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Wang LJ, Liu H, Zou X, Xu Q, Zhang CY. 3'-Terminal Repair-Powered Dendritic Nanoassembly of Polyadenine Molecular Beacons for One-Step Quantification of Alkaline Phosphatase in Human Serum. Anal Chem 2021; 93:10704-10711. [PMID: 34292701 DOI: 10.1021/acs.analchem.1c02285] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Alkaline phosphatase (ALP) is an important hydrolase with crucial roles in biological processes, and the dysregulation of ALP may cause various human diseases. The conventional ALP assays usually involve cumbersome procedures with poor sensitivity. Herein, taking advantage of intrinsic superiorities of molecular beacons (MBs) and unique features of terminal deoxynucleotidyl transferase (TdT), we demonstrate for the first time the 3'-terminal repair-powered dendritic nanoassembly of polyadenine (A) MBs for one-step quantification of ALP in human serum. When ALP is present, it catalyzes 3'-terminal dephosphorylation of poly-A MBs to induce TdT-mediated template-free polymerization, generating long chains of polythymidine (T) sequences. The long poly-T chains can function as the anchoring templates to hybridize with many poly-A MBs, leading to the unfolding of loop structures and the dissociation of FAM/BHQ1 pairs (the 1st amplification stage). Subsequently, all 3'-hydroxylated poly-A MBs can be extended with the assistance of TdT to generate the branched long poly-T chains, leading to the hybridization of more poly-A MBs and the dissociation of more FAM/BHQ1 pairs (the 2nd amplification stage). Through multiple rounds of extension, assembly, and activation of poly-A MBs, dendritic DNA nanostructures are automatically formed, resulting in the dissociation of abundant fluorophores from the FAM/BHQ1 pairs to generate an exponentially amplified fluorescence signal (the nth amplification stage). This strategy possesses high sensitivity and excellent specificity, and the detection limit can reach 1 cell. Moreover, it can evaluate kinetic parameters, screen inhibitors, estimate cellular inhibition effects, and measure ALP in human serums.
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Affiliation(s)
- Li-Juan Wang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China.,School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Hao Liu
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China
| | - Xiaoran Zou
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China
| | - Qinfeng Xu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China
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Lin W, Li Y, Yang L, Chen T. Development of BODIPY FL VH032 as a High-Affinity and Selective von Hippel-Lindau E3 Ligase Fluorescent Probe and Its Application in a Time-Resolved Fluorescence Resonance Energy-Transfer Assay. ACS OMEGA 2021; 6:680-695. [PMID: 33458521 PMCID: PMC7807814 DOI: 10.1021/acsomega.0c05221] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 12/16/2020] [Indexed: 05/06/2023]
Abstract
The von Hippel-Lindau (VHL) tumor suppressor associates with transcription factors elongin-C and elongin-B to form the VHL-elongin-C-elongin-B protein complex and carry out its functions, such as degradation of hypoxia-inducible factors. VHL ligands are used not only to modulate hypoxia-signaling pathways and potentially treat chronic anemia or ischemia but also to form bivalent ligands as proteolysis-targeting chimeras to degrade proteins for potential therapeutic applications. Sensitive and selective VHL-based binding assays are critical for identifying and characterizing VHL ligands with high-throughput screening approaches. VHL ligand-binding assays, such as isothermal titration calorimetry, surface plasmon resonance, and fluorescence polarization assays, are reported but with limitations. Isothermal titration calorimetry requires higher protein concentrations with a lower throughput than fluorescence-based assays do. Surface plasmon resonance requires protein immobilization, which introduces variation and is not suitable for testing a large number of ligands. Fluorescence polarization can be sensitive with high-throughput capability but is susceptible to assay interference, and small-molecule-based fluorescent probes are not available. We developed the first small-molecule-based high-affinity VHL fluorescent probe BODIPY FL VH032 (5), with a K d of 3.01 nM, for a time-resolved fluorescence resonance energy-transfer assay. This new assay is sensitive, selective, resistant to assay interference, and capable of characterizing VHL ligands with a wide range of affinities. It is also suitable for VHL ligand identification and characterization with high-throughput screening.
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Wang LJ, Wang ZY, Zhang CY. Primer dephosphorylation-initiated circular exponential amplification for ultrasensitive detection of alkaline phosphatase. Analyst 2018; 143:4606-4613. [PMID: 30191935 DOI: 10.1039/c8an01647j] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Alkaline phosphatase (ALP) is an important diagnostic indicator for various human diseases including bone diseases, liver dysfunction, diabetes, breast and prostatic cancers. However, the conventional methods for ALP assay are usually cumbersome and time-consuming with low sensitivity. Here, we develop a new fluorescent method for ultrasensitive detection of ALP activity on the basis of primer dephosphorylation-initiated isothermal circular exponential amplification. We design two dual-functional hairpin probes (HP1 and HP2), which function as both the templates for exponential amplification reaction (EXPAR) and the generators for signal output. In the presence of ALP, the 3'-phosphorylated primer is dephosphorylated and subsequently hybridizes with the 3' protruding end of HP1 to initiate the first strand displacement amplification (SDA), producing trigger 1 and fluorescence signal. The released trigger 1 is complementary to the 3' protruding end of HP2 for the initiation of the second SDA, producing trigger 2 and fluorescence signal. Notably, trigger 2 is complementary to the 3' protruding end of HP1 and may subsequently initiate two consecutive SDAs, enabling circular EXPAR to generate an amplified fluorescence signal. This method exhibits high sensitivity with a detection limit of 2.0 × 10-10 U μL-1 and a large dynamic range of 5 orders of magnitude from 1.0 × 10-9 to 1.0 × 10-4 U μL-1, and it can measure ALP at the single-cell level. Importantly, this method can be applied for the measurement of kinetic parameters and the screening of potential inhibitors, providing a powerful tool for ALP-related biomedical research and clinical diagnosis.
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Affiliation(s)
- Li-Juan Wang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China.
| | - Zi-Yue Wang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China.
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China.
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4
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Song P, Liu Q, Zhang Y, Liu W, Meng M, Yin Y, Xi R. The chemical redox modulated switch-on fluorescence of carbon dots for probing alkaline phosphatase and its application in an immunoassay. RSC Adv 2018. [DOI: 10.1039/c7ra11784a] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The chemical redox modulated switch-on fluorescence of carbon dots for detecting ALP and human IgG.
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Affiliation(s)
- Pei Song
- State Key Laboratory of Medicinal Chemical Biology
- College of Pharmacy
- Tianjin Key Laboratory of Molecular Drug Research
- Nankai University
- Tianjin 300353
| | - Qian Liu
- State Key Laboratory of Medicinal Chemical Biology
- College of Pharmacy
- Tianjin Key Laboratory of Molecular Drug Research
- Nankai University
- Tianjin 300353
| | - Ying Zhang
- State Key Laboratory of Medicinal Chemical Biology
- College of Pharmacy
- Tianjin Key Laboratory of Molecular Drug Research
- Nankai University
- Tianjin 300353
| | - Wei Liu
- State Key Laboratory of Medicinal Chemical Biology
- College of Pharmacy
- Tianjin Key Laboratory of Molecular Drug Research
- Nankai University
- Tianjin 300353
| | - Meng Meng
- State Key Laboratory of Medicinal Chemical Biology
- College of Pharmacy
- Tianjin Key Laboratory of Molecular Drug Research
- Nankai University
- Tianjin 300353
| | - Yongmei Yin
- State Key Laboratory of Medicinal Chemical Biology
- College of Pharmacy
- Tianjin Key Laboratory of Molecular Drug Research
- Nankai University
- Tianjin 300353
| | - Rimo Xi
- State Key Laboratory of Medicinal Chemical Biology
- College of Pharmacy
- Tianjin Key Laboratory of Molecular Drug Research
- Nankai University
- Tianjin 300353
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5
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Switchable fluorescence of gold nanoclusters for probing the activity of alkaline phosphatase and its application in immunoassay. Biosens Bioelectron 2016; 77:666-72. [DOI: 10.1016/j.bios.2015.10.046] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 09/25/2015] [Accepted: 10/14/2015] [Indexed: 12/27/2022]
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6
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Development of a highly selective fluorescence probe for alkaline phosphatase. Bioorg Med Chem Lett 2011; 21:5088-91. [DOI: 10.1016/j.bmcl.2011.03.070] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2011] [Revised: 03/16/2011] [Accepted: 03/17/2011] [Indexed: 11/22/2022]
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7
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Alkaline phosphatase assay using a near-infrared fluorescent substrate merocyanine 700 phosphate. Talanta 2011; 84:941-6. [DOI: 10.1016/j.talanta.2011.02.035] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Revised: 02/17/2011] [Accepted: 02/21/2011] [Indexed: 11/24/2022]
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8
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MacPhee DJ. Methodological considerations for improving Western blot analysis. J Pharmacol Toxicol Methods 2009; 61:171-7. [PMID: 20006725 DOI: 10.1016/j.vascn.2009.12.001] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2009] [Accepted: 12/07/2009] [Indexed: 10/20/2022]
Abstract
The need for a technique that could allow the determination of antigen specificity of antisera led to the development of a method that allowed the production of a replica of proteins, which had been separated electrophoretically on polyacrylamide gels, on to a nitrocellulose membrane. This method was coined Western blotting and is very useful to study the presence, relative abundance, relative molecular mass, post-translational modification, and interaction of specific proteins. As a result it is utilized routinely in many fields of scientific research such as chemistry, biology and biomedical sciences. This review serves to touch on some of the methodological conditions that should be considered to improve Western blot analysis, particularly as a guide for graduate students but also scientists who wish to continue adapting this now fundamental research tool.
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Affiliation(s)
- Daniel J MacPhee
- Division of BioMedical Sciences, Faculty of Medicine, Health Sciences Centre, Memorial University of Newfoundland, St. John's, NL, Canada A1B 3V6.
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9
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Kamiya M, Urano Y, Ebata N, Yamamoto M, Kosuge J, Nagano T. Extension of the applicable range of fluorescein: a fluorescein-based probe for Western blot analysis. Angew Chem Int Ed Engl 2006; 44:5439-41. [PMID: 16044483 DOI: 10.1002/anie.200501542] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Mako Kamiya
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Scrivener E, Boghigian BA, Golenko E, Bogdanova A, Jackson P, Mikulskis A, Denoyer E, Courtney P, Lopez MF, Patton WF. Performance validation of an improved Xenon-arc lamp-based CCD camera system for multispectral imaging in proteomics. Proteomics 2005; 5:4354-66. [PMID: 16206330 DOI: 10.1002/pmic.200500062] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Advances in gel-based nonradioactive protein expression and PTM detection using fluorophores has served as the impetus for developing analytical instrumentation with improved imaging capabilities. We describe a CCD camera-based imaging instrument, equipped with both a high-pressure Xenon arc lamp and a UV transilluminator, which provides broad-band wavelength coverage (380-700 nm and UV). With six-position filter wheels, both excitation and emission wavelengths may be selected, providing optimal measurement and quantitation of virtually any dye and allowing excellent spectral resolution among different fluorophores. While spatial resolution of conventional fixed CCD camera imaging systems is typically inferior to laser scanners, this problem is circumvented with the new instrument by mechanically scanning the CCD camera over the sample and collecting multiple images that are subsequently automatically reconstructed into a complete high-resolution image. By acquiring images in succession, as many as four different fluorophores may be evaluated from a gel. The imaging platform is suitable for analysis of the wide range of dyes and tags commonly encountered in proteomics investigations. The instrument is unique in its capabilities of scanning large areas at high resolution and providing accurate selectable illumination over the UV/visible spectral range, thus maximizing the efficiency of dye multiplexing protocols.
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11
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Kamiya M, Urano Y, Ebata N, Yamamoto M, Kosuge J, Nagano T. Extension of the Applicable Range of Fluorescein: A Fluorescein-Based Probe for Western Blot Analysis. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200501542] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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12
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Salerno D, Daban JR. Comparative study of different fluorescent dyes for the detection of proteins on membranes using the peroxyoxalate chemiluminescent reaction. J Chromatogr B Analyt Technol Biomed Life Sci 2003; 793:75-81. [PMID: 12880855 DOI: 10.1016/s1570-0232(03)00365-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We have previously shown that the bis(2,4,6-trichlorophenyl)oxalate (TCPO)-H(2)O(2) chemiluminescent reaction in acetone can be used for the detection of proteins labeled with the fluorescent reagent 2-methoxy-2,4-diphenyl-3(2H)-furanone (MDPF) on polyvinylidene difluoride (PVDF) membranes. To improve this method, in this work we have designed and constructed a cell that allows us to perform this chemiluminescent reaction on PVDF membranes with a homogeneous distribution of the reagents. Using this cell we have examined the analytical properties of several recently developed fluorescent protein dyes chemically different from MDPF. We have found that the metal chelate dye SYPRO Ruby can also be excited by the high-energy intermediate produced in the TCPO-H(2)O(2) reaction.
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Affiliation(s)
- Doris Salerno
- Departament de Bioquímica i Biologia Molecular, Facultat de Ciències, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
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Schulenberg B, Beechem JM, Patton WF. Mapping glycosylation changes related to cancer using the Multiplexed Proteomics technology: a protein differential display approach. J Chromatogr B Analyt Technol Biomed Life Sci 2003; 793:127-39. [PMID: 12880860 DOI: 10.1016/s1570-0232(03)00370-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The metastatic spread of tumor cells in malignant progression is known to be a major cause of cancer mortality. Protein glycosylation is increasingly being recognized as one of the most prominent biochemical alterations associated with malignant transformation and tumorigenesis. The Multiplexed Proteomics (MP) approach is a new technology that permits quantitative, multicolor fluorescence detection of proteins in two-dimensional (2-D) gels and on Western blots. This methodology allows the parallel determination of both altered glycosylation patterns and protein expression level changes within a single 2-D gel experiment. The linear responses of the fluorescent dyes utilized allow rigorous quantitation of changes in protein expression over a broad 3-log linear dynamic range. Global analysis of changes in protein glycosylation and total protein expression is followed by dichromatic, lectin-based profiling methods for rapidly categorizing glycan branching structures. The MP approach was applied to whole tissue extracts of normal and cancerous liver, so that altered glycosylation modification patterns and protein expression levels could be determined. One prominent glycoprotein determined to be up-regulated in the tumor tissue was haptoglobin, an acute-phase response protein. The detection methodologies associated with the MP technology radically increase the information content of 2-D gel experiments. This new information greatly enhances the applicability of these experiments in addressing fundamental questions associated with proteome-wide glycosylation changes related to cancer.
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Affiliation(s)
- Birte Schulenberg
- Proteomics Section, Molecular Probes Inc., 4849 Pitchford Avenue, Eugene, OR 97402, USA
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14
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Martin K, Hart C, Schulenberg B, Jones L, Patton WF. Simultaneous red/green dual fluorescence detection on electroblots using BODIPY TR-X succinimidyl ester and ELF 39 phosphate. Proteomics 2002; 2:499-512. [PMID: 11987124 DOI: 10.1002/1615-9861(200205)2:5<499::aid-prot499>3.0.co;2-h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A two-color fluorescence detection method is described based upon covalently coupling the succinimidyl ester of BODIPY TR-X dye to proteins immobilized on polyvinylidene difluoride membranes, followed by detection of target proteins using the fluorogenic, precipitating substrate ELF 39-phosphate in combination with alkaline phosphatase conjugated reporter molecules. This results in all proteins in the profile being visualized as fluorescent red signal while those detected specifically with the alkaline phosphatase conjugate appear as fluorescent green signal. The dichromatic detection system is broadly compatible with ultraviolet epi- or trans-illuminators combined with photographic or charge-coupled device cameras, and xenon-arc sources equipped with appropriate excitation/emission filters. The dichromatic method permits detection of low nanogram amounts of protein and allows for unambiguous identification of target proteins relative to the entire protein profile on a single electroblot, obviating the need to run replicate gels that would otherwise require visualization of total proteins by silver staining and subsequent alignment with chemiluminescent or colorimetric signals generated on electroblots. Combining the detection approach with an Alexa Fluor 350 dye conjugated monoclonal antibody permits simultaneous fluorescence detection of two antigens and the total protein profile on the same electroblot.
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Affiliation(s)
- Karen Martin
- Proteomics Section, Molecular Probes, Inc., Eugene, Oregon 97402, USA
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15
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Hanson BJ, Schulenberg B, Patton WF, Capaldi RA. A novel subfractionation approach for mitochondrial proteins: A three-dimensional mitochondrial proteome map. Electrophoresis 2001. [DOI: 10.1002/1522-2683()22:5%3c950::aid-elps950%3e3.0.co;2-d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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16
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Hanson BJ, Schulenberg B, Patton WF, Capaldi RA. A novel subfractionation approach for mitochondrial proteins: a three-dimensional mitochondrial proteome map. Electrophoresis 2001; 22:950-9. [PMID: 11332763 DOI: 10.1002/1522-2683()22:5<950::aid-elps950>3.0.co;2-d] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
As mitochondria play critical roles in both cell life and cell death, there is great interest in obtaining a human mitochondrial proteome map. Such a map could potentially be useful in diagnosing diseases, identifying targets for drug therapy, and in screening for unwanted drug side effects. In this paper, we present a novel approach to obtaining a human mitochondrial proteome map that combines sucrose gradient centrifugation with standard two-dimensional gel electrophoresis. The resulting three-dimensional separation of proteins allows us to address some of the problems encountered during previous attempts to obtain mitochondrial proteome maps such as resolution of proteins and solubility of hydrophobic proteins during isoelectric focusing. In addition, we show that this new approach provides functional information about protein complexes within the organelle that is not obtained with two-dimensional gel electrophoresis of whole mitochondria.
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Affiliation(s)
- B J Hanson
- Institute of Molecular Biology, University of Oregon, Eugene 97403-1229, USA
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