1
|
Zhang H, Zhang W, Zuo Z, Yang J. Towards ultra-low-cost smartphone microscopy. Microsc Res Tech 2024; 87:1521-1533. [PMID: 38419399 DOI: 10.1002/jemt.24535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/17/2023] [Accepted: 02/14/2024] [Indexed: 03/02/2024]
Abstract
The outbreak of COVID-19 exposed the inadequacy of our technical tools for home health surveillance, and recent studies have shown the potential of smartphones as a universal optical microscopic imaging platform for such applications. However, most of them use laboratory-grade optomechanical components and transmitted illuminations to ensure focus tuning capability and imaging quality, which keeps the cost of the equipment high. Here, we propose an ultra-low-cost solution for smartphone microscopy. To realize focus tunability, we designed a seesaw-like structure capable of converting large displacements on one side into small displacements on the other (reduced to ∼9.1%), which leverages the intrinsic flexibility of 3D printing materials. We achieved a focus-tuning accuracy of ∼5 𝜇m, which is 40 times higher than the machining accuracy of the 3D-printed lens holder itself. For microscopic imaging, we used an off-the-shelf smartphone camera lens as the objective and the built-in flashlight as the illumination. To compensate for the resulting image quality degradation, we developed a learning-based image enhancement method. We used the CycleGAN architecture to establish the mapping from smartphone microscope images to benchtop microscope images without pairing. We verified the imaging performance on different biomedical samples. Except for the smartphone, we kept the full costs of the device under 4 USD. We think these efforts to lower the costs of smartphone microscopes will benefit their applications in various scenarios, such as point-of-care testing, on-site diagnosis, and home health surveillance. RESEARCH HIGHLIGHTS: We propose a solution for ultra-low-cost smartphone microscopy. Utilizing the flexibility of 3D-printed material, we can achieve focusing accuracy of ∼5 𝜇m. Such a low-cost device will benefit point-of-care diagnosis and home health surveillance.
Collapse
Affiliation(s)
- Haoran Zhang
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Weiyi Zhang
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Zirui Zuo
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Jianlong Yang
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| |
Collapse
|
2
|
Raju G, Ranjan A, Banik S, Poddar A, Managuli V, Mazumder N. A commentary on the development and use of smartphone imaging devices. Biophys Rev 2024; 16:151-163. [PMID: 38737211 PMCID: PMC11078910 DOI: 10.1007/s12551-023-01175-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 12/04/2023] [Indexed: 05/14/2024] Open
Abstract
Current-age smartphones are known for their wide array of functionality and are now being utilized in the field of healthcare and medicine due to their proven capabilities as smartphone imaging devices (SIDs). Recent technical advancements enabled the integration of special add-on lenses with smartphones to transform them into SIDs. With the rising demand for efficient point-of-care (PoC) devices for better diagnostic applications, SIDs will be a one-stop solution. Additionally, portability, user-friendliness and low-cost make it accessible for all even at remote locations. Furthermore, improvements in resolution, magnification and field-of-view (FOV) have attracted the scientific community to use SIDs in various biomedical applications such as disease diagnosis, food quality control and pathogen detection. SIDs can be arranged in various combinational setups by using different illumination sources and optics to achieve suitable contrast and visibility of the specimen under study. This Commentary illustrates the various illumination sources used in SID and also spotlights their design and applications.
Collapse
Affiliation(s)
- Gagan Raju
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576104 India
| | - Aashrayi Ranjan
- Department of Mechanical and Industrial Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka 576104 India
| | - Soumyabrata Banik
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576104 India
| | - Ashmini Poddar
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576104 India
| | - Vishwanath Managuli
- Department of Mechanical and Industrial Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka 576104 India
| | - Nirmal Mazumder
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576104 India
| |
Collapse
|
3
|
Li C, Chen J, Man T, Chen B, Li J, Li Q, Yang X, Wan Y, Fan C, Shen J. DNA Framework-Engineered Assembly of Cyanine Dyes for Structural Identification of Nucleic Acids. JACS AU 2024; 4:1125-1133. [PMID: 38559725 PMCID: PMC10976577 DOI: 10.1021/jacsau.3c00826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 02/02/2024] [Accepted: 02/07/2024] [Indexed: 04/04/2024]
Abstract
DNA nanostructures serve as precise templates for organizing organic dyes, enabling the creation of programmable artificial photonic systems with efficient light-harvesting and energy transfer capabilities. However, regulating the organization of organic dyes on DNA frameworks remains a great challenge. In this study, we investigated the factors influencing the self-assembly behavior of cyanine dye K21 on DNA frameworks. We observed that K21 exhibited diverse assembly modes, including monomers, H-aggregates, J-aggregates, and excimers, when combined with DNA frameworks. By manipulating conditions such as the ion concentration, dye concentration, and structure of DNA frameworks, we successfully achieved precise control over the assembly modes of K21. Leveraging K21's microenvironment-sensitive fluorescence properties on DNA nanostructures, we successfully discriminated between the chirality and topology structures of physiologically relevant G-quadruplexes. This study provides valuable insights into the factors influencing the dynamic assembly behavior of organic dyes on DNA framework nanostructures, offering new perspectives for constructing functional supramolecular aggregates and identifying DNA secondary structures.
Collapse
Affiliation(s)
- Cong Li
- School
of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory,
Frontiers Science Center for Transformative Molecules and National
Center for Translational Medicine, Shanghai
Jiao Tong University, Shanghai 200240, China
| | - Jielin Chen
- School
of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory,
Frontiers Science Center for Transformative Molecules and National
Center for Translational Medicine, Shanghai
Jiao Tong University, Shanghai 200240, China
| | - Tiantian Man
- School
of Mechanical Engineering, Nanjing University
of Science and Technology, Nanjing 210094, China
| | - Bin Chen
- School
of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Jiang Li
- Institute
of Materiobiology, Department of Chemistry, College of Science, Shanghai University, Shanghai 200444, China
| | - Qian Li
- School
of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory,
Frontiers Science Center for Transformative Molecules and National
Center for Translational Medicine, Shanghai
Jiao Tong University, Shanghai 200240, China
| | - Xiurong Yang
- School
of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory,
Frontiers Science Center for Transformative Molecules and National
Center for Translational Medicine, Shanghai
Jiao Tong University, Shanghai 200240, China
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Ying Wan
- School
of Mechanical Engineering, Nanjing University
of Science and Technology, Nanjing 210094, China
| | - Chunhai Fan
- School
of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory,
Frontiers Science Center for Transformative Molecules and National
Center for Translational Medicine, Shanghai
Jiao Tong University, Shanghai 200240, China
| | - Jianlei Shen
- School
of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory,
Frontiers Science Center for Transformative Molecules and National
Center for Translational Medicine, Shanghai
Jiao Tong University, Shanghai 200240, China
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Grabenhorst L, Sturzenegger F, Hasler M, Schuler B, Tinnefeld P. Single-Molecule FRET at 10 MHz Count Rates. J Am Chem Soc 2024; 146:3539-3544. [PMID: 38266173 DOI: 10.1021/jacs.3c13757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
A bottleneck in many studies utilizing single-molecule Förster resonance energy transfer is the attainable photon count rate, as it determines the temporal resolution of the experiment. As many biologically relevant processes occur on time scales that are hardly accessible with currently achievable photon count rates, there has been considerable effort to find strategies to increase the stability and brightness of fluorescent dyes. Here, we use DNA nanoantennas to drastically increase the achievable photon count rates and observe fast biomolecular dynamics in the small volume between two plasmonic nanoparticles. As a proof of concept, we observe the coupled folding and binding of two intrinsically disordered proteins, which form transient encounter complexes with lifetimes on the order of 100 μs. To test the limits of our approach, we also investigated the hybridization of a short single-stranded DNA to its complementary counterpart, revealing a transition path time of 17 μs at photon count rates of around 10 MHz, which is an order-of-magnitude improvement compared to the state of the art. Concomitantly, the photostability was increased, enabling many seconds long megahertz fluorescence time traces. Due to the modular nature of the DNA origami method, this platform can be adapted to a broad range of biomolecules, providing a promising approach to study previously unobservable ultrafast biophysical processes.
Collapse
Affiliation(s)
- Lennart Grabenhorst
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, 81377 München, Germany
| | | | - Moa Hasler
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
- Department of Physics, University of Zurich, 8057 Zurich, Switzerland
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, 81377 München, Germany
| |
Collapse
|
6
|
Bauer J, Reichl A, Tinnefeld P. Kinetic Referencing Allows Identification of Epigenetic Cytosine Modifications by Single-Molecule Hybridization Kinetics and Superresolution DNA-PAINT Microscopy. ACS NANO 2024; 18:1496-1503. [PMID: 38157484 DOI: 10.1021/acsnano.3c08451] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
We develop a DNA origami-based internal kinetic referencing system with a colocalized reference and target molecule to provide increased sensitivity and robustness for transient binding kinetics. To showcase this, we investigate the subtle changes in binding strength of DNA oligonucleotide hybrids induced by cytosine modifications. These cytosine modifications, especially 5-methylcytosine but also its oxidized derivatives, have been increasingly studied in the context of epigenetics. Recently revealed correlations of epigenetic modifications and disease also render them interesting biomarkers for early diagnosis. Internal kinetic referencing allows us to probe and compare the influence of the different epigenetic cytosine modifications on the strengths of 7-nucleotide long DNA hybrids with one or two modified nucleotides by single-molecule imaging of their transient binding, revealing subtle differences in binding times. Interestingly, the influence of epigenetic modifications depends on their position in the DNA strand, and in the case of two modifications, effects are additive. The sensitivity of the assay indicates its potential for the direct detection of epigenetic disease markers.
Collapse
Affiliation(s)
- Julian Bauer
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
| | - Andreas Reichl
- Department of Chemistry, Ludwig-Maximilians-Universität München, Würmtalstraße 201, 81377 München, Germany
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
| |
Collapse
|
7
|
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.
Collapse
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.
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Kanehira Y, Tapio K, Wegner G, Kogikoski S, Rüstig S, Prietzel C, Busch K, Bald I. The Effect of Nanoparticle Composition on the Surface-Enhanced Raman Scattering Performance of Plasmonic DNA Origami Nanoantennas. ACS NANO 2023; 17:21227-21239. [PMID: 37847540 DOI: 10.1021/acsnano.3c05464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
A versatile generation of plasmonic nanoparticle dimers for surface-enhanced Raman scattering (SERS) is presented by combining a DNA origami nanofork and spherical and nonspherical Au or Ag nanoparticles. Combining different nanoparticle species with a DNA origami nanofork to form DNA origami nanoantennas (DONAs), the plasmonic nanoparticle dimers can be optimized for a specific excitation wavelength in SERS. The preparation of such nanoparticle dimers is robust enough to enable the characterization of SERS intensities and SERS enhancement factors of dye-modified DONAs on a single dimer level by measuring in total several thousands of dimers from five different dimer designs, each functionalized with three different Raman reporter molecules and measured at four different excitation wavelengths. Based on these data, SERS enhancement factor (EF) distributions have been determined for each dimer design and excitation wavelengths. The structures and measurement conditions with the highest EFs are suitable for single-molecule SERS (SM-SERS), which is realized by placing single dye molecules into hot spots. We demonstrate that the probability of placing single molecules in a strongly enhancing hot spot for SM-SERS can be increased by using anisotropic nanoparticles with several sharp edges, such as nanoflowers. Combining a Ag nanoparticle with a Au particle in one dimer structure allows for a broadband excitation covering almost the whole visible range. The most versatile plasmonic dimer structure for SERS combines a spherical Ag nanoparticle with a Au nanoflower. Employing the discontinuous Galerkin time domain method, we numerically investigate the bare, symmetric dimers with respect to spectral and near-field properties, showing that, indeed, the nanoflowers induce multiple hot spots located at the edges which surpass the intensity of the spherical dimers, indicating the possibility for SM-SERS. The presented DONA structures and SERS data provide a robust basis for applying such designs as versatile SERS tags and as substrates for SM-SERS measurements.
Collapse
Affiliation(s)
- Yuya Kanehira
- Hybrid Nanostructures Lab, Institute of Chemistry, University of Potsdam, 14476 Potsdam, Germany
| | - Kosti Tapio
- Hybrid Nanostructures Lab, Institute of Chemistry, University of Potsdam, 14476 Potsdam, Germany
| | - Gino Wegner
- AG Theoretical Optics & Photonics, Institute of Physics, Humboldt University of Berlin, 12489 Berlin, Germany
- Institute of Condensed Matter Theory and Optics, Friedrich-Schiller-University Jena, 07743 Jena, Germany
| | - Sergio Kogikoski
- Hybrid Nanostructures Lab, Institute of Chemistry, University of Potsdam, 14476 Potsdam, Germany
| | - Sibylle Rüstig
- Hybrid Nanostructures Lab, Institute of Chemistry, University of Potsdam, 14476 Potsdam, Germany
| | - Claudia Prietzel
- Hybrid Nanostructures Lab, Institute of Chemistry, University of Potsdam, 14476 Potsdam, Germany
| | - Kurt Busch
- AG Theoretical Optics & Photonics, Institute of Physics, Humboldt University of Berlin, 12489 Berlin, Germany
- Max Born Institute, 12489 Berlin, Germany
| | - Ilko Bald
- Hybrid Nanostructures Lab, Institute of Chemistry, University of Potsdam, 14476 Potsdam, Germany
| |
Collapse
|
10
|
Richter L, Szalai AM, Manzanares-Palenzuela CL, Kamińska I, Tinnefeld P. Exploring the Synergies of Single-Molecule Fluorescence and 2D Materials Coupled by DNA. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2303152. [PMID: 37670535 DOI: 10.1002/adma.202303152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/31/2023] [Indexed: 09/07/2023]
Abstract
The world of 2D materials is steadily growing, with numerous researchers attempting to discover, elucidate, and exploit their properties. Approaches relying on the detection of single fluorescent molecules offer a set of advantages, for instance, high sensitivity and specificity, that allow the drawing of conclusions with unprecedented precision. Herein, it is argued how the study of 2D materials benefits from fluorescence-based single-molecule modalities, and vice versa. A special focus is placed on DNA, serving as a versatile adaptor when anchoring single dye molecules to 2D materials. The existing literature on the fruitful combination of the two fields is reviewed, and an outlook on the additional synergies that can be created between them provided.
Collapse
Affiliation(s)
- Lars Richter
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, Haus E, 81377, München, Germany
| | - Alan M Szalai
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, Haus E, 81377, München, Germany
| | - C Lorena Manzanares-Palenzuela
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, Haus E, 81377, München, Germany
| | - Izabela Kamińska
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, Haus E, 81377, München, Germany
- Institute of Physical Chemistry of the Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, Haus E, 81377, München, Germany
| |
Collapse
|
11
|
Chen C, Luo X, Kaplan AE, Bawendi MG, Macfarlane RJ, Bathe M. Ultrafast dense DNA functionalization of quantum dots and rods for scalable 2D array fabrication with nanoscale precision. SCIENCE ADVANCES 2023; 9:eadh8508. [PMID: 37566651 PMCID: PMC10421044 DOI: 10.1126/sciadv.adh8508] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/14/2023] [Indexed: 08/13/2023]
Abstract
Scalable fabrication of two-dimensional (2D) arrays of quantum dots (QDs) and quantum rods (QRs) with nanoscale precision is required for numerous device applications. However, self-assembly-based fabrication of such arrays using DNA origami typically suffers from low yield due to inefficient QD and QR DNA functionalization. In addition, it is challenging to organize solution-assembled DNA origami arrays on 2D device substrates while maintaining their structural fidelity. Here, we reduced manufacturing time from a few days to a few minutes by preparing high-density DNA-conjugated QDs/QRs from organic solution using a dehydration and rehydration process. We used a surface-assisted large-scale assembly (SALSA) method to construct 2D origami lattices directly on solid substrates to template QD and QR 2D arrays with orientational control, with overall loading yields exceeding 90%. Our fabrication approach enables the scalable, high fidelity manufacturing of 2D addressable QDs and QRs with nanoscale orientational and spacing control for functional 2D photonic devices.
Collapse
Affiliation(s)
- Chi Chen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Xin Luo
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alexander E. K. Kaplan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Moungi G. Bawendi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Robert J. Macfarlane
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| |
Collapse
|
12
|
Semeniak D, Cruz DF, Chilkoti A, Mikkelsen MH. Plasmonic Fluorescence Enhancement in Diagnostics for Clinical Tests at Point-of-Care: A Review of Recent Technologies. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2107986. [PMID: 35332957 PMCID: PMC9986847 DOI: 10.1002/adma.202107986] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 01/26/2022] [Indexed: 05/31/2023]
Abstract
Fluorescence-based biosensors have widely been used in the life-sciences and biomedical applications due to their low limit of detection and a diverse selection of fluorophores that enable simultaneous measurements of multiple biomarkers. Recent research effort has been made to implement fluorescent biosensors into the exploding field of point-of-care testing (POCT), which uses cost-effective strategies for rapid and affordable diagnostic testing. However, fluorescence-based assays often suffer from their feeble signal at low analyte concentrations, which often requires sophisticated, costly, and bulky instrumentation to maintain high detection sensitivity. Metal- and metal oxide-based nanostructures offer a simple solution to increase the output signal from fluorescent biosensors due to the generation of high field enhancements close to a metal or metal oxide surface, which has been shown to improve the excitation rate, quantum yield, photostability, and radiation pattern of fluorophores. This article provides an overview of existing biosensors that employ various strategies for fluorescence enhancement via nanostructures and have demonstrated the potential for use as POCT. Biosensors using nanostructures such as planar substrates, freestanding nanoparticles, and metal-dielectric-metal nanocavities are discussed with an emphasis placed on technologies that have shown promise towards POCT applications without the need for centralized laboratories.
Collapse
Affiliation(s)
- Daria Semeniak
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Daniela F. Cruz
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Maiken H. Mikkelsen
- Department of Electrical and Computer Engineering, Duke University, Durham, NC 27708, USA
| |
Collapse
|
13
|
Nath P, Mahtaba KR, Ray A. Fluorescence-Based Portable Assays for Detection of Biological and Chemical Analytes. SENSORS (BASEL, SWITZERLAND) 2023; 23:s23115053. [PMID: 37299780 DOI: 10.3390/s23115053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/16/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023]
Abstract
Fluorescence-based detection techniques are part of an ever-expanding field and are widely used in biomedical and environmental research as a biosensing tool. These techniques have high sensitivity, selectivity, and a short response time, making them a valuable tool for developing bio-chemical assays. The endpoint of these assays is defined by changes in fluorescence signal, in terms of its intensity, lifetime, and/or shift in spectrum, which is monitored using readout devices such as microscopes, fluorometers, and cytometers. However, these devices are often bulky, expensive, and require supervision to operate, which makes them inaccessible in resource-limited settings. To address these issues, significant effort has been directed towards integrating fluorescence-based assays into miniature platforms based on papers, hydrogels, and microfluidic devices, and to couple these assays with portable readout devices like smartphones and wearable optical sensors, thereby enabling point-of-care detection of bio-chemical analytes. This review highlights some of the recently developed portable fluorescence-based assays by discussing the design of fluorescent sensor molecules, their sensing strategy, and the fabrication of point-of-care devices.
Collapse
Affiliation(s)
- Peuli Nath
- Department of Physics and Astronomy, University of Toledo, Toledo, OH 43606, USA
| | - Kazi Ridita Mahtaba
- Department of Physics and Astronomy, University of Toledo, Toledo, OH 43606, USA
| | - Aniruddha Ray
- Department of Physics and Astronomy, University of Toledo, Toledo, OH 43606, USA
| |
Collapse
|
14
|
Liu L, Tibbs J, Li N, Bacon A, Shepherd S, Lee H, Chauhan N, Demirci U, Wang X, Cunningham BT. A photonic resonator interferometric scattering microscope for label-free detection of nanometer-scale objects with digital precision in point-of-use environments. Biosens Bioelectron 2023; 228:115197. [PMID: 36905862 PMCID: PMC10072782 DOI: 10.1016/j.bios.2023.115197] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/27/2023] [Accepted: 03/04/2023] [Indexed: 03/08/2023]
Abstract
Label-free detection and digital counting of nanometer-scaled objects such as nanoparticles, viruses, extracellular vesicles, and protein molecules enable a wide range of applications in cancer diagnostics, pathogen detection, and life science research. Here, we report the design, implementation, and characterization of a compact Photonic Resonator Interferometric Scattering Microscope (PRISM) designed for point-of-use environments and applications. The contrast of interferometric scattering microscopy is amplified through a photonic crystal surface, upon which scattered light from an object combines with illumination from a monochromatic source. The use of a photonic crystal substrate for interferemetric scattering microscopy results in reduced requirements for high-intensity lasers or oil-immersion objectives, thus opening a pathway toward instruments that are more suitable for environments outside the optics laboratory. The instrument incorporates two innovative elements that facilitate operation on a desktop in ordinary laboratory environments by users that do not have optics expertise. First, because scattering microscopes are extremely sensitive to vibration, we incorporated an inexpensive but effective solution of suspending the instrument's main components from a rigid metal framework using elastic bands, resulting in an average of 28.7 dBV reduction in vibration amplitude compared to an office desk. Second, an automated focusing module based on the principle of total internal reflection maintains the stability of image contrast over time and spatial position. In this work, we characterize the system's performance by measuring the contrast from gold nanoparticles with diameters in the 10-40 nm range and by observing various biological analytes, including HIV virus, SARS-CoV-2 virus, exosome, and ferritin protein.
Collapse
Affiliation(s)
- Leyang Liu
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Joseph Tibbs
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Nantao Li
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Amanda Bacon
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Skye Shepherd
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Hankeun Lee
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Neha Chauhan
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Utkan Demirci
- Canary Center at Stanford for Cancer Early Detection, Stanford School of Medicine, Stanford University, Palo Alto, CA, 94304, USA
| | - Xing Wang
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Brian T Cunningham
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Cancer Center at Illinois, Urbana, IL, 61801, USA.
| |
Collapse
|
15
|
Kogikoski S, Ameixa J, Mostafa A, Bald I. Lab-on-a-DNA origami: nanoengineered single-molecule platforms. Chem Commun (Camb) 2023; 59:4726-4741. [PMID: 37000514 PMCID: PMC10111202 DOI: 10.1039/d3cc00718a] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 03/08/2023] [Indexed: 04/01/2023]
Abstract
DNA origami nanostructures are self-assembled into almost arbitrary two- and three-dimensional shapes from a long, single-stranded viral scaffold strand and a set of short artificial oligonucleotides. Each DNA strand can be functionalized individually using well-established DNA chemistry, representing addressable sites that allow for the nanometre precise placement of various chemical entities such as proteins, molecular chromophores, nanoparticles, or simply DNA motifs. By means of microscopic and spectroscopic techniques, these entities can be visualized or detected, and either their mutual interaction or their interaction with external stimuli such as radiation can be studied. This gives rise to the Lab-on-a-DNA origami approach, which is introduced in this Feature Article, and the state-of-the-art is summarized with a focus on light-harvesting nanoantennas and DNA platforms for single-molecule analysis either by optical spectroscopy or atomic force microscopy (AFM). Light-harvesting antennas can be generated by the precise arrangement of chromophores to channel and direct excitation energy. At the same time, plasmonic nanoparticles represent a complementary approach to focus light on the nanoscale. Plasmonic nanoantennas also allow for the observation of single molecules either by Raman scattering or fluorescence spectroscopy and DNA origami platforms provide unique opportunities to arrange nanoparticles and molecules to be studied. Finally, the analysis of single DNA motifs by AFM allows for an investigation of radiation-induced processes in DNA with unprecedented detail and accuracy.
Collapse
Affiliation(s)
- Sergio Kogikoski
- Institute of Chemistry, Hybrid Nanostructures, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany.
| | - João Ameixa
- Institute of Chemistry, Hybrid Nanostructures, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany.
| | - Amr Mostafa
- Institute of Chemistry, Hybrid Nanostructures, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany.
| | - Ilko Bald
- Institute of Chemistry, Hybrid Nanostructures, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany.
| |
Collapse
|
16
|
Mao M, Lin Z, Chen L, Zou Z, Zhang J, Dou Q, Wu J, Chen J, Wu M, Niu L, Fan C, Zhang Y. Modular DNA-Origami-Based Nanoarrays Enhance Cell Binding Affinity through the "Lock-and-Key" Interaction. J Am Chem Soc 2023; 145:5447-5455. [PMID: 36812464 DOI: 10.1021/jacs.2c13825] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Surface proteins of cells are generally recognized through receptor-ligand interactions (RLIs) in disease diagnosis, but their nonuniform spatial distribution and higher-order structure lead to low binding affinity. Constructing nanotopologies that match the spatial distribution of membrane proteins to improve the binding affinity remains a challenge. Inspired by the multiantigen recognition of immune synapses, we developed modular DNA-origami-based nanoarrays with multivalent aptamers. By adjusting the valency and interspacing of the aptamers, we constructed specific nanotopology to match the spatial distribution of target protein clusters and avoid potential steric hindrance. We found that the nanoarrays significantly enhanced the binding affinity of target cells and synergistically recognized low-affinity antigen-specific cells. In addition, DNA nanoarrays used for the clinical detection of circulating tumor cells successfully verified their precise recognition ability and high-affinity RLIs. Such nanoarrays will further promote the potential application of DNA materials in clinical detection and even cell membrane engineering.
Collapse
Affiliation(s)
- Miao Mao
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510006, China
| | - Zhun Lin
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510006, China
| | - Liang Chen
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510006, China
| | - Zhengyu Zou
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong 510080, China
| | - Jie Zhang
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510006, China
| | - Quanhao Dou
- Joint Laboratory of Optofluidic Technology and Systems, National Center for International Research on Green Optoelectronics, South China Academy of Advanced Optoelectronics, South China Normal University, Guangzhou, Guangdong 510006, China
| | - Jiacheng Wu
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510006, China
| | - Jinglin Chen
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510006, China
| | - Minhao Wu
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong 510080, China
| | - Li Niu
- Center for Advanced Analytical Science, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou, Guangdong 510006, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuanqing Zhang
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510006, China
| |
Collapse
|
17
|
Liu J, Zhan Y, Qiu B, Lin Z, Guo L. Portable Smartphone Platform Based on Aggregation-Induced Enhanced Emission Carbon Dots for Ratiometric Quantitative Sensing of Fluoride Ions. ACS Sens 2023; 8:884-892. [PMID: 36657970 DOI: 10.1021/acssensors.2c02589] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The development of an instrument-free, on-site, real-time, sensitive, and visualized fluoride-ion (F-) content rapid detection strategy is crucial to ensuring the health of the population. Smart microdevices that are portable, directly read, and easy to operate have recently attracted much attention. Herein, a ratiometric fluorescent probe (AA-CDs@[Ru(bpy)3]2+)-based smartphone sensing platform was developed for the detection of F-. The red fluorescent ruthenium bipyridine [Ru(bpy)3]2+ molecule was chosen as the reference signal, and the carbon dots (AA-CDs) with Al3+ aggregation-induced enhanced emission (AIE) were designed as the response signal. The ratiometric probe fluorescence changed continuously from red to cyan in response to different concentrations of F-, and the red-green-blue (RGB) channel values of the fluorescence image were extracted through the smartphone color recognition application (APP). There was a linear relationship between the blue-red (B/R) ratio and the F- concentration, with a limit of detection (LOD) of 1.53 μM, far below the allowable content of F- in drinking water prescribed by the World Health Organization. The F- content was rapidly detected on-site with satisfactory repeatability and relative standard deviation using several water and toothpaste samples as the real sample. The platform features low cost, portability, easy operation, and good stability, selectivity, and repeatability, which provides a powerful tool for the visual quantitative detection of smartphone-based microsensing platforms possibly in the fields of environmental protection, diagnosis, and food safety assessment.
Collapse
Affiliation(s)
- Jingjing Liu
- Fujian Universities and Colleges Engineering Research Center of Soft Plastic Packaging Technology for Food, Fujian Polytechnic Normal University, Fuqing, Fujian Province 350300, P. R. China
| | - Yuanjin Zhan
- Department of Chemistry, State Key Laboratory of Molecular Engineering of Polymers and Chem, Fudan University, Shanghai 200433, P. R. China
| | - Bin Qiu
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, College of Chemistry, Fuzhou University, Fuzhou 350116, PR China
| | - Zhenyu Lin
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, College of Chemistry, Fuzhou University, Fuzhou 350116, PR China
| | - Longhua Guo
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, College of Chemistry, Fuzhou University, Fuzhou 350116, PR China.,Jiaxing Key Laboratory of Molecular Recognition and Sensing, College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, PR China
| |
Collapse
|
18
|
Büber E, Schröder T, Scheckenbach M, Dass M, Franquelim HG, Tinnefeld P. DNA Origami Curvature Sensors for Nanoparticle and Vesicle Size Determination with Single-Molecule FRET Readout. ACS NANO 2023; 17:3088-3097. [PMID: 36735241 DOI: 10.1021/acsnano.2c11981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Particle size is an important characteristic of materials with a direct effect on their physicochemical features. Besides nanoparticles, particle size and surface curvature are particularly important in the world of lipids and cellular membranes as the cell membrane undergoes conformational changes in many biological processes which leads to diverging local curvature values. On account of that, it is important to develop cost-effective, rapid and sufficiently precise systems that can measure the surface curvature on the nanoscale that can be translated to size for spherical particles. As an alternative approach for particle characterization, we present flexible DNA nanodevices that can adapt to the curvature of the structure they are bound to. The curvature sensors use Fluorescence Resonance Energy Transfer (FRET) as the transduction mechanism on the single-molecule level. The curvature sensors consist of segmented DNA origami structures connected via flexible DNA linkers incorporating a FRET pair. The activity of the sensors was first demonstrated with defined binding to different DNA origami geometries used as templates. Then the DNA origami curvature sensors were applied to measure spherical silica beads having different size, and subsequently on lipid vesicles. With the designed sensors, we could reliably distinguish different sized nanoparticles within a size range of 50-300 nm as well as the bending angle range of 50-180°. This study helps with the development of more advanced modular-curvature sensing devices that are capable of determining the sizes of nanoparticles and biological complexes.
Collapse
Affiliation(s)
- Ece Büber
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-University, Butenandtstraße 5-13, 81377Munich, Germany
| | - Tim Schröder
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-University, Butenandtstraße 5-13, 81377Munich, Germany
| | - Michael Scheckenbach
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-University, Butenandtstraße 5-13, 81377Munich, Germany
| | - Mihir Dass
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-University, 80539Munich, Germany
| | - Henri G Franquelim
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152Martinsried, Germany
- Interfaculty Centre for Bioactive Matter, Leipzig University, c/o Deutscher Platz 5 (BBZ), 04109Leipzig, Germany
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-University, Butenandtstraße 5-13, 81377Munich, Germany
| |
Collapse
|
19
|
Dey S, Dolci M, Zijlstra P. Single-Molecule Optical Biosensing: Recent Advances and Future Challenges. ACS PHYSICAL CHEMISTRY AU 2023; 3:143-156. [PMID: 36968450 PMCID: PMC10037498 DOI: 10.1021/acsphyschemau.2c00061] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/22/2022] [Accepted: 12/22/2022] [Indexed: 01/13/2023]
Abstract
In recent years, the sensitivity and specificity of optical sensors has improved tremendously due to improvements in biochemical functionalization protocols and optical detection systems. As a result, single-molecule sensitivity has been reported in a range of biosensing assay formats. In this Perspective, we summarize optical sensors that achieve single-molecule sensitivity in direct label-free assays, sandwich assays, and competitive assays. We describe the advantages and disadvantages of single-molecule assays and summarize future challenges in the field including their optical miniaturization and integration, multimodal sensing capabilities, accessible time scales, and compatibility with real-life matrices such as biological fluids. We conclude by highlighting the possible application areas of optical single-molecule sensors that include not only healthcare but also the monitoring of the environment and industrial processes.
Collapse
Affiliation(s)
- Swayandipta Dey
- Eindhoven University of Technology, Department of Applied Physics, Eindhoven 5600 MB, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven, 5600 MB, The Netherlands
- Eindhoven Hendrik Casimir Institute, Eindhoven, 5600 MB, The Netherlands
| | - Mathias Dolci
- Eindhoven University of Technology, Department of Applied Physics, Eindhoven 5600 MB, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven, 5600 MB, The Netherlands
- Eindhoven Hendrik Casimir Institute, Eindhoven, 5600 MB, The Netherlands
| | - Peter Zijlstra
- Eindhoven University of Technology, Department of Applied Physics, Eindhoven 5600 MB, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven, 5600 MB, The Netherlands
- Eindhoven Hendrik Casimir Institute, Eindhoven, 5600 MB, The Netherlands
| |
Collapse
|
20
|
Trofymchuk K, Kołątaj K, Glembockyte V, Zhu F, Acuna GP, Liedl T, Tinnefeld P. Gold Nanorod DNA Origami Antennas for 3 Orders of Magnitude Fluorescence Enhancement in NIR. ACS NANO 2023; 17:1327-1334. [PMID: 36594816 DOI: 10.1021/acsnano.2c09577] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
DNA origami has taken a leading position in organizing materials at the nanoscale for various applications such as manipulation of light by exploiting plasmonic nanoparticles. We here present the arrangement of gold nanorods in a plasmonic nanoantenna dimer enabling up to 1600-fold fluorescence enhancement of a conventional near-infrared (NIR) dye positioned at the plasmonic hotspot between the nanorods. Transmission electron microscopy, dark-field spectroscopy, and fluorescence analysis together with numerical simulations give us insights on the heterogeneity of the observed enhancement values. The size of our hotspot region is ∼12 nm, granted by using the recently introduced design of NAnoantenna with Cleared HotSpot (NACHOS), which provides enough space for placing of tailored bioassays. Additionally, the possibility to synthesize nanoantennas in solution might allow for production upscaling.
Collapse
Affiliation(s)
- Kateryna Trofymchuk
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, 81377München, Germany
| | - Karol Kołątaj
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539Munich, Germany
- Département de Physique - Photonic Nanosystems, Université de Fribourg - Faculté des Sciences et Médicine, Chemin de Musée 3, CH-1700Fribourg, Switzerland
| | - Viktorija Glembockyte
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, 81377München, Germany
| | - Fangjia Zhu
- Département de Physique - Photonic Nanosystems, Université de Fribourg - Faculté des Sciences et Médicine, Chemin de Musée 3, CH-1700Fribourg, Switzerland
| | - Guillermo P Acuna
- Département de Physique - Photonic Nanosystems, Université de Fribourg - Faculté des Sciences et Médicine, Chemin de Musée 3, CH-1700Fribourg, Switzerland
| | - Tim Liedl
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539Munich, Germany
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, 81377München, Germany
| |
Collapse
|
21
|
Liu L, Tibbs J, Li N, Bacon A, Shepherd S, Lee H, Chauhan N, Demirci U, Wang X, Cunningham BT. A Photonic Resonator Interferometric Scattering Microscope for Label-free Detection of Nanometer-Scale Objects with Digital Precision in Point-of-Use Environments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.12.13.520266. [PMID: 36561182 PMCID: PMC9774210 DOI: 10.1101/2022.12.13.520266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Label-free detection and digital counting of nanometer-scaled objects such as nanoparticles, viruses, extracellular vesicles, and protein molecules enable a wide range of applications in cancer diagnostics, pathogen detection, and life science research. The contrast of interferometric scattering microscopy is amplified through a photonic crystal surface, upon which scattered light from an object combines with illumination from a monochromatic plane wave source. The use of a photonic crystal substrate for interference scattering microscopy results in reduced requirements for high-intensity lasers or oil-immersion objectives, thus opening a pathway toward instruments that are more suitable for environments outside the optics laboratory. Here, we report the design, implementation, and characterization of a compact Photonic Resonator Interferometric Scattering Microscope (PRISM) designed for point-of-use environments and applications. The instrument incorporates two innovative elements that facilitate operation on a desktop in ordinary laboratory environments by users that do not have optics expertise. First, because scattering microscopes are extremely sensitive to vibration, we incorporated an inexpensive but effective solution of suspending the instrument's main components from a rigid metal framework using elastic bands, resulting in an average of 28.7 dBV reduction in vibration amplitude compared to an office desk. Second, an automated focusing module based on the principle of total internal reflection maintains the stability of image contrast over time and spatial position, facilitating automated data collection. In this work, we characterize the system's performance by measuring the contrast from gold nanoparticles with diameters in the 10-40 nm range and by observing various biological analytes, including HIV virus, SARS-CoV-2 virus, exosomes, and ferritin protein.
Collapse
Affiliation(s)
- Leyang Liu
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Joseph Tibbs
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Nantao Li
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Amanda Bacon
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Skye Shepherd
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Hankeun Lee
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Neha Chauhan
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Utkan Demirci
- Canary Center at Stanford for Cancer Early Detection, Stanford School of Medicine, Stanford University, Palo Alto, California 94304, USA
| | - Xing Wang
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Brian T. Cunningham
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Cancer Center at Illinois, Urbana, Illinois 61801, USA
| |
Collapse
|
22
|
Bao M, Zhang S, Ten Pas C, Dollery SJ, Bushnell RV, Yuqing FNU, Liu R, Lu G, Tobin GJ, Du K. Computer vision enabled funnel adapted sensing tube (FAST) for power-free and pipette-free nucleic acid detection. LAB ON A CHIP 2022; 22:4849-4859. [PMID: 36111877 DOI: 10.1039/d2lc00586g] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A simple, portable, and low-cost microfluidic system-funnel adapted sensing tube (FAST) is developed as an integrated, power-free, and pipette-free biosensor for viral nucleic acids. This FAST chip consists of four reaction chambers separated by carbon fiber rods, and the reagents in each chamber are transferred and mixed by manually removing the rods. Rather than using electrical heaters, only a hand warmer pouch is used for an isothermal recombinase polymerase amplification (RPA) and CRISPR-Cas12a reaction. The signal produced by the RPA-CRISPR reaction is observed by the naked eye using an inexpensive flashlight as a light source. The FAST chip is fabricated using water-soluble polyvinyl alcohol (PVA) as a sacrificial core, which is simple and environmentally friendly. Using a SARS-CoV-2 fragment as a target, a ∼10 fM (6 × 103 copies per μL) detection limit is achieved. To generalize standard optical readout for individuals without training, a linear kernel algorithm is created, showing an accuracy of ∼100% for identifying both positive and negative samples in FAST. This power-free, pipette-free, disposable, and simple device will be a promising tool for nucleic acid diagnostics in either clinics or low-resource settings.
Collapse
Affiliation(s)
- Mengdi Bao
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521, USA.
| | - Shuhuan Zhang
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521, USA.
| | - Chad Ten Pas
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521, USA.
| | | | - Ruth V Bushnell
- Biological Mimetics, Inc., 124 Byte Drive, Frederick, MD 21702, USA
| | - F N U Yuqing
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521, USA.
| | - Rui Liu
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521, USA.
| | - Guoyu Lu
- Department of Electrical and Computer Engineering, University of Georgia, Athens, GA 30602, USA
| | - Gregory J Tobin
- Biological Mimetics, Inc., 124 Byte Drive, Frederick, MD 21702, USA
| | - Ke Du
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521, USA.
| |
Collapse
|
23
|
Domljanovic I, Loretan M, Kempter S, Acuna GP, Kocabey S, Ruegg C. DNA origami book biosensor for multiplex detection of cancer-associated nucleic acids. NANOSCALE 2022; 14:15432-15441. [PMID: 36219167 PMCID: PMC9612396 DOI: 10.1039/d2nr03985k] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/03/2022] [Indexed: 06/16/2023]
Abstract
DNA nanotechnology provides a promising approach for the development of biomedical point-of-care diagnostic nanoscale devices that are easy to use and cost-effective, highly sensitive and thus constitute an alternative to expensive, complex diagnostic devices. Moreover, DNA nanotechnology-based devices are particularly advantageous for applications in oncology, owing to being ideally suited for the detection of cancer-associated nucleic acids, including circulating tumor-derived DNA fragments (ctDNAs), circulating microRNAs (miRNAs) and other RNA species. Here, we present a dynamic DNA origami book biosensor that is precisely decorated with arrays of fluorophores acting as donors and acceptors and also fluorescence quenchers that produce a strong optical readout upon exposure to external stimuli for the single or dual detection of target oligonucleotides and miRNAs. This biosensor allowed the detection of target molecules either through the decrease of Förster resonance energy transfer (FRET) or an increase in the fluorescence intensity profile owing to a rotation of the constituent top layer of the structure. Single-DNA origami experiments showed that detection of two targets can be achieved simultaneously within 10 min with a limit of detection in the range of 1-10 pM. Overall, our DNA origami book biosensor design showed sensitive and specific detection of synthetic target oligonucleotides and natural miRNAs extracted from cancer cells. Based on these results, we foresee that our DNA origami biosensor may be developed into a cost-effective point-of-care diagnostic strategy for the specific and sensitive detection of a variety of DNAs and RNAs, such as ctDNAs, miRNAs, mRNAs, and viral DNA/RNAs in human samples.
Collapse
Affiliation(s)
- Ivana Domljanovic
- Laboratory of Experimental and Translational Oncology, Department of Oncology, Microbiology and Immunology, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 18, PER17, 1700 Fribourg, Switzerland.
| | - Morgane Loretan
- Photonic Nanosystems, Department of Physics, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 3, PER08, 1700 Fribourg, Switzerland.
| | - Susanne Kempter
- Department of Physics, Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539 Munich, Germany
| | - Guillermo P Acuna
- Photonic Nanosystems, Department of Physics, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 3, PER08, 1700 Fribourg, Switzerland.
| | - Samet Kocabey
- Laboratory of Experimental and Translational Oncology, Department of Oncology, Microbiology and Immunology, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 18, PER17, 1700 Fribourg, Switzerland.
| | - Curzio Ruegg
- Laboratory of Experimental and Translational Oncology, Department of Oncology, Microbiology and Immunology, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 18, PER17, 1700 Fribourg, Switzerland.
| |
Collapse
|
24
|
Adamczyk AK, Huijben TAPM, Sison M, Di Luca A, Chiarelli G, Vanni S, Brasselet S, Mortensen KI, Stefani FD, Pilo-Pais M, Acuna GP. DNA Self-Assembly of Single Molecules with Deterministic Position and Orientation. ACS NANO 2022; 16:16924-16931. [PMID: 36065997 DOI: 10.1021/acsnano.2c06936] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
An ideal nanofabrication method should allow the organization of nanoparticles and molecules with nanometric positional precision, stoichiometric control, and well-defined orientation. The DNA origami technique has evolved into a highly versatile bottom-up nanofabrication methodology that fulfils almost all of these features. It enables the nanometric positioning of molecules and nanoparticles with stoichiometric control, and even the orientation of asymmetrical nanoparticles along predefined directions. However, orienting individual molecules has been a standing challenge. Here, we show how single molecules, namely, Cy5 and Cy3 fluorophores, can be incorporated in a DNA origami with controlled orientation by doubly linking them to oligonucleotide strands that are hybridized while leaving unpaired bases in the scaffold. Increasing the number of bases unpaired induces a stretching of the fluorophore linkers, reducing its mobility freedom, and leaves more space for the fluorophore to accommodate and find different sites for interaction with the DNA. Particularly, we explore the effects of leaving 0, 2, 4, 6, and 8 bases unpaired and find extreme orientations for 0 and 8 unpaired bases, corresponding to the molecules being perpendicular and parallel to the DNA double-helix, respectively. We foresee that these results will expand the application field of DNA origami toward the fabrication of nanodevices involving a wide range of orientation-dependent molecular interactions, such as energy transfer, intermolecular electron transport, catalysis, exciton delocalization, or the electromagnetic coupling of a molecule to specific resonant nanoantenna modes.
Collapse
Affiliation(s)
- Aleksandra K Adamczyk
- Department of Physics, University of Fribourg, Chemin du Musée 3, FribourgCH-1700, Switzerland
| | - Teun A P M Huijben
- Department of Health Technology, Technical University of Denmark, Anker Engelunds Vej 101, 2800Kongens Lyngby, Denmark
| | - Miguel Sison
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, F-13013Marseille, France
| | - Andrea Di Luca
- Department of Biology, University of Fribourg, Chemin du Musée 10, FribourgCH-1700, Switzerland
| | - Germán Chiarelli
- Department of Physics, University of Fribourg, Chemin du Musée 3, FribourgCH-1700, Switzerland
| | - Stefano Vanni
- Department of Biology, University of Fribourg, Chemin du Musée 10, FribourgCH-1700, Switzerland
| | - Sophie Brasselet
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, F-13013Marseille, France
| | - Kim I Mortensen
- Department of Health Technology, Technical University of Denmark, Anker Engelunds Vej 101, 2800Kongens Lyngby, Denmark
| | - Fernando D Stefani
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQDCiudad Autónoma de Buenos Aires, Argentina
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Güiraldes 2620, C1428EHACiudad Autónoma de Buenos Aires, Argentina
| | - Mauricio Pilo-Pais
- Department of Physics, University of Fribourg, Chemin du Musée 3, FribourgCH-1700, Switzerland
| | - Guillermo P Acuna
- Department of Physics, University of Fribourg, Chemin du Musée 3, FribourgCH-1700, Switzerland
| |
Collapse
|
25
|
Hariri AA, Newman SS, Tan S, Mamerow D, Adams AM, Maganzini N, Zhong BL, Eisenstein M, Dunn AR, Soh HT. Improved immunoassay sensitivity and specificity using single-molecule colocalization. Nat Commun 2022; 13:5359. [PMID: 36097164 PMCID: PMC9468026 DOI: 10.1038/s41467-022-32796-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 08/12/2022] [Indexed: 11/29/2022] Open
Abstract
Enzyme-linked immunosorbent assays (ELISAs) are a cornerstone of modern molecular detection, but the technique still faces notable challenges. One of the biggest problems is discriminating true signal generated by target molecules versus non-specific background. Here, we developed a Single-Molecule Colocalization Assay (SiMCA) that overcomes this problem by employing total internal reflection fluorescence microscopy to quantify target proteins based on the colocalization of fluorescent signal from orthogonally labeled capture and detection antibodies. By specifically counting colocalized signals, we can eliminate the effects of background produced by non-specific binding of detection antibodies. Using TNF-α, we show that SiMCA achieves a three-fold lower limit of detection compared to conventional single-color assays and exhibits consistent performance for assays performed in complex specimens such as serum and blood. Our results help define the pernicious effects of non-specific background in immunoassays and demonstrate the diagnostic gains that can be achieved by eliminating those effects.
Collapse
Affiliation(s)
- Amani A Hariri
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA
| | - Sharon S Newman
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Steven Tan
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Dan Mamerow
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA
| | - Alexandra M Adams
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Nicolò Maganzini
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Brian L Zhong
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Michael Eisenstein
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Alexander R Dunn
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA.
| | - H Tom Soh
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA.
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
| |
Collapse
|
26
|
Chen X, Liu Y, Liu X, Lu C. Nanoparticle-based single molecule fluorescent probes. LUMINESCENCE 2022; 37:1808-1821. [PMID: 35982510 DOI: 10.1002/bio.4364] [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: 07/13/2022] [Revised: 08/13/2022] [Accepted: 08/16/2022] [Indexed: 11/11/2022]
Abstract
Single molecule fluorescent probes have attracted considerable attention duet to their ultimate sensitivity, fast response, low sample consumption, and high signal-to-noise ratio. Nanoparticles with outstanding optical properties make them perfect candidates for probes in application of single molecule detection. In this review, we focus on various kinds of nanoparticles acting as single molecule fluorescent probes, including quantum dots, upconverting fluorescent nanoparticles, carbon dots, single-wall carbon nanotubes, fluorescent nanodiamonds, polymeric nanoparticles, nanoclusters, and metallic nanoparticles. Optical properties of various nanoparticles and their recent application in single molecule fluorescent probes are explored. How nanoparticles boost the sensitivity of detection is emphasized in combination with different sensing strategies. Future trends of nanoparticles in single molecule detection are also discussed. We hope this review can provide practical guidance for researchers who work on nanoparticle-based single molecule fluorescent probes.
Collapse
Affiliation(s)
- Xueqian Chen
- Green Catalysis Center and College of Chemistry, Zhengzhou University, Zhengzhou, China
| | - Yuhao Liu
- Green Catalysis Center and College of Chemistry, Zhengzhou University, Zhengzhou, China
| | - Xiaoting Liu
- Green Catalysis Center and College of Chemistry, Zhengzhou University, Zhengzhou, China
| | - Chao Lu
- Green Catalysis Center and College of Chemistry, Zhengzhou University, Zhengzhou, China.,State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing, China
| |
Collapse
|
27
|
Kabusure KM, Piskunen P, Yang J, Kataja M, Chacha M, Ojasalo S, Shen B, Hakala TK, Linko V. Optical characterization of DNA origami-shaped silver nanoparticles created through biotemplated lithography. NANOSCALE 2022; 14:9648-9654. [PMID: 35718875 DOI: 10.1039/d1nr06256e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Here, we study optically resonant substrates fabricated using the previously reported BLIN (biotemplated lithography of inorganic nanostructures) technique with single triangle and bowtie DNA origami as templates. We present the first optical characterization of BLIN-fabricated origami-shaped silver nanoparticle patterns on glass surfaces, comprising optical transmission measurements and surface-enhanced Raman spectroscopy. The formed nanoparticle patterns are examined by optical transmission measurements and used for surface enhanced Raman spectroscopy (SERS) of Rhodamine 6G (R6G) dye molecules. Polarization-resolved simulations reveal that the higher SERS enhancement observed for the bowties is primarily due to spectral overlap of the optical resonances with the Raman transitions of R6G. The results manifest the applicability of the BLIN method and substantiate its potential in parallel and high-throughput substrate manufacturing with engineered optical properties. While the results demonstrate the crucial role of the formed nanogaps for SERS, the DNA origami may enable even more complex nanopatterns for various optical applications.
Collapse
Affiliation(s)
- Kabusure M Kabusure
- Department of Physics and Mathematics, University of Eastern Finland, Yliopistokatu 2, P.O Box 111, FI-80101, Joensuu, Finland.
| | - Petteri Piskunen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, FI-00076, Aalto, Finland.
| | - Jiaqi Yang
- Department of Physics and Mathematics, University of Eastern Finland, Yliopistokatu 2, P.O Box 111, FI-80101, Joensuu, Finland.
| | - Mikko Kataja
- Department of Physics and Mathematics, University of Eastern Finland, Yliopistokatu 2, P.O Box 111, FI-80101, Joensuu, Finland.
| | - Mwita Chacha
- Department of Physics and Mathematics, University of Eastern Finland, Yliopistokatu 2, P.O Box 111, FI-80101, Joensuu, Finland.
| | - Sofia Ojasalo
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, FI-00076, Aalto, Finland.
| | - Boxuan Shen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, FI-00076, Aalto, Finland.
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17165 Stockholm, Sweden
| | - Tommi K Hakala
- Department of Physics and Mathematics, University of Eastern Finland, Yliopistokatu 2, P.O Box 111, FI-80101, Joensuu, Finland.
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, FI-00076, Aalto, Finland.
- LIBER Center of Excellence, Aalto University, P.O. Box 16100, FI-00076, Aalto, Finland
| |
Collapse
|
28
|
Eiring P, McLaughlin R, Matikonda SS, Han Z, Grabenhorst L, Helmerich DA, Meub M, Beliu G, Luciano M, Bandi V, Zijlstra N, Shi ZD, Tarasov SG, Swenson R, Tinnefeld P, Glembockyte V, Cordes T, Sauer M, Schnermann MJ. Targetable Conformationally Restricted Cyanines Enable Photon-Count-Limited Applications*. Angew Chem Int Ed Engl 2021; 60:26685-26693. [PMID: 34606673 PMCID: PMC8649030 DOI: 10.1002/anie.202109749] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/18/2021] [Indexed: 12/15/2022]
Abstract
Cyanine dyes are exceptionally useful probes for a range of fluorescence-based applications, but their photon output can be limited by trans-to-cis photoisomerization. We recently demonstrated that appending a ring system to the pentamethine cyanine ring system improves the quantum yield and extends the fluorescence lifetime. Here, we report an optimized synthesis of persulfonated variants that enable efficient labeling of nucleic acids and proteins. We demonstrate that a bifunctional sulfonated tertiary amide significantly improves the optical properties of the resulting bioconjugates. These new conformationally restricted cyanines are compared to the parent cyanine derivatives in a range of contexts. These include their use in the plasmonic hotspot of a DNA-nanoantenna, in single-molecule Förster-resonance energy transfer (FRET) applications, far-red fluorescence-lifetime imaging microscopy (FLIM), and single-molecule localization microscopy (SMLM). These efforts define contexts in which eliminating cyanine isomerization provides meaningful benefits to imaging performance.
Collapse
Affiliation(s)
- Patrick Eiring
- Department of Biotechnology and Biophysics Biocenter, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Ryan McLaughlin
- Laboratory of Chemical Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Siddharth S Matikonda
- Laboratory of Chemical Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Zhongying Han
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Lennart Grabenhorst
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, München, Germany
| | - Dominic A Helmerich
- Department of Biotechnology and Biophysics Biocenter, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Mara Meub
- Department of Biotechnology and Biophysics Biocenter, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Gerti Beliu
- Department of Biotechnology and Biophysics Biocenter, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Michael Luciano
- Laboratory of Chemical Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Venu Bandi
- Laboratory of Chemical Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Niels Zijlstra
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Zhen-Dan Shi
- Chemistry and Synthesis Center, National Heart, Lung, and Blood Institute, NIH, Rockville, MD, 20850, USA
| | - Sergey G Tarasov
- Biophysics Resource in the Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Rolf Swenson
- Chemistry and Synthesis Center, National Heart, Lung, and Blood Institute, NIH, Rockville, MD, 20850, USA
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, München, Germany
| | - Viktorija Glembockyte
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, München, Germany
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Markus Sauer
- Department of Biotechnology and Biophysics Biocenter, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Martin J Schnermann
- Laboratory of Chemical Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| |
Collapse
|
29
|
Eiring P, McLaughlin R, Matikonda SS, Han Z, Grabenhorst L, Helmerich DA, Meub M, Beliu G, Luciano M, Bandi V, Zijlstra N, Shi Z, Tarasov SG, Swenson R, Tinnefeld P, Glembockyte V, Cordes T, Sauer M, Schnermann MJ. Targetable Conformationally Restricted Cyanines Enable Photon‐Count‐Limited Applications**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202109749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Patrick Eiring
- Department of Biotechnology and Biophysics Biocenter Julius-Maximilians-Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Ryan McLaughlin
- Laboratory of Chemical Biology Center for Cancer Research National Cancer Institute Frederick MD 21702 USA
| | - Siddharth S. Matikonda
- Laboratory of Chemical Biology Center for Cancer Research National Cancer Institute Frederick MD 21702 USA
| | - Zhongying Han
- Physical and Synthetic Biology Faculty of Biology Ludwig-Maximilians-Universität München Großhadernerstr. 2–4 82152 Planegg-Martinsried Germany
| | - Lennart Grabenhorst
- Department of Chemistry and Center for NanoScience Ludwig-Maximilians-Universität München Butenandtstr. 5–13 81377 München Germany
| | - Dominic A. Helmerich
- Department of Biotechnology and Biophysics Biocenter Julius-Maximilians-Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Mara Meub
- Department of Biotechnology and Biophysics Biocenter Julius-Maximilians-Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Gerti Beliu
- Department of Biotechnology and Biophysics Biocenter Julius-Maximilians-Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Michael Luciano
- Laboratory of Chemical Biology Center for Cancer Research National Cancer Institute Frederick MD 21702 USA
| | - Venu Bandi
- Laboratory of Chemical Biology Center for Cancer Research National Cancer Institute Frederick MD 21702 USA
| | - Niels Zijlstra
- Physical and Synthetic Biology Faculty of Biology Ludwig-Maximilians-Universität München Großhadernerstr. 2–4 82152 Planegg-Martinsried Germany
| | - Zhen‐Dan Shi
- Chemistry and Synthesis Center National Heart, Lung, and Blood Institute NIH Rockville MD 20850 USA
| | - Sergey G. Tarasov
- Biophysics Resource in the Center for Structural Biology Center for Cancer Research National Cancer Institute Frederick MD 21702 USA
| | - Rolf Swenson
- Chemistry and Synthesis Center National Heart, Lung, and Blood Institute NIH Rockville MD 20850 USA
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience Ludwig-Maximilians-Universität München Butenandtstr. 5–13 81377 München Germany
| | - Viktorija Glembockyte
- Department of Chemistry and Center for NanoScience Ludwig-Maximilians-Universität München Butenandtstr. 5–13 81377 München Germany
| | - Thorben Cordes
- Physical and Synthetic Biology Faculty of Biology Ludwig-Maximilians-Universität München Großhadernerstr. 2–4 82152 Planegg-Martinsried Germany
| | - Markus Sauer
- Department of Biotechnology and Biophysics Biocenter Julius-Maximilians-Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Martin J. Schnermann
- Laboratory of Chemical Biology Center for Cancer Research National Cancer Institute Frederick MD 21702 USA
| |
Collapse
|
30
|
Hepp C, Shiaelis N, Robb NC, Vaughan A, Matthews PC, Stoesser N, Crook D, Kapanidis AN. Viral detection and identification in 20 min by rapid single-particle fluorescence in-situ hybridization of viral RNA. Sci Rep 2021; 11:19579. [PMID: 34599242 PMCID: PMC8486776 DOI: 10.1038/s41598-021-98972-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 09/09/2021] [Indexed: 12/24/2022] Open
Abstract
The increasing risk from viral outbreaks such as the ongoing COVID-19 pandemic exacerbates the need for rapid, affordable and sensitive methods for virus detection, identification and quantification; however, existing methods for detecting virus particles in biological samples usually depend on multistep protocols that take considerable time to yield a result. Here, we introduce a rapid fluorescence in situ hybridization (FISH) protocol capable of detecting influenza virus, avian infectious bronchitis virus and SARS-CoV-2 specifically and quantitatively in approximately 20 min, in virus cultures, combined nasal and throat swabs with added virus and likely patient samples without previous purification. This fast and facile workflow can be adapted both as a lab technique and a future diagnostic tool in enveloped viruses with an accessible genome.
Collapse
Affiliation(s)
- Christof Hepp
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK.
| | - Nicolas Shiaelis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK
| | - Nicole C Robb
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Alison Vaughan
- Nuffield Department for Medicine, University of Oxford, Oxford, OX3 9DU, UK
| | | | - Nicole Stoesser
- Nuffield Department for Medicine, University of Oxford, Oxford, OX3 9DU, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford in Partnership With Public Health England, University of Oxford, Oxford, UK
| | - Derrick Crook
- Nuffield Department for Medicine, University of Oxford, Oxford, OX3 9DU, UK
- NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford in Partnership With Public Health England, University of Oxford, Oxford, UK
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK.
| |
Collapse
|
31
|
Heintz J, Markešević N, Gayet EY, Bonod N, Bidault S. Few-Molecule Strong Coupling with Dimers of Plasmonic Nanoparticles Assembled on DNA. ACS NANO 2021; 15:14732-14743. [PMID: 34469108 DOI: 10.1021/acsnano.1c04552] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Hybrid nanostructures, in which a known number of quantum emitters are strongly coupled to a plasmonic resonator, should feature optical properties at room temperature such as few-photon nonlinearities or coherent superradiant emission. We demonstrate here that this coupling regime can only be reached with dimers of gold nanoparticles in stringent experimental conditions, when the interparticle spacing falls below 2 nm. Using a short transverse DNA double-strand, we introduce five dye molecules in the gap between two 40 nm gold particles and actively decrease its length down to sub-2 nm values by screening electrostatic repulsion between the particles at high ionic strengths. Single-nanostructure scattering spectroscopy then evidence the observation of a strong-coupling regime in excellent agreement with electrodynamic simulations. Furthermore, we highlight the influence of the planar facets of polycrystalline gold nanoparticles on the probability of observing strongly coupled hybrid nanostructures.
Collapse
Affiliation(s)
- Jeanne Heintz
- Institut Langevin, ESPCI Paris, Université PSL, CNRS, 1 rue Jussieu, 75005 Paris, France
| | - Nemanja Markešević
- Institut Langevin, ESPCI Paris, Université PSL, CNRS, 1 rue Jussieu, 75005 Paris, France
| | - Elise Y Gayet
- Institut Langevin, ESPCI Paris, Université PSL, CNRS, 1 rue Jussieu, 75005 Paris, France
| | - Nicolas Bonod
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, 52 Avenue Escadrille Normandie Niemen, 13013 Marseille, France
| | - Sébastien Bidault
- Institut Langevin, ESPCI Paris, Université PSL, CNRS, 1 rue Jussieu, 75005 Paris, France
| |
Collapse
|
32
|
Single antibody detection in a DNA origami nanoantenna. iScience 2021; 24:103072. [PMID: 34568793 PMCID: PMC8449233 DOI: 10.1016/j.isci.2021.103072] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/26/2021] [Accepted: 08/27/2021] [Indexed: 12/24/2022] Open
Abstract
DNA nanotechnology offers new biosensing approaches by templating different sensor and transducer components. Here, we combine DNA origami nanoantennas with label-free antibody detection by incorporating a nanoswitch in the plasmonic hotspot of the nanoantenna. The nanoswitch contains two antigens that are displaced by antibody binding, thereby eliciting a fluorescent signal. Single-antibody detection is demonstrated with a DNA origami integrated anti-digoxigenin antibody nanoswitch. In combination with the nanoantenna, the signal generated by the antibody is additionally amplified. This allows the detection of single antibodies on a portable smartphone microscope. Overall, fluorescence-enhanced antibody detection in DNA origami nanoantennas shows that fluorescence-enhanced biosensing can be expanded beyond the scope of the nucleic acids realm. Single-antibody detection with nanoswitch sensor incorporated in DNA origami structures Fluorescence-enhanced single antibody detection in DNA origami nanoantennas Detection of single antibodies on a portable smartphone microscope
Collapse
|
33
|
Wang H, Guo Y, Zang J, Hao H, Wang L, Liu T, Bian H, Jiang R, Wen R, Li H, Tong Y, Wang H. Nanoantennas Involved Optical Plasmonic Cavity for Improved Luminescence of Quantum Dots Light-Emitting Diodes. ACS APPLIED MATERIALS & INTERFACES 2021; 13:44760-44767. [PMID: 34505502 DOI: 10.1021/acsami.1c11995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The optical plasmonic cavity (OPC) including the metallic optical nanoantennas and a metal film exhibits extreme field enhancement for the increased spontaneous emission rate of emitters. The resonance wavelength of the OPC can be easily controlled by the volume of the OPC and the localized surface plasmonic resonances (LSPRs) of the nanoantennas, facilitating the effective coupling of OPC and the emitters. However, involving the OPC into the light emission-enhanced solution-processed devices is still a difficult challenge. The trade-off between the metallic structure of OPC and the solution procedures limits the performance enhancement of the electrical-driven devices. In this work, we construct a device-compatible OPC that allows the characterization of the carrier dynamics of quantum dot (QD) films in the real devices in-suit. The radiative recombination rate and relaxation rate of carriers in QDs are increased by the LSPR effect of the silver nanocubes for luminescence enhancement. The OPC further increases the spontaneous emission rate of QD films, achieving a Purcell factor of 166 and improving the electroluminescence of the OPC-based QD light-emitting diodes (QLEDs). The design of the OPC-involved QLEDs offers a solution for addressing the limitation of fabrication of OPC-combined solution-processed optoelectronic light sources.
Collapse
Affiliation(s)
- Hongyue Wang
- State Key Laboratory of Solidification Processing, Center for Nano Energy Materials, School of Materials Science and Engineering, Shaanxi Joint Laboratory of Graphene (NPU), Northwestern Polytechnical University, Xi'an 710072, P. R. China
| | - Yangyang Guo
- State Key Laboratory of Solidification Processing, Center for Nano Energy Materials, School of Materials Science and Engineering, Shaanxi Joint Laboratory of Graphene (NPU), Northwestern Polytechnical University, Xi'an 710072, P. R. China
| | - Jianyang Zang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China
| | - Hongxing Hao
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China
| | - Le Wang
- Shaanxi Key Laboratory for Advanced Energy Devices, Shaanxi Engineering Laboratory for Advanced Energy Technology, School of Materials Science and Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China
| | - Taihong Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China
| | - Hongtao Bian
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China
| | - Ruibin Jiang
- Shaanxi Key Laboratory for Advanced Energy Devices, Shaanxi Engineering Laboratory for Advanced Energy Technology, School of Materials Science and Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China
| | - Ruijuan Wen
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China
| | - Huixin Li
- State Key Laboratory of Solidification Processing, Center for Nano Energy Materials, School of Materials Science and Engineering, Shaanxi Joint Laboratory of Graphene (NPU), Northwestern Polytechnical University, Xi'an 710072, P. R. China
| | - Yu Tong
- State Key Laboratory of Solidification Processing, Center for Nano Energy Materials, School of Materials Science and Engineering, Shaanxi Joint Laboratory of Graphene (NPU), Northwestern Polytechnical University, Xi'an 710072, P. R. China
| | - Hongqiang Wang
- State Key Laboratory of Solidification Processing, Center for Nano Energy Materials, School of Materials Science and Engineering, Shaanxi Joint Laboratory of Graphene (NPU), Northwestern Polytechnical University, Xi'an 710072, P. R. China
| |
Collapse
|
34
|
Glembockyte V, Grabenhorst L, Trofymchuk K, Tinnefeld P. DNA Origami Nanoantennas for Fluorescence Enhancement. Acc Chem Res 2021; 54:3338-3348. [PMID: 34435769 DOI: 10.1021/acs.accounts.1c00307] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The possibility to increase fluorescence by plasmonic effects in the near-field of metal nanostructures was recognized more than half a century ago. A major challenge, however, was to use this effect because placing single quantum emitters in the nanoscale plasmonic hotspot remained unsolved for a long time. This not only presents a chemical problem but also requires the nanostructure itself to be coaligned with the polarization of the excitation light. Additional difficulties arise from the complex distance dependence of fluorescence emission: in contrast to other surface-enhanced spectroscopies (such as Raman spectroscopy), the emitter should not be placed as close as possible to the metallic nanostructure but rather needs to be at an optimal distance on the order of a few nanometers to avoid undesired quenching effects.Our group addressed these challenges almost a decade ago by exploiting the unique positioning ability of DNA nanotechnology and reported the first self-assembled DNA origami nanoantennas. This Account summarizes our work spanning from this first proof-of-principle study to recent advances in utilizing DNA origami nanoantennas for single DNA molecule detection on a portable smartphone microscope.We summarize different aspects of DNA origami nanoantennas that are essential for achieving strong fluorescence enhancement and discuss how single-molecule fluorescence studies helped us to gain a better understanding of the interplay between fluorophores and plasmonic hotspots. Practical aspects of preparing the DNA origami nanoantennas and extending their utility are also discussed.Fluorescence enhancement in DNA origami nanoantennas is especially exciting for signal amplification in molecular diagnostic assays or in single-molecule biophysics, which could strongly benefit from higher time resolution. Additionally, biophysics can greatly profit from the ultrasmall effective detection volumes provided by DNA nanoantennas that allow single-molecule detection at drastically elevated concentrations as is required, e.g., in single-molecule DNA sequencing approaches.Finally, we describe our most recent progress in developing DNA NanoAntennas with Cleared HOtSpots (NACHOS) that are fully compatible with biomolecular assays. The developed DNA origami nanoantennas have proven robustness and remain functional after months of storage. As an example, we demonstrated for the first time the single-molecule detection of DNA specific to antibiotic-resistant bacteria on a portable and battery-driven smartphone microscope enabled by DNA origami nanoantennas. These recent developments mark a perfect moment to summarize the principles and the synthesis of DNA origami nanoantennas and give an outlook of new exciting directions toward using different nanomaterials for the construction of nanoantennas as well as for their emerging applications.
Collapse
Affiliation(s)
- Viktorija Glembockyte
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
| | - Lennart Grabenhorst
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
| | - Kateryna Trofymchuk
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
| |
Collapse
|
35
|
Momenbeitollahi N, Cloet T, Li H. Pushing the detection limits: strategies towards highly sensitive optical-based protein detection. Anal Bioanal Chem 2021; 413:5995-6011. [PMID: 34363087 PMCID: PMC8346249 DOI: 10.1007/s00216-021-03566-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 07/14/2021] [Accepted: 07/19/2021] [Indexed: 01/07/2023]
Abstract
Proteins are one of the main constituents of living cells. Studying the quantities of proteins under physiological and pathological conditions can give valuable insights into health status, since proteins are the functional molecules of life. To be able to detect and quantify low-abundance proteins in biofluids for applications such as early disease diagnostics, sensitive analytical techniques are desired. An example of this application is using proteins as biomarkers for detecting cancer or neurological diseases, which can provide early, lifesaving diagnoses. However, conventional methods for protein detection such as ELISA, mass spectrometry, and western blotting cannot offer enough sensitivity for certain applications. Recent advances in optical-based micro- and nano-biosensors have demonstrated promising results to detect proteins at low quantities down to the single-molecule level, shining lights on their capacities for ultrasensitive disease diagnosis and rare protein detection. However, to date, there is a lack of review articles synthesizing and comparing various optical micro- and nano-sensing methods of enhancing the limits of detections of the antibody-based protein assays. The purpose of this article is to critically review different strategies of improving assay sensitivity using miniaturized biosensors, such as assay miniaturization, improving antibody binding capacity, sample purification, and signal amplification. The pros and cons of different methods are compared, and the future perspectives of this research field are discussed.
Collapse
Affiliation(s)
| | - Teran Cloet
- School of Engineering, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Huiyan Li
- School of Engineering, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.
| |
Collapse
|
36
|
Liu G. Grand Challenges in Biosensors and Biomolecular Electronics. Front Bioeng Biotechnol 2021; 9:707615. [PMID: 34422782 PMCID: PMC8377753 DOI: 10.3389/fbioe.2021.707615] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 07/28/2021] [Indexed: 11/25/2022] Open
Affiliation(s)
- Guozhen Liu
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, China
| |
Collapse
|
37
|
Cellphone enabled point-of-care assessment of breast tumor cytology and molecular HER2 expression from fine-needle aspirates. NPJ Breast Cancer 2021; 7:85. [PMID: 34215753 PMCID: PMC8253731 DOI: 10.1038/s41523-021-00290-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 06/03/2021] [Indexed: 12/13/2022] Open
Abstract
Management of breast cancer in limited-resource settings is hindered by a lack of low-cost, logistically sustainable approaches toward molecular and cellular diagnostic pathology services that are needed to guide therapy. To address these limitations, we have developed a multimodal cellphone-based platform—the EpiView-D4—that can evaluate both cellular morphology and molecular expression of clinically relevant biomarkers directly from fine-needle aspiration (FNA) of breast tissue specimens within 1 h. The EpiView-D4 is comprised of two components: (1) an immunodiagnostic chip built upon a “non-fouling” polymer brush-coating (the “D4”) which quantifies expression of protein biomarkers directly from crude cell lysates, and (2) a custom cellphone-based optical microscope (“EpiView”) designed for imaging cytology preparations and D4 assay readout. As a proof-of-concept, we used the EpiView-D4 for assessment of human epidermal growth factor receptor-2 (HER2) expression and validated the performance using cancer cell lines, animal models, and human tissue specimens. We found that FNA cytology specimens (prepared in less than 5 min with rapid staining kits) imaged by the EpiView-D4 were adequate for assessment of lesional cellularity and tumor content. We also found our device could reliably distinguish between HER2 expression levels across multiple different cell lines and animal xenografts. In a pilot study with human tissue (n = 19), we were able to accurately categorize HER2-negative and HER2-positve tumors from FNA specimens. Taken together, the EpiView-D4 offers a promising alternative to invasive—and often unavailable—pathology services and may enable the democratization of effective breast cancer management in limited-resource settings.
Collapse
|
38
|
Dass M, Gür FN, Kołątaj K, Urban MJ, Liedl T. DNA Origami-Enabled Plasmonic Sensing. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2021; 125:5969-5981. [PMID: 33828635 PMCID: PMC8016175 DOI: 10.1021/acs.jpcc.0c11238] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/31/2021] [Indexed: 05/02/2023]
Abstract
The reliable programmability of DNA origami makes it an extremely attractive tool for bottom-up self-assembly of complex nanostructures. Utilizing this property for the tuned arrangement of plasmonic nanoparticles holds great promise particularly in the field of biosensing. Plasmonic particles are beneficial for sensing in multiple ways, from enhancing fluorescence to enabling a visualization of the nanoscale dynamic actuation via chiral rearrangements. In this Perspective, we discuss the recent developments and possible future directions of DNA origami-enabled plasmonic sensing systems. We start by discussing recent advancements in the area of fluorescence-based plasmonic sensing using DNA origami. We then move on to surface-enhanced Raman spectroscopy sensors followed by chiral sensing, both utilizing DNA origami nanostructures. We conclude by providing our own views on the future prospects for plasmonic biosensors enabled using DNA origami.
Collapse
Affiliation(s)
- Mihir Dass
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539 Munich, Germany
| | - Fatih N. Gür
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539 Munich, Germany
| | - Karol Kołątaj
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539 Munich, Germany
| | - Maximilian J. Urban
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539 Munich, Germany
| | - Tim Liedl
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539 Munich, Germany
| |
Collapse
|
39
|
Abstract
Structural DNA nanotechnology is a pioneering biotechnology that presents the opportunity to engineer DNA-based hardware that will mediate a profound interface to the nanoscale. To date, an enormous library of shaped 3D DNA nanostructures have been designed and assembled. Moreover, recent research has demonstrated DNA nanostructures that are not only static but can exhibit specific dynamic motion. DNA nanostructures have thus garnered significant research interest as a template for pursuing shape and motion-dependent nanoscale phenomena. Potential applications have been explored in many interdisciplinary areas spanning medicine, biosensing, nanofabrication, plasmonics, single-molecule chemistry, and facilitating biophysical studies. In this review, we begin with a brief overview of general and versatile design techniques for 3D DNA nanostructures as well as some techniques and studies that have focused on improving the stability of DNA nanostructures in diverse environments, which is pivotal for its reliable utilization in downstream applications. Our main focus will be to compile a wide body of existing research on applications of 3D DNA nanostructures that demonstrably rely on the versatility of their mechanical design. Furthermore, we frame reviewed applications into three primary categories, namely encapsulation, surface templating, and nanomechanics, that we propose to be archetypal shape- or motion-related functions of DNA nanostructures found in nanoscience applications. Our intent is to identify core concepts that may define and motivate specific directions of progress in this field as we conclude the review with some perspectives on the future.
Collapse
|