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Xu S, Lee I, Kwon SJ, Kim E, Nevo L, Straight L, Murata H, Matyjaszewski K, Dordick JS. Split fluorescent protein-mediated multimerization of cell wall binding domain for highly sensitive and selective bacterial detection. N Biotechnol 2024; 82:54-64. [PMID: 38750815 DOI: 10.1016/j.nbt.2024.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 04/22/2024] [Accepted: 05/08/2024] [Indexed: 05/18/2024]
Abstract
Cell wall peptidoglycan binding domains (CBDs) of cell lytic enzymes, including bacteriocins, autolysins and bacteriophage endolysins, enable highly selective bacterial binding, and thus, have potential as biorecognition molecules for nondestructive bacterial detection. Here, a novel design for a self-complementing split fluorescent protein (FP) complex is proposed, where a multimeric FP chain fused with specific CBDs ((FP-CBD)n) is assembled inside the cell, to improve sensitivity by enhancing the signal generated upon Staphylococcus aureus or Bacillus anthracis binding. Flow cytometry shows enhanced fluorescence on the cell surface with increasing FP stoichiometry and surface plasmon resonance reveals nanomolar binding affinity to isolated peptidoglycan. The breadth of function of these complexes is demonstrated through the use of CBD modularity and the ability to attach enzymatic detection modalities. Horseradish peroxidase-coupled (FP-CBD)n complexes generate a catalytic amplification, with the degree of amplification increasing as a function of FP length, reaching a limit of detection (LOD) of 103 cells/droplet (approximately 0.1 ng S. aureus or B. anthracis) within 15 min on a polystyrene surface. These fusion proteins can be multiplexed for simultaneous detection. Multimeric split FP-CBD fusions enable use as a biorecognition molecule with enhanced signal for use in bacterial biosensing platforms.
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Affiliation(s)
- Shirley Xu
- Department of Chemical and Biological Engineering, and Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY, USA
| | - Inseon Lee
- Department of Chemical and Biological Engineering, and Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY, USA
| | - Seok-Joon Kwon
- Department of Chemical and Biological Engineering, and Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY, USA
| | - Eunsol Kim
- Department of Chemical and Biological Engineering, and Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY, USA
| | - Liv Nevo
- Department of Chemical and Biological Engineering, and Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY, USA
| | - Lorelli Straight
- Department of Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY, USA
| | - Hironobu Murata
- Department of Chemistry, Carnegie Mellon University, 5000 Forbes Ave, Pittsburgh, PA, USA
| | | | - Jonathan S Dordick
- Department of Chemical and Biological Engineering, and Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY, USA; Department of Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY, USA.
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2
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Liu D, Yu X, Li C, Wang Y, Huang C, Li M, Huang Y, Yang C. Au-Pt Coating Improved Catalytic Stability of Au@AuPt Nanoparticles for Pressure-Based Point-of-Care Detection of Escherichia coli O157:H7. ACS APPLIED MATERIALS & INTERFACES 2024; 16:34632-34640. [PMID: 38916478 DOI: 10.1021/acsami.4c05351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Point-of-care testing (POCT) technologies facilitate onsite detection of pathogens in minutes to hours. Among various POCT approaches, pressure-based sensors that utilize gas-generating reactions, particularly those catalyzed by nanozymes (e.g., platinum nanoparticles, PtNPs, or platinum-coated gold nanoparticles, and Au@PtNPs) have been shown to provide rapid and sensitive detection capabilities. The current study introduces Au-Pt alloy-coated gold nanoparticles (Au@AuPtNPs), an innovative nanozyme with enhanced catalytic activity and relatively high stability. For pathogen detection, Au@AuPtNPs are modified with H1 or H2 hairpin DNAs that can be triggered to undergo a hybridization chain reaction (HCR) that leads to their aggregation upon recognition by an initiator strand (Ini) with H1-/H2-complementary aptamers tethered to magnetic beads (MBs). Pathogen binding to the aptamer exposes Ini, which then binds Au@AuPtNPs and initiates a HCR, resulting in Au@AuPtNP aggregation on MBs. These Au@AuPtNP aggregates exhibit strong catalysis of O2 from the H2O2 substrate, which is measured by a pressure meter, enabling detection of Escherichia coli (E. coli) O157:H7 at concentrations as low as 3 CFU/mL with high specificity. Additionally, E. coli O157:H7 could also be detected in simulated water and tea samples. This method eliminates the need for costly, labor- and training-intensive instruments, supporting its further testing and validation for deployment as a rapid-response POCT application in the detection of bacterial contaminants.
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Affiliation(s)
- Dan Liu
- Engineering Research Centre of Molecular Medicine of Ministry of Education, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, School of Medicine, Huaqiao University, Xiamen, Fujian 362021, China
| | - Xingbo Yu
- Engineering Research Centre of Molecular Medicine of Ministry of Education, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, School of Medicine, Huaqiao University, Xiamen, Fujian 362021, China
| | - Congying Li
- Institute of Analytical Technology and Smart Instruments, Xiamen Key Laboratory of Food and Drug Safety, College of Environment and Public Health, Xiamen Huaxia University, Xiamen, Fujian 361024, China
| | - Ying Wang
- Engineering Research Centre of Molecular Medicine of Ministry of Education, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, School of Medicine, Huaqiao University, Xiamen, Fujian 362021, China
| | - Chenyi Huang
- Institute of Analytical Technology and Smart Instruments, Xiamen Key Laboratory of Food and Drug Safety, College of Environment and Public Health, Xiamen Huaxia University, Xiamen, Fujian 361024, China
| | - Mengmeng Li
- Engineering Research Centre of Molecular Medicine of Ministry of Education, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, School of Medicine, Huaqiao University, Xiamen, Fujian 362021, China
| | - Yishun Huang
- Institute of Analytical Technology and Smart Instruments, Xiamen Key Laboratory of Food and Drug Safety, College of Environment and Public Health, Xiamen Huaxia University, Xiamen, Fujian 361024, China
| | - Chaoyong Yang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, the Key Laboratory of Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
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3
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Karoń S, Drozd M, Malinowska E. A Careful Insight into DDI-Type Receptor Layers on the Way to Improvement of Click-Biology-Based Immunosensors. BIOSENSORS 2024; 14:136. [PMID: 38534243 DOI: 10.3390/bios14030136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 02/26/2024] [Accepted: 03/02/2024] [Indexed: 03/28/2024]
Abstract
Protein-based microarrays are important tools for high-throughput medical diagnostics, offering versatile platforms for multiplex immunodetection. However, challenges arise in protein microarrays due to the heterogeneous nature of proteins and, thus, differences in their immobilization conditions. This article advocates DNA-directed immobilization (DDI) as a solution, emphasizing its rapid and cost-effective fabrication of biosensing platforms. Thiolated single-stranded DNA and its analogues, such as ZNA® and PNA probes, were used to immobilize model proteins (anti-CRP antibodies and SARS-CoV nucleoprotein). The study explores factors influencing DDI-based immunosensor performance, including the purity of protein-DNA conjugates and the stability of their duplexes with DNA and analogues. It also provides insight into backfilling agent type and probe surface density. The research reveals that single-component monolayers lack protection against protein adsorption, while mixing the probes with long-chain ligands may hinder DNA-protein conjugate anchoring. Conventional DNA probes offer slightly higher surface density, while ZNA® probes exhibit better binding efficiency. Despite no enhanced stability in different ionic strength media, the cost-effectiveness of DNA probes led to their preference. The findings contribute to advancing microarray technology, paving the way for new generations of DDI-based multiplex platforms for rapid and robust diagnostics.
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Affiliation(s)
- Sylwia Karoń
- Department of Medical Diagnostics, Centre for Advanced Materials and Technologies CEZAMAT, Warsaw University of Technology, Poleczki 19, 02-822 Warsaw, Poland
- Chair of Medical Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - Marcin Drozd
- Department of Medical Diagnostics, Centre for Advanced Materials and Technologies CEZAMAT, Warsaw University of Technology, Poleczki 19, 02-822 Warsaw, Poland
- Chair of Medical Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - Elżbieta Malinowska
- Department of Medical Diagnostics, Centre for Advanced Materials and Technologies CEZAMAT, Warsaw University of Technology, Poleczki 19, 02-822 Warsaw, Poland
- Chair of Medical Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
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4
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Komiya E, Takamatsu S, Miura D, Tsukakoshi K, Tsugawa W, Sode K, Ikebukuro K, Asano R. Exploration and Application of DNA-Binding Proteins to Make a Versatile DNA-Protein Covalent-Linking Patch (D-Pclip): The Case of a Biosensing Element. J Am Chem Soc 2024; 146:4087-4097. [PMID: 38295327 PMCID: PMC10870700 DOI: 10.1021/jacs.3c12668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 01/06/2024] [Accepted: 01/08/2024] [Indexed: 02/02/2024]
Abstract
DNA-protein complexes are attractive components with broad applications in various research fields, such as DNA aptamer-enzyme complexes as biosensing elements. However, noncovalent DNA-protein complexes often decrease detection sensitivity because they are highly susceptible to environmental conditions. In this study, we developed a versatile DNA-protein covalent-linking patch (D-Pclip) for fabricating covalent and stoichiometric DNA-protein complexes. We comprehensively explored the database to determine the DNA-binding ability of the candidates and selected UdgX as the only uracil-DNA glycosylase known to form covalent bonds with DNA via uracil, with a binding efficiency >90%. We integrated a SpyTag/SpyCatcher protein-coupling system into UdgX to create a universal and convenient D-Pclip. The usability of D-Pclip was shown by preparing a stoichiometric model complex of a hemoglobin (Hb)-binding aptamer and glucose oxidase (GOx) by mixing at 4 °C. The prepared aptamer-GOx complexes detected Hb in a dose-dependent manner within the clinically required detection range in buffer and human serum without any washing procedures. D-Pclip covalently connects any uracil-inserted DNA sequence and any SpyCatcher-fused protein stoichiometrically; therefore, it has a high potential for various applications.
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Affiliation(s)
- Erika Komiya
- Department
of Biotechnology and Life Science, Tokyo
University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Shouhei Takamatsu
- Department
of Biotechnology and Life Science, Tokyo
University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Daimei Miura
- Department
of Biotechnology and Life Science, Tokyo
University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Kaori Tsukakoshi
- Department
of Biotechnology and Life Science, Tokyo
University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Wakako Tsugawa
- Department
of Biotechnology and Life Science, Tokyo
University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Koji Sode
- Joint
Department of Biomedical Engineering, University
of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, North Carolina 27599, United States
- Institute
of Global Innovation Research, Tokyo University
of Agriculture and Technology, 3-8-1 Harumi-cho, Fuchu, Tokyo 183-8509, Japan
| | - Kazunori Ikebukuro
- Department
of Biotechnology and Life Science, Tokyo
University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Ryutaro Asano
- Department
of Biotechnology and Life Science, Tokyo
University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
- Institute
of Global Innovation Research, Tokyo University
of Agriculture and Technology, 3-8-1 Harumi-cho, Fuchu, Tokyo 183-8509, Japan
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5
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Miao Q, Ding W, Bao X, Wang S, Lin Q, Xu Y, Lu J, Lyu M, Wang S. An efficient
DNAzyme
for the fluorescence detection of
Vibrio cholerae. Food Sci Nutr 2023. [DOI: 10.1002/fsn3.3304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023] Open
Affiliation(s)
- Qingzhen Miao
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology Jiangsu Ocean University Lianyungang China
- Co‐Innovation Center of Jiangsu Marine Bio‐industry Technology Jiangsu Ocean University Lianyungang China
| | - Wen Ding
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology Jiangsu Ocean University Lianyungang China
- Co‐Innovation Center of Jiangsu Marine Bio‐industry Technology Jiangsu Ocean University Lianyungang China
| | - Xiuli Bao
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology Jiangsu Ocean University Lianyungang China
- Co‐Innovation Center of Jiangsu Marine Bio‐industry Technology Jiangsu Ocean University Lianyungang China
| | - Siyuan Wang
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology Jiangsu Ocean University Lianyungang China
- Co‐Innovation Center of Jiangsu Marine Bio‐industry Technology Jiangsu Ocean University Lianyungang China
| | - Qianru Lin
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology Jiangsu Ocean University Lianyungang China
- Co‐Innovation Center of Jiangsu Marine Bio‐industry Technology Jiangsu Ocean University Lianyungang China
| | - Yingying Xu
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology Jiangsu Ocean University Lianyungang China
- Co‐Innovation Center of Jiangsu Marine Bio‐industry Technology Jiangsu Ocean University Lianyungang China
| | - Jing Lu
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology Jiangsu Ocean University Lianyungang China
- Co‐Innovation Center of Jiangsu Marine Bio‐industry Technology Jiangsu Ocean University Lianyungang China
| | - Mingsheng Lyu
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology Jiangsu Ocean University Lianyungang China
- Co‐Innovation Center of Jiangsu Marine Bio‐industry Technology Jiangsu Ocean University Lianyungang China
| | - Shujun Wang
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology Jiangsu Ocean University Lianyungang China
- Co‐Innovation Center of Jiangsu Marine Bio‐industry Technology Jiangsu Ocean University Lianyungang China
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6
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A Novel Nanobody-Horseradish Peroxidase Fusion Based-Competitive ELISA to Rapidly Detect Avian Corona-Virus-Infectious Bronchitis Virus Antibody in Chicken Serum. Int J Mol Sci 2022; 23:ijms23147589. [PMID: 35886935 PMCID: PMC9321063 DOI: 10.3390/ijms23147589] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 07/04/2022] [Accepted: 07/07/2022] [Indexed: 02/04/2023] Open
Abstract
Avian coronavirus-infectious bronchitis virus (AvCoV-IBV) is the causative agent of infectious bronchitis (IB) that has brought great threat and economic losses to the global poultry industry. Rapid and accurate diagnostic methods are very necessary for effective disease monitoring. At the present study, we screened a novel nanobody against IBV-N protein for development of a rapid, simple, sensitive, and specific competitive ELISA for IBV antibody detection in order to enable the assessment of inoculation effect and early warning of disease infection. Using the phage display technology and bio-panning, we obtained 7 specific nanobodies fused with horseradish peroxidase (HRP) which were expressed in culture supernatant of HEK293T cells. Out of which, the nanobody of IBV-N-Nb66-vHRP has highly binding with IBV-N protein and was easily blocked by the IBV positive serums, which was finally employed as an immunoprobe for development of the competitive ELISA (cELISA). In the newly developed cELISA, we reduce the use of enzyme-conjugated secondary antibody, and the time of whole operation process is approximately 1 h. Moreover, the IBV positive serums diluted at 1:1000 can still be detected by the developed cELISA, and it has no cross reactivity with others chicken disease serums including Newcastle disease virus, Fowl adenovirus, Avian Influenza Virus, Infectious bursal disease virus and Hepatitis E virus. The cut-off value of the established cELISA was 36%, and the coefficient of variation of intra- and inter-assay were 0.55–1.65% and 2.58–6.03%, respectively. Compared with the commercial ELISA (IDEXX kit), the agreement rate of two methods was defined as 98% and the kappa value was 0.96, indicating the developed cELISA has high consistency with the commercial ELISA. Taken together, the novel cELISA for IBV antibody detection is a simple, rapid, sensitive, and specific immunoassay, which has the potential to rapidly test IBV antibody contributing to the surveillance and control of the disease.
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7
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Cytoplasmic Production of Nanobodies and Nanobody-Based Reagents by Co-Expression of Sulfhydryl Oxidase and DsbC Isomerase. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2446:145-157. [PMID: 35157272 DOI: 10.1007/978-1-0716-2075-5_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Nanobodies are stable molecules that can often fold correctly even in the absence of the disulfide bond(s) that stabilize their three-dimensional conformation. Nevertheless, some nanobodies require the formation of disulfide bonds, and therefore they are commonly expressed from vectors that promote their secretion into the oxidizing environment of the Escherichia coli periplasm. As an alternative, the bacterial cytoplasm can be an effective compartment for producing correctly folded nanobodies when sulfhydryl oxidase and disulfide-bond isomerase activities are co-expressed from a recombinant vector. The larger volume and wider chaperone/foldase availability of the cytoplasm enable the achievement of high yields of both nanobodies and nanobody-tag fusions, independently of their redox requirements. Among other examples, the protocol described here was used to successfully produce nanobody fusions with fluorescent proteins that do not fold correctly in the periplasm, nanobodies with Fc domains, and nanobodies containing free cysteine tags.
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8
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Kosman J, Żukowski K, Csáki A, Fritzsche W, Juskowiak B. Sequence Effect on the Activity of DNAzyme with Covalently Attached Hemin and Their Potential Bioanalytical Application. SENSORS (BASEL, SWITZERLAND) 2022; 22:500. [PMID: 35062461 PMCID: PMC8780643 DOI: 10.3390/s22020500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/30/2021] [Accepted: 01/07/2022] [Indexed: 06/14/2023]
Abstract
In this work we investigated the effect of a DNA oligonucleotide sequence on the activity of a DNAzyme with covalently attached hemin. For this purpose, we synthesized seven DNA-hemin conjugates. All DNA-hemin conjugates as well as DNA/hemin complexes were characterized using circular dichroism, determination of melting temperatures and pKa of hemin. We observed that hemin conjugation in most cases led to the formation of parallel G-quadruplexes in the presence of potassium and increased thermal stability of all studied systems. Although the activity of DNA-hemin conjugates depended on the sequence used, the highest activity was observed for the DNA-hemin conjugate based on a human telomeric sequence. We used this DNAzyme for development of "sandwich" assay for detection of DNA sequence. For this assay, we used electric chip which could conduct electricity after silver deposition catalyzed by DNAzyme. This method was proved to be selective towards DNA oligonucleotides with mismatches and could be used for the detection of the target. To prove the versatility of our DNAzyme probe we also performed experiments with streptavidin-coated microplates. Our research proved that DNAzyme with covalently attached hemin can be used successfully in the development of heterogeneous assays.
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Affiliation(s)
- Joanna Kosman
- Department of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614 Poznan, Poland; (K.Ż.); (B.J.)
| | - Krzysztof Żukowski
- Department of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614 Poznan, Poland; (K.Ż.); (B.J.)
| | - Andrea Csáki
- Leibniz Institute of Photonic Technology, Albert-Einstein-Strasse 9, 07745 Jena, Germany; (A.C.); (W.F.)
| | - Wolfgang Fritzsche
- Leibniz Institute of Photonic Technology, Albert-Einstein-Strasse 9, 07745 Jena, Germany; (A.C.); (W.F.)
| | - Bernard Juskowiak
- Department of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614 Poznan, Poland; (K.Ż.); (B.J.)
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9
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Nanobody-Dependent Detection of Microcystis aeruginosa by ELISA and Thermal Lens Spectrometry. Appl Biochem Biotechnol 2021; 193:2729-2741. [PMID: 33871768 DOI: 10.1007/s12010-021-03552-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 03/22/2021] [Indexed: 12/26/2022]
Abstract
Nanobodies against cell surface antigens of toxic cyanobacteria Microcystis aeruginosa were recovered by whole-cell biopanning of a naïve phage display library of nanobodies. Six unique sequences were identified and three sub-cloned and purified as fusion immunoreagents together with either green fluorescent protein or AviTag to be used for diagnostics. The yields of nanobody constructs were in the range of 5-10 mg/l and their specificity and sensitivity was initially evaluated by immunofluorescence and by fluorescent enzyme-linked immunosorbent assay (ELISA) using fluorescent nanobodies. The ELISA data confirmed the nanobody specificity but showed that the saturation of the fluorescence signal already in the presence of few hundreds of cells limited the dynamic range of the method. As an alternative, Avi-tagged nanobodies were used in combination with streptavidin-linked horseradish peroxidase for developing a diagnostic colorimetric cell ELISA, the limit-of-detection of which was 3.2 and 4.5 cells/ml for the two tested cyanobacteria strains, whereas the linear range of the assay was expanded from 10 to 10,000 cells. The fluorescent nanobodies were finally exploited for quantifying cyanobacteria by thermal lens spectrometry (TLS) that enabled to reach a limit-of-detection of 1.2 cells/ml and provided a linear range of measurement between 0 and 10,000 cells. No cross-reactivity with unrelated microalgae was detected and both colorimetric ELISA and TLS provided a linear range of detection of few logs. The data indicate that nanobodies are suitable capture reagents and that both TLS and colorimetric ELISA are reliable to monitor variations of cyanobacteria populations.
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10
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Yu S, Chen T, Zhang Q, Zhou M, Zhu X. Application of DNA nanodevices for biosensing. Analyst 2020; 145:3481-3489. [PMID: 32319463 DOI: 10.1039/d0an00159g] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Deoxyribonucleic acid (DNA), the carrier of genetic information in living life, is an essential biomacromolecule in almost all living systems. DNA has advantages including, programmability, predictability, high rigidity, and stability. Through self-assembly or combination with other nanomaterials (such as gold nanoparticles, graphene oxides, quantum dots, and polymers), DNA can be applied to construct specific, stable, biocompatible, and functional nanodevices. DNA nanodevices have made greater contributions in a plethora of fields. In this review, we discuss the recent progress of DNA nanodevices in molecular detection and analysis. Meanwhile, we prospect the development of various DNA devices in biological analysis, clinical diagnosis and biomedical research.
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Affiliation(s)
- Sinuo Yu
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China.
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11
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de Marco A. Recombinant expression of nanobodies and nanobody-derived immunoreagents. Protein Expr Purif 2020; 172:105645. [PMID: 32289357 PMCID: PMC7151424 DOI: 10.1016/j.pep.2020.105645] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 04/06/2020] [Accepted: 04/09/2020] [Indexed: 12/12/2022]
Abstract
Antibody fragments for which the sequence is available are suitable for straightforward engineering and expression in both eukaryotic and prokaryotic systems. When produced as fusions with convenient tags, they become reagents which pair their selective binding capacity to an orthogonal function. Several kinds of immunoreagents composed by nanobodies and either large proteins or short sequences have been designed for providing inexpensive ready-to-use biological tools. The possibility to choose among alternative expression strategies is critical because the fusion moieties might require specific conditions for correct folding or post-translational modifications. In the case of nanobody production, the trend is towards simpler but reliable (bacterial) methods that can substitute for more cumbersome processes requiring the use of eukaryotic systems. The use of these will not disappear, but will be restricted to those cases in which the final immunoconstructs must have features that cannot be obtained in prokaryotic cells. At the same time, bacterial expression has evolved from the conventional procedure which considered exclusively the nanobody and nanobody-fusion accumulation in the periplasm. Several reports show the advantage of cytoplasmic expression, surface-display and secretion for at least some applications. Finally, there is an increasing interest to use as a model the short nanobody sequence for the development of in silico methodologies aimed at optimizing the yields, stability and affinity of recombinant antibodies. There is an increasing request for immunoreagents based on nanobodies. The multiplicity of their applications requires constructs with different structural complexity. Alternative expression methods are necessary to achieve such structural requirements. In silico optimization of nanobody biophysical characteristics becomes more and more reliable.
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Affiliation(s)
- Ario de Marco
- Laboratory for Environmental and Life Sciences, University of Nova Gorica, Vipavska cesta 13, S-5000, Nova Gorica, Slovenia.
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