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Zhang X, Yarman A, Kovács N, Bognár Z, Gyurcsányi RE, Bier FF, Scheller FW. Specific features of epitope-MIPs and whole-protein MIPs as illustrated for AFP and RBD of SARS-CoV-2. Mikrochim Acta 2024; 191:242. [PMID: 38573524 DOI: 10.1007/s00604-024-06325-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 03/22/2024] [Indexed: 04/05/2024]
Abstract
Molecularly imprinted polymer (MIP) nanofilms for alpha-fetoprotein (AFP) and the receptor binding domain (RBD) of the spike protein of SARS-CoV-2 using either a peptide (epitope-MIP) or the whole protein (protein-MIP) as the template were prepared by electropolymerization of scopoletin. Conducting atomic force microscopy revealed after template removal and electrochemical deposition of gold a larger surface density of imprinted cavities for the epitope-imprinted polymers than when using the whole protein as template. However, comparable affinities towards the respective target protein (AFP and RBD) were obtained for both types of MIPs as expressed by the KD values in the lower nanomolar range. On the other hand, while the cross reactivity of both protein-MIPs towards human serum albumin (HSA) amounts to around 50% in the saturation region, the nonspecific binding to the respective epitope-MIPs is as low as that for the non-imprinted polymer (NIP). This effect might be caused by the different sizes of the imprinted cavities. Thus, in addition to the lower costs the reduced nonspecific binding is an advantage of epitope-imprinted polymers for the recognition of proteins.
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Affiliation(s)
- Xiaorong Zhang
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht Str. 24-25, 14476, Potsdam, Germany.
| | - Aysu Yarman
- Molecular Biotechnology, Faculty of Science, Turkish-German University, Sahinkaya Cad. Beykoz, Istanbul, 34820, Turkey
| | - Norbert Kovács
- BME "Lendület" Chemical Nanosensors Research Group, Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Műegyetem rkp. 3, 1111, Budapest, Hungary
| | - Zsófia Bognár
- BME "Lendület" Chemical Nanosensors Research Group, Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Műegyetem rkp. 3, 1111, Budapest, Hungary
| | - Róbert E Gyurcsányi
- BME "Lendület" Chemical Nanosensors Research Group, Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Műegyetem rkp. 3, 1111, Budapest, Hungary
- HUN-REN-BME Computation Driven Chemistry Research Group, Műegyetem rkp. 3, 1111, Budapest, Hungary
| | - Frank F Bier
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht Str. 24-25, 14476, Potsdam, Germany
| | - Frieder W Scheller
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht Str. 24-25, 14476, Potsdam, Germany
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2
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Altattan B, Ullrich J, Mattig E, Poppe A, Martins R, Bier FF. Direct TAMRA-dUTP labeling of M. tuberculosis genes using loop-mediated isothermal amplification (LAMP). Sci Rep 2024; 14:5611. [PMID: 38454089 PMCID: PMC10920756 DOI: 10.1038/s41598-024-55289-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 02/22/2024] [Indexed: 03/09/2024] Open
Abstract
Fluorescent molecule-based direct labeling of amplified DNA is a sensitive method employed across diverse DNA detection and diagnostics systems. However, using pre-labeled primers only allows for the attachment of a single fluorophore to each DNA strand and any modifications of the system are less flexible, requiring new sets of primers. As an alternative, direct labeling of amplified products with modified nucleotides is available, but still poorly characterized. To address these limitations, we sought a direct and adaptable approach to label amplicons produced through Loop-mediated isothermal amplification (LAMP), using labeled nucleotides (dUTPs) rather than primers. The focus of this study was the development and examination of a direct labeling technique of specific genes, including those associated with drug resistance in Mycobacterium tuberculosis. We used 5-(3-Aminoallyl)-2'-deoxyuridine-5'triphosphate, tagged with 5/6-TAMRA (TAMRA-dUTP) for labeling LAMP amplicons during the amplification process and characterized amplification and incorporation efficiency. The optimal TAMRA-dUTP concentration was first determined based on amplification efficiency (0.5% to total dNTPs). Higher concentrations of modified nucleotides reduced or completely inhibited the amplification yield. Target size also showed to be determinant to the success of amplification, as longer sequences showed lower amplification rates, thus less TAMRA incorporated amplicons. Finally, we were able to successfully amplify all four M. tuberculosis target genes using LAMP and TAMRA-modified dUTPs.
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Affiliation(s)
- Basma Altattan
- Institute for Molecular Diagnostics und Bioanalysis (IMDB), 14476, Potsdam, Germany.
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany.
| | - Jasmin Ullrich
- Institute for Molecular Diagnostics und Bioanalysis (IMDB), 14476, Potsdam, Germany
| | - Emily Mattig
- Fraunhofer Institute for Cell Therapy and Immunology-Bioanalytics and Bioprocesses (IZI-BB), 14476, Potsdam, Germany
| | - Aline Poppe
- Fraunhofer Institute for Cell Therapy and Immunology-Bioanalytics and Bioprocesses (IZI-BB), 14476, Potsdam, Germany
| | - Renata Martins
- Institute for Molecular Diagnostics und Bioanalysis (IMDB), 14476, Potsdam, Germany
| | - Frank F Bier
- Institute for Molecular Diagnostics und Bioanalysis (IMDB), 14476, Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
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3
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Agarwal S, Hamidizadeh M, Bier FF. Detection of Reverse Transcriptase LAMP-Amplified Nucleic Acid from Oropharyngeal Viral Swab Samples Using Biotinylated DNA Probes through a Lateral Flow Assay. Biosensors (Basel) 2023; 13:988. [PMID: 37998163 PMCID: PMC10669123 DOI: 10.3390/bios13110988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/06/2023] [Accepted: 11/10/2023] [Indexed: 11/25/2023]
Abstract
This study focuses on three key aspects: (a) crude throat swab samples in a viral transport medium (VTM) as templates for RT-LAMP reactions; (b) a biotinylated DNA probe with enhanced specificity for LFA readouts; and (c) a digital semi-quantification of LFA readouts. Throat swab samples from SARS-CoV-2 positive and negative patients were used in their crude (no cleaning or pre-treatment) forms for the RT-LAMP reaction. The samples were heat-inactivated but not treated for any kind of nucleic acid extraction or purification. The RT-LAMP (20 min processing time) product was read out by an LFA approach using two labels: FITC and biotin. FITC was enzymatically incorporated into the RT-LAMP amplicon with the LF-LAMP primer, and biotin was introduced using biotinylated DNA probes, specifically for the amplicon region after RT-LAMP amplification. This assay setup with biotinylated DNA probe-based LFA readouts of the RT-LAMP amplicon was 98.11% sensitive and 96.15% specific. The LFA result was further analysed by a smartphone-based IVD device, wherein the T-line intensity was recorded. The LFA T-line intensity was then correlated with the qRT-PCR Ct value of the positive swab samples. A digital semi-quantification of RT-LAMP-LFA was reported with a correlation coefficient of R2 = 0.702. The overall RT-LAMP-LFA assay time was recorded to be 35 min with a LoD of three RNA copies/µL (Ct-33). With these three advancements, the nucleic acid testing-point of care technique (NAT-POCT) is exemplified as a versatile biosensor platform with great potential and applicability for the detection of pathogens without the need for sample storage, transportation, or pre-processing.
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Affiliation(s)
- Saloni Agarwal
- Institute for Biochemistry and Biology, Chair of Molecular Bioanalysis and Bioelectronics, University of Potsdam, Karl-Liebknecht-Strasse 24/25, 14476 Potsdam, Germany; (S.A.); (M.H.)
| | - Mojdeh Hamidizadeh
- Institute for Biochemistry and Biology, Chair of Molecular Bioanalysis and Bioelectronics, University of Potsdam, Karl-Liebknecht-Strasse 24/25, 14476 Potsdam, Germany; (S.A.); (M.H.)
| | - Frank F. Bier
- Institute for Biochemistry and Biology, Chair of Molecular Bioanalysis and Bioelectronics, University of Potsdam, Karl-Liebknecht-Strasse 24/25, 14476 Potsdam, Germany; (S.A.); (M.H.)
- Institute for Molecular Diagnostics and Bioanalysis-IMDB gGmbH, Am Mühlenberg 10, 14476 Potsdam, Germany
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4
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Zhang X, Yarman A, Bagheri M, El-Sherbiny IM, Hassan RYA, Kurbanoglu S, Waffo AFT, Zebger I, Karabulut TC, Bier FF, Lieberzeit P, Scheller FW. Imprinted Polymers on the Route to Plastibodies for Biomacromolecules (MIPs), Viruses (VIPs), and Cells (CIPs). Adv Biochem Eng Biotechnol 2023. [PMID: 37884758 DOI: 10.1007/10_2023_234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Around 30% of the scientific papers published on imprinted polymers describe the recognition of proteins, nucleic acids, viruses, and cells. The straightforward synthesis from only one up to six functional monomers and the simple integration into a sensor are significant advantages as compared with enzymes or antibodies. Furthermore, they can be synthesized against toxic substances and structures of low immunogenicity and allow multi-analyte measurements via multi-template synthesis. The affinity is sufficiently high for protein biomarkers, DNA, viruses, and cells. However, the cross-reactivity of highly abundant proteins is still a challenge.
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Affiliation(s)
- Xiaorong Zhang
- Institute for Biochemistry and Biology, Universität Potsdam, Potsdam, Germany
| | - Aysu Yarman
- Molecular Biotechnology, Faculty of Science, Turkish-German University, Istanbul, Turkey
| | - Mahdien Bagheri
- Department of Physical Chemistry, Faculty for Chemistry, University of Vienna, Vienna, Austria
| | - Ibrahim M El-Sherbiny
- Nanoscience Program, University of Science and Technology (UST), Zewail City of Science and Technology, Giza, Egypt
- Center for Materials Science (CMS), Zewail City of Science and Technology, Giza, Egypt
| | - Rabeay Y A Hassan
- Nanoscience Program, University of Science and Technology (UST), Zewail City of Science and Technology, Giza, Egypt
- Center for Materials Science (CMS), Zewail City of Science and Technology, Giza, Egypt
| | - Sevinc Kurbanoglu
- Department of Analytical Chemistry, Faculty of Pharmacy, Ankara University, Ankara, Turkey
| | | | - Ingo Zebger
- Institut für Chemie, PC 14 Technische Universität Berlin, Berlin, Germany
| | | | - Frank F Bier
- Institute for Biochemistry and Biology, Universität Potsdam, Potsdam, Germany
| | - Peter Lieberzeit
- Department of Physical Chemistry, Faculty for Chemistry, University of Vienna, Vienna, Austria.
| | - Frieder W Scheller
- Institute for Biochemistry and Biology, Universität Potsdam, Potsdam, Germany.
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5
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Bognár Z, Supala E, Yarman A, Zhang X, Bier FF, Scheller FW, Gyurcsányi RE. Correction: Peptide epitope-imprinted polymer microarrays for selective protein recognition. Application for SARS-CoV-2 RBD protein. Chem Sci 2023; 14:9980. [PMID: 37736654 PMCID: PMC10510652 DOI: 10.1039/d3sc90170j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 08/25/2023] [Indexed: 09/23/2023] Open
Abstract
[This corrects the article DOI: 10.1039/D1SC04502D.].
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Affiliation(s)
- Zsófia Bognár
- BME "Lendület" Chemical Nanosensors Research Group, Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics Szt. Gellért tér 4 1111 Budapest Hungary
| | - Eszter Supala
- BME "Lendület" Chemical Nanosensors Research Group, Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics Szt. Gellért tér 4 1111 Budapest Hungary
| | - Aysu Yarman
- Institute of Biochemistry and Biology, University of Potsdam Karl-Liebknecht-Str. 24-25 14476 Potsdam OT Golm Germany
| | - Xiaorong Zhang
- Institute of Biochemistry and Biology, University of Potsdam Karl-Liebknecht-Str. 24-25 14476 Potsdam OT Golm Germany
| | - Frank F Bier
- Institute of Biochemistry and Biology, University of Potsdam Karl-Liebknecht-Str. 24-25 14476 Potsdam OT Golm Germany
| | - Frieder W Scheller
- Institute of Biochemistry and Biology, University of Potsdam Karl-Liebknecht-Str. 24-25 14476 Potsdam OT Golm Germany
| | - Róbert E Gyurcsányi
- BME "Lendület" Chemical Nanosensors Research Group, Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics Szt. Gellért tér 4 1111 Budapest Hungary
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6
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Prüfer M, Stanke S, Bier FF, Hölzel R. Catalytic activity of glucose oxidase after dielectrophoretic immobilization on nanoelectrodes. Electrophoresis 2023. [PMID: 36892276 DOI: 10.1002/elps.202300010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/13/2023] [Accepted: 02/27/2023] [Indexed: 03/10/2023]
Abstract
Dielectrophoresis (DEP) is an AC electrokinetic effect that is proven to be effective for the immobilization of not only cells, but also of macromolecules, for example, antibodies and enzyme molecules. In our previous work, we have already demonstrated the high catalytic activity of immobilized horseradish peroxidase after DEP. To evaluate the suitability of the immobilization method for sensing or research in general, we want to test it for other enzymes, too. In this study, glucose oxidase (GOX) from Aspergillus niger was immobilized on TiN nanoelectrode arrays by DEP. Fluorescence microscopy showed the intrinsic fluorescence of the immobilized enzymes flavin cofactor on the electrodes. The catalytic activity of immobilized GOX was detectable, but a fraction of less than 1.3% of the maximum activity that was expected for a full monolayer of immobilized enzymes on all electrodes was stable for multiple measurement cycles. Therefore, the effect of DEP immobilization on the catalytic activity strongly depends on the used enzyme.
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Affiliation(s)
- Mareike Prüfer
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam-Golm, Germany.,Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
| | - Sandra Stanke
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam-Golm, Germany.,Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
| | - Frank F Bier
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
| | - Ralph Hölzel
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam-Golm, Germany
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7
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Zhang X, Waffo AT, Yarman A, Kovács N, Bognár Z, Wollenberger U, El-Sherbiny IM, Hassan RYA, Bier FF, Gyurcsányi RE, Zebger I, Scheller FW. How an ACE2 mimicking epitope-MIP nanofilm recognizes template-related peptides and the receptor binding domain of SARS-CoV-2. Nanoscale 2022; 14:18106-18114. [PMID: 36448745 DOI: 10.1039/d2nr03898f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Here we aim to gain a mechanistic understanding of the formation of epitope-imprinted polymer nanofilms using a non-terminal peptide sequence, i.e. the peptide GFNCYFP (G485 to P491) of the SARS-CoV-2 receptor binding domain (RBD). This epitope is chemisorbed on the gold surface through the central cysteine 488 followed by the electrosynthesis of a ∼5 nm thick polyscopoletin film around the surface confined templates. The interaction of peptides and the parent RBD and spike protein with the imprinted polyscopoletin nanofilm was followed by electrochemical redox marker gating, surface enhanced infrared absorption spectroscopy and conductive AFM. Because the use of non-terminal epitopes is especially intricate, here we characterize the binding pockets through their interaction with 5 peptides rationally derived from the template sequence, i.e. implementing central single amino acid mismatch as well as elongations and truncations at its C- and N- termini. Already a single amino acid mismatch, i.e. the central Cys488 substituted by a serine, results in ca. 15-fold lower affinity. Further truncation of the peptides to tetrapeptide (EGFN) and hexapeptide (YFPLQS) results also in a significantly lower affinity. We concluded that the affinity towards the different peptides is mainly determined by the four amino acid motif CYFP present in the sequence of the template peptide. A higher affinity than that for the peptides is found for the parent proteins RBD and spike protein, which seems to be due to out of cavity effects caused by their larger footprint on the nanofilm surface.
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Affiliation(s)
- Xiaorong Zhang
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht Str. 24-25, 14476 Potsdam, Germany.
| | - Armel T Waffo
- Institut für Chemie, PC 14 Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Aysu Yarman
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht Str. 24-25, 14476 Potsdam, Germany.
- Molecular Biotechnology, Faculty of Science, Turkish-German University, Sahinkaya Cad, 86, Beykoz, Istanbul 34820, Turkey
| | - Norbert Kovács
- Department of Inorganic and Analytical Chemistry, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary.
| | - Zsófia Bognár
- Department of Inorganic and Analytical Chemistry, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary.
- ELKH-BME Computation Driven Chemistry Research Group, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - Ulla Wollenberger
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht Str. 24-25, 14476 Potsdam, Germany.
| | - Ibrahim M El-Sherbiny
- Nanoscience Program, University of Science and Technology (UST) & Center for Materials Science (CMS), Zewail City of Science and Technology, Giza 12578, Egypt
| | - Rabeay Y A Hassan
- Nanoscience Program, University of Science and Technology (UST) & Center for Materials Science (CMS), Zewail City of Science and Technology, Giza 12578, Egypt
| | - Frank F Bier
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht Str. 24-25, 14476 Potsdam, Germany.
| | - Róbert E Gyurcsányi
- Department of Inorganic and Analytical Chemistry, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary.
- ELKH-BME Computation Driven Chemistry Research Group, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - Ingo Zebger
- Institut für Chemie, PC 14 Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Frieder W Scheller
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht Str. 24-25, 14476 Potsdam, Germany.
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8
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Prüfer M, Wenger C, Bier FF, Laux EM, Hölzel R. Activity of AC electrokinetically immobilized horseradish peroxidase. Electrophoresis 2022; 43:1920-1933. [PMID: 35904497 DOI: 10.1002/elps.202200073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 06/22/2022] [Accepted: 07/18/2022] [Indexed: 12/14/2022]
Abstract
Dielectrophoresis (DEP) is an AC electrokinetic effect mainly used to manipulate cells. Smaller particles, like virions, antibodies, enzymes, and even dye molecules can be immobilized by DEP as well. In principle, it was shown that enzymes are active after immobilization by DEP, but no quantification of the retained activity was reported so far. In this study, the activity of the enzyme horseradish peroxidase (HRP) is quantified after immobilization by DEP. For this, HRP is immobilized on regular arrays of titanium nitride ring electrodes of 500 nm diameter and 20 nm widths. The activity of HRP on the electrode chip is measured with a limit of detection of 60 fg HRP by observing the enzymatic turnover of Amplex Red and H2 O2 to fluorescent resorufin by fluorescence microscopy. The initial activity of the permanently immobilized HRP equals up to 45% of the activity that can be expected for an ideal monolayer of HRP molecules on all electrodes of the array. Localization of the immobilizate on the electrodes is accomplished by staining with the fluorescent product of the enzyme reaction. The high residual activity of enzymes after AC field induced immobilization shows the method's suitability for biosensing and research applications.
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Affiliation(s)
- Mareike Prüfer
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam-Golm, Germany
| | - Christian Wenger
- IHP GmbH - Leibniz Institute for Innovative Microelectronics, Frankfurt/Oder, Germany
| | - Frank F Bier
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
| | - Eva-Maria Laux
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam-Golm, Germany
| | - Ralph Hölzel
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam-Golm, Germany
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9
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Stanke S, Wenger C, Bier FF, Hölzel R. AC electrokinetic immobilization of influenza virus. Electrophoresis 2022; 43:1309-1321. [DOI: 10.1002/elps.202100324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 12/26/2021] [Accepted: 01/06/2022] [Indexed: 11/05/2022]
Affiliation(s)
- Sandra Stanke
- Fraunhofer Institute for Cell Therapy and Immunology Branch Bioanalytics and Bioprocesses (IZI‐BB) Potsdam‐Golm Germany
- Institute of Biochemistry and Biology University of Potsdam Potsdam‐Golm Germany
| | - Christian Wenger
- IHP – Leibnizinstitut für innovative Mikroelektronik Frankfurt/Oder Germany
- Brandenburg University of Technology Cottbus–Senftenberg Cottbus Germany
| | - Frank F. Bier
- Institute of Biochemistry and Biology University of Potsdam Potsdam‐Golm Germany
| | - Ralph Hölzel
- Fraunhofer Institute for Cell Therapy and Immunology Branch Bioanalytics and Bioprocesses (IZI‐BB) Potsdam‐Golm Germany
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10
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Bognár Z, Supala E, Yarman A, Zhang X, Bier FF, Scheller FW, Gyurcsányi RE. Peptide epitope-imprinted polymer microarrays for selective protein recognition. Application for SARS-CoV-2 RBD protein. Chem Sci 2022; 13:1263-1269. [PMID: 35222909 PMCID: PMC8809392 DOI: 10.1039/d1sc04502d] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 11/23/2021] [Indexed: 12/18/2022] Open
Abstract
We introduce a practically generic approach for the generation of epitope-imprinted polymer-based microarrays for protein recognition on surface plasmon resonance imaging (SPRi) chips. The SPRi platform allows the subsequent rapid screening of target binding kinetics in a multiplexed and label-free manner. The versatility of such microarrays, both as synthetic and screening platform, is demonstrated through developing highly affine molecularly imprinted polymers (MIPs) for the recognition of the receptor binding domain (RBD) of SARS-CoV-2 spike protein. A characteristic nonapeptide GFNCYFPLQ from the RBD and other control peptides were microspotted onto gold SPRi chips followed by the electrosynthesis of a polyscopoletin nanofilm to generate in one step MIP arrays. A single chip screening of essential synthesis parameters, including the surface density of the template peptide and its sequence led to MIPs with dissociation constants (K D) in the lower nanomolar range for RBD, which exceeds the affinity of RBD for its natural target, angiotensin-convertase 2 enzyme. Remarkably, the same MIPs bound SARS-CoV-2 virus like particles with even higher affinity along with excellent discrimination of influenza A (H3N2) virus. While MIPs prepared with a truncated heptapeptide template GFNCYFP showed only a slightly decreased affinity for RBD, a single mismatch in the amino acid sequence of the template, i.e. the substitution of the central cysteine with a serine, fully suppressed the RBD binding.
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Affiliation(s)
- Zsófia Bognár
- BME "Lendület" Chemical Nanosensors Research Group, Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics Szt. Gellért tér 4 1111 Budapest Hungary
| | - Eszter Supala
- BME "Lendület" Chemical Nanosensors Research Group, Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics Szt. Gellért tér 4 1111 Budapest Hungary
| | - Aysu Yarman
- Institute of Biochemistry and Biology, University of Potsdam Karl-Liebknecht-Str. 24-25 14476 Potsdam OT Golm Germany
| | - Xiaorong Zhang
- Institute of Biochemistry and Biology, University of Potsdam Karl-Liebknecht-Str. 24-25 14476 Potsdam OT Golm Germany
| | - Frank F Bier
- Institute of Biochemistry and Biology, University of Potsdam Karl-Liebknecht-Str. 24-25 14476 Potsdam OT Golm Germany
| | - Frieder W Scheller
- Institute of Biochemistry and Biology, University of Potsdam Karl-Liebknecht-Str. 24-25 14476 Potsdam OT Golm Germany
| | - Róbert E Gyurcsányi
- BME "Lendület" Chemical Nanosensors Research Group, Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics Szt. Gellért tér 4 1111 Budapest Hungary
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11
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Peter H, Mattig E, Guest PC, Bier FF. Lab-on-a-Chip Immunoassay for Prediction of Severe COVID-19 Disease. Methods Mol Biol 2022; 2511:235-244. [PMID: 35838964 DOI: 10.1007/978-1-0716-2395-4_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Most people infected by the SARS-CoV-2 virus which causes COVID-19 disease experience mild or no symptoms. Severe forms of the disease are often marked by a hyper-inflammatory response known as a cytokine storm. Thus, biomarker tests which can identify these patients and place them on the appropriate treatment regime at the earliest possible phase would help to improve outcomes. Here we describe an automated microarray-based immunoassay using the Fraunhofer lab-on-a-chip platform for analysis of C-reactive protein due to its role in the hyper-inflammatory response.
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Affiliation(s)
- Harald Peter
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany.
| | - Emily Mattig
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
| | - Paul C Guest
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Frank F Bier
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Institute of Molecular Diagnostics and Bioanalysis (IMDB gGmbH), Berlin, Germany
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12
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Holenya P, Lange PJ, Reimer U, Woltersdorf W, Panterodt T, Glas M, Wasner M, Eckey M, Drosch M, Hollidt J, Naumann M, Kern F, Wenschuh H, Lange R, Schnatbaum K, Bier FF. Peptide microarray-based analysis of antibody responses to SARS-CoV-2 identifies unique epitopes with potential for diagnostic test development. Eur J Immunol 2021; 51:1839-1849. [PMID: 33772767 PMCID: PMC8250065 DOI: 10.1002/eji.202049101] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/11/2021] [Accepted: 03/22/2021] [Indexed: 12/17/2022]
Abstract
Humoral immunity to the Severe Adult Respiratory Syndrome (SARS) Coronavirus (CoV)-2 is not fully understood yet but is a crucial factor of immune protection. The possibility of antibody cross-reactivity between SARS-CoV-2 and other human coronaviruses (HCoVs) would have important implications for immune protection but also for the development of specific diagnostic ELISA tests. Using peptide microarrays, n = 24 patient samples and n = 12 control samples were screened for antibodies against the entire SARS-CoV-2 proteome as well as the Spike (S), Nucleocapsid (N), VME1 (V), R1ab, and Protein 3a (AP3A) of the HCoV strains SARS, MERS, OC43, and 229E. While widespread cross-reactivity was revealed across several immunodominant regions of S and N, IgG binding to several SARS-CoV-2-derived peptides provided statistically significant discrimination between COVID-19 patients and controls. Selected target peptides may serve as capture antigens for future, highly COVID-19-specific diagnostic antibody tests.
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Affiliation(s)
| | - Paul Joris Lange
- Institute for Molecular Diagnostics and Bioanalysis‐IMDB gGmbHHennigsdorfGermany
- KH Labor GmbHBernburgGermany
- Medical FacultyInstitute of Experimental Internal MedicineOtto von Guericke UniversityMagdeburgGermany
- Institute for Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
| | - Ulf Reimer
- JPT Peptide Technologies GmbHBerlinGermany
| | | | | | | | | | | | | | - Jörg‐Michael Hollidt
- Institute for Molecular Diagnostics and Bioanalysis‐IMDB gGmbHHennigsdorfGermany
- in.vent GmbHHennigsdorfGermany
| | - Michael Naumann
- Medical FacultyInstitute of Experimental Internal MedicineOtto von Guericke UniversityMagdeburgGermany
| | - Florian Kern
- JPT Peptide Technologies GmbHBerlinGermany
- Department of Clinical and Experimental MedicineBrighton and Sussex Medical SchoolBrightonUK
| | | | - Robert Lange
- Institute for Molecular Diagnostics and Bioanalysis‐IMDB gGmbHHennigsdorfGermany
- KH Labor GmbHBernburgGermany
| | | | - Frank F. Bier
- Institute for Molecular Diagnostics and Bioanalysis‐IMDB gGmbHHennigsdorfGermany
- Institute for Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
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13
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Behm LVJ, Gerike S, Grauel MK, Uhlig K, Pfisterer F, Baumann W, Bier FF, Duschl C, Kirschbaum M. Micropatterned Thermoresponsive Cell Culture Substrates for Dynamically Controlling Neurite Outgrowth and Neuronal Connectivity in Vitro. ACS Appl Bio Mater 2019; 2:2853-2861. [DOI: 10.1021/acsabm.9b00246] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Laura V. J. Behm
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Potsdam IZI-BB, Am Muehlenberg 13, 14476 Potsdam, Germany
| | - Susanna Gerike
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Potsdam IZI-BB, Am Muehlenberg 13, 14476 Potsdam, Germany
| | - M. Katharina Grauel
- Institute of Neurophysiology, Charité-Universitätsmedizin, Charitéplatz 1, 10117 Berlin, Germany
| | - Katja Uhlig
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Potsdam IZI-BB, Am Muehlenberg 13, 14476 Potsdam, Germany
| | - Felix Pfisterer
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Potsdam IZI-BB, Am Muehlenberg 13, 14476 Potsdam, Germany
| | - Werner Baumann
- Chair for Biophysics, University of Rostock, Gertrudenstr. 11a, 18057 Rostock, Germany
| | - Frank F. Bier
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Potsdam IZI-BB, Am Muehlenberg 13, 14476 Potsdam, Germany
| | - Claus Duschl
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Potsdam IZI-BB, Am Muehlenberg 13, 14476 Potsdam, Germany
| | - Michael Kirschbaum
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Potsdam IZI-BB, Am Muehlenberg 13, 14476 Potsdam, Germany
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14
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Kersting S, Rausch V, Bier FF, von Nickisch-Rosenegk M. A recombinase polymerase amplification assay for the diagnosis of atypical pneumonia. Anal Biochem 2018; 550:54-60. [DOI: 10.1016/j.ab.2018.04.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 04/11/2018] [Accepted: 04/12/2018] [Indexed: 12/15/2022]
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15
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Soria J, Acera A, Merayo-LLoves J, Durán JA, González N, Rodriguez S, Bistolas N, Schumacher S, Bier FF, Peter H, Stöcklein W, Suárez T. Tear proteome analysis in ocular surface diseases using label-free LC-MS/MS and multiplexed-microarray biomarker validation. Sci Rep 2017. [PMID: 29234088 PMCID: PMC5727318 DOI: 10.1038/s41598-017-17536-2 10.1038/s41598-017-17536-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
We analyzed the tear film proteome of patients with dry eye (DE), meibomian gland dysfunction (MGD), and normal volunteers (CT). Tear samples were collected from 70 individuals. Of these, 37 samples were analyzed using spectral-counting-based LC-MS/MS label-free quantitation, and 33 samples were evaluated in the validation of candidate biomarkers employing customized antibody microarray assays. Comparative analysis of tear protein profiles revealed differences in the expression levels of 26 proteins, including protein S100A6, annexin A1, cystatin-S, thioredoxin, phospholipase A2, antileukoproteinase, and lactoperoxidase. Antibody microarray validation of CST4, S100A6, and MMP9 confirmed the accuracy of previously reported ELISA assays, with an area under ROC curve (AUC) of 87.5%. Clinical endpoint analysis showed a good correlation between biomarker concentrations and clinical parameters. In conclusion, different sets of proteins differentiate between the groups. Apolipoprotein D, S100A6, S100A8, and ceruloplasmin discriminate best between the DE and CT groups. The differences between antileukoproteinase, phospholipase A2, and lactoperoxidase levels allow the distinction between MGD and DE, and the changes in the levels of annexin A1, clusterin, and alpha-1-acid glycoprotein 1, between MGD and CT groups. The functional network analysis revealed the main biological processes that should be examined to identify new candidate biomarkers and therapeutic targets.
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Affiliation(s)
- Javier Soria
- Bioftalmik Applied Research, Bizkaia Science and Technology Park, Building 612, E-48160, Derio, Bizkaia, Spain
| | - Arantxa Acera
- Bioftalmik Applied Research, Bizkaia Science and Technology Park, Building 612, E-48160, Derio, Bizkaia, Spain
| | - Jesús Merayo-LLoves
- Instituto Universitario Fernández-Vega, Avda Dres Fernández-Vega num 34, Oviedo, E-33012, Principado de Asturias, Spain
| | - Juan A Durán
- Instituto Clínico Quirúrgico de Oftalmología (ICQO), Virgen de Begoña N° 34, E-48006, Bilbao, Bizkaia, Spain.,Department of Ophthalmology, School of Medicine, University of the Basque Country (UPV/EHU), Leioa, Bizkaia, Spain
| | - Nerea González
- Bioftalmik Applied Research, Bizkaia Science and Technology Park, Building 612, E-48160, Derio, Bizkaia, Spain
| | - Sandra Rodriguez
- Bioftalmik Applied Research, Bizkaia Science and Technology Park, Building 612, E-48160, Derio, Bizkaia, Spain
| | - Nikitas Bistolas
- Department of automatization, Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses, Am Muehlenberg 13, 14476, Potsdam-Golm, Germany
| | - Soeren Schumacher
- Department of automatization, Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses, Am Muehlenberg 13, 14476, Potsdam-Golm, Germany
| | - Frank F Bier
- Department of automatization, Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses, Am Muehlenberg 13, 14476, Potsdam-Golm, Germany
| | - Harald Peter
- Department of automatization, Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses, Am Muehlenberg 13, 14476, Potsdam-Golm, Germany
| | - Walter Stöcklein
- Department of automatization, Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses, Am Muehlenberg 13, 14476, Potsdam-Golm, Germany
| | - Tatiana Suárez
- Bioftalmik Applied Research, Bizkaia Science and Technology Park, Building 612, E-48160, Derio, Bizkaia, Spain.
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16
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Soria J, Acera A, Merayo-LLoves J, Durán JA, González N, Rodriguez S, Bistolas N, Schumacher S, Bier FF, Peter H, Stöcklein W, Suárez T. Tear proteome analysis in ocular surface diseases using label-free LC-MS/MS and multiplexed-microarray biomarker validation. Sci Rep 2017; 7:17478. [PMID: 29234088 PMCID: PMC5727318 DOI: 10.1038/s41598-017-17536-2] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 11/20/2017] [Indexed: 12/02/2022] Open
Abstract
We analyzed the tear film proteome of patients with dry eye (DE), meibomian gland dysfunction (MGD), and normal volunteers (CT). Tear samples were collected from 70 individuals. Of these, 37 samples were analyzed using spectral-counting-based LC-MS/MS label-free quantitation, and 33 samples were evaluated in the validation of candidate biomarkers employing customized antibody microarray assays. Comparative analysis of tear protein profiles revealed differences in the expression levels of 26 proteins, including protein S100A6, annexin A1, cystatin-S, thioredoxin, phospholipase A2, antileukoproteinase, and lactoperoxidase. Antibody microarray validation of CST4, S100A6, and MMP9 confirmed the accuracy of previously reported ELISA assays, with an area under ROC curve (AUC) of 87.5%. Clinical endpoint analysis showed a good correlation between biomarker concentrations and clinical parameters. In conclusion, different sets of proteins differentiate between the groups. Apolipoprotein D, S100A6, S100A8, and ceruloplasmin discriminate best between the DE and CT groups. The differences between antileukoproteinase, phospholipase A2, and lactoperoxidase levels allow the distinction between MGD and DE, and the changes in the levels of annexin A1, clusterin, and alpha-1-acid glycoprotein 1, between MGD and CT groups. The functional network analysis revealed the main biological processes that should be examined to identify new candidate biomarkers and therapeutic targets.
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Affiliation(s)
- Javier Soria
- Bioftalmik Applied Research, Bizkaia Science and Technology Park, Building 612, E-48160, Derio, Bizkaia, Spain
| | - Arantxa Acera
- Bioftalmik Applied Research, Bizkaia Science and Technology Park, Building 612, E-48160, Derio, Bizkaia, Spain
| | - Jesús Merayo-LLoves
- Instituto Universitario Fernández-Vega, Avda Dres Fernández-Vega num 34, Oviedo, E-33012, Principado de Asturias, Spain
| | - Juan A Durán
- Instituto Clínico Quirúrgico de Oftalmología (ICQO), Virgen de Begoña N° 34, E-48006, Bilbao, Bizkaia, Spain.,Department of Ophthalmology, School of Medicine, University of the Basque Country (UPV/EHU), Leioa, Bizkaia, Spain
| | - Nerea González
- Bioftalmik Applied Research, Bizkaia Science and Technology Park, Building 612, E-48160, Derio, Bizkaia, Spain
| | - Sandra Rodriguez
- Bioftalmik Applied Research, Bizkaia Science and Technology Park, Building 612, E-48160, Derio, Bizkaia, Spain
| | - Nikitas Bistolas
- Department of automatization, Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses, Am Muehlenberg 13, 14476, Potsdam-Golm, Germany
| | - Soeren Schumacher
- Department of automatization, Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses, Am Muehlenberg 13, 14476, Potsdam-Golm, Germany
| | - Frank F Bier
- Department of automatization, Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses, Am Muehlenberg 13, 14476, Potsdam-Golm, Germany
| | - Harald Peter
- Department of automatization, Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses, Am Muehlenberg 13, 14476, Potsdam-Golm, Germany
| | - Walter Stöcklein
- Department of automatization, Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses, Am Muehlenberg 13, 14476, Potsdam-Golm, Germany
| | - Tatiana Suárez
- Bioftalmik Applied Research, Bizkaia Science and Technology Park, Building 612, E-48160, Derio, Bizkaia, Spain.
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17
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Fischbach J, Loh Q, Bier FF, Lim TS, Frohme M, Glökler J. Alizarin Red S for Online Pyrophosphate Detection Identified by a Rapid Screening Method. Sci Rep 2017; 7:45085. [PMID: 28338022 PMCID: PMC5364467 DOI: 10.1038/srep45085] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 02/20/2017] [Indexed: 12/29/2022] Open
Abstract
We identified Alizarin Red S and other well known fluorescent dyes useful for the online detection of pyrophosphate in enzymatic assays, including the loop mediated isothermal amplification (LAMP) and polymerase chain reaction (PCR) assays. An iterative screening was used for a selected set of compounds to first secure enzyme compatibility, evaluate inorganic pyrophosphate sensitivity in the presence of manganese as quencher and optimize conditions for an online detection. Of the selected dyes, the inexpensive alizarin red S was found to selectively detect pyrophosphate under LAMP and PCR conditions and is superior with respect to its defined red-shifted spectrum, long shelf life and low toxicity. In addition, the newly identified properties may also be useful in other enzymatic assays which do not generate nucleic acids but are based on inorganic pyrophosphate. Finally, we propose that our screening method may provide a blueprint for rapid screening of compounds for detecting inorganic pyrophosphate.
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Affiliation(s)
- Jens Fischbach
- Division Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany
| | - Qiuting Loh
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Frank F. Bier
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476 Potsdam, Germany
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Marcus Frohme
- Division Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany
| | - Jörn Glökler
- Division Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany
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18
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Abstract
Lab-on-a-chip multiplex assays allow a rapid identification of multiple parameters in an automated manner. Here we describe a lab-based preparation followed by a rapid and fully automated DNA microarray hybridization and readout in less than 10 min using the Fraunhofer in vitro diagnostics (ivD) platform to enable rapid identification of bacterial species and detection of antibiotic resistance. The use of DNA microarrays allows a fast adaptation of new biomarkers enabling the identification of different genes as well as single-nucleotide-polymorphisms (SNPs) within these genes. In this protocol we describe a DNA microarray developed for identification of Staphylococcus aureus and the mecA resistance gene.
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Affiliation(s)
- Harald Peter
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany.
| | - Julia Wienke
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Frank F Bier
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
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19
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Memczak H, Lauster D, Kar P, Di Lella S, Volkmer R, Knecht V, Herrmann A, Ehrentreich-Förster E, Bier FF, Stöcklein WFM. Anti-Hemagglutinin Antibody Derived Lead Peptides for Inhibitors of Influenza Virus Binding. PLoS One 2016; 11:e0159074. [PMID: 27415624 PMCID: PMC4944999 DOI: 10.1371/journal.pone.0159074] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 06/27/2016] [Indexed: 12/23/2022] Open
Abstract
Antibodies against spike proteins of influenza are used as a tool for characterization of viruses and therapeutic approaches. However, development, production and quality control of antibodies is expensive and time consuming. To circumvent these difficulties, three peptides were derived from complementarity determining regions of an antibody heavy chain against influenza A spike glycoprotein. Their binding properties were studied experimentally, and by molecular dynamics simulations. Two peptide candidates showed binding to influenza A/Aichi/2/68 H3N2. One of them, termed PeB, with the highest affinity prevented binding to and infection of target cells in the micromolar region without any cytotoxic effect. PeB matches best the conserved receptor binding site of hemagglutinin. PeB bound also to other medical relevant influenza strains, such as human-pathogenic A/California/7/2009 H1N1, and avian-pathogenic A/Mute Swan/Rostock/R901/2006 H7N1. Strategies to improve the affinity and to adapt specificity are discussed and exemplified by a double amino acid substituted peptide, obtained by substitutional analysis. The peptides and their derivatives are of great potential for drug development as well as biosensing.
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Affiliation(s)
- Henry Memczak
- Department of Bioanalytics and Biosensorics, Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses, Potsdam, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Daniel Lauster
- Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Parimal Kar
- Department of Theory and Bio-Systems, Max-Planck-Institute of Colloids and Interfaces, Potsdam, Germany
| | - Santiago Di Lella
- Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
- Departamento de Química Biológica e IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | | | - Volker Knecht
- Department of Theory and Bio-Systems, Max-Planck-Institute of Colloids and Interfaces, Potsdam, Germany
| | - Andreas Herrmann
- Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Eva Ehrentreich-Förster
- Department of Bioanalytics and Biosensorics, Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses, Potsdam, Germany
| | - Frank F. Bier
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Department of Biosystem Integration and Automation, Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses, Potsdam, Germany
| | - Walter F. M. Stöcklein
- Department of Bioanalytics and Biosensorics, Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses, Potsdam, Germany
- * E-mail:
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20
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Laux EM, Knigge X, Bier FF, Wenger C, Hölzel R. Aligned Immobilization of Proteins Using AC Electric Fields. Small 2016; 12:1514-1520. [PMID: 26779699 DOI: 10.1002/smll.201503052] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 12/01/2015] [Indexed: 06/05/2023]
Abstract
Protein molecules are aligned and immobilized from solution by AC electric fields. In a single-step experiment, the enhanced green fluorescent proteins are immobilized on the surface as well as at the edges of planar nanoelectrodes. Alignment is found to follow the molecules' geometrical shape with their longitudinal axes parallel to the electric field. Simultaneous dielectrophoretic attraction and AC electroosmotic flow are identified as the dominant forces causing protein movement and alignment. Molecular orientation is determined by fluorescence microscopy based on polarized excitation of the proteins' chromophores. The chromophores' orientation with respect to the whole molecule supports X-ray crystal data.
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Affiliation(s)
- Eva-Maria Laux
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476, Potsdam-Golm, Germany
| | - Xenia Knigge
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476, Potsdam-Golm, Germany
| | - Frank F Bier
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476, Potsdam-Golm, Germany
| | - Christian Wenger
- IHP GmbH-Leibniz Institute for Innovative Microelectronics, Im Technologiepark 25, 15235, Frankfurt/Oder, Germany
| | - Ralph Hölzel
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476, Potsdam-Golm, Germany
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21
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Connor DO, Zantow J, Hust M, Bier FF, von Nickisch-Rosenegk M. Identification of Novel Immunogenic Proteins of Neisseria gonorrhoeae by Phage Display. PLoS One 2016; 11:e0148986. [PMID: 26859666 PMCID: PMC4747489 DOI: 10.1371/journal.pone.0148986] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 01/26/2016] [Indexed: 12/14/2022] Open
Abstract
Neisseria gonorrhoeae is one of the most prevalent sexually transmitted diseases worldwide with more than 100 million new infections per year. A lack of intense research over the last decades and increasing resistances to the recommended antibiotics call for a better understanding of gonococcal infection, fast diagnostics and therapeutic measures against N. gonorrhoeae. Therefore, the aim of this work was to identify novel immunogenic proteins as a first step to advance those unresolved problems. For the identification of immunogenic proteins, pHORF oligopeptide phage display libraries of the entire N. gonorrhoeae genome were constructed. Several immunogenic oligopeptides were identified using polyclonal rabbit antibodies against N. gonorrhoeae. Corresponding full-length proteins of the identified oligopeptides were expressed and their immunogenic character was verified by ELISA. The immunogenic character of six proteins was identified for the first time. Additional 13 proteins were verified as immunogenic proteins in N. gonorrhoeae.
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Affiliation(s)
- Daniel O. Connor
- Department of Bioanalytics and Biosensorics, Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
| | - Jonas Zantow
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Michael Hust
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Frank F. Bier
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Department of Biosystem Integration and Automation, Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
| | - Markus von Nickisch-Rosenegk
- Department of Bioanalytics and Biosensorics, Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
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22
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Georgi V, Georgi L, Blechert M, Bergmeister M, Zwanzig M, Wüstenhagen DA, Bier FF, Jung E, Kubick S. On-chip automation of cell-free protein synthesis: new opportunities due to a novel reaction mode. Lab Chip 2016; 16:269-81. [PMID: 26554896 DOI: 10.1039/c5lc00700c] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Many pharmaceuticals are proteins or their development is based on proteins. Cell-free protein synthesis (CFPS) is an innovative alternative to conventional cell based systems which enables the production of proteins with complex and even new characteristics. However, the short lifetime, low protein production and expensive reagent costs are still limitations of CFPS. Novel automated microfluidic systems might allow continuous, controllable and resource conserving CFPS. The presented microfluidic TRITT platform (TRITT for Transcription - RNA Immobilization & Transfer - Translation) addresses the individual biochemical requirements of the transcription and the translation step of CFPS in separate compartments, and combines the reaction steps by quasi-continuous transfer of RNA templates to enable automated CFPS. In detail, specific RNA templates with 5' and 3' hairpin structures for stabilization against nucleases were immobilized during in vitro transcription by newly designed and optimized hybridization oligonucleotides coupled to magnetizable particles. Transcription compatibility and reusability for immobilization of these functionalized particles was successfully proven. mRNA transfer was realized on-chip by magnetic actuated particle transfer, RNA elution and fluid flow to the in vitro translation compartment. The applicability of the microfluidic TRITT platform for the production of the cytotoxic protein Pierisin with simultaneous incorporation of a non-canonical amino acid for fluorescence labeling was demonstrated. The new reaction mode (TRITT mode) is a modified linked mode that fulfills the precondition for an automated modular reactor system. By continual transfer of new mRNA, the novel procedure overcomes problems caused by nuclease digestion and hydrolysis of mRNA during TL in standard CFPS reactions.
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Affiliation(s)
- V Georgi
- Fraunhofer Institute for Reliability Microintegration, Department System Integration & Interconnection Technologies, Working Group Medical Microystems, Berlin, Germany. and Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB), Potsdam, Germany.
| | - L Georgi
- Technische Universität Berlin, Faculty Electrical Engineering Computer Science, Microperipheric Technologies, Berlin, Germany
| | - M Blechert
- Fraunhofer Institute for Reliability Microintegration, Department System Integration & Interconnection Technologies, Working Group Medical Microystems, Berlin, Germany.
| | - M Bergmeister
- Fraunhofer Institute for Reliability Microintegration, Department System Integration & Interconnection Technologies, Working Group Medical Microystems, Berlin, Germany.
| | - M Zwanzig
- Technische Universität Berlin, Faculty Electrical Engineering Computer Science, Microperipheric Technologies, Berlin, Germany
| | - D A Wüstenhagen
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB), Potsdam, Germany.
| | - F F Bier
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB), Potsdam, Germany.
| | - E Jung
- Fraunhofer Institute for Reliability Microintegration, Department System Integration & Interconnection Technologies, Working Group Medical Microystems, Berlin, Germany.
| | - S Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB), Potsdam, Germany.
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Laux EM, Knigge X, Bier FF, Wenger C, Hölzel R. Dielectrophoretic immobilization of proteins: Quantification by atomic force microscopy. Electrophoresis 2015; 36:2094-101. [DOI: 10.1002/elps.201500108] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 04/29/2015] [Accepted: 05/02/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Eva-Maria Laux
- Fraunhofer Institute for Cell Therapy and Immunology; Branch Bioanalytics and Bioprocesses (IZI-BB); Potsdam-Golm Germany
| | - Xenia Knigge
- Fraunhofer Institute for Cell Therapy and Immunology; Branch Bioanalytics and Bioprocesses (IZI-BB); Potsdam-Golm Germany
| | - Frank F. Bier
- Fraunhofer Institute for Cell Therapy and Immunology; Branch Bioanalytics and Bioprocesses (IZI-BB); Potsdam-Golm Germany
| | - Christian Wenger
- IHP GmbH-Leibniz Institute for Innovative Microelectronics; Frankfurt (Oder) Germany
| | - Ralph Hölzel
- Fraunhofer Institute for Cell Therapy and Immunology; Branch Bioanalytics and Bioprocesses (IZI-BB); Potsdam-Golm Germany
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Tan C, Schenk JA, Gajovic-Eichelmann N, Sellrie F, Bier FF. A new one-step antigen heterologous homogeneous fluorescence immunoassay for progesterone detection in serum. Talanta 2015; 134:508-513. [DOI: 10.1016/j.talanta.2014.11.062] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 11/24/2014] [Accepted: 11/28/2014] [Indexed: 11/29/2022]
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Jeenduang N, Porntadavity S, von Nickisch-Rosenegk M, Bier FF, Promptmas C. Two-dye based arrayed primer extension for simultaneous multigene detection in lipid metabolism. Clin Chim Acta 2015; 442:36-43. [PMID: 25591965 DOI: 10.1016/j.cca.2015.01.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 01/08/2015] [Accepted: 01/08/2015] [Indexed: 01/24/2023]
Abstract
BACKGROUND Cardiovascular disease (CVD) is one of the major causes of death worldwide. Numerous genetic risk factors in lipid metabolism, including mutations of LDLR, APOB, and PCSK9, as well as polymorphisms of CETP and APOE, have been found to associate with CVD. METHODS In this study, a two-dye based arrayed primer extension (APEX) microarray assay for simultaneous multigene (LDLR, APOB, PCSK9, CETP, and APOE) detection was developed. The DNA templates, originating from 1 DNA sample of known genotype and 7 blind DNA samples, were amplified by uniplex PCR. RESULTS Optimized conditions for the APEX reaction were determined to include a hybridization temperature of 55°C and a DNA template size of 50-150bp. The total assay including PCR, purification, fragmentation, APEX reaction, and image analysis could be performed in 6h. In total, 48 genotypes were identified among 8 individual DNA samples by APEX analysis. CONCLUSIONS The data suggest that this APEX microarray offers a robust, fast, and versatile option for screening these genotypes in hypercholesterolemia patients.
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Affiliation(s)
- Nutjaree Jeenduang
- School of Allied Health Science and Public Health, Walailak University, Nakhon Si Thammarat 80161, Thailand; Department of Nanobiotechnology and Nanomedicine, Fraunhofer Institute for Biomedical Engineering (IBMT), Potsdam-Golm 14476, Germany
| | - Sureerut Porntadavity
- Department of Clinical Chemistry, Faculty of Medical Technology, Mahidol University, Nakhon Pathom 73170, Thailand
| | - Markus von Nickisch-Rosenegk
- Department of Nanobiotechnology and Nanomedicine, Fraunhofer Institute for Biomedical Engineering (IBMT), Potsdam-Golm 14476, Germany
| | - Frank F Bier
- Department of Nanobiotechnology and Nanomedicine, Fraunhofer Institute for Biomedical Engineering (IBMT), Potsdam-Golm 14476, Germany
| | - Chamras Promptmas
- Department of Biomedical Engineering, Faculty of Engineering, Mahidol University, Nakhon Pathom 73170, Thailand.
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26
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Abstract
Einleitung
Sowohl demografische Entwicklungen als auch neue Erkenntnisse in der molekularen Medizin stellen an die Biosensorik hohe Anforderungen. in vitro-Diagnostik muss schnell, personalisiert und nah am Ort der Probenentnahme geschehen, um den Therapieerfolg einhergehend mit Kostenersparnis und einer höheren Lebensqualität für den Patienten sicherzustellen. Somit müssen neue Wege beschritten werden, die ein Höchstmaß an transdisziplinärem Denken und Handeln fordern wie etwa bei der Konvergenz etablierter Technologien oder der vollständigen Integration aller (Prozess- und Analytik-) Komponenten.
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Affiliation(s)
- Frank F. Bier
- ⁎ Frank F. Bier Fraunhofer-Institut für Biomedizinische Technik Institutsteil Potsdam und Institut für Biochemie und Biologie der Universität Potsdam Am Mühlenberg 13 14476 Potsdam-Golm
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27
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Tanne J, Kracher D, Dietzel B, Schulz B, Ludwig R, Lisdat F, Scheller FW, Bier FF. Carboxylated or aminated polyaniline-multiwalled carbon nanotubes nanohybrids for immobilization of cellobiose dehydrogenase on gold electrodes. Biosensors (Basel) 2014; 4:370-86. [PMID: 25587429 PMCID: PMC4287708 DOI: 10.3390/bios4040370] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/18/2014] [Accepted: 10/14/2014] [Indexed: 11/23/2022]
Abstract
Polymer-multiwalled carbon nanotube (MWCNT) nanohybrids, which differ in surface charge have been synthesized to study the bioelectrocatalysis of adsorbed cellobiose dehydrogenase (CDH) from Phanerochaete sordida on gold electrodes. To obtain negatively charged nanohybrids, poly(3-amino-4-methoxybenzoic acid-co-aniline) (P(AMB-A)) was covalently linked to the surface of MWCNTs while modification with p-phenylenediamine (PDA) converted the COOH-groups to positively charged amino groups. Fourier transform infrared spectroscopy (FTIR) measurements verified the p-phenylenediamine (PDA) modification of the polymer-CNT nanohybrids. The positively charged nanohybrid MWCNT-P(AMB-A)-PDA promoted direct electron transfer (DET) of CDH to the electrode and bioelectrocatalysis of lactose was observed. Amperometric measurements gave an electrochemical response with KMapp = 8.89 mM and a current density of 410 nA/cm(2) (15 mM lactose). The catalytic response was tested at pH 3.5 and 4.5. Interference by ascorbic acid was not observed. The study proves that DET between the MWCNT-P(AMB-A)-PDA nanohybrids and CDH is efficient and allows the sensorial detection of lactose.
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Affiliation(s)
- Johannes Tanne
- Fraunhofer Institute for Cell Therapy and Immunology (IZI-BB), Branch Bioanalytics and Bioprocesses Potsdam-Golm, Am Mühlenberg 13, 14476 Potsdam, Germany; E-Mail:
| | - Daniel Kracher
- Food Biotechnology Laboratory, Department of Food Sciences and Technology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria; E-Mails: (D.K.); (R.L.)
| | - Birgit Dietzel
- Institute for Thin Film and Microsensoric Technology, Kantstr. 55, 14513 Teltow, Germany; E-Mails: (B.D.); (B.S.)
| | - Burkhard Schulz
- Institute for Thin Film and Microsensoric Technology, Kantstr. 55, 14513 Teltow, Germany; E-Mails: (B.D.); (B.S.)
| | - Roland Ludwig
- Food Biotechnology Laboratory, Department of Food Sciences and Technology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria; E-Mails: (D.K.); (R.L.)
| | - Fred Lisdat
- Biosystems Technology, Institute of Applied Life Sciences, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany; E-Mail:
| | - Frieder W Scheller
- Fraunhofer Institute for Cell Therapy and Immunology (IZI-BB), Branch Bioanalytics and Bioprocesses Potsdam-Golm, Am Mühlenberg 13, 14476 Potsdam, Germany; E-Mail:
| | - Frank F Bier
- Fraunhofer Institute for Cell Therapy and Immunology (IZI-BB), Branch Bioanalytics and Bioprocesses Potsdam-Golm, Am Mühlenberg 13, 14476 Potsdam, Germany; E-Mail:
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Hüttl C, Hettrich C, Riedel M, Henklein P, Rawel H, Bier FF. Development of Peptidyl Lysine Dendrons: 1,3-Dipolar Cycloaddition for Peptide Coupling and Antibody Recognition. Chem Biol Drug Des 2014; 85:565-73. [DOI: 10.1111/cbdd.12444] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 08/20/2014] [Accepted: 09/12/2014] [Indexed: 01/16/2023]
Affiliation(s)
- Christine Hüttl
- Fraunhofer Institute for Cell Therapy and Immunology; Branch Bioanalytics and Bioprocesses (Fraunhofer IZI-BB); Am Mühlenberg 13 Potsdam 14476 Germany
- Institute for Biochemistry und Biology; University of Potsdam; Maulbeerallee 2 Potsdam 14469 Germany
| | - Cornelia Hettrich
- Fraunhofer Institute for Cell Therapy and Immunology; Branch Bioanalytics and Bioprocesses (Fraunhofer IZI-BB); Am Mühlenberg 13 Potsdam 14476 Germany
| | - Melanie Riedel
- Fraunhofer Institute for Cell Therapy and Immunology; Branch Bioanalytics and Bioprocesses (Fraunhofer IZI-BB); Am Mühlenberg 13 Potsdam 14476 Germany
| | - Petra Henklein
- Institute of Biochemistry; Charité - Universitätsmedizin Berlin; Virchowweg 6 Berlin 10117 Germany
| | - Harshadrai Rawel
- Institute of Nutritional Sciences; University of Potsdam; Arthur-Scheunert-Allee 114-116 Nuthetal 14558 Germany
| | - Frank F. Bier
- Fraunhofer Institute for Cell Therapy and Immunology; Branch Bioanalytics and Bioprocesses (Fraunhofer IZI-BB); Am Mühlenberg 13 Potsdam 14476 Germany
- Institute for Biochemistry und Biology; University of Potsdam; Maulbeerallee 2 Potsdam 14469 Germany
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Hoppe S, Bier FF, von Nickisch-Rosenegk M. Identification of antigenic proteins of the nosocomial pathogen Klebsiella pneumoniae. PLoS One 2014; 9:e110703. [PMID: 25333280 PMCID: PMC4205017 DOI: 10.1371/journal.pone.0110703] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 09/24/2014] [Indexed: 12/17/2022] Open
Abstract
The continuous expansion of nosocomial infections around the globe has become a precarious situation. Key challenges include mounting dissemination of multiple resistances to antibiotics, the easy transmission and the growing mortality rates of hospital-acquired bacterial diseases. Thus, new ways to rapidly detect these infections are vital. Consequently, researchers around the globe pursue innovative approaches for point-of-care devices. In many cases the specific interaction of an antigen and a corresponding antibody is pivotal. However, the knowledge about suitable antigens is lacking. The aim of this study was to identify novel antigens as specific diagnostic markers. Additionally, these proteins might be aptly used for the generation of vaccines to improve current treatment options. Hence, a cDNA-based expression library was constructed and screened via microarrays to detect novel antigens of Klebsiella pneumoniae, a prominent agent of nosocomial infections well-known for its extensive antibiotics resistance, especially by extended-spectrum beta-lactamases (ESBL). After screening 1536 clones, 14 previously unknown immunogenic proteins were identified. Subsequently, each protein was expressed in full-length and its immunodominant character examined by ELISA and microarray analyses. Consequently, six proteins were selected for epitope mapping and three thereof possessed linear epitopes. After specificity analysis, homology survey and 3d structural modelling, one epitope sequence GAVVALSTTFA of KPN_00363, an ion channel protein, was identified harboring specificity for K. pneumoniae. The remaining epitopes showed ambiguous results regarding the specificity for K. pneumoniae. The approach adopted herein has been successfully utilized to discover novel antigens of Campylobacter jejuni and Salmonella enterica antigens before. Now, we have transferred this knowledge to the key nosocomial agent, K. pneumoniae. By identifying several novel antigens and their linear epitope sites, we have paved the way for crucial future research and applications including the design of point-of-care devices, vaccine development and serological screenings for a highly relevant nosocomial pathogen.
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Affiliation(s)
- Sebastian Hoppe
- Department of Bioanalytics and Biosensorics, Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
| | - Frank F. Bier
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Department of Biosystem Integration and Automation, Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocess (IZI-BB), Potsdam, Germany
| | - Markus von Nickisch-Rosenegk
- Department of Bioanalytics and Biosensorics, Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
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30
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Hovestädt M, Memczak H, Pleiner D, Zhang X, Rappich J, Bier FF, Stöcklein WFM. Characterization of a new maleimido functionalization of gold for surface plasmon resonance spectroscopy. J Mol Recognit 2014; 27:707-13. [PMID: 25319618 DOI: 10.1002/jmr.2396] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 05/16/2014] [Accepted: 05/16/2014] [Indexed: 11/06/2022]
Abstract
Para-maleimidophenyl (p-MP) modified gold surfaces have been prepared by one-step electrochemical deposition and used in surface plasmon resonance (SPR) studies. Therefore, a FITC mimotope peptide (MP1, 12 aa), a human mucin 1 epitope peptide (MUC, 9 aa) and a protein with their specific antibodies were used as model systems. The peptides were modified with an N-terminal cysteine for covalent and directed coupling to the maleimido functionalized surface by means of Michael addition. The coupling yield of the peptide, the binding characteristics of antibody and the unspecific adsorption of the analytes were investigated. The results expand the spectrum of biosensors usable with p-MP by widely used SPR and support its potential to be versatile for several electrochemical and optical biosensors. This allows the combination of an electrochemical and optical read-out for a broad variety of biomolecular interactions on the same chip.
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Affiliation(s)
- Marc Hovestädt
- Fraunhofer Institute for Biomedical Engineering IBMT, Branch Potsdam, Department of Molecular Bioanalytics and Bioelectronics, Am Mühlenberg 13, 14476, Potsdam, Germany; University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Straße 24/25, 14476, Potsdam, Germany
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31
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Rapsch K, Bier FF, von Nickisch-Rosenegk M. Rational design of artificial β-strand-forming antimicrobial peptides with biocompatible properties. Mol Pharm 2014; 11:3492-502. [PMID: 25192319 DOI: 10.1021/mp500271c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Because the intensive use of antibiotics has led to a large variety of resistant bacterial strains, therapeutic measures have become increasingly challenging. In order to ensure reliable treatment of diseases, alternative antimicrobial agents need to be explored. In this context, antimicrobial peptides have been discussed as novel bioactive molecules, which, however, may be limited in their applicability due to their high manufacturing costs and poor pharmacokinetic properties. Consequently, the design of artificial antimicrobial peptides featuring two flanking cationic regions and a hydrophobic center is presented. These sequences led to distinct antimicrobial activity on the same order of magnitude as that of naturally occurring reference peptides but with less cytotoxic or cytostatic drawbacks. Furthermore, a deletion and substitution library revealed the minimal sequence requirements. By analysis of the computed 3D structures of these peptides, a single characteristic β-strand was identified. This structural motif was pivotal for antimicrobial activity. Consequently, an optimized peptide sequence with antimicrobial and biocompatible properties was derived, and its application was demonstrated in a mixed culture experiment. Thus, it was shown that the optimized artificial antimicrobial peptide is suitable as a therapeutic agent and may be used as template for the development of new antimicrobial peptides with unique secondary structures.
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Affiliation(s)
- Karsten Rapsch
- Fraunhofer Institute for Biomedical Engineering IBMT , Branch Potsdam, Am Muehlenberg 13, 14476 Potsdam, Germany
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32
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Dechtrirat D, Gajovic-Eichelmann N, Wojcik F, Hartmann L, Bier FF, Scheller FW. Electrochemical displacement sensor based on ferrocene boronic acid tracer and immobilized glycan for saccharide binding proteins and E. coli. Biosens Bioelectron 2014; 58:1-8. [DOI: 10.1016/j.bios.2014.02.028] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 02/11/2014] [Accepted: 02/11/2014] [Indexed: 02/07/2023]
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Scheller FW, Yarman A, Bachmann T, Hirsch T, Kubick S, Renneberg R, Schumacher S, Wollenberger U, Teller C, Bier FF. Future of biosensors: a personal view. Adv Biochem Eng Biotechnol 2014; 140:1-28. [PMID: 24196315 DOI: 10.1007/10_2013_251] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Biosensors representing the technological counterpart of living senses have found routine application in amperometric enzyme electrodes for decentralized blood glucose measurement, interaction analysis by surface plasmon resonance in drug development, and to some extent DNA chips for expression analysis and enzyme polymorphisms. These technologies have already reached a highly advanced level and need minor improvement at most. The dream of the "100-dollar" personal genome may come true in the next few years provided that the technological hurdles of nanopore technology or of polymerase-based single molecule sequencing can be overcome. Tailor-made recognition elements for biosensors including membrane-bound enzymes and receptors will be prepared by cell-free protein synthesis. As alternatives for biological recognition elements, molecularly imprinted polymers (MIPs) have been created. They have the potential to substitute antibodies in biosensors and biochips for the measurement of low-molecular-weight substances, proteins, viruses, and living cells. They are more stable than proteins and can be produced in large amounts by chemical synthesis. Integration of nanomaterials, especially of graphene, could lead to new miniaturized biosensors with high sensitivity and ultrafast response. In the future individual therapy will include genetic profiling of isoenzymes and polymorphic forms of drug-metabolizing enzymes especially of the cytochrome P450 family. For defining the pharmacokinetics including the clearance of a given genotype enzyme electrodes will be a useful tool. For decentralized online patient control or the integration into everyday "consumables" such as drinking water, foods, hygienic articles, clothing, or for control of air conditioners in buildings and cars and swimming pools, a new generation of "autonomous" biosensors will emerge.
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Affiliation(s)
- Frieder W Scheller
- Fraunhofer Institute for Biomedical Engineering IBMT, 14476, Potsdam, Germany,
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34
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Füllbrandt M, Ermilova E, Asadujjaman A, Hölzel R, Bier FF, von Klitzing R, Schönhals A. Dynamics of Linear Poly(N-isopropylacrylamide) in Water around the Phase Transition Investigated by Dielectric Relaxation Spectroscopy. J Phys Chem B 2014; 118:3750-9. [DOI: 10.1021/jp501325x] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marieke Füllbrandt
- BAM
Bundesanstalt für Materialforschung und -prüfung, Unter den Eichen 87, 12205 Berlin, Germany
- Stranski-Laboratorium
für Physikalische und Theoretische Chemie/Institut für
Chemie, Technische Universität Berlin, Straße des 17. Juni 124, 10623 Berlin, Germany
| | - Elena Ermilova
- Fraunhofer-Institut
für Biomedizinische Technik IBMT, Institutsteil Potsdam-Golm, Am Mühlenberg 13, 14476 Potsdam-Golm, Germany
| | - Asad Asadujjaman
- BAM
Bundesanstalt für Materialforschung und -prüfung, Unter den Eichen 87, 12205 Berlin, Germany
| | - Ralph Hölzel
- Fraunhofer-Institut
für Biomedizinische Technik IBMT, Institutsteil Potsdam-Golm, Am Mühlenberg 13, 14476 Potsdam-Golm, Germany
| | - Frank F. Bier
- Fraunhofer-Institut
für Biomedizinische Technik IBMT, Institutsteil Potsdam-Golm, Am Mühlenberg 13, 14476 Potsdam-Golm, Germany
| | - Regine von Klitzing
- Stranski-Laboratorium
für Physikalische und Theoretische Chemie/Institut für
Chemie, Technische Universität Berlin, Straße des 17. Juni 124, 10623 Berlin, Germany
| | - Andreas Schönhals
- BAM
Bundesanstalt für Materialforschung und -prüfung, Unter den Eichen 87, 12205 Berlin, Germany
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Abstract
A silicon based chip device with a regular array of more than 100,000 cylindrical sub-microelectrodes has been developed for the dielectrophoretic (DEP) manipulation of nanoparticles and molecules in solution. It was fabricated by a standard CMOS (complementary metal oxide semiconductor) compatible process. The distribution of the electrical field gradient was calculated to predict the applicability of the setup. Heating due to field application was determined microscopically using a temperature sensitive fluorescent dye. Depending on voltage and frequency, temperature increase was found to be compatible with protein function. Successful field controlled immobilisation of biomolecules from solution was demonstrated with the autofluorescent protein R-phycoerythrin (RPE) and with fluorescently labelled IgG antibodies. Biological activity after DEP application was proven by immobilisation of an anti-RPE antibody and subsequent binding of RPE. These results demonstrate that the developed chip system allows the directed immobilisation of proteins onto microelectrodes by dielectrophoresis without the need for any chemical modification and that protein function is preserved. Being based on standard lithographical methods, further miniaturisation and on-chip integration of electronics towards a multiparameter single cell analysis system appear near at hand.
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Affiliation(s)
- Saskia Otto
- Fraunhofer Institute for Biomedical Engineering (IBMT), Branch Potsdam-Golm, 14476 Potsdam, Germany.
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Kersting S, Rausch V, Bier FF, von Nickisch-Rosenegk M. Multiplex isothermal solid-phase recombinase polymerase amplification for the specific and fast DNA-based detection of three bacterial pathogens. Mikrochim Acta 2014; 181:1715-1723. [PMID: 25253912 PMCID: PMC4167443 DOI: 10.1007/s00604-014-1198-5] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 01/30/2014] [Indexed: 12/24/2022]
Abstract
We report on the development of an on-chip RPA (recombinase polymerase amplification) with simultaneous multiplex isothermal amplification and detection on a solid surface. The isothermal RPA was applied to amplify specific target sequences from the pathogens Neisseria gonorrhoeae, Salmonella enterica and methicillin-resistant Staphylococcus aureus (MRSA) using genomic DNA. Additionally, a positive plasmid control was established as an internal control. The four targets were amplified simultaneously in a quadruplex reaction. The amplicon is labeled during on-chip RPA by reverse oligonucleotide primers coupled to a fluorophore. Both amplification and spatially resolved signal generation take place on immobilized forward primers bount to expoxy-silanized glass surfaces in a pump-driven hybridization chamber. The combination of microarray technology and sensitive isothermal nucleic acid amplification at 38 °C allows for a multiparameter analysis on a rather small area. The on-chip RPA was characterized in terms of reaction time, sensitivity and inhibitory conditions. A successful enzymatic reaction is completed in <20 min and results in detection limits of 10 colony-forming units for methicillin-resistant Staphylococcus aureus and Salmonella enterica and 100 colony-forming units for Neisseria gonorrhoeae. The results show this method to be useful with respect to point-of-care testing and to enable simplified and miniaturized nucleic acid-based diagnostics. The combination of multiplex isothermal nucleic acid amplification with RPA and spatially-resolved signal generation on specific immobilized oligonucleotides ![]()
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Affiliation(s)
- Sebastian Kersting
- Fraunhofer Institute for Biomedical Engineering IBMT, Branch Potsdam, Am Muehlenberg 13, 14476 Potsdam-Golm, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24–25, 14476 Potsdam, Germany
| | - Valentina Rausch
- Fraunhofer Institute for Biomedical Engineering IBMT, Branch Potsdam, Am Muehlenberg 13, 14476 Potsdam-Golm, Germany
| | - Frank F. Bier
- Fraunhofer Institute for Biomedical Engineering IBMT, Branch Potsdam, Am Muehlenberg 13, 14476 Potsdam-Golm, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24–25, 14476 Potsdam, Germany
| | - Markus von Nickisch-Rosenegk
- Fraunhofer Institute for Biomedical Engineering IBMT, Branch Potsdam, Am Muehlenberg 13, 14476 Potsdam-Golm, Germany
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Danckert L, Hoppe S, Bier FF, von Nickisch-Rosenegk M. Rapid identification of novel antigens of Salmonella Enteritidis by microarray-based immunoscreening. Mikrochim Acta 2014; 181:1707-1714. [PMID: 25253911 PMCID: PMC4167438 DOI: 10.1007/s00604-014-1197-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 01/30/2014] [Indexed: 01/13/2023]
Abstract
We report on an approach to rapidly screen thousands of Salmonella Enteritidis proteins with the goal of identifying novel immunodominant proteins. We used a microarray-based system that warrants high throughput and easy handling. Seven immunogenic candidates were selected after screening. Comparative analyses by ELISA and microarrays manifested their immunodominant character. The large repetitive protein (SEN4030) that plays a role as a putative adhesin in initial cell surface interaction and is highly specific to Salmonella is considered to be the most suitable protein for a diagnostic approach. The results further demonstrate that the strategy applied herein is convenient for specifically identifying immunogenic proteins of pathogenic microorganisms. Consequently, it enables a sound assessment of promising candidates for diagnostic applications and vaccine development. Moreover, the elucidation of immunogenic proteins may assist in unveiling unknown virulence-associated factors, thus furthering the understanding of the underlying pathogenicity of Salmonella in general, and of S. Enteritidis, one of the most frequently detected serovars of this pathogen, in particular. The microarray-based approach was aimed at identifying novel immunodominant proteins of S. Enteritidis. Seven antigens were revealed by screening a cDNA expression library. SEN4030, a large repetitive protein specific for salmonella, is considered an optimal candidate for future applications. ![]()
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Affiliation(s)
- Lena Danckert
- Fraunhofer IBMT, Am Mühlenberg 13., 14476 Potsdam, Germany
| | | | - Frank F Bier
- Fraunhofer IBMT, Am Mühlenberg 13., 14476 Potsdam, Germany
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Rapsch K, Bier FF, Tadros M, von Nickisch-Rosenegk M. Identification of antimicrobial peptides and immobilization strategy suitable for a covalent surface coating with biocompatible properties. Bioconjug Chem 2014; 25:308-19. [PMID: 24372365 DOI: 10.1021/bc4004469] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Bacterial accumulation on solid material displays a major source of biomaterial associated infections, cross contamination, and spreading. To overcome these problems, different investigations on surface modifications for the containment of bacterial adhesion have been done. The aim of this research is the development of a rapid and efficient screening procedure to identify and investigate biologically active peptides in an immobilized state in order to produce an antimicrobial surface coating. We figured out that the antimicrobial mode of action is the most important parameter because only peptides with pronounced membrane disruption abilities displayed meaningful activity in an immobilized state. In addition, we highlighted the influence of the coupling reaction chemistry on the activity and amount of the immobilized peptide. Thereupon we developed an optimized antimicrobial surface coating with unrestricted antimicrobial properties by adjusting the immobilization strategy in combination with lowering the necessary peptide amount. Moreover we demonstrated that this antimicrobial surface coating displayed no cytotoxic activity against a eukaryotic cell line and thereby indicates a promising biocompatibility. Furthermore, different antimicrobial peptides obtained either by chemical peptide synthesis or by recombinant DNA technology were used in this study and their activities as well as their potential applications were discussed.
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Affiliation(s)
- Karsten Rapsch
- Fraunhofer Institute for Biomedical Engineering IBMT, Branch Potsdam , Am Muehlenberg 13, 14476 Potsdam, Germany
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Andresen D, Nickisch-Rosenegk MV, Bier FF. Helicase-dependent amplification: use in OnChip amplification and potential for point-of-care diagnostics. Expert Rev Mol Diagn 2014; 9:645-50. [DOI: 10.1586/erm.09.46] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Laux EM, Kaletta UC, Bier FF, Wenger C, Hölzel R. Functionality of dielectrophoretically immobilized enzyme molecules. Electrophoresis 2013; 35:459-66. [PMID: 24254805 DOI: 10.1002/elps.201300447] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 11/04/2013] [Accepted: 11/11/2013] [Indexed: 11/10/2022]
Abstract
The enzyme horseradish peroxidase has been immobilized on nanoelectrode arrays by alternating current dielectrophoresis (DEP). Preservation of its enzymatic function after field application was demonstrated by oxidizing dihydrorhodamine 123 with hydrogen peroxide as co-oxidant to create its fluorescent form, rhodamine 123 (Rh123). Localization of the fluorescently labeled enzyme and its product was conducted by fluorescence microscopy. Nanoelectrodes were prepared as tungsten pins arranged in square arrays. Experimental parameters for dielectrophoretic immobilization were optimized for even enzyme distribution and for enzymatic efficiency. Enzyme activity was quantified by determination of fluorescence intensities of immobilized enzyme molecules and of Rh123 produced. These results demonstrate that DEP can be applied to immobilize enzyme molecules while retaining their activity and rendering any chemical modifications unnecessary. This introduces a novel way for the preparation of bioactive surfaces for processes such as biosensing.
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Affiliation(s)
- Eva-Maria Laux
- Fraunhofer Institute for Biomedical Engineering (IBMT), Branch Potsdam-Golm, Potsdam, Germany
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Schmitz-Hertzberg ST, Mak WC, Lai KK, Teller C, Bier FF. Multifactorial design of poly( d,l-lactic- co-glycolic acid) capsules with various release properties for differently sized filling agents. J Appl Polym Sci 2013. [DOI: 10.1002/app.39537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | - Kwok Kei Lai
- Department of Chemistry; Hong Kong University of Science and Technology; Clear Water Bay; Hong Kong; People's Republic of China
| | - Carsten Teller
- Fraunhofer Institute for Biomedical Engineering; Branch Potsdam, Am Mühlenberg 13; 14476; Potsdam; Germany
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Hüttl C, Hettrich C, Miller R, Paulke BR, Henklein P, Rawel H, Bier FF. Self-assembled peptide amphiphiles function as multivalent binder with increased hemagglutinin affinity. BMC Biotechnol 2013; 13:51. [PMID: 23777281 PMCID: PMC3689634 DOI: 10.1186/1472-6750-13-51] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Accepted: 06/13/2013] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND A promising way in diagnostic and therapeutic applications is the development of peptide amphiphiles (PAs). Peptides with a palmitic acid alkylchain were designed and characterized to study the effect of the structure modifications on self-assembling capabilities and the multiple binding capacity to hemagglutinin (HA), the surface protein of influenza virus type A. The peptide amphiphiles consists of a hydrophilic headgroup with a biological functionality of the peptide sequence and a chemically conjugated hydrophobic tail. In solution they self-assemble easily to micelles with a hydrophobic core surrounded by a closely packed peptide-shell. RESULTS In this study the effect of a multiple peptide binding partner to the receptor binding site of HA could be determined with surface plasmon resonance measurements. The applied modification of the peptides causes signal amplification in relationship to the unmodified peptide wherein the high constant specificity persists. The molecular assembly of the peptides was characterized by the determination of critical micelle concentration (CMC) with concentration of 10⁻⁵ M and the colloidal size distribution. CONCLUSION The modification of the physico-chemical parameters by producing peptide amphiphiles form monomeric structures which enhances the binding affinity and allows a better examination of the interaction with the virus surface protein hemagglutinin.
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Affiliation(s)
- Christine Hüttl
- Fraunhofer Institute for Biomedical Engineering IBMT, Am Mühlenberg 13, 14476, Potsdam, Germany
- Institute for Biochemistry und Biology, University of Potsdam, Maulbeerallee 2, 14469, Potsdam, Germany
| | - Cornelia Hettrich
- Fraunhofer Institute for Biomedical Engineering IBMT, Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Reinhard Miller
- Max Planck Institute for Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Bernd-Reiner Paulke
- Fraunhofer Institute for Applied Polymer Research IAP, Geiselbergstr. 69, 14476, Potsdam, Germany
| | - Petra Henklein
- Institute for Biochemistry, Charité – Universitätsmedizin Berlin, Virchowweg 6, 10117, Berlin, Germany
| | - Harshadrai Rawel
- Institute of Nutritional Sciences, University of Potsdam, Arthur-Scheunert-Allee 114-116, 14558, Nuthetal, Germany
| | - Frank F Bier
- Fraunhofer Institute for Biomedical Engineering IBMT, Am Mühlenberg 13, 14476, Potsdam, Germany
- Institute for Biochemistry und Biology, University of Potsdam, Maulbeerallee 2, 14469, Potsdam, Germany
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Hoppe S, Bier FF, Nickisch-Rosenegk MV. Rapid identification of novel immunodominant proteins and characterization of a specific linear epitope of Campylobacter jejuni. PLoS One 2013; 8:e65837. [PMID: 23734261 PMCID: PMC3667084 DOI: 10.1371/journal.pone.0065837] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 04/30/2013] [Indexed: 01/03/2023] Open
Abstract
Campylobacter jejuni remains one of the major gut pathogens of our time. Its zoonotic nature and wide-spread distribution in industrialized countries calls for a quick and reliable diagnostic tool. Antibody-based detection presents a suitable means to identify pathogenic bacteria. However, the knowledge about immunodominant targets is limited. Thus, an approach is presented, which allows for the rapid screening of numerous cDNA derived expression clones to identify novel antigens. The deeper understanding of immunodominant proteins assists in the design of diagnostic tools and furthers the insight into the bacterium's pathogenicity as well as revealing potential candidates for vaccination. We have successfully screened 1536 clones of an expression library to identify 22 proteins that have not been described as immunodominant before. After subcloning the corresponding 22 genes and expression of full-length proteins, we investigated the immunodominant character by microarrays and ELISA. Subsequently, seven proteins were selected for epitope mapping. For cj0669 and cj0920c linear epitopes were identified. For cj0669, specificity assays revealed a specific linear epitope site. Consequently, an eleven amino acid residue sequence TLIKELKRLGI was analyzed via alanine scan, which revealed the glycine residue to be significant for binding of the antibody. The innovative approach presented herein of generating cDNAs of prokaryotes in combination with a microarray platform rendering time-consuming purification steps obsolete has helped to illuminate novel immunodominant proteins of C.jejuni. The findings of a specific linear epitope pave the way for a plethora of future research and the potential use in diagnostic applications such as serological screenings. Moreover, the current approach is easily adaptable to other highly relevant bacteria making it a formidable tool for the future discovery of antigens and potential biomarkers. Consequently, it is desirable to simplify the identification of structural epitopes, as this would extend the spectrum of novel epitopes to be detected.
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Affiliation(s)
- Sebastian Hoppe
- Fraunhofer Institute for Biomedical Engineering, Am Muehlenberg, Potsdam, Germany
| | - Frank F. Bier
- Fraunhofer Institute for Biomedical Engineering, Am Muehlenberg, Potsdam, Germany
- University Potsdam, Institute of Biochemistry and Biology, Potsdam, Germany
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Kozma P, Lehmann A, Wunderlich K, Michel D, Schumacher S, Ehrentreich-Förster E, Bier FF. A novel handheld fluorescent microarray reader for point-of-care diagnostic. Biosens Bioelectron 2013; 47:415-20. [PMID: 23612063 DOI: 10.1016/j.bios.2013.03.043] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 03/14/2013] [Accepted: 03/15/2013] [Indexed: 10/27/2022]
Abstract
A novel handheld optical sensor for quantification of fluorescent microarrays, the so-called portMD-113 has been developed. On the surface of a planar waveguide, the spots of different fluorescently labeled biological complexes are excited by the evanescent field of the guided light. The emitted fluorescence signals of the spots are independently and simultaneously detected applying our system, which consists of a pinehole array, a microlens array, an interference filter and a detector array. As it is demonstrated in comparative measurements, the detection limit of this sensor is close to that of commercial top microarray readers, e.g. of modern laser scanners, while it has remarkable and important advantages over them. Namely, the device comprises only a few low-cost, lightweight and small components without applying any moving or energy-intensive elements, which results in turn in a commercially competitive, handheld and compact design and in the possibility to be supplied simply by a battery or a personal computer. These advantageous properties open prospects e.g. for point-of-care medical checks, as well.
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Affiliation(s)
- P Kozma
- Fraunhofer Institute for Biomedical Engineering (IBMT), Am Mühlenberg 13, 14476 Potsdam-Golm, Germany.
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Schumacher S, Sartorius D, Ehrentreich-Förster E, Bier FF. Miniaturization for Point-of-Care Analysis: Platform Technology for Almost Every Biomedical Assay. EJIFCC 2012; 23:70-5. [PMID: 27683418 PMCID: PMC4975254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Platform technologies for the changing need of diagnostics are one of the main challenges in medical device technology. From one point-of-view the demand for new and more versatile diagnostic is increasing due to a deeper knowledge of biomarkers and their combination with diseases. From another point-of-view a decentralization of diagnostics will occur since decisions can be made faster resulting in higher success of therapy. Hence, new types of technologies have to be established which enables a multiparameter analysis at the point-of-care. Within this review-like article a system called Fraunhofer ivD-platform is introduced. It consists of a credit-card sized cartridge with integrated reagents, sensors and pumps and a read-out/processing unit. Within the cartridge the assay runs fully automated within 15-20 minutes. Due to the open design of the platform different analyses such as antibody, serological or DNA-assays can be performed. Specific examples of these three different assay types are given to show the broad applicability of the system.
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Affiliation(s)
- Soeren Schumacher
- Fraunhofer Institute for Biomedical Engineering, Branch Potsdam Am Mühlenberg 13 14476 Potsdam, Germany www.ivd-plattform.de
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Affiliation(s)
- Rita Sachse
- Fraunhofer Institute for Biomedical Engineering (IBMT) Potsdam Germany
| | | | - Mária Šamalíková
- Fraunhofer Institute for Biomedical Engineering (IBMT) Potsdam Germany
| | | | - Frank F. Bier
- Fraunhofer Institute for Biomedical Engineering (IBMT) Potsdam Germany
- University of Potsdam Institute for Biochemistry and Biology Potsdam Germany
| | - Stefan Kubick
- Fraunhofer Institute for Biomedical Engineering (IBMT) Potsdam Germany
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Hoppe S, Bier FF, von Nickisch-Rosenegk M. Microarray-based method for screening of immunogenic proteins from bacteria. J Nanobiotechnology 2012; 10:12. [PMID: 22436172 PMCID: PMC3368735 DOI: 10.1186/1477-3155-10-12] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Accepted: 03/21/2012] [Indexed: 12/12/2022] Open
Abstract
Background Detection of immunogenic proteins remains an important task for life sciences as it nourishes the understanding of pathogenicity, illuminates new potential vaccine candidates and broadens the spectrum of biomarkers applicable in diagnostic tools. Traditionally, immunoscreenings of expression libraries via polyclonal sera on nitrocellulose membranes or screenings of whole proteome lysates in 2-D gel electrophoresis are performed. However, these methods feature some rather inconvenient disadvantages. Screening of expression libraries to expose novel antigens from bacteria often lead to an abundance of false positive signals owing to the high cross reactivity of polyclonal antibodies towards the proteins of the expression host. A method is presented that overcomes many disadvantages of the old procedures. Results Four proteins that have previously been described as immunogenic have successfully been assessed immunogenic abilities with our method. One protein with no known immunogenic behaviour before suggested potential immunogenicity. We incorporated a fusion tag prior to our genes of interest and attached the expressed fusion proteins covalently on microarrays. This enhances the specific binding of the proteins compared to nitrocellulose. Thus, it helps to reduce the number of false positives significantly. It enables us to screen for immunogenic proteins in a shorter time, with more samples and statistical reliability. We validated our method by employing several known genes from Campylobacter jejuni NCTC 11168. Conclusions The method presented offers a new approach for screening of bacterial expression libraries to illuminate novel proteins with immunogenic features. It could provide a powerful and attractive alternative to existing methods and help to detect and identify vaccine candidates, biomarkers and potential virulence-associated factors with immunogenic behaviour furthering the knowledge of virulence and pathogenicity of studied bacteria.
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Affiliation(s)
- Sebastian Hoppe
- Fraunhofer Institute for Biomedical Engineering, Branch Potsdam, Am Mühlenberg 13, 14476 Potsdam, Germany.
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