protein surface, were probed by varying the length of the spacer. A reduction of the excited-state lifetime, stronger in Sav than in Avi, was observed with the long spacer construct. Transient absorption measurements show that this effect originates from an electron transfer quenching of LY, most probably by a nearby tryptophan residue. The local environment of the LY chromophore could be probed by measuring the time-dependent polarisation anisotropy and Stokes shift of the fluorescence. Substantial differences in both dynamics were observed. The fluorescence anisotropy decays analysed by using the wobbling-in-a-cone model reveal a much more constrained environment of the chromophore with the short spacer. Moreover, the dynamic Stokes shift is multiphasic in all cases, with a approximately 1 ps component that can be ascribed to diffusive motion of bulk-like water molecules, and with slower components with time constants varying not only with the spacer, but with the protein as well. These slow components, which depend strongly on the local environment of the probe, are ascribed to the motion of the hydration layer coupled to the conformational dynamics of the protein.
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Affiliation(s)
- Alexandre Fürstenberg
- Department of Physical Chemistry, University of Geneva, 30, quai Ernest-Ansermet, CH-1211 Geneva, 4, Switzerland
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Waner MJ, Mascotti DP. A simple spectrophotometric streptavidin–biotin binding assay utilizing biotin-4-fluorescein. ACTA ACUST UNITED AC 2008; 70:873-7. [PMID: 17669504 DOI: 10.1016/j.jbbm.2007.06.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2007] [Revised: 05/24/2007] [Accepted: 06/28/2007] [Indexed: 11/19/2022]
Abstract
A new assay for biotin binding capacity of Streptavidin (SA) is presented in this work. The assay is based on the large decrease in the extinction coefficient at 493 nm that accompanies binding of biotin-4-fluorescein (B4F) to SA. This decrease is attributed to formation of a charge transfer complex between the B4F-donor and one or more SA residues. We show that one may observe the stoichiometric binding via monitoring the absorbance at 493 nm using either SA or B4F as the titrant. The sensitivity of the assay is at the lower end of similar fluorimetric and photometric assays. Though the sensitivity is not substantially lower than other comparable techniques, this assay allows one added flexibility in working range and instrumentation, since the same stock solutions may be used for this new photometric assay or the fluorescence assay for which this ligand was first developed.
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Affiliation(s)
- Mark J Waner
- Department of Chemistry, John Carroll University, 20700 North Park Blvd., University Heights, OH 44118 USA.
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45
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Smith DS, Eremin SA. Fluorescence polarization immunoassays and related methods for simple, high-throughput screening of small molecules. Anal Bioanal Chem 2008; 391:1499-507. [PMID: 18264817 DOI: 10.1007/s00216-008-1897-z] [Citation(s) in RCA: 167] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2007] [Revised: 01/14/2008] [Accepted: 01/17/2008] [Indexed: 11/24/2022]
Abstract
Fluorescence polarization immunoassay (FPIA) is a homogeneous (without separation) competitive immunoassay method based on the increase in fluorescence polarization (FP) of fluorescent-labeled small antigens when bound by specific antibody. The minimum detectable quantity of FPIAs with fluorescein label (about 0.1 ng analyte) is comparable with chromatography and ELISA methods, although this may be limited by sample matrix interference. Because of its simplicity and speed, FPIA is readily automated and therefore suitable for high-throughput screening (HTS) in a variety of application areas. Systems that involve binding of ligands to receptor proteins are also susceptible to analysis by analogous FP methods employing fluorescent-labeled ligand and HTS applications have been developed, notably for use in candidate drug screening.
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Affiliation(s)
- David S Smith
- MicroPharm Ltd, 51-53 Bartholomew Close, St. Bartholomew's Hospital, London, EC1A 7BE, UK
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46
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Application of biotin-4-fluorescein in homogeneous fluorescence assays for avidin, streptavidin, and biotin or biotin derivatives. Methods Mol Biol 2008; 418:73-88. [PMID: 18287651 DOI: 10.1007/978-1-59745-579-4_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Biotin-4-fluorescein (B4F) is a convenient molecular probe for (strept)avidin and for unlabeled biotin in homogeneous fluorescence assays. The primary standard is a 16 microM working solution of d-biotin which is used to titrate an aliquot of a (strept)avidin stock solution while monitoring the tryptophane fluorescence of (strept)avidin. This serves to standardize the (strept)avidin stock solution, an aliquot of which is then titrated with a roughly 16 microM working solution of B4F while monitoring the fluorescence of B4F. Specific binding is accompanied by quenching, but after saturation of all binding sites, the appearance of free ligand causes a sharp rise of intense fluorescence, the beginning of which allows to calculate the effective concentration of B4F in the working solution. Measurement of avidin in a crude sample is exemplified by mixing 8 pmol of B4F with various amounts of diluted egg white in a volume of 1 mL. Hereby, the extent of fluorescence quenching linearly correlates with the concentration of functional avidin. Moreover, a sharp minimum of fluorescence is observed when exactly 2 pmol of avidin is present in the sample. The latter assay has been adapted to measure between 0.5 and 5 pmol of d-biotin in 1 mL of sample by adding 1.9 pmol of avidin and 8 pmol of B4F. This competitive assay correctly measures the small dose of d-biotin in multivitamin tablets (e.g., 150 microg in 5 g of solid) after subtracting the background fluorescence of the colored aqueous solution.
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Mak WC, Yangzhong H, Trau D. Real time observation of diffusion and bioaffinity binding processes in single polyelectrolyte-coated microcapsules: A fluorescence-based approach. Colloids Surf B Biointerfaces 2007; 60:125-30. [PMID: 17698329 DOI: 10.1016/j.colsurfb.2007.05.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2007] [Revised: 05/24/2007] [Accepted: 05/26/2007] [Indexed: 10/23/2022]
Abstract
We report on using fluorescence microscopy to study, visualize and determine the diffusion phenomena into and bioaffinity binding within single microcapsules in real time by using biotin-fluorescein as diffusive species and encapsulated avidin as binding partner. Microcapsules were constructed by entrapment of avidin within an agarose matrix and encapsulated with polyelectrolyte layers by Layer-by-Layer (LbL) polyelectrolyte self assembly. A "ring" of high fluorescence intensity advancing with time towards the capsule centre was observed during incubation of capsules with fluorescent-labeled biotin. Fluorescence intensity was build up in capsule areas where binding to avidin occurred and was visualized in real time. A model for the diffusion process in microcapsules was developed and experimental data was plotted and fitted well with trends predicted by the model. The value of the diffusion coefficient for biotin-fluorescein was determined to be 3.5x10(-8)cm(2)/s, which is comparable to literature values of similar sized molecules.
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Affiliation(s)
- Wing Cheung Mak
- Division of Bioengineering, Faculty of Engineering, National University of Singapore, 7 Engineering Drive 1, Singapore 117574, Singapore
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48
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Highly efficient fluorescent label unquenched by protein interaction to probe the avidin rotational motion. J Photochem Photobiol A Chem 2006. [DOI: 10.1016/j.jphotochem.2006.04.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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49
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Hwang LC, Wohland T. Single wavelength excitation fluorescence cross-correlation spectroscopy with spectrally similar fluorophores: resolution for binding studies. J Chem Phys 2006; 122:114708. [PMID: 15836244 DOI: 10.1063/1.1862614] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
It was shown recently that fluorescence cross-correlation spectroscopy (FCCS) can be performed using a single laser wavelength for excitation (SW-FCCS) [L. C. Hwang and T. Wohland, Chem. Phys. Chem 5, 549 (2004).]. This method simplifies the FCCS setup since it does not require the simultaneous alignment of two lasers to the same focal spot. But up to now the method was shown to work only with dyes possessing large Stokes' shifts, and thus was limited to the use of quantum dots and tandem dyes. In this work we show that standard organic dyes with overlapping emission spectra, for instance fluorescein and tetramethylrhodamine, can be used as fluorescent pairs in SW-FCCS. As a biological model system for ligand-receptor interactions we studied the binding of biotin to streptavidin. To investigate the applicability of SW-FCCS for binding studies we adapt the existing FCCS theory for SW-FCCS and calculate limits for the measurement of dissociation constants in dependence on sample concentration, sample purity, and spectral cross talk between the different detection channels.
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50
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An L, Tang Y, Wang S, Li Y, Zhu D. A Fluorescence Ratiometric Protein Assay Using Light-Harvesting Conjugated Polymers. Macromol Rapid Commun 2006. [DOI: 10.1002/marc.200600214] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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