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Reuter C, Hauswald W, Burgold-Voigt S, Hübner U, Ehricht R, Weber K, Popp J. Imaging Diffractometric Biosensors for Label-Free, Multi-Molecular Interaction Analysis. BIOSENSORS 2024; 14:398. [PMID: 39194627 DOI: 10.3390/bios14080398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Revised: 07/26/2024] [Accepted: 08/14/2024] [Indexed: 08/29/2024]
Abstract
Biosensors are used for the specific and sensitive detection of biomolecules. In conventional approaches, the suspected target molecules are bound to selected capture molecules and successful binding is indicated by additional labelling to enable optical readout. This labelling requires additional processing steps tailored to the application. While numerous label-free interaction assays exist, they often compromise on detection characteristics. In this context, we introduce a novel diffractometric biosensor, comprising a diffractive biosensor chip and an associated optical reader assembly. This innovative system can capture an entire assay, detecting various types of molecules in a label-free manner and present the results within in a single, comprehensive image. The applicability of the biosensor is assessed for the detection of viral DNA as well as proteins directly in human plasma, investigating different antigens. In our experiments, we achieve a detection limit of 4.2 pg/mm², which is comparable to other label-free optical biosensors. The simplicity and robustness of the method make it a compelling option for advancing biosensing technologies. This work contributes to the development of an imaging diffractometric biosensor with the potential for multiple applications in molecular interaction analysis.
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Affiliation(s)
- Cornelia Reuter
- Leibniz Institute of Photonic Technology, Member of Leibniz Health Technologies, Member of the Leibniz Centre for Photonics in Infection Research (LPI), 07745 Jena, Germany
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Walter Hauswald
- Leibniz Institute of Photonic Technology, Member of Leibniz Health Technologies, Member of the Leibniz Centre for Photonics in Infection Research (LPI), 07745 Jena, Germany
| | - Sindy Burgold-Voigt
- Leibniz Institute of Photonic Technology, Member of Leibniz Health Technologies, Member of the Leibniz Centre for Photonics in Infection Research (LPI), 07745 Jena, Germany
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Uwe Hübner
- Leibniz Institute of Photonic Technology, Member of Leibniz Health Technologies, Member of the Leibniz Centre for Photonics in Infection Research (LPI), 07745 Jena, Germany
| | - Ralf Ehricht
- Leibniz Institute of Photonic Technology, Member of Leibniz Health Technologies, Member of the Leibniz Centre for Photonics in Infection Research (LPI), 07745 Jena, Germany
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, 07743 Jena, Germany
- InfectoGnostics Research Campus Jena, Center for Applied Research, 07743 Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Karina Weber
- Leibniz Institute of Photonic Technology, Member of Leibniz Health Technologies, Member of the Leibniz Centre for Photonics in Infection Research (LPI), 07745 Jena, Germany
| | - Juergen Popp
- Leibniz Institute of Photonic Technology, Member of Leibniz Health Technologies, Member of the Leibniz Centre for Photonics in Infection Research (LPI), 07745 Jena, Germany
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, 07743 Jena, Germany
- InfectoGnostics Research Campus Jena, Center for Applied Research, 07743 Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07743 Jena, Germany
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A Model System for Sensitive Detection of Viable E. coli Bacteria Combining Direct Viability PCR and a Novel Microarray-Based Detection Approach. CHEMOSENSORS 2021. [DOI: 10.3390/chemosensors9120357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We established an innovative approach that included direct, viability, and nested PCR for rapid and reliable identification of the fecal indicator organism Escherichia coli (E. coli). Direct PCR enabled successful amplification of the target uidA gene, omitting a prior DNA isolation or purification step. Furthermore, we applied viability PCR (v-PCR) to ensure the detection of only relevant viable bacterial cells. The principle involves the binding of propidium monoazide (PMA), a selective nucleic acid intercalating dye, to accessible DNA of heat killed bacteria cells and, consequently, allows viable and heat killed E. coli cells to be discriminated. To ensure high sensitivity, direct v-PCR was followed by a nested PCR step. The resulting amplicons were analyzed by a rapid 30 min microarray-based DNA hybridization assay for species-specific DNA detection of E. coli. A positive signal was indicated by enzymatically generated silver nanoparticle deposits, which served as robust endpoint signals allowing an immediate visual readout. The presented novel protocol allows the detection of 1 × 101 viable E. coli cells per PCR run.
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Kim J, Jung S, Kim MY, Kim BK, Kwon SH, Kim SK. Thermo-Responsive Polymer Capsules in Real-Time One-Step RT-PCR for Highly Multiplex RNA Analysis. Adv Healthc Mater 2020; 9:e1900790. [PMID: 32134572 DOI: 10.1002/adhm.201900790] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 12/13/2019] [Indexed: 11/09/2022]
Abstract
Rapid and simple detection of RNA targets is in high demand due to the growing threat of pandemic viruses. One-step real-time, reverse transcription-polymerase chain reaction (One-step RT-qPCR) using a controlled release system of thermo-responsive materials is developed in this paper to enable high-fidelity RNA analysis as suppressing by-products. The nanocapsules, consisting of upper critical solution temperature (UCST) material and PCR primers, carry or release the primers depending upon the temperature. The UCST nanocapsules are introduced into hydrogel microparticles incorporated with RT primers and then the target RNA is selectively amplified in the microparticle through one-step RT-qPCR. Severe side products are sharply subdued by separating the PCR primers from the RT process by means of the microparticles with nanocapsules. Because the one-step assay is now implemented in a single microparticle, multiple target RNAs can be analyzed in a simple RT-qPCR of multiple particles. Reliable 18-plex one-step RT-qPCR is successfully conducted within 30 min using single-color fluorescent optics. This work also explains the facile fabrication processes used for the thermo-responsive nanocapsules and hydrogel microparticles by the blending polymerization method. Extensible multiplex analysis of influenza virus demonstrates the versatile uses of this one-step RT-qPCR platform.
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Affiliation(s)
- Junsun Kim
- Center for Molecular Recognition ResearchMaterials and Life Science Research DivisionKorea Institute of Science and Technology Seoul 02792 Republic of Korea
- Chemical and Biological EngineeringKorea University Seoul 02841 Republic of Korea
| | - Seungwon Jung
- Center for Molecular Recognition ResearchMaterials and Life Science Research DivisionKorea Institute of Science and Technology Seoul 02792 Republic of Korea
- Applied ChemistryKyung Hee University Yongin 17104 Republic of Korea
| | - Mi Yeon Kim
- Center for Molecular Recognition ResearchMaterials and Life Science Research DivisionKorea Institute of Science and Technology Seoul 02792 Republic of Korea
- Chemical and Biological EngineeringKorea University Seoul 02841 Republic of Korea
| | - Bong Kyun Kim
- Center for Molecular Recognition ResearchMaterials and Life Science Research DivisionKorea Institute of Science and Technology Seoul 02792 Republic of Korea
- Biomedical EngineeringUniversity of Science and Technology (UST) Daejeon 34113 Republic of Korea
| | - Soon Hwan Kwon
- Armed Forces Medical Research Institute Daejeon 34059 Republic of Korea
| | - Sang Kyung Kim
- Center for Molecular Recognition ResearchMaterials and Life Science Research DivisionKorea Institute of Science and Technology Seoul 02792 Republic of Korea
- Biomedical EngineeringUniversity of Science and Technology (UST) Daejeon 34113 Republic of Korea
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Steinbach C, Steinbrücker C, Pollok S, Walther K, Clement JH, Chen Y, Petersen I, Cialla-May D, Weber K, Popp J. KRAS mutation screening by chip-based DNA hybridization--a further step towards personalized oncology. Analyst 2015; 140:2747-54. [PMID: 25706807 DOI: 10.1039/c4an02086c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The use of predictive biomarkers can help to improve therapeutic options for the individual cancer patient. For the treatment of colon cancer patients with anti-EGFR-based drugs, the KRAS mutation status has to be determined to pre-select responders that will benefit from this medication. Amongst others, array-based tests have been established for profiling of the KRAS mutation status. Within this article we describe an on-chip hybridization technique to screen therapeutic relevant KRAS codon 12 mutations. The DNA chip-based platform enables the reliable discrimination of selected mutations by allele-specific hybridization. Here, silver deposits represent robust endpoint signals that allow for a simple naked eye rating. With the here presented assay concept a precise identification of heterozygous and homozygous KRAS mutations, even against a background of up to 95% wild-type DNA, was realizable. The applicability of the test was successfully proven for various cancer cell lines as well as clinical tumour samples. Thus, the chip-based DNA hybridization technique seems to be a promising tool for KRAS mutation analysis to further improve personalized cancer treatment.
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Affiliation(s)
- Christine Steinbach
- Leibniz Institute of Photonic Technology Jena, Albert-Einstein-Str. 9, 07745 Jena, Germany
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Beyer A, Pollok S, Berg A, Weber K, Popp J. Easy daylight fabricated hydrogel array for colorimetric DNA analysis. Macromol Biosci 2014; 14:889-98. [PMID: 24497199 DOI: 10.1002/mabi.201300487] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Revised: 12/17/2013] [Indexed: 12/13/2022]
Abstract
The fabrication of 3D hydrogel microarrays for DNA analytics that allow simple visual signal readout for on-site applications is described. A convenient one-step polymerization of the hydrogel including in situ capture oligonucleotide immobilization is accomplished by using N,N'-dimethylacrylamide/polyethylene glycol (PEG1900 )-bisacrylamide monomers. The implementation of an acylphosphine-oxide photoinitiator even allows polymerization at daylight, whereas other approaches require exposure with light in the UV-range. This minimizes the risk of UV-caused DNA damages within the capture DNA-strand that could adversely affect the subsequent hybridization step. The porous network of these gel segments allows DNA as well as protein penetration. Thus, the successful in-gel DNA hybridization is monitored by the deposition of silver nanoparticles. These metal particles allow naked eye signal readout.
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Affiliation(s)
- Antje Beyer
- Leibniz Institute of Photonic Technology e.V., Albert-Einstein-Strasse 9, 07745, Jena, Germany; Institute of Physical Chemistry and Abbe Centre of Photonics, Friedrich-Schiller-University Jena, Helmholtzweg 4, 07743, Jena, Germany
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Wünscher S, Seise B, Pretzel D, Pollok S, Perelaer J, Weber K, Popp J, Schubert US. Chip-on-foil devices for DNA analysis based on inkjet-printed silver electrodes. LAB ON A CHIP 2014; 14:392-401. [PMID: 24276694 DOI: 10.1039/c3lc50886b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
For a rapid on-site diagnosis of pathogens, low-cost chip-based devices are of great interest. Here, we report the successful fabrication of inkjet printed silver electrodes on polymer foils as disposable chips for molecular DNA analytics. In order to manufacture these electrode structures, silver nanoparticle inks were inkjet printed onto planar polypropylene substrates. Due to the low thermal stability of the foils, substrate preserving sintering techniques, including low temperature thermal sintering and low pressure argon plasma sintering, were implemented. Thus, sufficient electrical conductance of the printed structures at processing temperatures ≤100 °C was achieved. To test the applicability of the manufactured chips, specific capture DNA was immobilized within the gaps of the conductive electrode paths and hybridized in the next step with biotin-labeled target DNA. Subsequently, an enzymatically generated silver nanoparticle deposition was induced that bridges the electrode gap. This enabled both conductance measurement and gray value analysis as a fast, simple and robust electrical and optical read-out system. The proof-of-principle experiments successfully demonstrated the applicability of these convenient chip-on-foil devices for nucleic acid based pathogen detection.
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Affiliation(s)
- Sebastian Wünscher
- Laboratory of Organic and Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Humboldtstr. 10, 07743 Jena, Germany.
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Roeber F, Jex AR, Gasser RB. Advances in the diagnosis of key gastrointestinal nematode infections of livestock, with an emphasis on small ruminants. Biotechnol Adv 2013; 31:1135-52. [PMID: 23376340 PMCID: PMC7126997 DOI: 10.1016/j.biotechadv.2013.01.008] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 01/21/2013] [Accepted: 01/22/2013] [Indexed: 12/19/2022]
Abstract
Parasitic nematodes (roundworms) of livestock have major economic impact globally. In spite of the diseases caused by these nematodes and some advances in the design of new therapeutic agents (anthelmintics) and attempts to develop vaccines against some of them, there has been limited progress in the establishment of practical diagnostic techniques. The specific and sensitive diagnosis of gastrointestinal nematode infections of livestock underpins effective disease control, which is highly relevant now that anthelmintic resistance (AR) is a major problem. Traditional diagnostic techniques have major constraints, in terms of sensitivity and specificity. The purpose of this article is to provide a brief background on gastrointestinal nematodes (Strongylida) of livestock and their control; to summarize conventional methods used for the diagnosis and discuss their constraints; to review key molecular-diagnostic methods and recent progress in the development of advanced amplification-based and sequencing technologies, and their implications for epidemiological investigations and the control of parasitic diseases.
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Affiliation(s)
| | | | - Robin B. Gasser
- Faculty of Veterinary Science, The University of Melbourne, Victoria 3010, Australia
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On-site detection of Phytophthora spp.—single-stranded target DNA as the limiting factor to improve on-chip hybridization. Mikrochim Acta 2013. [DOI: 10.1007/s00604-013-1107-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Seise B, Pollok S, Seyboldt C, Weber K. Dry-reagent-based PCR as a novel tool for the rapid detection of Clostridium spp. J Med Microbiol 2013; 62:1588-1591. [DOI: 10.1099/jmm.0.060061-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Improved conventional PCR techniques are required for the rapid on-site detection of human and animal diseases. In this context, a PCR method using dry-stored reagents intended for the detection of Clostridium spp. is presented. Basic PCR reagents (BSA, PCR buffer, MgCl2 and primers), which were dried on polyolefin matrices, showed stability at ambient temperatures for up to 10 months without any loss of functionality. An outstanding advantage of our amelioration is the elimination of PCR process errors caused by the improper storage and handling of liquid reagents. Moreover, our PCR-based amplification can be performed in less than 30 min, saving time compared with conventional detection methods. Thus, dry-reagent-based PCR is implementable in a suitcase-like modular device for the rapid on-site detection of microbial pathogens such as blackleg of ruminants caused by Clostridium chauvoei.
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Affiliation(s)
- Barbara Seise
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller-University Jena, Helmholtzweg 4, 07743 Jena, Germany
- Institute of Photonic Technology Jena, Albert-Einstein-Straße 9, 07745 Jena, Germany
| | - Sibyll Pollok
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller-University Jena, Helmholtzweg 4, 07743 Jena, Germany
- Institute of Photonic Technology Jena, Albert-Einstein-Straße 9, 07745 Jena, Germany
| | - Christian Seyboldt
- Institute of Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health (Friedrich-Loeffler-Institut), Naumburger Strasse 96a, 07743 Jena, Germany
| | - Karina Weber
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller-University Jena, Helmholtzweg 4, 07743 Jena, Germany
- Institute of Photonic Technology Jena, Albert-Einstein-Straße 9, 07745 Jena, Germany
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Liberski AR, Delaney JT, Liberska A, Perelaer J, Schwarz M, Schüler T, Möller R, Schubert US. Printed conductive features for DNA chip applications prepared on PET without sintering. RSC Adv 2012. [DOI: 10.1039/c2ra01191c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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Köhler JM. Editorial: Microtechnology for life science applications. Eng Life Sci 2011. [DOI: 10.1002/elsc.201190011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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BiotecVisions 2011, April. Biotechnol J 2011. [DOI: 10.1002/biot.201100142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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