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de Stigter Y, van der Veer HJ, Rosier BJHM, Merkx M. Bioluminescent Intercalating Dyes for Ratiometric Nucleic Acid Detection. ACS Chem Biol 2024; 19:575-583. [PMID: 38315567 PMCID: PMC10877566 DOI: 10.1021/acschembio.3c00755] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 02/07/2024]
Abstract
Rapid and sensitive DNA detection methods that can be conducted at the point of need may aid in disease diagnosis and monitoring. However, translation of current assays has proven challenging, as they typically require specialized equipment or probe-specific modifications for every new target DNA. Here, we present Luminescent Multivalent Intercalating Dye (LUMID), off-the-shelf bioluminescent sensors consisting of intercalating dyes conjugated to a NanoLuc luciferase, which allow for nonspecific detection of double-stranded DNA through a blue-to-green color change. Through the incorporation of multiple, tandem-arranged dyes separated by positively charged linkers, DNA-binding affinities were improved by over 2 orders of magnitude, detecting nanomolar DNA concentrations with an 8-fold change in green/blue ratio. We show that LUMID is easily combined with loop-mediated isothermal amplification (LAMP), enabling sequence-specific detection of viral DNA with attomolar sensitivity and a smartphone-based readout. With LUMID, we have thus developed a tool for simple and sensitive DNA detection that is particularly attractive for point-of-need applications.
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Affiliation(s)
- Yosta de Stigter
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Harmen J. van der Veer
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Bas J. H. M. Rosier
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Maarten Merkx
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
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Flipse J, Tromp AT, Thijssen D, van Xanten-Jans-Beken N, Pauwelsen R, van der Veer HJ, Schlaghecke JM, Swanink CMA. Optimization of the STARlet workflow for semi-automatic SARS-CoV-2 screening of swabs and deep respiratory materials using the RealAccurate Quadruplex SARS-CoV-2 PCR kit and Allplex SARS-CoV-2 PCR kit. Microbiol Spectr 2024; 12:e0329623. [PMID: 38193688 PMCID: PMC10846099 DOI: 10.1128/spectrum.03296-23] [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] [Received: 10/04/2023] [Accepted: 12/01/2023] [Indexed: 01/10/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic triggered the implementation of large-scale screenings in the health care and in the general population. Consequently, medical laboratories have to apply lean laboratory management to design workflows that are able to process large batches within short turnaround times while maintaining flexibility to use different SARS-CoV-2 reverse transcription polymerase chain reactions (RT-PCRs) and to be able to process a variety of clinical samples. We validated two SARS-CoV-2 PCR assays on the STARlet workflow: Allplex SARS-CoV-2 PCR kit and RealAccurate Quadruplex SARS-CoV-2 PCR kit. Furthermore, we optimized and validated the STARlet workflow for semi-automatic screening for SARS-CoV-2 in upper respiratory swabs and deep respiratory materials (sputa, bronchoalveolar lavage, and aspirate). Strikingly, guanidine-containing lysis buffers allow for easy processing and can enhance sensitivity of SARS-COV-2 screening since sampling in these buffers may preserve viral transcripts as evident by the higher copy numbers of the SARS-CoV-2 N gene. Moreover, using the principles of lean laboratory management, several bottlenecks that are typical for medical laboratories were addressed. We show that lean laboratory management resulted in significant reduction of the turnaround times of the SARS-CoV-2 PCR in our laboratory. This report thus describes a useful framework for laboratories to implement similar semi-automated workflows.IMPORTANCEThe SARS-CoV-2 pandemic triggered the implementation of large-scale screenings in the health care and in the general population. Consequently, medical laboratories had to adapt and evolve workflows that are able to process large batches within short turnaround times while maintaining flexibility to use different assays and to be able to process a variety of clinical samples. We describe how the need for increased outputs and greater flexibility was addressed with respect to clinical samples and assays (Allplex SARS-CoV-2 PCR and RealAccurate Quadruplex SARS-CoV-2 PCR). Strikingly, we found that upper respiratory swabs collected in guanidine-containing lysis buffers both improved the ease of processing as well as enhanced the sensitivity of the SARS-CoV-2 screening. This report thus describes a useful framework for laboratories to implement and optimize similar semi-automated workflows.
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Affiliation(s)
- Jacky Flipse
- Laboratory for Medical Microbiology and Immunology, Rijnstate Hospital, Velp, the Netherlands
| | - Angelino T. Tromp
- Laboratory for Medical Microbiology and Immunology, Rijnstate Hospital, Velp, the Netherlands
| | - Danique Thijssen
- Laboratory for Medical Microbiology and Immunology, Rijnstate Hospital, Velp, the Netherlands
| | | | - Roy Pauwelsen
- Laboratory for Medical Microbiology and Immunology, Rijnstate Hospital, Velp, the Netherlands
| | - Harmen J. van der Veer
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Juliëtte M. Schlaghecke
- Research Group Applied Natural Sciences, Fontys University of Applied Sciences, Eindhoven, the Netherlands
| | - Caroline M. A. Swanink
- Laboratory for Medical Microbiology and Immunology, Rijnstate Hospital, Velp, the Netherlands
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van Aalen EA, Rosier BJHM, Jansen T, Wouters SFA, Vermathen RT, van der Veer HJ, Yeste Lozano J, Mughal S, Fernández-Costa JM, Ramón-Azcón J, den Toonder JMJ, Merkx M. Integrated Bioluminescent Immunoassays for High-Throughput Sampling and Continuous Monitoring of Cytokines. Anal Chem 2023. [PMID: 37253113 DOI: 10.1021/acs.analchem.3c00745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Immunoassays show great potential for the detection of low levels of cytokines, due to their high sensitivity and excellent specificity. There is a particular demand for biosensors that enable both high-throughput screening and continuous monitoring of clinically relevant cytokines such as interleukin-6 (IL-6) and tumor necrosis factor-α (TNFα). To this end, we here introduce a novel bioluminescent immunoassay based on the ratiometric plug-and-play immunodiagnostics (RAPPID) platform, with an improved intrinsic signal-to-background and an >80-fold increase in the luminescent signal. The new dRAPPID assay, comprising a dimeric protein G adapter connected via a semiflexible linker, was applied to detect the secretion of IL-6 by breast carcinoma cells upon TNFα stimulation and the production of low concentrations of IL-6 (∼18 pM) in an endotoxin-stimulated human 3D muscle tissue model. Moreover, we integrated the dRAPPID assay in a newly developed microfluidic device for the simultaneous and continuous monitoring of changes in IL-6 and TNFα in the low-nanomolar range. The luminescence-based read-out and the homogeneous nature of the dRAPPID platform allowed for detection with a simple measurement setup, consisting of a digital camera and a light-sealed box. This permits the usage of the continuous dRAPPID monitoring chip at the point of need, without the requirement for complex or expensive detection techniques.
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Affiliation(s)
- Eva A van Aalen
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O Box 513, 5600 MB Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O Box 513, 5600 MB Eindhoven, The Netherlands
| | - Bas J H M Rosier
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O Box 513, 5600 MB Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O Box 513, 5600 MB Eindhoven, The Netherlands
| | - Tom Jansen
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O Box 513, 5600 MB Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O Box 513, 5600 MB Eindhoven, The Netherlands
| | - Simone F A Wouters
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O Box 513, 5600 MB Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O Box 513, 5600 MB Eindhoven, The Netherlands
| | - Robin T Vermathen
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O Box 513, 5600 MB Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O Box 513, 5600 MB Eindhoven, The Netherlands
| | - Harmen J van der Veer
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O Box 513, 5600 MB Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O Box 513, 5600 MB Eindhoven, The Netherlands
| | - José Yeste Lozano
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), C/Baldiri Reixac 10-12, Barcelona E08028, Spain
| | - Sheeza Mughal
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), C/Baldiri Reixac 10-12, Barcelona E08028, Spain
| | - Juan M Fernández-Costa
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), C/Baldiri Reixac 10-12, Barcelona E08028, Spain
| | - Javier Ramón-Azcón
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), C/Baldiri Reixac 10-12, Barcelona E08028, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig de Lluís Companys, 23,O Barcelona E08010, Spain
| | - Jaap M J den Toonder
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O Box 513, 5600 MB Eindhoven, The Netherlands
- Microsystems, Department of Mechanical Engineering, Eindhoven University of Technology, P.O Box 513, 5600 MB Eindhoven, The Netherlands
| | - Maarten Merkx
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O Box 513, 5600 MB Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O Box 513, 5600 MB Eindhoven, The Netherlands
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