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Napoletano S, Battista E, Netti PA, Causa F. MicroLOCK: Highly stable microgel biosensor using locked nucleic acids as bioreceptors for sensitive and selective detection of let-7a. Biosens Bioelectron 2024; 260:116406. [PMID: 38805889 DOI: 10.1016/j.bios.2024.116406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 05/30/2024]
Abstract
Chemically modified oligonucleotides can solve biosensing issues for the development of capture probes, antisense, CRISPR/Cas, and siRNA, by enhancing their duplex-forming ability, their stability against enzymatic degradation, and their specificity for targets with high sequence similarity as microRNA families. However, the use of modified oligonucleotides such as locked nucleic acids (LNA) for biosensors is still limited by hurdles in design and from performances on the material interface. Here we developed a fluorogenic biosensor for non-coding RNAs, represented by polymeric PEG microgels conjugated with molecular beacons (MB) modified with locked nucleic acids (MicroLOCK). By 3D modeling and computational analysis, we designed molecular beacons (MB) inserting spot-on LNAs for high specificity among targets with high sequence similarity (95%). MicroLOCK can reversibly detect microRNA targets in a tiny amount of biological sample (2 μL) at 25 °C with a higher sensitivity (LOD 1.3 fM) without any reverse transcription or amplification. MicroLOCK can hybridize the target with fast kinetic (about 30 min), high duplex stability without interferences from the polymer interface, showing high signal-to-noise ratio (up to S/N = 7.3). MicroLOCK also demonstrated excellent resistance to highly nuclease-rich environments, in real samples. These findings represent a great breakthrough for using the LNA in developing low-cost biosensing approaches and can be applied not only for nucleic acids and protein detection but also for real-time imaging and quantitative assessment of gene targeting both in vitro and in vivo.
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Affiliation(s)
- Sabrina Napoletano
- Interdisciplinary Research Centre on Biomaterials (CRIB), Università degli Studi di Napoli "Federico II", Piazzale Tecchio 80, 80125, Naples, Italy; Center for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125, Naples, Italy
| | - Edmondo Battista
- Department of Innovative Technologies in Medicine & Dentistry, University "G. d'Annunzio" Chieti-Pescara, Via dei Vestini, 31, 66100, Chieti, Italy
| | - Paolo Antonio Netti
- Interdisciplinary Research Centre on Biomaterials (CRIB), Università degli Studi di Napoli "Federico II", Piazzale Tecchio 80, 80125, Naples, Italy; Dipartimento di Ingegneria Chimica del Materiali e della Produzione Industriale (DICMAPI), University "Federico II", Piazzale Tecchio 80, 80125, Naples, Italy; Center for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125, Naples, Italy
| | - Filippo Causa
- Interdisciplinary Research Centre on Biomaterials (CRIB), Università degli Studi di Napoli "Federico II", Piazzale Tecchio 80, 80125, Naples, Italy; Dipartimento di Ingegneria Chimica del Materiali e della Produzione Industriale (DICMAPI), University "Federico II", Piazzale Tecchio 80, 80125, Naples, Italy; Center for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125, Naples, Italy.
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2
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Dey S, Rivas-Barbosa R, Sciortino F, Zaccarelli E, Zijlstra P. Biomolecular interactions on densely coated nanoparticles: a single-molecule perspective. NANOSCALE 2024; 16:4872-4879. [PMID: 38318671 DOI: 10.1039/d3nr06140j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
DNA-modified gold nanoparticles (AuNPs) play a pivotal role in bio-nanotechnology, driving advancements in bio-sensing, bio-imaging, and drug delivery. Synthetic protocols have focused on maximizing the receptor density on particles by fine-tuning chemical conditions, particularly for DNA. Despite their significance, the understanding of hybridization kinetics on functionalized AuNPs is lacking, particularly how this kinetics depends on DNA density and to what extent it varies from particle-to-particle. This study explores the molecular mechanisms of DNA hybridization on densely coated AuNPs by employing a combination of single-molecule microscopy and coarse-grained molecular dynamics simulations providing a quantification of the molecular rate constants for single particles. Our findings demonstrate that DNA receptor density and the presence of spacer strands profoundly impact association kinetics, with short spacers enhancing association rates by up to ∼15-fold. In contrast, dissociation kinetics are largely unaffected by receptor density within the studied range. Single-particle analysis directly reveals variability in hybridization kinetics, which is analyzed in terms of intra- and inter-particle heterogeneity. A coarse-grained DNA model that quantifies hybridization kinetics on densely coated surfaces further corroborates our experimental results, additionally shedding light on how transient base pairing within the DNA coating influences kinetics. This integrated approach underscores the value of single-molecule studies and simulations for understanding DNA dynamics on densely coated nanoparticle surfaces, offering guidance for designing DNA-functionalized nanoparticles in sensor applications.
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Affiliation(s)
- Swayandipta Dey
- Eindhoven University of Technology, Department of Applied Physics and Science Education, Postbus 513, 5600 MB, Eindhoven, The Netherlands.
- Institute for Complex Molecular Systems and Eindhoven Hendrik Casimir Institute, Eindhoven University of Technology, The Netherlands
| | - Rodrigo Rivas-Barbosa
- Dipartmento di Fisica, Universita' di Roma "La Sapienza", Piazzale Moro 5, Roma I-00185, Italy
| | - Francesco Sciortino
- Dipartmento di Fisica, Universita' di Roma "La Sapienza", Piazzale Moro 5, Roma I-00185, Italy
| | - Emanuela Zaccarelli
- Dipartmento di Fisica, Universita' di Roma "La Sapienza", Piazzale Moro 5, Roma I-00185, Italy
- CNR Institute of Complex Systems, Uos Sapienza, Piazzale Aldo Moro 2, 00185 Roma, Italy
| | - Peter Zijlstra
- Eindhoven University of Technology, Department of Applied Physics and Science Education, Postbus 513, 5600 MB, Eindhoven, The Netherlands.
- Institute for Complex Molecular Systems and Eindhoven Hendrik Casimir Institute, Eindhoven University of Technology, The Netherlands
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3
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Lamberti V, Dolci M, Zijlstra P. Continuous Monitoring Biosensing Mediated by Single-Molecule Plasmon-Enhanced Fluorescence in Complex Matrices. ACS NANO 2024. [PMID: 38334312 PMCID: PMC10883122 DOI: 10.1021/acsnano.3c12428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
Continuous detection of critical markers directly at the point of interest and in undiluted biological fluids represents the next fundamental step in biosensing. The goal of realizing such a platform is utterly challenging because it requires a reversible biosensor that enables the tracking of pico- to nanomolar molecular concentrations over long time spans in a compact device. Here we describe a sensing method based on plasmon-enhanced fluorescence capable of single-molecule detection of unlabeled analyte by employing biofunctionalized gold nanoparticles. The very strong plasmon-enhanced fluorescence signals allow for single-molecule sensing in unaltered biological media, while the use of low-affinity interactions ensures the continuous tracking of increasing and decreasing analyte concentrations with picomolar sensitivity. We demonstrate the use of a sandwich assay for a DNA cancer marker with a limit of detection of picomolar and a time response of 10 min. The enhanced single-molecule signals will allow for miniaturization into a small and cheap platform with multiplexing capability for application in point-of-care diagnostics, monitoring of industrial processes, and safe keeping of the environment.
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Affiliation(s)
- Vincenzo Lamberti
- Eindhoven University of Technology, Department of Applied Physics and Science Education and Institute for Complex Molecular Systems, 5600 MB Eindhoven, The Netherlands
| | - Mathias Dolci
- Eindhoven University of Technology, Department of Applied Physics and Science Education and Institute for Complex Molecular Systems, 5600 MB Eindhoven, The Netherlands
| | - Peter Zijlstra
- Eindhoven University of Technology, Department of Applied Physics and Science Education and Institute for Complex Molecular Systems, 5600 MB Eindhoven, The Netherlands
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4
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Barulin A, Kim Y, Oh DK, Jang J, Park H, Rho J, Kim I. Dual-wavelength metalens enables Epi-fluorescence detection from single molecules. Nat Commun 2024; 15:26. [PMID: 38167868 PMCID: PMC10761847 DOI: 10.1038/s41467-023-44407-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 12/12/2023] [Indexed: 01/05/2024] Open
Abstract
Single molecule fluorescence spectroscopy is at the heart of molecular biophysics research and the most sensitive biosensing assays. The growing demand for precision medicine and environmental monitoring requires the creation of miniaturized and portable sensing platforms. However, the need for highly sophisticated objective lenses has precluded the development of single molecule detection systems for truly portable devices. Here, we propose a dielectric metalens device of submicrometer thickness to excite and collect light from fluorescent molecules instead of an objective lens. The high numerical aperture, high focusing efficiency, and dual-wavelength operation of the metalens enable the implementation of fluorescence correlation spectroscopy with a single Alexa 647 molecule in the focal volume. Moreover, the metalens enables real-time monitoring of individual fluorescent nanoparticle transitions and identification of hydrodynamic diameters ranging from a few to hundreds of nanometers. This advancement in sensitivity extends the application of the metalens technology to ultracompact single-molecule sensors.
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Affiliation(s)
- Aleksandr Barulin
- Department of Biophysics, Institute of Quantum Biophysics, Sungkyunkwan University, Suwon, 16419, Republic of Korea
- Department of Intelligent Precision Healthcare Convergence, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Yeseul Kim
- Department of Mechanical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Dong Kyo Oh
- Department of Mechanical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Jaehyuck Jang
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
- POSCO-POSTECH-RIST Convergence Research Center for Flat Optics and Metaphotonics, Pohang, 37673, Republic of Korea
| | - Hyemi Park
- Department of Biophysics, Institute of Quantum Biophysics, Sungkyunkwan University, Suwon, 16419, Republic of Korea
- Department of Intelligent Precision Healthcare Convergence, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Junsuk Rho
- Department of Mechanical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea.
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea.
- POSCO-POSTECH-RIST Convergence Research Center for Flat Optics and Metaphotonics, Pohang, 37673, Republic of Korea.
- National Institute of Nanomaterials Technology (NINT), Pohang, 37673, Republic of Korea.
| | - Inki Kim
- Department of Biophysics, Institute of Quantum Biophysics, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
- Department of Intelligent Precision Healthcare Convergence, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
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5
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Roy P, Zhu S, Claude JB, Liu J, Wenger J. Ultraviolet Resonant Nanogap Antennas with Rhodium Nanocube Dimers for Enhancing Protein Intrinsic Autofluorescence. ACS NANO 2023; 17:22418-22429. [PMID: 37931219 PMCID: PMC10690780 DOI: 10.1021/acsnano.3c05008] [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: 06/04/2023] [Accepted: 09/07/2023] [Indexed: 11/08/2023]
Abstract
Plasmonic optical nanoantennas offer compelling solutions for enhancing light-matter interactions at the nanoscale. However, until now, their focus has been mainly limited to the visible and near-infrared regions, overlooking the immense potential of the ultraviolet (UV) range, where molecules exhibit their strongest absorption. Here, we present the realization of UV resonant nanogap antennas constructed from paired rhodium nanocubes. Rhodium emerges as a robust alternative to aluminum, offering enhanced stability in wet environments and ensuring reliable performance in the UV range. Our results showcase the nanoantenna's ability to enhance the UV autofluorescence of label-free streptavidin and hemoglobin proteins. We achieve significant enhancements of the autofluorescence brightness per protein by up to 120-fold and reach zeptoliter detection volumes, enabling UV autofluorescence correlation spectroscopy (UV-FCS) at high concentrations of several tens of micromolar. We investigate the modulation of fluorescence photokinetic rates and report excellent agreement between the experimental results and numerical simulations. This work expands the applicability of plasmonic nanoantennas to the deep UV range, unlocking the investigation of label-free proteins at physiological concentrations.
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Affiliation(s)
- Prithu Roy
- Aix
Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, AMUTech, 13013 Marseille, France
| | - Siyuan Zhu
- Department
of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Jean-Benoît Claude
- Aix
Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, AMUTech, 13013 Marseille, France
| | - Jie Liu
- Department
of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Jérôme Wenger
- Aix
Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, AMUTech, 13013 Marseille, France
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6
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Dolci M, Wang Y, Nooteboom SW, Soto Rodriguez PED, Sánchez S, Albertazzi L, Zijlstra P. Real-Time Optical Tracking of Protein Corona Formation on Single Nanoparticles in Serum. ACS NANO 2023; 17:20167-20178. [PMID: 37802067 PMCID: PMC10604089 DOI: 10.1021/acsnano.3c05872] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 09/22/2023] [Indexed: 10/08/2023]
Abstract
The formation of a protein corona, where proteins spontaneously adhere to the surface of nanomaterials in biological environments, leads to changes in their physicochemical properties and subsequently affects their intended biomedical functionalities. Most current methods to study protein corona formation are ensemble-averaging and either require fluorescent labeling, washing steps, or are only applicable to specific types of particles. Here we introduce real-time all-optical nanoparticle analysis by scattering microscopy (RONAS) to track the formation of protein corona in full serum, at the single-particle level, without any labeling. RONAS uses optical scattering microscopy and enables real-time and in situ tracking of protein adsorption on metallic and dielectric nanoparticles with different geometries directly in blood serum. We analyzed the adsorbed protein mass, the affinity, and the kinetics of the protein adsorption at the single particle level. While there is a high degree of heterogeneity from particle to particle, the predominant factor in protein adsorption is surface chemistry rather than the underlying nanoparticle material or size. RONAS offers an in-depth understanding of the mechanisms related to protein coronas and, thus, enables the development of strategies to engineer efficient bionanomaterials.
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Affiliation(s)
- Mathias Dolci
- Department
of Applied Physics and Science Education, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Yuyang Wang
- Department
of Applied Physics and Science Education, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Sjoerd W. Nooteboom
- Department
of Applied Physics and Science Education, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | | | - Samuel Sánchez
- Institute
for Bioengineering of Catalonia (IBEC), The Barcelona Institute for
Science and Technology (BIST), Baldiri Reixac 10-12, 08028 Barcelona, Spain
- Institució
Catalana de Recerca i Estudis Avançats (ICREA), Passeig de Lluís Companys,
23, 08010 Barcelona, Spain
| | - Lorenzo Albertazzi
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
- Department
of Biomedical Engineering, Eindhoven University
of Technology, 5600 MB Eindhoven The Netherlands
| | - Peter Zijlstra
- Department
of Applied Physics and Science Education, 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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7
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Bergkamp MH, Cajigas S, van IJzendoorn LJ, Prins MW. High-Throughput Single-Molecule Sensors: How Can the Signals Be Analyzed in Real Time for Achieving Real-Time Continuous Biosensing? ACS Sens 2023; 8:2271-2281. [PMID: 37216442 PMCID: PMC10294250 DOI: 10.1021/acssensors.3c00245] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/05/2023] [Indexed: 05/24/2023]
Abstract
Single-molecule sensors collect statistics of single-molecule interactions, and the resulting data can be used to determine concentrations of analyte molecules. The assays are generally end-point assays and are not designed for continuous biosensing. For continuous biosensing, a single-molecule sensor needs to be reversible, and the signals should be analyzed in real time in order to continuously report output signals, with a well-controlled time delay and measurement precision. Here, we describe a signal processing architecture for real-time continuous biosensing based on high-throughput single-molecule sensors. The key aspect of the architecture is the parallel computation of multiple measurement blocks that enables continuous measurements over an endless time span. Continuous biosensing is demonstrated for a single-molecule sensor with 10,000 individual particles that are tracked as a function of time. The continuous analysis includes particle identification, particle tracking, drift correction, and detection of the discrete timepoints where individual particles switch between bound and unbound states, yielding state transition statistics that relate to the analyte concentration in solution. The continuous real-time sensing and computation were studied for a reversible cortisol competitive immunosensor, showing how the precision and time delay of cortisol monitoring are controlled by the number of analyzed particles and the size of the measurement blocks. Finally, we discuss how the presented signal processing architecture can be applied to various single-molecule measurement methods, allowing these to be developed into continuous biosensors.
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Affiliation(s)
- Max H. Bergkamp
- Department
of Biomedical Engineering, Eindhoven University
of Technology, Eindhoven 5612 AE, The Netherlands
- Institute
for Complex Molecular Systems (ICMS), Eindhoven
University of Technology, Eindhoven 5612 AE, The Netherlands
| | | | - Leo J. van IJzendoorn
- Department
of Applied Physics and Science Education, Eindhoven University of Technology, Eindhoven 5612 AE, The Netherlands
- Institute
for Complex Molecular Systems (ICMS), Eindhoven
University of Technology, Eindhoven 5612 AE, The Netherlands
| | - Menno W.J. Prins
- Department
of Biomedical Engineering, Eindhoven University
of Technology, Eindhoven 5612 AE, The Netherlands
- Department
of Applied Physics and Science Education, Eindhoven University of Technology, Eindhoven 5612 AE, The Netherlands
- Institute
for Complex Molecular Systems (ICMS), Eindhoven
University of Technology, Eindhoven 5612 AE, The Netherlands
- Helia
Biomonitoring, Eindhoven 5612 AR, The Netherlands
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8
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Herrera-Domínguez M, Morales-Luna G, Mahlknecht J, Cheng Q, Aguilar-Hernández I, Ornelas-Soto N. Optical Biosensors and Their Applications for the Detection of Water Pollutants. BIOSENSORS 2023; 13:bios13030370. [PMID: 36979582 PMCID: PMC10046542 DOI: 10.3390/bios13030370] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/01/2023] [Accepted: 03/02/2023] [Indexed: 05/14/2023]
Abstract
The correct detection and quantification of pollutants in water is key to regulating their presence in the environment. Biosensors offer several advantages, such as minimal sample preparation, short measurement times, high specificity and sensibility and low detection limits. The purpose of this review is to explore the different types of optical biosensors, focusing on their biological elements and their principle of operation, as well as recent applications in the detection of pollutants in water. According to our literature review, 33% of the publications used fluorescence-based biosensors, followed by surface plasmon resonance (SPR) with 28%. So far, SPR biosensors have achieved the best results in terms of detection limits. Although less common (22%), interferometers and resonators (4%) are also highly promising due to the low detection limits that can be reached using these techniques. In terms of biological recognition elements, 43% of the published works focused on antibodies due to their high affinity and stability, although they could be replaced with molecularly imprinted polymers. This review offers a unique compilation of the most recent work in the specific area of optical biosensing for water monitoring, focusing on both the biological element and the transducer used, as well as the type of target contaminant. Recent technological advances are discussed.
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Affiliation(s)
- Marcela Herrera-Domínguez
- Tecnológico de Monterrey, Escuela de Ingeniería y Ciencias, Ave. Eugenio Garza Sada 2501, Monterrey 64849, Mexico
| | - Gesuri Morales-Luna
- Departamento de Física y Matemáticas, Universidad Iberoamericana, Prolongación Paseo de la Reforma 880, Mexico City 01219, Mexico
| | - Jürgen Mahlknecht
- Tecnológico de Monterrey, Escuela de Ingeniería y Ciencias, Ave. Eugenio Garza Sada 2501, Monterrey 64849, Mexico
| | - Quan Cheng
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Iris Aguilar-Hernández
- Tecnológico de Monterrey, Escuela de Ingeniería y Ciencias, Ave. Eugenio Garza Sada 2501, Monterrey 64849, Mexico
- Correspondence: (I.A.-H.); (N.O.-S.)
| | - Nancy Ornelas-Soto
- Tecnológico de Monterrey, Escuela de Ingeniería y Ciencias, Ave. Eugenio Garza Sada 2501, Monterrey 64849, Mexico
- Correspondence: (I.A.-H.); (N.O.-S.)
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