1
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Dai L, Johnson-Buck A, Laird PW, Tewari M, Walter NG. Ultrasensitive amplification-free quantification of a methyl CpG-rich cancer biomarker by single-molecule kinetic fingerprinting. bioRxiv 2024:2024.04.06.587997. [PMID: 38645159 PMCID: PMC11030368 DOI: 10.1101/2024.04.06.587997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
The most well-studied epigenetic marker in humans is the 5-methyl modification of cytosine in DNA, which has great potential as a disease biomarker in liquid biopsies of cell-free DNA. Currently, quantification of DNA methylation relies heavily on bisulfite conversion followed by PCR amplification and NGS or microarray analysis. PCR is subject to potential bias in differential amplification of bisulfite-converted methylated versus unmethylated sequences. Here, we combine bisulfite conversion with single-molecule kinetic fingerprinting to develop an amplification-free assay for DNA methylation at the branched-chain amino acid transaminase 1 (BCAT1) promoter. Our assay selectively responds to methylated sequences with a limit of detection below 1 fM and a specificity of 99.9999%. Evaluating complex genomic DNA matrices, we reliably distinguish 2-5% DNA methylation at the BCAT1 promoter in whole blood DNA from completely unmethylated whole-genome amplified DNA. Taken together, these results demonstrate the feasibility and sensitivity of our amplification-free, single-molecule quantification approach to improve the early detection of methylated cancer DNA biomarkers.
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Affiliation(s)
- Liuhan Dai
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
- Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alexander Johnson-Buck
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter W. Laird
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, 49503, USA
| | - Muneesh Tewari
- Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nils G. Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
- Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
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2
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Rinauro DJ, Chiti F, Vendruscolo M, Limbocker R. Misfolded protein oligomers: mechanisms of formation, cytotoxic effects, and pharmacological approaches against protein misfolding diseases. Mol Neurodegener 2024; 19:20. [PMID: 38378578 PMCID: PMC10877934 DOI: 10.1186/s13024-023-00651-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 08/17/2023] [Indexed: 02/22/2024] Open
Abstract
The conversion of native peptides and proteins into amyloid aggregates is a hallmark of over 50 human disorders, including Alzheimer's and Parkinson's diseases. Increasing evidence implicates misfolded protein oligomers produced during the amyloid formation process as the primary cytotoxic agents in many of these devastating conditions. In this review, we analyze the processes by which oligomers are formed, their structures, physicochemical properties, population dynamics, and the mechanisms of their cytotoxicity. We then focus on drug discovery strategies that target the formation of oligomers and their ability to disrupt cell physiology and trigger degenerative processes.
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Affiliation(s)
- Dillon J Rinauro
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Fabrizio Chiti
- Section of Biochemistry, Department of Experimental and Clinical Biomedical Sciences, University of Florence, 50134, Florence, Italy
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
| | - Ryan Limbocker
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY, 10996, USA.
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3
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Chen J, Zeng Q, Zhang Y, Xu Y, Yang Y, Yu H. Classification of Molecular Binding Traces for Dynamic Single-Molecule Sensing. Anal Chem 2024; 96:2327-2332. [PMID: 38308847 DOI: 10.1021/acs.analchem.3c03534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2024]
Abstract
Interference from nonspecific binding imposes a fundamental limit in the sensitivity of biosensors that is dependent on the affinity and specificity of the available sensing probes. The dynamic single-molecule sensing (DSMS) strategy allows ultrasensitive detection of biomarkers at the femtomolar level by identifying specific binding according to molecular binding traces. However, the accuracy in classifying binding traces is not sufficient from separate features, such as the bound lifetime. Here, we establish a DSMS workflow to improve the sensitivity and linearity by classifying molecular binding traces in surface plasmon resonance microscopy with multiple kinetic features. The improvement is achieved by correlation analysis to select key features of binding traces, followed by unsupervised k-clustering. The results show that this unsupervised classification approach improves the sensitivity and linearity in microRNA (hsa-miR155-5p, hsa-miR21-5p, and hsa-miR362-5p) detection to achieve a limit of detection at the subfemtomolar level.
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Affiliation(s)
- Juntao Chen
- College of Automation, Hangzhou Dianzi University, Hangzhou, Zhejiang 310018, China
| | - Qiang Zeng
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Yiyang Zhang
- School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Ying Xu
- College of Automation, Hangzhou Dianzi University, Hangzhou, Zhejiang 310018, China
| | - Yuting Yang
- School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Hui Yu
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
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4
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Lamberti V, Dolci M, Zijlstra P. Continuous Monitoring Biosensing Mediated by Single-Molecule Plasmon-Enhanced Fluorescence in Complex Matrices. ACS Nano 2024. [PMID: 38334312 PMCID: PMC10883122 DOI: 10.1021/acsnano.3c12428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
Continuous detection of critical markers directly at the point of interest and in undiluted biological fluids represents the next fundamental step in biosensing. The goal of realizing such a platform is utterly challenging because it requires a reversible biosensor that enables the tracking of pico- to nanomolar molecular concentrations over long time spans in a compact device. Here we describe a sensing method based on plasmon-enhanced fluorescence capable of single-molecule detection of unlabeled analyte by employing biofunctionalized gold nanoparticles. The very strong plasmon-enhanced fluorescence signals allow for single-molecule sensing in unaltered biological media, while the use of low-affinity interactions ensures the continuous tracking of increasing and decreasing analyte concentrations with picomolar sensitivity. We demonstrate the use of a sandwich assay for a DNA cancer marker with a limit of detection of picomolar and a time response of 10 min. The enhanced single-molecule signals will allow for miniaturization into a small and cheap platform with multiplexing capability for application in point-of-care diagnostics, monitoring of industrial processes, and safe keeping of the environment.
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Affiliation(s)
- Vincenzo Lamberti
- Eindhoven University of Technology, Department of Applied Physics and Science Education and Institute for Complex Molecular Systems, 5600 MB Eindhoven, The Netherlands
| | - Mathias Dolci
- Eindhoven University of Technology, Department of Applied Physics and Science Education and Institute for Complex Molecular Systems, 5600 MB Eindhoven, The Netherlands
| | - Peter Zijlstra
- Eindhoven University of Technology, Department of Applied Physics and Science Education and Institute for Complex Molecular Systems, 5600 MB Eindhoven, The Netherlands
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5
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Lee Y, Buchheim J, Hellenkamp B, Lynall D, Yang K, Young EF, Penkov B, Sia S, Stojanovic MN, Shepard KL. Carbon-nanotube field-effect transistors for resolving single-molecule aptamer-ligand binding kinetics. Nat Nanotechnol 2024:10.1038/s41565-023-01591-0. [PMID: 38233588 DOI: 10.1038/s41565-023-01591-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 12/11/2023] [Indexed: 01/19/2024]
Abstract
Small molecules such as neurotransmitters are critical for biochemical functions in living systems. While conventional ultraviolet-visible spectroscopy and mass spectrometry lack portability and are unsuitable for time-resolved measurements in situ, techniques such as amperometry and traditional field-effect detection require a large ensemble of molecules to reach detectable signal levels. Here we demonstrate the potential of carbon-nanotube-based single-molecule field-effect transistors (smFETs), which can detect the charge on a single molecule, as a new platform for recognizing and assaying small molecules. smFETs are formed by the covalent attachment of a probe molecule, in our case a DNA aptamer, to a carbon nanotube. Conformation changes on binding are manifest as discrete changes in the nanotube electrical conductance. By monitoring the kinetics of conformational changes in a binding aptamer, we show that smFETs can detect and quantify serotonin at the single-molecule level, providing unique insights into the dynamics of the aptamer-ligand system. In particular, we show the involvement of G-quadruplex formation and the disruption of the native hairpin structure in the conformational changes of the serotonin-aptamer complex. The smFET is a label-free approach to analysing molecular interactions at the single-molecule level with high temporal resolution, providing additional insights into complex biological processes.
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Affiliation(s)
- Yoonhee Lee
- Department of Electrical Engineering, Columbia University, New York, NY, USA
- Division of Electronics & Information System, ICT Research Institute, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Republic of Korea
| | - Jakob Buchheim
- Department of Electrical Engineering, Columbia University, New York, NY, USA
- Deutsches Zentrum für Luft- und Raumfahrt e.V. (DLR), Institute of Quantum Technologies, Ulm, Germany
| | - Björn Hellenkamp
- Department of Electrical Engineering, Columbia University, New York, NY, USA
| | - David Lynall
- Department of Electrical Engineering, Columbia University, New York, NY, USA
| | - Kyungae Yang
- Department of Medicine, Columbia University, New York, NY, USA
| | - Erik F Young
- Quicksilver Biosciences, Inc., New York, NY, USA
| | - Boyan Penkov
- Department of Electrical Engineering, Columbia University, New York, NY, USA
| | - Samuel Sia
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | | | - Kenneth L Shepard
- Department of Electrical Engineering, Columbia University, New York, NY, USA.
- Department of Biomedical Engineering, Columbia University, New York, NY, USA.
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6
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Nie C, Shaw I, Chen C. Application of microfluidic technology based on surface-enhanced Raman scattering in cancer biomarker detection: A review. J Pharm Anal 2023; 13:1429-1451. [PMID: 38223444 PMCID: PMC10785256 DOI: 10.1016/j.jpha.2023.08.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/02/2023] [Accepted: 08/10/2023] [Indexed: 01/16/2024] Open
Abstract
With the continuous discovery and research of predictive cancer-related biomarkers, liquid biopsy shows great potential in cancer diagnosis. Surface-enhanced Raman scattering (SERS) and microfluidic technology have received much attention among the various cancer biomarker detection methods. The former has ultrahigh detection sensitivity and can provide a unique fingerprint. In contrast, the latter has the characteristics of miniaturization and integration, which can realize accurate control of the detection samples and high-throughput detection through design. Both have the potential for point-of-care testing (POCT), and their combination (lab-on-a-chip SERS (LoC-SERS)) shows good compatibility. In this paper, the basic situation of circulating proteins, circulating tumor cells, exosomes, circulating tumor DNA (ctDNA), and microRNA (miRNA) in the diagnosis of various cancers is reviewed, and the detection research of these biomarkers by the LoC-SERS platform in recent years is described in detail. At the same time, the challenges and future development of the platform are discussed at the end of the review. Summarizing the current technology is expected to provide a reference for scholars engaged in related work and interested in this field.
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Affiliation(s)
- Changhong Nie
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, China
| | - Ibrahim Shaw
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, China
| | - Chuanpin Chen
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, China
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7
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Zhai C, Long J, He J, Zheng Y, Wang B, Xu J, Yang Y, Jiang L, Yu H, Ding X. Precise Identification and Profiling of Surface Proteins of Ultra Rare Tumor Specific Extracellular Vesicle with Dynamic Quantitative Plasmonic Imaging. ACS Nano 2023; 17:16656-16667. [PMID: 37638659 DOI: 10.1021/acsnano.3c02853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/29/2023]
Abstract
Specific detection of tumor-derived EVs (tEVs) in plasma is complicated by nontumor EVs and non-EV particles. To accurately identify tEVs and profile their surface protein expression at single tEV resolution directly with clinical plasma is still an unmet need. Here, we present a Dynamic Immunoassay for Single tEV surface protein Profiling (DISEP), a kinetic assay based on surface plasmon resonance microscopy (SPRM) for specific single tEV profiling. DISEP adopts a pair of low-affinity oligonucleotide probes to respectively label EV surface proteins and functionalize an SPRM biosensor interface. tEVs labeled with the oligonucleotide probes possess distinctive binding kinetics from nonspecific particles in plasma, which permits accurate digital plasmonic counting of single EVs. We demonstrate DISEP for recognizing target EVs among 350-fold background plasma particles with high sensitivity (4677 EVs per μL). Clinical plasma samples were analyzed to discriminate between pancreatic cancer patients (n = 40) and healthy donors (n = 45). With a panel of biomarker signatures (EpCAM, HER2, and GPC1), DISEP only requires 10 μL primary sample from each donor to classify tumor patients with an area under the curve of 0.98. DISEP provides a highly specific EV detection and surface protein profiling strategy for early cancer diagnosis.
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Affiliation(s)
- Chunhui Zhai
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, People's Republic of China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai 200030, People's Republic of China
| | - Jiang Long
- Department of Pancreatic Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, People's Republic of China
- Shanghai Key Laboratory of Pancreatic Disease, Institute of Pancreatic Disease, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, People's Republic of China
| | - Jie He
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, People's Republic of China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai 200030, People's Republic of China
| | - Yan Zheng
- Department of Pancreatic Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, People's Republic of China
- Shanghai Key Laboratory of Pancreatic Disease, Institute of Pancreatic Disease, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, People's Republic of China
| | - Boqian Wang
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, People's Republic of China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai 200030, People's Republic of China
| | - Jiaying Xu
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, People's Republic of China
| | - Yuting Yang
- Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200030, People's Republic of China
| | - Lai Jiang
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, People's Republic of China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai 200030, People's Republic of China
| | - Hui Yu
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, People's Republic of China
| | - Xianting Ding
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, People's Republic of China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai 200030, People's Republic of China
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8
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Bergkamp MH, Cajigas S, van IJzendoorn LJ, Prins MW. High-Throughput Single-Molecule Sensors: How Can the Signals Be Analyzed in Real Time for Achieving Real-Time Continuous Biosensing? ACS Sens 2023; 8:2271-2281. [PMID: 37216442 PMCID: PMC10294250 DOI: 10.1021/acssensors.3c00245] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/05/2023] [Indexed: 05/24/2023]
Abstract
Single-molecule sensors collect statistics of single-molecule interactions, and the resulting data can be used to determine concentrations of analyte molecules. The assays are generally end-point assays and are not designed for continuous biosensing. For continuous biosensing, a single-molecule sensor needs to be reversible, and the signals should be analyzed in real time in order to continuously report output signals, with a well-controlled time delay and measurement precision. Here, we describe a signal processing architecture for real-time continuous biosensing based on high-throughput single-molecule sensors. The key aspect of the architecture is the parallel computation of multiple measurement blocks that enables continuous measurements over an endless time span. Continuous biosensing is demonstrated for a single-molecule sensor with 10,000 individual particles that are tracked as a function of time. The continuous analysis includes particle identification, particle tracking, drift correction, and detection of the discrete timepoints where individual particles switch between bound and unbound states, yielding state transition statistics that relate to the analyte concentration in solution. The continuous real-time sensing and computation were studied for a reversible cortisol competitive immunosensor, showing how the precision and time delay of cortisol monitoring are controlled by the number of analyzed particles and the size of the measurement blocks. Finally, we discuss how the presented signal processing architecture can be applied to various single-molecule measurement methods, allowing these to be developed into continuous biosensors.
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Affiliation(s)
- Max H. Bergkamp
- Department
of Biomedical Engineering, Eindhoven University
of Technology, Eindhoven 5612 AE, The Netherlands
- Institute
for Complex Molecular Systems (ICMS), Eindhoven
University of Technology, Eindhoven 5612 AE, The Netherlands
| | | | - Leo J. van IJzendoorn
- Department
of Applied Physics and Science Education, Eindhoven University of Technology, Eindhoven 5612 AE, The Netherlands
- Institute
for Complex Molecular Systems (ICMS), Eindhoven
University of Technology, Eindhoven 5612 AE, The Netherlands
| | - Menno W.J. Prins
- Department
of Biomedical Engineering, Eindhoven University
of Technology, Eindhoven 5612 AE, The Netherlands
- Department
of Applied Physics and Science Education, Eindhoven University of Technology, Eindhoven 5612 AE, The Netherlands
- Institute
for Complex Molecular Systems (ICMS), Eindhoven
University of Technology, Eindhoven 5612 AE, The Netherlands
- Helia
Biomonitoring, Eindhoven 5612 AR, The Netherlands
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9
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Gunasekara H, Perera T, Anderson J, Saed B, Ramseier N, Keshta N, Hu YS. Superresolution Imaging with Single-Antibody Labeling. Bioconjug Chem 2023; 34:825-833. [PMID: 37145839 PMCID: PMC10859171 DOI: 10.1021/acs.bioconjchem.3c00178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
We present a versatile single-molecule localization microscopy technique utilizing time-lapse imaging of single-antibody labeling. By performing single-molecule imaging in the subminute time scale and tuning the antibody concentration to create sparse single-molecule binding, we captured antibody labeling of subcellular targets to generate superresolution images. Single-antibody labeling enabled dual-target superresolution imaging using dye-conjugated monoclonal and polyclonal antibodies. We further demonstrate a dual-color strategy to increase the sample labeling density. Single-antibody labeling paves a new way to evaluate antibody binding for superresolution imaging in the native cellular environment.
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Affiliation(s)
| | - Thilini Perera
- Department of Chemistry, College of Liberal Arts and Sciences
| | - Jesse Anderson
- Department of Chemical Engineering, College of Engineering
| | - Badeia Saed
- Department of Chemistry, College of Liberal Arts and Sciences
| | - Neal Ramseier
- Department of Chemistry, College of Liberal Arts and Sciences
| | - Neama Keshta
- Department of Biological Sciences, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL, 60607, USA
| | - Ying S. Hu
- Department of Chemistry, College of Liberal Arts and Sciences
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10
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Abstract
There has been a recent surge of advances in biomolecular assays based on the measurement of discrete molecular targets as opposed to signals averaged across molecular ensembles. Many of these "digital" assay designs derive from now-mature technologies involving single-molecule imaging and microfluidics and provide an assortment of new modalities to quantify nucleic acids and proteins in biospecimens such as blood and tissue homogenates. A primary new benefit is the robust detection of trace analytes at attomolar to femtomolar concentrations for which many ensemble assays cannot distinguish signals above noise levels. In addition, multiple biomolecules can be differentiated within a mixture using optical barcodes, with much faster and simpler readouts compared with sequencing methods. In ideal digital assays, signals should, in theory, further represent absolute molecular counts, rather than relative levels, eliminating the need for calibration standards that are the mainstay of typical assays. Several digital assay platforms have now been commercialized but challenges hinder the adoption and diversification of these new formats, as there are broad needs to balance sensitivity and dynamic range of detection, increase analyte multiplexing, improve sample throughput, and reduce cost. Our lab and others have developed technologies to address these challenges by redesigning molecular probes and labels, improving molecular transport within detection focal volumes, and applying solution-based readout methods in flow.This Account describes the principles, formats, and design constraints of digital biomolecular assays that apply optical labels toward the goal of simple and routine target counting that may ultimately approach absolute readout standards. The primary challenges can be understood from fundamental concepts in thermodynamics and kinetics of association reactions, mass transport, and discrete statistics. Major advances include (1) new inorganic nanocrystal probes for more robust counting compared with dyes, (2) diverse molecular amplification tools that endow attachment of numerous labels to single targets, (3) specialized surfaces with patterned features for electromagnetic coupling to labels for signal amplification, (4) surface capture enhancement methods to concentrate targets through disruption of diffusion depletion zones, and (5) flow counting in which analytes are rapidly counted in solution without pull-down to a surface. Further progress and integration of these tools for biomolecular counting could improve the precision of laboratory measurements in life sciences research and benefit clinical diagnostic assays for low abundance biomarkers in limiting biospecimen volumes that are out of reach of traditional ensemble-level bioassays.
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Affiliation(s)
- Chia-Wei Kuo
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Micro and Nanotechnology Laboratory, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Andrew M Smith
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Micro and Nanotechnology Laboratory, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Materials Science & Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Carle Illinois College of Medicine, Urbana, Illinois 61801, United States
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11
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Li Q, Qiang W, Yuan J, Xiao L. Nanoparticle-Coupled Single-Molecule Kinetic Fingerprinting for Enzymatic Activity Detection. Anal Chem 2023; 95:7796-7803. [PMID: 37129996 DOI: 10.1021/acs.analchem.3c01385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The sensitive and accurate detection of biomarkers plays an important role in clinical diagnosis and drug discovery. Currently, amplification-based methods for biomarker detection are widely explored. However, the key challenges of these methods are limited reproducibility and high background noise. To overcome these limitations, we develop a robust plasmonic nanoparticle-coupled single-molecule kinetic fingerprinting (PNP-SMKF) method to achieve ultrasensitive detection of protein kinase A (PKA). Transient binding of a short fluorescent probe with the genuine target produces a distinct kinetic signature that is completely different from that of the background signal, allowing us to recognize PKA sensitively. Importantly, integrating a plasmonic nanoparticle efficiently breaks the concentration limit of the imager strand for single-molecule imaging, thus achieving a much faster imaging speed. A limit of detection (LOD) of as low as 0.0005 U/mL is readily realized. This method holds great potential as a versatile platform for enzyme detection and inhibitor screening in the future.
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Affiliation(s)
- Qingnan Li
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
- College of Chemistry, Nankai University, Tianjin 300071, China
| | - Wenzhi Qiang
- College of Chemistry, Nankai University, Tianjin 300071, China
| | - Jie Yuan
- School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, China
| | - Lehui Xiao
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
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12
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Ahmad M, Ha JH, Mayse LA, Presti MF, Wolfe AJ, Moody KJ, Loh SN, Movileanu L. A generalizable nanopore sensor for highly specific protein detection at single-molecule precision. Nat Commun 2023; 14:1374. [PMID: 36941245 PMCID: PMC10027671 DOI: 10.1038/s41467-023-36944-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 02/23/2023] [Indexed: 03/23/2023] Open
Abstract
Protein detection has wide-ranging implications in molecular diagnostics. Substantial progress has been made in protein analytics using nanopores and the resistive-pulse technique. Yet, a long-standing challenge is implementing specific interfaces for detecting proteins without the steric hindrance of the pore interior. Here, we formulate a class of sensing elements made of a programmable antibody-mimetic binder fused to a monomeric protein nanopore. This way, such a modular design significantly expands the utility of nanopore sensors to numerous proteins while preserving their architecture, specificity, and sensitivity. We prove the power of this approach by developing and validating nanopore sensors for protein analytes that drastically vary in size, charge, and structural complexity. These analytes produce unique electrical signatures that depend on their identity and quantity and the binder-analyte assembly at the nanopore tip. The outcomes of this work could impact biomedical diagnostics by providing a fundamental basis for biomarker detection in biofluids.
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Affiliation(s)
- Mohammad Ahmad
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY, 13244-1130, USA
| | - Jeung-Hoi Ha
- Department of Biochemistry and Molecular Biology, State University of New York-Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, NY, 13210, USA
| | - Lauren A Mayse
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY, 13244-1130, USA
- Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, NY, 13244, USA
| | - Maria F Presti
- Department of Biochemistry and Molecular Biology, State University of New York-Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, NY, 13210, USA
| | - Aaron J Wolfe
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY, 13244-1130, USA
- Ichor Life Sciences, Inc., 2561 US Route 11, LaFayette, NY, 13084, USA
- Lewis School of Health Sciences, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, 13699, USA
- Department of Chemistry, College of Environmental Science and Forestry, State University of New York, 1 Forestry Drive, Syracuse, NY, 13210, USA
| | - Kelsey J Moody
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY, 13244-1130, USA
- Ichor Life Sciences, Inc., 2561 US Route 11, LaFayette, NY, 13084, USA
- Lewis School of Health Sciences, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, 13699, USA
- Department of Chemistry, College of Environmental Science and Forestry, State University of New York, 1 Forestry Drive, Syracuse, NY, 13210, USA
| | - Stewart N Loh
- Department of Biochemistry and Molecular Biology, State University of New York-Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, NY, 13210, USA
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY, 13244-1130, USA.
- Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, NY, 13244, USA.
- The BioInspired Institute, Syracuse University, Syracuse, NY, 13244, USA.
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13
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Abstract
This paper reviews methods for detecting proteins based on molecular digitization, i.e., the isolation and detection of single protein molecules or singulated ensembles of protein molecules. The single molecule resolution of these methods has resulted in significant improvements in the sensitivity of immunoassays beyond what was possible using traditional "analog" methods: the sensitivity of some digital immunoassays approach those of methods for measuring nucleic acids, such as the polymerase chain reaction (PCR). The greater sensitivity of digital protein detection has resulted in immuno-diagnostics with high potential societal impact, e.g., the early diagnosis and therapeutic intervention of Alzheimer's Disease. In this review, we will first provide the motivation for developing digital protein detection methods given the limitations in the sensitivity of analog methods. We will describe the paradigm shift catalyzed by single molecule detection, and will describe in detail one digital approach - which we call digital bead assays (DBA) - based on the capture and labeling of proteins on beads, identifying "on" and "off" beads, and quantification using Poisson statistics. DBA based on the single molecule array (Simoa) technology have sensitivities down to attomolar concentrations, equating to ∼10 proteins in a 200 μL sample. We will describe the concept behind DBA, the different single molecule labels used, the ways of analyzing beads (imaging of arrays and flow), the binding reagents and substrates used, and integration of these technologies into fully automated and miniaturized systems. We provide an overview of emerging approaches to digital protein detection, including those based on digital detection of nucleic acids labels, single nanoparticle detection, measurements using nanopores, and methods that exploit the kinetics of single molecule binding. We outline the initial impact of digital protein detection on clinical measurements, highlighting the importance of customized assay development and translational clinical research. We highlight the use of DBA in the measurement of neurological protein biomarkers in blood, and how these higher sensitivity methods are changing the diagnosis and treatment of neurological diseases. We conclude by summarizing the status of digital protein detection and suggest how the lab-on-a-chip community might drive future innovations in this field.
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Affiliation(s)
- David C Duffy
- Quanterix Corporation, 900 Middlesex Turnpike, Billerica, MA 01821, USA.
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14
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Zhao W, Huang C, Zhao B, Wen J, Lu Y, Li N, He Q, Bao J, Zhang X, Pi Z, Dong Y, Chen Y. Magnetic Relaxation Switching Immunosensors via a Click Chemistry-Mediated Controllable Aggregation Strategy for Direct Detection of Chlorpyrifos. J Agric Food Chem 2023; 71:1727-1734. [PMID: 36638207 DOI: 10.1021/acs.jafc.2c06858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Chlorpyrifos (CPF) is the most frequently found organophosphate pesticide residue in solid food samples and can cause increasing public concerns about potential risks to human health. Traditional detection signals of such small molecules are mostly generated by target-mediated indirect conversion, which tends to be detrimental to sensitivity and accuracy. Herein, a novel magnetic relaxation switching detection platform was developed for target-mediated direct and sensitive detection of CPF with a controllable aggregation strategy based on a bioorthogonal ligation reaction between tetrazine (Tz) and trans-cyclooctene (TCO) ligands. Under optimal conditions, this sensor can achieve a detection limit of 37 pg/mL with a broad linear range of 0.1-500 ng/mL in 45 min, which is approximately 51-fold lower than that of the gas chromatography analysis and 13-fold lower than that of the enzyme-linked immunosorbent assay. The proposed click chemistry-mediated controllable aggregation strategy is direct, rapid, and sensitive, indicating great potential for residue screening in food matrices.
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Affiliation(s)
- Weiqi Zhao
- Key Laboratory of Environment Correlative Dietology, Huazhong Agricultural University, Wuhan, 430070 Hubei, China
| | - Chenxi Huang
- Key Laboratory of Environment Correlative Dietology, Huazhong Agricultural University, Wuhan, 430070 Hubei, China
| | - Binjie Zhao
- Key Laboratory of Environment Correlative Dietology, Huazhong Agricultural University, Wuhan, 430070 Hubei, China
| | - Junping Wen
- Key Laboratory of Environment Correlative Dietology, Huazhong Agricultural University, Wuhan, 430070 Hubei, China
| | - Yingying Lu
- Key Laboratory of Environment Correlative Dietology, Huazhong Agricultural University, Wuhan, 430070 Hubei, China
| | - Nan Li
- Daye Public Inspection and Test Center, Daye, 435100 Hubei, China
| | - Qifu He
- Daye Public Inspection and Test Center, Daye, 435100 Hubei, China
| | - Junwang Bao
- Daye Public Inspection and Test Center, Daye, 435100 Hubei, China
| | - Xiuwen Zhang
- Daye Public Inspection and Test Center, Daye, 435100 Hubei, China
| | - Zhixiong Pi
- Daye Public Inspection and Test Center, Daye, 435100 Hubei, China
| | - Yongzhen Dong
- Key Laboratory of Environment Correlative Dietology, Huazhong Agricultural University, Wuhan, 430070 Hubei, China
| | - Yiping Chen
- Key Laboratory of Environment Correlative Dietology, Huazhong Agricultural University, Wuhan, 430070 Hubei, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Shenzhen Institute of Food Nutrition and Health, Huazhong Agricultural University, Shenzhen 518120, Guangdong, China
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15
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Dey S, Dolci M, Zijlstra P. Single-Molecule Optical Biosensing: Recent Advances and Future Challenges. ACS Phys Chem Au 2023; 3:143-156. [PMID: 36968450 PMCID: PMC10037498 DOI: 10.1021/acsphyschemau.2c00061] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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16
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He H, Wu C, Saqib M, Hao R. Single-molecule fluorescence methods for protein biomarker analysis. Anal Bioanal Chem 2023:10.1007/s00216-022-04502-9. [PMID: 36609860 DOI: 10.1007/s00216-022-04502-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/07/2022] [Accepted: 12/20/2022] [Indexed: 01/09/2023]
Abstract
Proteins have been considered key building blocks of life. In particular, the protein content of an organism and a cell offers significant information for the in-depth understanding of the disease and biological processes. Single-molecule protein detection/sequencing tools will revolutionize clinical (proteomics) research, offering ultrasensitivity for low-abundance biomarker (protein) detection, which is important for the realization of early-stage disease diagnosis and single-cell proteomics. This improved detection/measurement capability delivers new sets of techniques to explore new frontiers and address important challenges in various interdisciplinary areas including nanostructured materials, molecular medicine, molecular biology, and chemistry. Importantly, fluorescence-based methods have emerged as indispensable tools for single protein detection/sequencing studies, providing a higher signal-to-noise ratio (SNR). Improvements in fluorescent dyes/probes and detector capabilities coupled with advanced (image) analysis strategies have fueled current developments for single protein biomarker detections. For example, in comparison to conventional ELISA (i.e., based on ensembled measurements), single-molecule fluorescence detection is more sensitive, faster, and more accurate with reduced background, high-throughput, and so on. In comparison to MS sequencing, fluorescence-based single-molecule protein sequencing can achieve the sequencing of peptides themselves with higher sensitivity. This review summarizes various typical single-molecule detection technologies including their methodology (modes of operation), detection limits, advantages and drawbacks, and current challenges with recent examples. We describe the fluorescence-based single-molecule protein sequencing/detection based on five kinds of technologies such as fluorosequencing, N-terminal amino acid binder, nanopore light sensing, and DNA nanotechnology. Finally, we present our perspective for developing high-performance fluorescence-based sequencing/detection techniques.
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Affiliation(s)
- Haihan He
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China.,Research Center for Chemical Biology and Omics Analysis, School of Science, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Chuhong Wu
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China.,Research Center for Chemical Biology and Omics Analysis, School of Science, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Muhammad Saqib
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China.,Research Center for Chemical Biology and Omics Analysis, School of Science, Southern University of Science and Technology, Shenzhen, 518055, China.,Institute of Chemistry, Khwaja Fareed University of Engineering & Information Technology, Rahim Yar Khan 64200, Pakistan
| | - Rui Hao
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China. .,Research Center for Chemical Biology and Omics Analysis, School of Science, Southern University of Science and Technology, Shenzhen, 518055, China.
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17
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Schaub JM, Ruan Q, Tetin SY. Epifluorescent single-molecule counting with Streptavidin-Phycoerythrin conjugates. Anal Biochem 2022; 659:114955. [PMID: 36265689 DOI: 10.1016/j.ab.2022.114955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 10/10/2022] [Indexed: 12/14/2022]
Abstract
Single-molecule methods, specifically single-molecule counting, convey high sensitivity in research applications. However, single-molecule counting experiments require specialized equipment or consumables to perform. We demonstrate the utility of using bright Streptavidin-Phycoerythrin (SA-PE) conjugates and an epifluorescence microscope, for single-molecule counting applications. In this work, we show that we can visualize single-molecules on glass surfaces, perform single-molecule diagnostic assays on magnetic microparticles, and image individual foci on cell surfaces. This approach is simple and effective for researchers interested in single-molecule counting.
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Affiliation(s)
- Jeffrey M Schaub
- Applied Research and Technology, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, IL, 60064, USA
| | - Qiaoqiao Ruan
- Applied Research and Technology, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, IL, 60064, USA
| | - Sergey Y Tetin
- Applied Research and Technology, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, IL, 60064, USA.
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18
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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 DOI: 10.1038/s41467-022-32796-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [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. A major challenge of enzyme-linked immunosorbent assays is discriminating true signal from non-specific binding. Here the authors present a Single-Molecule Colocalization Assay (SiMCA) which eliminates such effects, enabling reproducible detection of picomolar protein concentrations.
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19
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Chatterjee T, Johnson-Buck A, Walter NG. Highly sensitive protein detection by aptamer-based single-molecule kinetic fingerprinting. Biosens Bioelectron 2022; 216:114639. [PMID: 36037714 DOI: 10.1016/j.bios.2022.114639] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/21/2022] [Accepted: 08/13/2022] [Indexed: 11/28/2022]
Abstract
Sensitive assays of protein biomarkers play critical roles in clinical diagnostics and biomedical research. Such assays typically employ immunoreagents such as monoclonal antibodies that suffer from several drawbacks, including relatively tedious production, significant batch-to-batch variability, and challenges in site-specific, stoichiometric modification with fluorophores or other labels. One proposed alternative to such immunoreagents, nucleic acid aptamers generated by systematic evolution of ligand by exponential enrichment (SELEX), can be chemically synthesized with much greater ease, precision, and reproducibility than antibodies. However, most aptamers exhibit relatively poor affinity, yielding low sensitivity in the assays employing them. Recently, single molecule recognition through equilibrium Poisson sampling (SiMREPS) has emerged as a platform for detecting proteins and other biomarkers with high sensitivity without requiring high-affinity detection probes. In this manuscript, we demonstrate the applicability and advantages of aptamers as detection probes in SiMREPS as applied to two clinically relevant biomarkers, VEGF165 and IL-8, using a wash-free protocol with limits of detection in the low femtomolar range (3-9 fM). We show that the kinetics of existing RNA aptamers can be rationally optimized for use as SiMREPS detection probes by mutating a single nucleotide in the conserved binding region or by shortening the aptamer sequence. Finally, we demonstrate the detection of endogenous IL-8 from human serum at a concentration below the detection limit of commercial ELISAs.
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Affiliation(s)
- Tanmay Chatterjee
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, United States
| | - Alexander Johnson-Buck
- aLight Sciences, Inc., 333 Jackson Plaza Suite 460, Ann Arbor, Michigan, 48103, United States.
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, United States.
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20
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Blanchard AT, Li Z, Duran EC, Scull CE, Hoff JD, Wright KR, Pan V, Walter NG. Ultra-photostable DNA FluoroCubes: Mechanism of Photostability and Compatibility with FRET and Dark Quenching. Nano Lett 2022; 22:6235-6244. [PMID: 35881934 PMCID: PMC10080265 DOI: 10.1021/acs.nanolett.2c01757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
DNA-based FluoroCubes were recently developed as a solution to photobleaching, a ubiquitous limitation of fluorescence microscopy (Niekamp; ; Stuurman; ; Vale Nature Methods, 2020). FluoroCubes, that is, compact ∼4 × 4 × 5.4 nm3 four-helix bundles coupled to ≤6 fluorescent dyes, remain fluorescent up to ∼50× longer than single dyes and emit up to ∼40× as many photons. The current work answers two important questions about the FluoroCubes. First, what is the mechanism by which photostability is enhanced? Second, are FluoroCubes compatible with Förster resonance energy transfer (FRET) and similar techniques? We use single particle photobleaching studies to show that photostability arises through interactions between the fluorophores and the four-helix DNA bundle. Supporting this, we discover that smaller ∼4 × 4 × 2.7 nm3 FluoroCubes also confer ultraphotostability. However, we find that certain dye-dye interactions negatively impact FluoroCube performance. Accordingly, 4-dye FluoroCubes lacking these interactions perform better than 6-dye FluoroCubes. We also demonstrate that FluoroCubes are compatible with FRET and dark quenching applications.
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Affiliation(s)
- Aaron T. Blanchard
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, United States
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, 48109, United States
- Michigan Society of Fellows, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Zi Li
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, United States
| | - Elizabeth C. Duran
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, United States
| | - Catherine E. Scull
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, United States
| | - J. Damon Hoff
- Single Molecule Analysis in Real-Time (SMART) Center, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Keenan R. Wright
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, United States
| | - Victor Pan
- Department of Biomedical Engineering, Emory University and the Georgia Institute of Technology, Atlanta, Georgia, 30322
| | - Nils G. Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, United States
- Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan, 48109, United States
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21
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Yang Y, Zeng Q, Luo Q, Wang C, Yu H. Dynamic Single-Molecule Sensors: A Theoretical Study. ACS Sens 2022; 7:2069-2074. [PMID: 35709486 DOI: 10.1021/acssensors.2c00929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
One of the key advantages of single-molecule sensors over conventional ensemble technologies is their capability of revealing the heterogeneity among molecular events. In dynamic single-molecule sensing, heterogeneity in molecular interaction kinetics is quantified as the fingerprint to specifically detect target molecules. This strategy offers a unique approach to develop ultrasensitive biosensors with a limit of detection at the fM level, which is three orders of magnitude lower than that of conventional assays. However, due to the lack of a comprehensive theoretical model, the rational design of dynamic single-molecule sensors is challenging. Herein, we present the theoretical study of sensing performance with a hydrodynamic model. We quantitatively show that there is a dilemma regarding the probe design. High-affinity probes offer higher specificity but require extremely long assay time, while low-affinity probes could shorten the assay time but are prone to the interference from unwanted molecules. This study also suggests that one possible solution to solve this dilemma is by applying external disturbance to the system, as we have recently demonstrated by experiments. We anticipate that this work could inspire the rational design of single-molecule sensors to further improve the sensitivity, specificity, and multiplexing capability.
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Affiliation(s)
- Yuting Yang
- Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200030, People's Republic of China
| | - Qiang Zeng
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, People's Republic of China
| | - Qingqing Luo
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, People's Republic of China
| | - Chen Wang
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, People's Republic of China
| | - Hui Yu
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, People's Republic of China
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22
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Li Z, McNeely M, Sandford E, Tewari M, Johnson-Buck A, Walter NG. Attomolar Sensitivity in Single Biomarker Counting upon Aqueous Two-Phase Surface Enrichment. ACS Sens 2022; 7:1419-1430. [PMID: 35438959 DOI: 10.1021/acssensors.2c00135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
From longstanding techniques like enzyme-linked immunosorbent assay (ELISA) to modern next-generation sequencing, many of the most sensitive and specific biomarker detection assays require capture of the analyte at a surface. While surface-based assays provide advantages, including the ability to reduce background by washing away excess reagents and/or increase specificity through analyte-specific capture probes, the limited efficiency of capture from dilute solution often restricts assay sensitivity to the femtomolar-to-nanomolar range. Although assays for many nucleic acid analytes can decrease limits of detection (LODs) to the subfemtomolar range using polymerase chain reaction, such amplification may introduce biases, errors, and an increased risk of sample cross-contamination. Furthermore, many analytes cannot be amplified easily, including short nucleic acid fragments, epigenetic modifications, and proteins. To address the challenge of achieving subfemtomolar LODs in surface-based assays without amplification, we exploit an aqueous two-phase system (ATPS) to concentrate target molecules in a smaller-volume phase near the assay surface, thus increasing capture efficiency compared to passive diffusion from the original solution. We demonstrate the utility of ATPS-enhanced capture via single molecule recognition through equilibrium Poisson sampling (SiMREPS), a microscopy technique previously shown to possess >99.9999% detection specificity for DNA mutations but an LOD of only ∼1-5 fM. By combining ATPS-enhanced capture with a Förster resonance energy transfer (FRET)-based probe design for rapid data acquisition over many fields of view, we improve the LOD ∼ 300-fold to <10 aM for an EGFR exon 19 deletion mutation. We further validate this ATPS-assisted FRET-SiMREPS assay by detecting endogenous exon 19 deletion molecules in cancer patient blood plasma.
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Affiliation(s)
- Zi Li
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Molly McNeely
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Erin Sandford
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Muneesh Tewari
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan, Ann Arbor, Michigan 48109, United States
- Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Alexander Johnson-Buck
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan, Ann Arbor, Michigan 48109, United States
- Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Nils G. Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan 48109, United States
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
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23
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Liu X, Lin X, Pan X, Gai H. Multiplexed Homogeneous Immunoassay Based on Counting Single Immunocomplexes together with Dark-Field and Fluorescence Microscopy. Anal Chem 2022; 94:5830-5837. [PMID: 35380795 DOI: 10.1021/acs.analchem.1c05269] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The development of multiplexed immunoassays is impeded by the difficulty in distinguishing labeled immunocomplexes from free probes and nonspecifically bound probes. Here, we attempted to overcome this issue by counting core-satellite-structured immunocomplexes simultaneously using dark-field and fluorescence microscopy. The tumor biomarkers of carcinoembryonic antigen (CEA), α-fetoprotein (AFP), and prostate-specific antigen (PSA) were chosen as model targets. Gold nanoparticles (AuNPs) with diameters of 70 nm were coated with the detection antibodies of the three targets. Quantum dot (QD) 525, QD 585, and QD 655 were modified with the capture antibodies of CEA, AFP, and PSA, respectively. Then, an immunocomplex containing one AuNP and one or several QDs was formed, whereas free and nonspecifically bound probes had either one AuNP or one QD. When observed with a transmission grating-based spectral microscope, the immunocomplexes had overlapping scattering and fluorescent spectral images and were therefore identified and quantified precisely. The biomarkers inside the immunocomplexes were recognized on the basis of the fluorescent first-order streaks of the QDs. Model biomarkers in buffer and in 12.6% blank plasma were quantified for validation. The limits of detection for CEA, PSA, and AFP in buffer were in dozens of femtomolar and were close to those in blank plasma. The results demonstrated that our approach worked well in distinguishing immunocomplexes from free and nonspecifically bound probes. The successful quantification of the three targets in five human plasma samples verified the reliability of our method in clinical applications.
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Affiliation(s)
- Xiaojun Liu
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, Jiangsu, China
| | - Xinyi Lin
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, Jiangsu, China
| | - Xiaoyan Pan
- School of Medicine, the Second Affiliated Hospital of Zhejiang University, Hangzhou 310009, Zhejiang, China
| | - Hongwei Gai
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, Jiangsu, China
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24
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Zeng Q, Zhou X, Yang Y, Sun Y, Wang J, Zhai C, Li J, Yu H. Dynamic single-molecule sensing by actively tuning binding kinetics for ultrasensitive biomarker detection. Proc Natl Acad Sci U S A 2022; 119:e2120379119. [PMID: 35238650 DOI: 10.1073/pnas.2120379119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
SignificanceThe detection of low-abundance molecular biomarkers is key to the liquid-biopsy-based disease diagnosis. Existing methods are limited by the affinity and specificity of recognition probes and the mass transportation of analyte molecules onto the sensor surfaces, resulting in insufficient sensitivity and long assay time. This work establishes a rapid and ultrasensitive approach by actively tuning binding kinetics and accelerating the mass transportation via nanoparticle micromanipulations. This is significant because it permits extremely sensitive measurements within clinically acceptable assay time. It is incubation-free, washing-free, and compatible with low- and high-affinity probes.
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Stein J, Stehr F, Jungmann R, Schwille P. Calibration-free counting of low molecular copy numbers in single DNA-PAINT localization clusters. Biophys Rep (N Y) 2021; 1:100032. [PMID: 36425461 PMCID: PMC9680712 DOI: 10.1016/j.bpr.2021.100032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 11/04/2021] [Indexed: 06/16/2023]
Abstract
Single-molecule localization microscopy (SMLM) has revolutionized light microscopy by enabling optical resolution down to a few nanometer. Yet, localization precision commonly does not suffice to visually resolve single subunits in molecular assemblies or multimeric complexes. Because each targeted molecule contributes localizations during image acquisition, molecular counting approaches to reveal the target copy numbers within localization clusters have been persistently proposed since the early days of SMLM, most of which rely on preliminary knowledge of the dye photophysics or on a calibration to a reference. Previously, we developed localization-based fluorescence correlation spectroscopy (lbFCS) as an absolute ensemble counting approach for the SMLM-variant DNA-PAINT (points accumulation for imaging in nanoscale topography), for the first time, to our knowledge, circumventing the necessity for reference calibrations. Here, we present an extended concept termed lbFCS+, which allows absolute counting of copy numbers for individual localization clusters in a single DNA-PAINT image. In lbFCS+, absolute counting of fluorescent loci contained in individual nanoscopic volumes is achieved via precise measurement of the local hybridization rates of the fluorescently labeled oligonucleotides ("imagers") employed in DNA-PAINT imaging. In proof-of-principle experiments on DNA origami nanostructures, we demonstrate the ability of lbFCS+ to truthfully determine molecular copy numbers and imager association and dissociation rates in well-separated localization clusters containing up to 10 docking strands. For N ≤ 4 target molecules, lbFCS+ is even able to resolve integers, providing the potential to study the composition of up to tetrameric molecular complexes. Furthermore, we show that lbFCS+ allows resolving heterogeneous binding dynamics, enabling the distinction of stochastically generated and a priori indistinguishable DNA assemblies. Beyond advancing quantitative DNA-PAINT imaging, we believe that lbFCS+ could find promising applications ranging from biosensing to DNA computing.
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Affiliation(s)
- Johannes Stein
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Florian Stehr
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ralf Jungmann
- Max Planck Institute of Biochemistry, Martinsried, Germany
- Faculty of Physics, Ludwig Maximilian University, Munich, Germany
| | - Petra Schwille
- Max Planck Institute of Biochemistry, Martinsried, Germany
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Hentrich C, Kellmann SJ, Putyrski M, Cavada M, Hanuschka H, Knappik A, Ylera F. Periplasmic expression of SpyTagged antibody fragments enables rapid modular antibody assembly. Cell Chem Biol 2021; 28:813-824.e6. [PMID: 33529581 DOI: 10.1016/j.chembiol.2021.01.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/16/2020] [Accepted: 01/06/2021] [Indexed: 12/15/2022]
Abstract
Antibodies are essential tools in research and diagnostics. Although antibody fragments typically obtained from in vitro selection can be rapidly produced in bacteria, the generation of full-length antibodies or the modification of antibodies with probes is time and labor intensive. Protein ligation such as SpyTag technology could covalently attach domains and labels to antibody fragments equipped with a SpyTag. However, we found that the established periplasmic expression of antibody fragments in E. coli led to quantitative cleavage of the SpyTag by the proteases Tsp and OmpT. Here we report successful periplasmic expression of SpyTagged Fab fragments and demonstrate the coupling to separately prepared SpyCatcher modules. We used this modular toolbox of SpyCatcher proteins to generate reagents for a variety of immunoassays and measured their performance in comparison with traditional reagents. Furthermore, we demonstrate surface immobilization, high-throughput screening of antibody libraries, and rapid prototyping of antibodies based on modular antibody assembly.
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Affiliation(s)
| | | | - Mateusz Putyrski
- Bio-Rad AbD Serotec GmbH, Zeppelinstraße 4, 82178 Puchheim, Germany
| | - Manuel Cavada
- Bio-Rad AbD Serotec GmbH, Zeppelinstraße 4, 82178 Puchheim, Germany
| | - Hanh Hanuschka
- Bio-Rad AbD Serotec GmbH, Zeppelinstraße 4, 82178 Puchheim, Germany
| | - Achim Knappik
- Bio-Rad AbD Serotec GmbH, Zeppelinstraße 4, 82178 Puchheim, Germany
| | - Francisco Ylera
- Bio-Rad AbD Serotec GmbH, Zeppelinstraße 4, 82178 Puchheim, Germany.
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Mandal S, Li Z, Chatterjee T, Khanna K, Montoya K, Dai L, Petersen C, Li L, Tewari M, Johnson-Buck A, Walter NG. Direct Kinetic Fingerprinting for High-Accuracy Single-Molecule Counting of Diverse Disease Biomarkers. Acc Chem Res 2021; 54:388-402. [PMID: 33382587 DOI: 10.1021/acs.accounts.0c00621] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Methods for detecting and quantifying disease biomarkers in biofluids with high specificity and sensitivity play a pivotal role in enabling clinical diagnostics, including point-of-care tests. The most widely used molecular biomarkers include proteins, nucleic acids, hormones, metabolites, and other small molecules. While numerous methods have been developed for analyzing biomarkers, most techniques are challenging to implement for clinical use due to insufficient analytical performance, high cost, and/or other practical shortcomings. For instance, the detection of cell-free nucleic acid (cfNA) biomarkers by digital PCR and next-generation sequencing (NGS) requires time-consuming nucleic acid extraction steps, often introduces enzymatic amplification bias, and can be costly when high specificity is required. While several amplification-free methods for detecting cfNAs have been reported, these techniques generally suffer from low specificity and sensitivity. Meanwhile, the quantification of protein biomarkers is generally performed using immunoassays such as enzyme-linked immunosorbent assay (ELISA); the analytical performance of these methods is often limited by the availability of antibodies with high affinity and specificity as well as the significant nonspecific binding of antibodies to assay surfaces. To address the drawbacks of existing biomarker detection methods and establish a universal diagnostics platform capable of detecting different types of analytes, we have developed an amplification-free approach, named single-molecule recognition through equilibrium Poisson sampling (SiMREPS), for the detection of diverse biomarkers with arbitrarily high specificity and single-molecule sensitivity. SiMREPS utilizes the transient, reversible binding of fluorescent detection probes to immobilized target molecules to generate kinetic fingerprints that are detected by single-molecule fluorescence microscopy. The analysis of these kinetic fingerprints enables nearly perfect discrimination between specific binding to target molecules and any nonspecific binding. Early proof-of-concept studies demonstrated the in vitro detection of miRNAs with a limit of detection (LOD) of approximately 1 fM and >500-fold selectivity for single-nucleotide polymorphisms. The SiMREPS approach was subsequently expanded to the detection of rare mutant DNA alleles from biofluids at mutant allele fractions of as low as 1 in 1 million, corresponding to a specificity of >99.99999%. Recently, SiMREPS was generalized to protein quantification using dynamically binding antibody probes, permitting LODs in the low-femtomolar to attomolar range. Finally, SiMREPS has been demonstrated to be suitable for the in situ detection of miRNAs in cultured cells, the quantification of small-molecule toxins and drugs, and the monitoring of telomerase activity at the single-molecule level. In this Account, we discuss the principles of SiMREPS for the highly specific and sensitive detection of molecular analytes, including considerations for assay design. We discuss the generality of SiMREPS for the detection of very disparate analytes and provide an overview of data processing methods, including the expansion of the dynamic range using super-resolution analysis and the improvement of performance using deep learning algorithms. Finally, we describe current challenges, opportunities, and future directions for the SiMREPS approach.
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