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Finocchiaro G, Špringer T, Krejčík Z, Bocková M, Merkerová MD, Homola J. Large gold nanoparticle release assay for attomolar detection of miRNA related to myelodysplastic neoplasms. Talanta 2025; 293:128037. [PMID: 40199123 DOI: 10.1016/j.talanta.2025.128037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2025] [Revised: 03/21/2025] [Accepted: 03/27/2025] [Indexed: 04/10/2025]
Abstract
MicroRNAs (miRNAs) hold potential as biomarkers for numerous cancer types, including myelodysplastic neoplasms (MDS). Here, we present a highly sensitive assay based on the oligonucleotide-triggered release of gold nanoparticles (AuNPs) for the detection of hsa-miR-451a with a surface plasmon resonance biosensor. The performance of the assay is in large part determined by the size and functional coating of AuNPs. Therefore, we investigate AuNPs in a size range from 43 to 170 nm, functionalized with thiol- or biotin-terminated oligonucleotides (AuNPsSdT or AuNPsBdT). Our study reveals that 103 nm AuNPsSdT are the best option to improve the assay performance due to their high colloidal stability, a release efficiency exceeding 90%, and a sensor response enhancement factor exceeding 105. We demonstrate that in conjunction with 103 nm AuNPsSdT, the AuNP release assay can detect hsa-miR-451a at levels down to 40 aM and quantify hsa-miR-451a physiological levels in human blood plasma. Moreover, we use the assay to demonstrate a significant down-regulation of hsa-miR-451a in blood plasma of MDS patients compared to healthy individuals, suggesting the potential relevance of hsa-miR-451a as a prospective MDS biomarker.
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Affiliation(s)
- Giusy Finocchiaro
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberská 1014/57, 182 00, Prague, Czech Republic
| | - Tomáš Špringer
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberská 1014/57, 182 00, Prague, Czech Republic
| | - Zdeněk Krejčík
- Institute of Hematology and Blood Transfusion, U Nemocnice 2094/1, 128 20, Prague, Czech Republic
| | - Markéta Bocková
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberská 1014/57, 182 00, Prague, Czech Republic
| | | | - Jiří Homola
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberská 1014/57, 182 00, Prague, Czech Republic.
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2
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Lee H, Li S, Liu L, Wang W, Ayupova T, Tibbs J, Kim C, Fang Y, Do MN, Cunningham BT. Physically grounded deep learning-enabled gold nanoparticle localization and quantification in photonic resonator absorption microscopy for digital resolution molecular diagnostics. Biosens Bioelectron 2025; 281:117455. [PMID: 40233489 DOI: 10.1016/j.bios.2025.117455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2025] [Revised: 03/31/2025] [Accepted: 04/04/2025] [Indexed: 04/17/2025]
Abstract
Accurate molecular biomarker detection with digital-resolution sensitivity is essential for applications such as disease diagnostics, therapeutic studies, and biomedical research. Here, we present LOCA-PRAM (LOcalization with Context Awareness), a deep learning-based method integrated with a Photonic Resonator Absorption Microscope (PRAM) to achieve digital-resolution detection of biomolecules using gold nanoparticles (AuNPs) as molecular tags. LOCA-PRAM leverages photonic crystal (PC)-AuNP resonant-coupling to enhance signal contrast, facilitating precise quantification of target molecules without partitioning the sample into droplets or enzymatic amplification. Through registration of PRAM images with Scanning Electron Microscopy (SEM) images, we empirically obtain the point spread function (PSF) of AuNP tags, enabling realistic training data generation for the deep learning framework. LOCA-PRAM surpasses conventional image processing method in accuracy and sensitivity, achieving reliable AuNP detection and localization even in high-density conditions, minimizing false-positive and false-negative quantifications and expending the dynamic range of assay. Benchmarking with SEM-derived ground truth confirms LOCA-PRAM's sub-pixel resolution and ability to accurately quantify AuNPs with overlapping PSF. Overall, the PRAM combined with LOCA-based AuNP digital counting enables real-time, high-precision detection of molecular biomarkers, advancing digital-resolution biosensing for biomedical research and diagnostics.
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Affiliation(s)
- Hankeun Lee
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Nick Holonyak Jr. Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Siyan Li
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Leyang Liu
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Nick Holonyak Jr. Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Weijing Wang
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Nick Holonyak Jr. Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Takhmina Ayupova
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Nick Holonyak Jr. Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Joseph Tibbs
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Nick Holonyak Jr. Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Chansong Kim
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Ying Fang
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Minh N Do
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Grainger College of Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Siebel School of Computing and Data Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA; VinUni-Illinois Smart Health Center, VinUniversity, Ha Noi, Viet Nam
| | - Brian T Cunningham
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Nick Holonyak Jr. Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Center for Genomic Diagnostics, Woese Institute for Genomic Biology, Urbana, IL, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Grainger College of Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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3
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Cao LM, Qiu YZ, Li ZZ, Wang GR, Xiao Y, Luo HY, Liu B, Wu Q, Bu LL. Extracellular Vesicles: Hermes between cancers and lymph nodes. Cancer Lett 2025; 623:217735. [PMID: 40268131 DOI: 10.1016/j.canlet.2025.217735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2025] [Revised: 04/16/2025] [Accepted: 04/19/2025] [Indexed: 04/25/2025]
Abstract
Cancer is one of the main causes of death and a major obstacle to increasing life expectancy in all countries of the world. Lymph node metastasis (LNM) of in cancer patients indicates poor prognosis and it is an important indication to determine the therapeutic regime. Therefore, more attention should be given to the molecular mechanics of tumor lymphangiogenesis and LNM. Extracellular vesicles (EVs) are nanoscale cargo-bearing membrane vesicles that can serve as key mediators for the intercellular communication. Like Hermes, the messenger of the Greek gods, EVs can be secreted by tumor cells to regulate the LNM process. Many evidence has proved the clinical correlation between EVs and LNM in various cancer types. EVs plays an active role in the process of metastasis by expressing its connotative molecules, including proteins, nucleic acids, and metabolites. However, the clear role of EVs in the process of cancer LNM has not been thoroughly studied yet. In this review, we will summarize the clinical and mechanical findings of EVs regulating role on cancer LNM, and discuss the advanced modification of the research proposal. We propose the "PUMP" principle of EVs in LNM, including Preparation, Unleash, Migration, and Planting.
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Affiliation(s)
- Lei-Ming Cao
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
| | - Yu-Zhong Qiu
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
| | - Zi-Zhan Li
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
| | - Guang-Rui Wang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
| | - Yao Xiao
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
| | - Han-Yue Luo
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
| | - Bing Liu
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China; Department of Oral & Maxillofacial Head Neck Oncology, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
| | - Qiuji Wu
- Department of Radiation and Medical Oncology, Hubei Key Laboratory of Tumor Biological Behavior, Hubei Provincial Clinical Research Center for Cancer, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
| | - Lin-Lin Bu
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China; Department of Oral & Maxillofacial Head Neck Oncology, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China.
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4
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Hu C, Dief EM, Soliman BG, Romanazzo S, Rana S, Kilian KA, Tilley RD, Gooding JJ. Direct detection of microRNA in liquid biopsies from single cancer spheroids. Chem Sci 2025; 16:8970-8978. [PMID: 40271030 PMCID: PMC12013504 DOI: 10.1039/d5sc01036e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2025] [Accepted: 04/12/2025] [Indexed: 04/25/2025] Open
Abstract
Exploring cancer heterogeneity is crucial for both understanding cancer and developing prognostic tools to monitor cancer progression during treatment through the liquid biopsy concept. Herein, a nanoparticle-based "dispersible electrodes" biosensor was used to detect ultra-low concentrations of microRNA-155 (miRNA-155) from a single breast cancer spheroid for the first time. The results from the sensor were comparable to the standard real-time polymerase chain reaction analysis, but in a much shorter detection time and without any sample purification or amplification. Owing to the unique ability of the sensor to measure biomarker expression from unaltered and undiluted cancer liquid biopsy from a single cancer spheroid, we then tracked dynamic changes in miRNA-155 expression in a single spheroid treated with the anti-cancer drug doxorubicin. The ability to track dynamic biomarker changes in a single cancer spheroid opens the door to understanding key biological processes such as response to treatment on the cellular and molecular levels, paving the way for adapting liquid biopsy insights to guide oncologists and more personalised treatment strategies.
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Affiliation(s)
- Chen Hu
- School of Chemistry, Australian Centre for NanoMedicine, University of New South Wales Sydney NSW 2052 Australia
| | - Essam M Dief
- School of Chemistry, Australian Centre for NanoMedicine, University of New South Wales Sydney NSW 2052 Australia
| | - Bram G Soliman
- School of Chemistry, Australian Centre for NanoMedicine, University of New South Wales Sydney NSW 2052 Australia
| | - Sara Romanazzo
- School of Chemistry, Australian Centre for NanoMedicine, University of New South Wales Sydney NSW 2052 Australia
| | - Shilpa Rana
- School of Chemistry, Australian Centre for NanoMedicine, University of New South Wales Sydney NSW 2052 Australia
| | - Kristopher A Kilian
- School of Chemistry, Australian Centre for NanoMedicine, University of New South Wales Sydney NSW 2052 Australia
- School of Materials Science and Engineering, University of New South Wales Sydney NSW 2052 Australia
| | - Richard D Tilley
- School of Chemistry, Australian Centre for NanoMedicine, University of New South Wales Sydney NSW 2052 Australia
- Electron Microscope Unit, Mark Wainwright Analytical Centre, University of New South Wales Sydney NSW 2052 Australia
| | - J Justin Gooding
- School of Chemistry, Australian Centre for NanoMedicine, University of New South Wales Sydney NSW 2052 Australia
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5
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Zhou L, Xiong Y, Dwivedy A, Zheng M, Cooper L, Shepherd S, Song T, Hong W, Le LTP, Chen X, Umrao S, Rong L, Wang T, Cunningham BT, Wang X. Bioinspired designer DNA NanoGripper for virus sensing and potential inhibition. Sci Robot 2024; 9:eadi2084. [PMID: 39602515 PMCID: PMC11750070 DOI: 10.1126/scirobotics.adi2084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 10/25/2024] [Indexed: 11/29/2024]
Abstract
DNA has shown great biocompatibility, programmable mechanical properties, and precise structural addressability at the nanometer scale, rendering it a material for constructing versatile nanorobots for biomedical applications. Here, we present the design principle, synthesis, and characterization of a DNA nanorobotic hand, called DNA NanoGripper, that contains a palm and four bendable fingers as inspired by naturally evolved human hands, bird claws, and bacteriophages. Each NanoGripper finger consists of three phalanges connected by three rotatable joints that are bendable in response to the binding of other entities. NanoGripper functions are enabled and driven by the interactions between moieties attached to the fingers and their binding partners. We demonstrate that the NanoGripper can be engineered to effectively interact with and capture nanometer-scale objects, including gold nanoparticles, gold NanoUrchins, and SARS-CoV-2 virions. With multiple DNA aptamer nanoswitches programmed to generate a fluorescent signal that is enhanced on a photonic crystal platform, the NanoGripper functions as a highly sensitive biosensor that selectively detects intact SARS-CoV-2 virions in human saliva with a limit of detection of ~100 copies per milliliter, providing a sensitivity equal to that of reverse transcription quantitative polymerase chain reaction (RT-qPCR). Quantified by flow cytometry assays, we demonstrated that the NanoGripper-aptamer complex can effectively block viral entry into the host cells, suggesting its potential for inhibiting virus infections. The design, synthesis, and characterization of a sophisticated nanomachine that can be tailored for specific applications highlight a promising pathway toward feasible and efficient solutions to the detection and potential inhibition of virus infections.
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Affiliation(s)
- Lifeng Zhou
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yanyu Xiong
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Abhisek Dwivedy
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Mengxi Zheng
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Laura Cooper
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Skye Shepherd
- Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tingjie Song
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Wei Hong
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Linh T. P. Le
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- VinUni-Illinois Smart Health Center, VinUniversity, Hanoi, Vietnam
| | - Xin Chen
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Saurabh Umrao
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Lijun Rong
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Tong Wang
- Advanced Science Research Center at Graduate Center, City University of New York, New York, NY 10031, USA
| | - Brian T. Cunningham
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Xing Wang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Khemtonglang K, Liu W, Lee H, Wang W, Li S, Li ZY, Shepherd S, Yang Y, Diel DG, Fang Y, Cunningham BT. Portable, smartphone-linked, and miniaturized photonic resonator absorption microscope (PRAM Mini) for point-of-care diagnostics. BIOMEDICAL OPTICS EXPRESS 2024; 15:5691-5705. [PMID: 39421766 PMCID: PMC11482178 DOI: 10.1364/boe.531388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 08/13/2024] [Accepted: 08/25/2024] [Indexed: 10/19/2024]
Abstract
We report the design, development, and characterization of a miniaturized version of the photonic resonator absorption microscope (PRAM Mini), whose cost, size, and functionality are compatible with point-of-care (POC) diagnostic assay applications. Compared to previously reported versions of the PRAM instrument, the PRAM Mini components are integrated within an optical framework comprised of an acrylic breadboard and plastic alignment fixtures. The instrument incorporates a Raspberry Pi microprocessor and Bluetooth communication circuit board for wireless control and data connection to a linked smartphone. PRAM takes advantage of enhanced optical absorption of ∼80 nm diameter gold nanoparticles (AuNP) whose localized surface plasmon resonance overlaps with the ∼625 nm resonant reflection wavelength of a photonic crystal (PC) surface. When illuminated with wide-field low-intensity collimated light from a ∼617 nm wavelength red LED, each AuNP linked to the PC surface results in locally reduced reflection intensity, which is visualized by observing dark spots in the PC-reflected image with an inexpensive CMOS image sensor. Each AuNP in the image field of view can be easily counted with digital resolution. We report upon the selection of optical/electronic components, image processing algorithm, and contrast achieved for single AuNP detection. The instrument is operated via a wireless connection to a linked mobile device using a custom-developed software application that runs on an Android smartphone. As a representative POC application, we used the PRAM Mini as the detection instrument for an assay that measures the presence of antibodies against SARS-CoV-2 infection in cat serum samples, where each dark spot in the image represents a complex between one immobilized viral antigen, one antibody molecule, and one AuNP tag. With dimensions of 23 × 21 × 10 cm3, the PRAM Mini offers a compact detection instrument for POC diagnostics.
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Affiliation(s)
- Kodchakorn Khemtonglang
- Nick Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Weinan Liu
- Nick Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Hankeun Lee
- Nick Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Weijing Wang
- Nick Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Siyan Li
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Zhao Yuan Li
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Skye Shepherd
- Nick Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Yihong Yang
- Nick Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Zhejiang University-University of Illinois Urbana-Champaign Institute, Zhejiang, China
| | - Diego G. Diel
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, New York, USA
| | - Ying Fang
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Brian T. Cunningham
- Nick Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Cancer Center at Illinois, Urbana, Illinois, USA
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7
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Li S, Wang W, Liu W, Chen C, Shephard S, Yuan F, Reinhart JM, Diel D, Cunningham BT, Fang Y. Digital Immunoassay for Rapid Detection of SARS-CoV-2 Infection in a Broad Spectrum of Animals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.21.600129. [PMID: 38979300 PMCID: PMC11230178 DOI: 10.1101/2024.06.21.600129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
The ability of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) to infect a wide-range of species raises significant concerns regarding both human-to-animal and animal-to-human transmission. There is an increasing demand for highly sensitive, rapid, and simple diagnostic assays that can detect viral infection across various species. In this study, we developed a biosensor assay that adapted a monoclonal-antibody (mAb)-based blocking ELISA format into an Activate Capture + Digital Counting (AC + DC)-based immunoassay. The assay employs a photonic crystal (PC) biosensor, gold-nanoparticle (AuNP) tags, SARS-CoV-2 nucleocapsid (N) protein, and specific anti-N mAb to detect antibody responses in animals exposed with SARS-CoV-2. We demonstrated a simple 2-step 15-min test that was capable of detecting as low as 12.5 ng of antibody in controlled standard serum samples. Based on an evaluation of 176 cat serum samples with known antibody status, an optimal percentage of inhibition (PI) cut-off value of 0.588 resulted in a diagnostic sensitivity of 98.3% and a diagnostic specificity of 96.5%. The test is highly repeatable with low variation coefficients of 2.04%, 2.73%, and 4.87% across different runs, within a single run, and on a single chip, respectively. The test was further employed to detect antibody responses in multiple animal species as well as investigate dynamics of antibody response in experimentally infected cats. This test platform provides an important tool for rapid field surveillance of SARS-CoV-2 infection across multiple species.
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Ganesh KM, Bhaskar S, Cheerala VSK, Battampara P, Reddy R, Neelakantan SC, Reddy N, Ramamurthy SS. Review of Gold Nanoparticles in Surface Plasmon-Coupled Emission Technology: Effect of Shape, Hollow Nanostructures, Nano-Assembly, Metal-Dielectric and Heterometallic Nanohybrids. NANOMATERIALS (BASEL, SWITZERLAND) 2024; 14:111. [PMID: 38202566 PMCID: PMC10780701 DOI: 10.3390/nano14010111] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/23/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024]
Abstract
Point-of-care (POC) diagnostic platforms are globally employed in modern smart technologies to detect events or changes in the analyte concentration and provide qualitative and quantitative information in biosensing. Surface plasmon-coupled emission (SPCE) technology has emerged as an effective POC diagnostic tool for developing robust biosensing frameworks. The simplicity, robustness and relevance of the technology has attracted researchers in physical, chemical and biological milieu on account of its unique attributes such as high specificity, sensitivity, low background noise, highly polarized, sharply directional, excellent spectral resolution capabilities. In the past decade, numerous nano-fabrication methods have been developed for augmenting the performance of the conventional SPCE technology. Among them the utility of plasmonic gold nanoparticles (AuNPs) has enabled the demonstration of plethora of reliable biosensing platforms. Here, we review the nano-engineering and biosensing applications of AuNPs based on the shape, hollow morphology, metal-dielectric, nano-assembly and heterometallic nanohybrids under optical as well as biosensing competencies. The current review emphasizes the recent past and evaluates the latest advancements in the field to comprehend the futuristic scope and perspectives of exploiting Au nano-antennas for plasmonic hotspot generation in SPCE technology.
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Affiliation(s)
- Kalathur Mohan Ganesh
- STAR Laboratory, Department of Chemistry, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam Campus, Sri Sathya Sai District, Puttaparthi 515134, India;
| | - Seemesh Bhaskar
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory (HMNTL), 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
| | - Vijay Sai Krishna Cheerala
- Department of Chemistry, Sri Sathya Sai Institute of Higher Learning, Brindavan Campus, Kadugodi, Bengaluru 560067, India; (V.S.K.C.); (S.C.N.)
| | - Prajwal Battampara
- Center for Incubation Innovation Research and Consultancy, Jyothy Institute of Technology, Thataguni Post, Bengaluru 560109, India; (P.B.); (R.R.); (N.R.)
| | - Roopa Reddy
- Center for Incubation Innovation Research and Consultancy, Jyothy Institute of Technology, Thataguni Post, Bengaluru 560109, India; (P.B.); (R.R.); (N.R.)
| | - Sundaresan Chittor Neelakantan
- Department of Chemistry, Sri Sathya Sai Institute of Higher Learning, Brindavan Campus, Kadugodi, Bengaluru 560067, India; (V.S.K.C.); (S.C.N.)
| | - Narendra Reddy
- Center for Incubation Innovation Research and Consultancy, Jyothy Institute of Technology, Thataguni Post, Bengaluru 560109, India; (P.B.); (R.R.); (N.R.)
| | - Sai Sathish Ramamurthy
- STAR Laboratory, Department of Chemistry, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam Campus, Sri Sathya Sai District, Puttaparthi 515134, India;
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9
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Greten TF, Villanueva A, Korangy F, Ruf B, Yarchoan M, Ma L, Ruppin E, Wang XW. Biomarkers for immunotherapy of hepatocellular carcinoma. Nat Rev Clin Oncol 2023; 20:780-798. [PMID: 37726418 DOI: 10.1038/s41571-023-00816-4] [Citation(s) in RCA: 83] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/29/2023] [Indexed: 09/21/2023]
Abstract
Immune-checkpoint inhibitors (ICIs) are now widely used for the treatment of patients with advanced-stage hepatocellular carcinoma (HCC). Two different ICI-containing regimens, atezolizumab plus bevacizumab and tremelimumab plus durvalumab, are now approved standard-of-care first-line therapies in this setting. However, and despite substantial improvements in survival outcomes relative to sorafenib, most patients with advanced-stage HCC do not derive durable benefit from these regimens. Advances in genome sequencing including the use of single-cell RNA sequencing (both of tumour material and blood samples), as well as immune cell identification strategies and other techniques such as radiomics and analysis of the microbiota, have created considerable potential for the identification of novel predictive biomarkers enabling the accurate selection of patients who are most likely to derive benefit from ICIs. In this Review, we summarize data on the immunology of HCC and the outcomes in patients receiving ICIs for the treatment of this disease. We then provide an overview of current biomarker use and developments in the past 5 years, including gene signatures, circulating tumour cells, high-dimensional flow cytometry, single-cell RNA sequencing as well as approaches involving the microbiome, radiomics and clinical markers. Novel concepts for further biomarker development in HCC are then discussed including biomarker-driven trials, spatial transcriptomics and integrated 'big data' analysis approaches. These concepts all have the potential to better identify patients who are most likely to benefit from ICIs and to promote the development of new treatment approaches.
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Affiliation(s)
- Tim F Greten
- Gastrointestinal Malignancies Section, Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
- Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
| | - Augusto Villanueva
- Divisions of Liver Disease and Hematology/Medical Oncology, Tisch Cancer Institute, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Firouzeh Korangy
- Gastrointestinal Malignancies Section, Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Benjamin Ruf
- Gastrointestinal Malignancies Section, Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Mark Yarchoan
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lichun Ma
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Xin W Wang
- Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
- Liver Carcinogenesis Section, Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
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10
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Liang Y, Chen D, Wang H, Pian H, Liu W, Wang F, Wang H, Li Z. Single-microbead space-confined digital quantification strategy (SMSDQ) for counting microRNAs at the single-molecule level. Biosens Bioelectron 2023; 238:115578. [PMID: 37573644 DOI: 10.1016/j.bios.2023.115578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/03/2023] [Accepted: 08/05/2023] [Indexed: 08/15/2023]
Abstract
Quantification of microRNAs (miRNAs) at the single-molecule level is of great significance for clinical diagnostics and biomedical research. The challenges lie in the limits to transforming single-molecule measurements into quantitative signals. To address these limits, here, we report a new approach called a Single Microbead-based Space-confined Digital Quantification (SMSDQ) to measure individual miRNA molecules by counting gold nanoparticles (AuNPs) with localized surface plasmon resonance (LSPR) light-scattering imaging. One miRNA target hybridizes with the alkynyl-modified capture DNA probe immobilized on a microbead (60 μm) and the azide-modified report DNA probe anchored on AuNP (50 nm), respectively. Through the click reaction between the alkynyl and azide group, a single microbead can covalently link the AuNPs in the confined space within the view of the microscope. By digitally counting the light-scattering spots of AuNPs, we demonstrated the proposed approach with single-molecule detection sensitivity and high specificity of single-base discrimination. Taking the advantages of ultrahigh sensitivity, specificity, and the digital detection manner, the approach is suitable for evaluating cell heterogeneity and small variations of miRNA expression and has been successfully applied to direct quantification of miRNAs in one-tenth single-cell lysates and serum samples without RNA-isolated and nucleic acid amplification steps.
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Affiliation(s)
- Yuanwen Liang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Desheng Chen
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Honghong Wang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Hongru Pian
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Weiliang Liu
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Fangfang Wang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Hui Wang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China.
| | - Zhengping Li
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China.
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11
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Huang K, Li Q, Xue Y, Wang Q, Chen Z, Gu Z. Application of colloidal photonic crystals in study of organoids. Adv Drug Deliv Rev 2023; 201:115075. [PMID: 37625595 DOI: 10.1016/j.addr.2023.115075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 07/09/2023] [Accepted: 08/20/2023] [Indexed: 08/27/2023]
Abstract
As alternative disease models, other than 2D cell lines and patient-derived xenografts, organoids have preferable in vivo physiological relevance. However, both endogenous and exogenous limitations impede the development and clinical translation of these organoids. Fortunately, colloidal photonic crystals (PCs), which benefit from favorable biocompatibility, brilliant optical manipulation, and facile chemical decoration, have been applied to the engineering of organoids and have achieved the desirable recapitulation of the ECM niche, well-defined geometrical onsets for initial culture, in situ multiphysiological parameter monitoring, single-cell biomechanical sensing, and high-throughput drug screening with versatile functional readouts. Herein, we review the latest progress in engineering organoids fabricated from colloidal PCs and provide inputs for future research.
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Affiliation(s)
- Kai Huang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Qiwei Li
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Yufei Xue
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Qiong Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Zaozao Chen
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China; Institute of Biomaterials and Medical Devices, Southeast University, Suzhou, Jiangsu 215163, China.
| | - Zhongze Gu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
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12
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Wang H, Sun Y, Zhang Z, Yang X, Ning B, Senyushkin P, Bogdanov B, Zmaga G, Xue Y, Chi J, Xie H, Chen S, Wu T, Lian Z, Pan Q, Chen B, Tan Z, Pan X, Su M, Song Y. Molecular Recognition-Modulated Hetero-Assembly of Nanostructures for Visualizable and Portable Detection of Circulating miRNAs. Anal Chem 2023; 95:11769-11776. [PMID: 37489945 DOI: 10.1021/acs.analchem.3c01996] [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: 07/26/2023]
Abstract
Biomolecular markers, particularly circulating microRNAs (miRNAs) play an important role in diagnosis, monitoring, and therapeutic intervention of cancers. However, existing detection strategies remain intricate, laborious, and far from being developed for point-of-care testing. Here, we report a portable colorimetric sensor that utilizes the hetero-assembly of nanostructures driven by base pairing and recognition for direct detection of miRNAs. Following hybridization, two sizes of nanoparticles modified with single-strand DNA can be robustly assembled into heterostructures with strong optical resonance, exhibiting distinct structure colors. Particularly, the large nanoparticles are first arranged into nanochains to enhance scattering signals of small nanoparticles, which allows for sensitive detection and quantification of miRNAs without the requirement of target extraction, amplification, and fluorescent labels. Furthermore, we demonstrate the high specificity and single-base selectivity of testing different miRNA samples, which shows great potential in the diagnosis, staging, and monitoring of cancers. These heterogeneous assembled nanostructures provide an opportunity to develop simple, fast, and convenient tools for miRNAs detection, which is suitable for many scenarios, especially in low-resource setting.
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Affiliation(s)
- Huadong Wang
- Key Laboratory of Green Printing, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, P. R. China
- University of Chinese Academy of Sciences (UCAS), Beijing 100049, P. R. China
| | - Yali Sun
- School of Physics and Engineering, ITMO University, Saint Petersburg 197101, Russia
| | - Zeying Zhang
- Key Laboratory of Green Printing, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, P. R. China
| | - Xu Yang
- Key Laboratory of Green Printing, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, P. R. China
- University of Chinese Academy of Sciences (UCAS), Beijing 100049, P. R. China
| | - Bobing Ning
- Department of General Surgery, Chinese PLA General Hospital, Beijing 100853, P. R. China
| | - Pavel Senyushkin
- School of Physics and Engineering, ITMO University, Saint Petersburg 197101, Russia
| | - Bogdan Bogdanov
- School of Physics and Engineering, ITMO University, Saint Petersburg 197101, Russia
| | - Georgii Zmaga
- School of Physics and Engineering, ITMO University, Saint Petersburg 197101, Russia
| | - Yonggan Xue
- Department of General Surgery, Chinese PLA General Hospital, Beijing 100853, P. R. China
| | - Jimei Chi
- Key Laboratory of Green Printing, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, P. R. China
- University of Chinese Academy of Sciences (UCAS), Beijing 100049, P. R. China
| | - Hongfei Xie
- Key Laboratory of Green Printing, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, P. R. China
- University of Chinese Academy of Sciences (UCAS), Beijing 100049, P. R. China
| | - Sisi Chen
- Key Laboratory of Green Printing, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, P. R. China
- University of Chinese Academy of Sciences (UCAS), Beijing 100049, P. R. China
| | - Tingqing Wu
- Key Laboratory of Green Printing, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, P. R. China
- University of Chinese Academy of Sciences (UCAS), Beijing 100049, P. R. China
| | - Zewei Lian
- Key Laboratory of Green Printing, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, P. R. China
- University of Chinese Academy of Sciences (UCAS), Beijing 100049, P. R. China
| | - Qi Pan
- Key Laboratory of Green Printing, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, P. R. China
| | - Bingda Chen
- Key Laboratory of Green Printing, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, P. R. China
| | - Zhiyu Tan
- Key Laboratory of Green Printing, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, P. R. China
- University of Chinese Academy of Sciences (UCAS), Beijing 100049, P. R. China
| | - Xiangyu Pan
- Key Laboratory of Green Printing, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, P. R. China
- University of Chinese Academy of Sciences (UCAS), Beijing 100049, P. R. China
| | - Meng Su
- Key Laboratory of Green Printing, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, P. R. China
| | - Yanlin Song
- Key Laboratory of Green Printing, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, P. R. China
- University of Chinese Academy of Sciences (UCAS), Beijing 100049, P. R. China
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13
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Nava G, Casiraghi L, Carzaniga T, Zanchetta G, Chiari M, Damin F, Bollati V, Signorini L, Delbue S, Bellini T, Buscaglia M. Digital Detection of Single Virus Particles by Multi-Spot, Label-Free Imaging Biosensor on Anti-Reflective Glass. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2300947. [PMID: 37060208 DOI: 10.1002/smll.202300947] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/21/2023] [Indexed: 06/19/2023]
Abstract
Rapid detection of whole virus particles in biological or environmental samples represents an unmet need for the containment of infectious diseases. Here, an optical device enabling the enumeration of single virion particles binding on antibody or aptamers immobilized on a surface with anti-reflective coating is described. In this regime, nanoparticles adhering to the sensor surface provide localized contributions to the reflected field that become detectable because of their mixing with the interfering waves in the reflection direction. Thus, these settings are exploited to realize a scan-free, label-free, micro-array-type digital assay on a disposable cartridge, in which the virion counting takes place in wide field-of-view imaging. With this approach we could quantify, by enumeration, different variants of SARS-CoV-2 virions interacting with antibodies and aptamers immobilized on different spots. For all tested variants, the aptamers showed larger affinity but lower specificity relative to the antibodies. It is found that the combination of different probes on the same surface enables increasing specificity of detection and dynamic range.
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Affiliation(s)
- Giovanni Nava
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Universitá degli Studi di Milano, via F.lli Cervi, 93, Segrate, Milano, 20054, Italy
| | - Luca Casiraghi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Universitá degli Studi di Milano, via F.lli Cervi, 93, Segrate, Milano, 20054, Italy
| | - Thomas Carzaniga
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Universitá degli Studi di Milano, via F.lli Cervi, 93, Segrate, Milano, 20054, Italy
| | - Giuliano Zanchetta
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Universitá degli Studi di Milano, via F.lli Cervi, 93, Segrate, Milano, 20054, Italy
| | - Marcella Chiari
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta", National Research Council of Italy (SCITEC-CNR), via Mario Bianco 11, Milano, 20131, Italy
| | - Francesco Damin
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta", National Research Council of Italy (SCITEC-CNR), via Mario Bianco 11, Milano, 20131, Italy
| | - Valentina Bollati
- Dipartimento di Scienze Cliniche e di Comunitá, Universitá degli Studi di Milano, via S. Barnaba 8, Milano, 20122, Italy
| | - Lucia Signorini
- Dipartimento di Scienze Biomediche, Chirurgiche ed Odontoiatriche, Universitá degli Studi di Milano, via Pascal 36, Milano, 20133, Italy
| | - Serena Delbue
- Dipartimento di Scienze Biomediche, Chirurgiche ed Odontoiatriche, Universitá degli Studi di Milano, via Pascal 36, Milano, 20133, Italy
| | - Tommaso Bellini
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Universitá degli Studi di Milano, via F.lli Cervi, 93, Segrate, Milano, 20054, Italy
| | - Marco Buscaglia
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Universitá degli Studi di Milano, via F.lli Cervi, 93, Segrate, Milano, 20054, Italy
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14
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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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15
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Zhou L, Xiong Y, Cooper L, Shepherd S, Song T, Dwivedy A, Rong L, Wang T, Cunningham BT, Wang X. Designer DNA NanoGripper. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.26.538490. [PMID: 37162861 PMCID: PMC10168355 DOI: 10.1101/2023.04.26.538490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
DNA has shown great biocompatibility, programmable mechanical properties, and structural addressability at the nanometer scale, making it a versatile material for building high precision nanorobotics for biomedical applications. Herein, we present design principle, synthesis, and characterization of a DNA nanorobotic hand, called the "NanoGripper", that contains a palm and four bendable fingers as inspired by human hands, bird claws, and bacteriophages evolved in nature. Each NanoGripper finger has three phalanges connected by two flexible and rotatable joints that are bendable in response to binding to other entities. Functions of the NanoGripper have been enabled and driven by the interactions between moieties attached to the fingers and their binding partners. We showcase that the NanoGripper can be engineered to interact with and capture various objects with different dimensions, including gold nanoparticles, gold NanoUrchins, and SARS-CoV-2 virions. When carrying multiple DNA aptamer nanoswitches programmed to generate fluorescent signal enhanced on a photonic crystal platform, the NanoGripper functions as a sensitive viral biosensor that detects intact SARS-CoV-2 virions in human saliva with a limit of detection of ~ 100 copies/mL, providing RT-PCR equivalent sensitivity. Additionally, we use confocal microscopy to visualize how the NanoGripper-aptamer complex can effectively block viral entry into the host cells, indicating the viral inhibition. In summary, we report the design, synthesis, and characterization of a complex nanomachine that can be readily tailored for specific applications. The study highlights a path toward novel, feasible, and efficient solutions for the diagnosis and therapy of other diseases such as HIV and influenza.
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Affiliation(s)
- Lifeng Zhou
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yanyu Xiong
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Laura Cooper
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Skye Shepherd
- Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tingjie Song
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Abhisek Dwivedy
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Lijun Rong
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Tong Wang
- Advanced Science Research Center at Graduate Center, City University of New York, New York, NY 10031, USA
| | - Brian T. Cunningham
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Xing Wang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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16
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Wang X, Shepherd S, Li N, Che C, Song T, Xiong Y, Palm IR, Zhao B, Kohli M, Demirci U, Lu Y, Cunningham BT. A Target Recycling Amplification Process for the Digital Detection of Exosomal MicroRNAs through Photonic Resonator Absorption Microscopy. Angew Chem Int Ed Engl 2023; 62:e202217932. [PMID: 36622783 PMCID: PMC10073263 DOI: 10.1002/anie.202217932] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/05/2023] [Accepted: 01/09/2023] [Indexed: 01/10/2023]
Abstract
Exosomal microRNAs (miRNAs) have considerable potential as pivotal biomarkers to monitor cancer development, dis-ease progression, treatment effects and prognosis. Here, we report an efficient target recycling amplification process (TRAP) for the digital detection of miRNAs using photonic resonator absorption microscopy. We achieve multiplex digital detection with sub-attomolar sensitivity in 20 minutes, robust selectivity for single nucleotide variants, and a broad dynamic range from 1 aM to 1 pM. Compared with traditional qRT-PCR, TRAP showed similar accuracy in profiling exosomal miRNAs derived from cancer cells, but also exhibited at least 31-fold and 61-fold enhancement in the limits of miRNA-375 and miRNA-21 detection, respectively. The TRAP approach is ideal for exosomal or circulating miRNA biomarker quantification, where the miRNAs are present in low concentrations or sample volume, with potentials for frequent, low-cost, and minimally invasive point-of-care testing.
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Affiliation(s)
- Xiaojing Wang
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, Department of Electrical and Computer Engineering, Department of Chemistry, Department of Bioengineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Skye Shepherd
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, Department of Electrical and Computer Engineering, Department of Chemistry, Department of Bioengineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Nantao Li
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, Department of Electrical and Computer Engineering, Department of Chemistry, Department of Bioengineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Congnyu Che
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, Department of Electrical and Computer Engineering, Department of Chemistry, Department of Bioengineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Tingjie Song
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, Department of Electrical and Computer Engineering, Department of Chemistry, Department of Bioengineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Yanyu Xiong
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, Department of Electrical and Computer Engineering, Department of Chemistry, Department of Bioengineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Isabella Rose Palm
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, Department of Electrical and Computer Engineering, Department of Chemistry, Department of Bioengineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Bin Zhao
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, Department of Electrical and Computer Engineering, Department of Chemistry, Department of Bioengineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Manish Kohli
- Department of Oncology, Mayo Clinic Rochester, MN 55905, USA; Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center, Tampa, FL 12902, USA
| | - Utkan Demirci
- Bio-Acoustic MEMS in Medicine (BAMM) Laboratory, Canary Center at Stanford for Cancer Early Detection, Department of Radiology School of Medicine, Stanford University, Palo Alto, CA 94304, USA
| | - Yi Lu
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, Department of Electrical and Computer Engineering, Department of Chemistry, Department of Bioengineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Brian T. Cunningham
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, Department of Electrical and Computer Engineering, Department of Chemistry, Department of Bioengineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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17
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Xiong Y, Shepherd S, Tibbs J, Bacon A, Liu W, Akin LD, Ayupova T, Bhaskar S, Cunningham BT. Photonic Crystal Enhanced Fluorescence: A Review on Design Strategies and Applications. MICROMACHINES 2023; 14:668. [PMID: 36985075 PMCID: PMC10059769 DOI: 10.3390/mi14030668] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/03/2023] [Accepted: 03/13/2023] [Indexed: 05/25/2023]
Abstract
Nanoscale fluorescence emitters are efficient for measuring biomolecular interactions, but their utility for applications requiring single-unit observations is constrained by the need for large numerical aperture objectives, fluorescence intermittency, and poor photon collection efficiency resulting from omnidirectional emission. Photonic crystal (PC) structures hold promise to address the aforementioned challenges in fluorescence enhancement. In this review, we provide a broad overview of PCs by explaining their structures, design strategies, fabrication techniques, and sensing principles. Furthermore, we discuss recent applications of PC-enhanced fluorescence-based biosensors incorporated with emerging technologies, including nucleic acids sensing, protein detection, and steroid monitoring. Finally, we discuss current challenges associated with PC-enhanced fluorescence and provide an outlook for fluorescence enhancement with photonic-plasmonics coupling and their promise for point-of-care biosensing as well monitoring analytes of biological and environmental relevance. The review presents the transdisciplinary applications of PCs in the broad arena of fluorescence spectroscopy with broad applications in photo-plasmonics, life science research, materials chemistry, cancer diagnostics, and internet of things.
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Affiliation(s)
- Yanyu Xiong
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, Urbana, IL 61801, USA
| | - Skye Shepherd
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, Urbana, IL 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Joseph Tibbs
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, Urbana, IL 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Amanda Bacon
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, Urbana, IL 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Weinan Liu
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, Urbana, IL 61801, USA
| | - Lucas D. Akin
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, Urbana, IL 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Takhmina Ayupova
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, Urbana, IL 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Seemesh Bhaskar
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, 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, Urbana, IL 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, Urbana, IL 61801, USA
- Cancer Center at Illinois, Urbana, IL 61801, USA
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18
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Bacon A, Wang W, Lee H, Umrao S, Sinawang PD, Akin D, Khemtonglang K, Tan A, Hirshfield S, Demirci U, Wang X, Cunningham BT. Review of HIV Self Testing Technologies and Promising Approaches for the Next Generation. BIOSENSORS 2023; 13:298. [PMID: 36832064 PMCID: PMC9954708 DOI: 10.3390/bios13020298] [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] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/06/2023] [Accepted: 02/14/2023] [Indexed: 05/28/2023]
Abstract
The ability to self-test for HIV is vital to preventing transmission, particularly when used in concert with HIV biomedical prevention modalities, such as pre-exposure prophylaxis (PrEP). In this paper, we review recent developments in HIV self-testing and self-sampling methods, and the potential future impact of novel materials and methods that emerged through efforts to develop more effective point-of-care (POC) SARS-CoV-2 diagnostics. We address the gaps in existing HIV self-testing technologies, where improvements in test sensitivity, sample-to-answer time, simplicity, and cost are needed to enhance diagnostic accuracy and widespread accessibility. We discuss potential paths toward the next generation of HIV self-testing through sample collection materials, biosensing assay techniques, and miniaturized instrumentation. We discuss the implications for other applications, such as self-monitoring of HIV viral load and other infectious diseases.
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Affiliation(s)
- Amanda Bacon
- Department of Bioengineering, 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
| | - Weijing Wang
- Department of Bioengineering, 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
| | - Hankeun Lee
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Saurabh Umrao
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Center for Genomic Diagnostics, Woese Institute for Genomic Biology, Urbana, IL 61801, USA
| | - Prima Dewi Sinawang
- Center at Stanford for Cancer Early Detection, Department of Radiology, School of Medicine, Stanford University, Palo Alto, CA 94304, USA
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Demir Akin
- Center at Stanford for Cancer Early Detection, Department of Radiology, School of Medicine, Stanford University, Palo Alto, CA 94304, USA
- Center for Cancer Nanotechnology Excellence for Translational Diagnostics (CCNE-TD), School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Kodchakorn Khemtonglang
- Department of Bioengineering, 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
| | - Anqi Tan
- Department of Bioengineering, 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
| | - Sabina Hirshfield
- Special Treatment and Research (STAR) Program, Department of Medicine, SUNY Downstate Health Sciences University, Brooklyn, New York, NY 11203, USA
| | - Utkan Demirci
- Center at Stanford for Cancer Early Detection, Department of Radiology, School of Medicine, Stanford University, Palo Alto, CA 94304, USA
| | - Xing Wang
- Department of Bioengineering, 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
- Center for Genomic Diagnostics, Woese Institute for Genomic Biology, Urbana, IL 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Brian T. Cunningham
- Department of Bioengineering, 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 Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Center for Genomic Diagnostics, Woese Institute for Genomic Biology, Urbana, IL 61801, USA
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19
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Joo S, Lee UJ, Son HY, Kim M, Huh YM, Lee TG, Lee M. Highly Selective FRET-Aided Single-Molecule Counting of MicroRNAs Labeled by Splinted Ligation. ACS Sens 2022; 7:3409-3415. [PMID: 36279317 DOI: 10.1021/acssensors.2c01526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
MicroRNAs (miRNAs) are short non-coding RNAs that play an important role in regulating gene expression. Since miRNAs are abnormally expressed in various cancers, they are considered to be promising biomarkers for early cancer diagnosis. However, the short length and strong sequence similarity among miRNAs make their reliable quantification very challenging. We developed a highly selective amplification-free miRNA detection method based on Förster resonance energy transfer (FRET)-aided single-molecule counting. miRNAs were selectively labeled with FRET probes using splinted ligation. When imaged with a single-molecule FRET setup, the miRNA molecules were accurately identified by the probe's FRET. miRNA concentrations were estimated from the count of molecules. The high sensitivity of the method in finding sparse molecules enabled us to achieve a limit of detection of 31-56 amol for miR-125b, miR-100, and miR-99a. Single nucleotide mismatch could be discriminated with a very high target-to-mismatch ratio. The method accurately measured the high expression of miR-125b in gastric cancer cells, which agreed well with previous reports. The high sensitivity and accuracy of this technique demonstrated its clinical potential as a robust miRNA detection method.
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Affiliation(s)
- Sihwa Joo
- Safety Measurement Institute, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, South Korea
| | - Ui Jin Lee
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, South Korea
| | - Hye Young Son
- Department of Radiology, College of Medicine, Yonsei University, Seoul 03722, South Korea.,Severance Biomedical Science Institute, College of Medicine, Yonsei University, Seoul 03722, South Korea
| | - Moonil Kim
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, South Korea.,Department of Biotechnology, University of Science and Technology (UST), Daejeon 34113, South Korea
| | - Yong-Min Huh
- Department of Radiology, College of Medicine, Yonsei University, Seoul 03722, South Korea.,Severance Biomedical Science Institute, College of Medicine, Yonsei University, Seoul 03722, South Korea.,Department of Biochemistry and Molecular Biology, College of Medicine, Yonsei University, Seoul 03722, South Korea.,YUHS-KRIBB Medical Convergence Research Institute, Seoul 03722, South Korea
| | - Tae Geol Lee
- Safety Measurement Institute, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, South Korea.,Department of Nano Science, University of Science and Technology (UST), Daejeon 34113, South Korea
| | - Mina Lee
- Safety Measurement Institute, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, South Korea
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20
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Attomolar sensitivity microRNA detection using real-time digital microarrays. Sci Rep 2022; 12:16220. [PMID: 36171215 PMCID: PMC9519543 DOI: 10.1038/s41598-022-19912-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 09/06/2022] [Indexed: 11/08/2022] Open
Abstract
MicroRNAs (miRNAs) are a family of noncoding, functional RNAs. With recent developments in molecular biology, miRNA detection has attracted significant interest, as hundreds of miRNAs and their expression levels have shown to be linked to various diseases such as infections, cardiovascular disorders and cancers. A powerful and high throughput tool for nucleic acid detection is the DNA microarray technology. However, conventional methods do not meet the demands in sensitivity and specificity, presenting significant challenges for the adaptation of miRNA detection for diagnostic applications. In this study, we developed a highly sensitive and multiplexed digital microarray using plasmonic gold nanorods as labels. For proof of concept studies, we conducted experiments with two miRNAs, miRNA-451a (miR-451) and miRNA-223-3p (miR-223). We demonstrated improvements in sensitivity in comparison to traditional end-point assays that employ capture on solid phase support, by implementing real-time tracking of the target molecules on the sensor surface. Particle tracking overcomes the sensitivity limitations for detection of low-abundance biomarkers in the presence of low-affinity but high-abundance background molecules, where endpoint assays fall short. The absolute lowest measured concentration was 100 aM. The measured detection limit being well above the blank samples, we performed theoretical calculations for an extrapolated limit of detection (LOD). The dynamic tracking improved the extrapolated LODs from femtomolar range to \documentclass[12pt]{minimal}
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\begin{document}$$\sim$$\end{document}∼ 10 attomolar (less than 1300 copies in 0.2 ml of sample) for both miRNAs and the total incubation time was decreased from 5 h to 35 min.
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21
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Nava G, Zanchetta G, Giavazzi F, Buscaglia M. Label-free optical biosensors in the pandemic era. NANOPHOTONICS (BERLIN, GERMANY) 2022; 11:4159-4181. [PMID: 39634532 PMCID: PMC11502114 DOI: 10.1515/nanoph-2022-0354] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/01/2022] [Indexed: 12/07/2024]
Abstract
The research in the field of optical biosensors is continuously expanding, thanks both to the introduction of brand new technologies and the ingenious use of established methods. A new awareness on the potential societal impact of this research has arisen as a consequence of the Covid-19 pandemic. The availability of a new generation of analytical tools enabling a more accurate understanding of bio-molecular processes or the development of distributed diagnostic devices with improved performance is now in greater demand and more clearly envisioned, but not yet achieved. In this review, we focus on emerging innovation opportunities conveyed by label-free optical biosensors. We review the most recent innovations in label-free optical biosensor technology in consideration of their competitive potential in selected application areas. The operational simplicity implicit to label-free detection can be exploited in novel rapid and compact devices for distributed diagnostic applications. The adaptability to any molecular recognition or conformational process facilitates the integration of DNA nanostructures carrying novel functions. The high sensitivity to nanoscale objects stimulates the development of ultrasensitive systems down to digital detection of single molecular binding events enhanced by nanoparticles and direct enumeration of bio-nanoparticles like viruses.
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Affiliation(s)
- Giovanni Nava
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Segrate, MI, Italy
| | - Giuliano Zanchetta
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Segrate, MI, Italy
| | - Fabio Giavazzi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Segrate, MI, Italy
| | - Marco Buscaglia
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Segrate, MI, Italy
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22
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Jin G, Hong S, Rich J, Xia J, Kim K, You L, Zhao C, Huang TJ. Intelligent nanoscope for rapid nanomaterial identification and classification. LAB ON A CHIP 2022; 22:2978-2985. [PMID: 35647808 PMCID: PMC9378457 DOI: 10.1039/d2lc00206j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Machine learning image recognition and classification of particles and materials is a rapidly expanding field. However, nanomaterial identification and classification are dependent on the image resolution, the image field of view, and the processing time. Optical microscopes are one of the most widely utilized technologies in laboratories across the world, due to their nondestructive abilities to identify and classify critical micro-sized objects and processes, but identifying and classifying critical nano-sized objects and processes with a conventional microscope are outside of its capabilities, due to the diffraction limit of the optics and small field of view. To overcome these challenges of nanomaterial identification and classification, we developed an intelligent nanoscope that combines machine learning and microsphere array-based imaging to: (1) surpass the diffraction limit of the microscope objective with microsphere imaging to provide high-resolution images; (2) provide large field-of-view imaging without the sacrifice of resolution by utilizing a microsphere array; and (3) rapidly classify nanomaterials using a deep convolution neural network. The intelligent nanoscope delivers more than 46 magnified images from a single image frame so that we collected more than 1000 images within 2 seconds. Moreover, the intelligent nanoscope achieves a 95% nanomaterial classification accuracy using 1000 images of training sets, which is 45% more accurate than without the microsphere array. The intelligent nanoscope also achieves a 92% bacteria classification accuracy using 50 000 images of training sets, which is 35% more accurate than without the microsphere array. This platform accomplished rapid, accurate detection and classification of nanomaterials with miniscule size differences. The capabilities of this device wield the potential to further detect and classify smaller biological nanomaterial, such as viruses or extracellular vesicles.
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Affiliation(s)
- Geonsoo Jin
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA.
| | - Seongwoo Hong
- Office of Biomedical Graduate Education, Duke University School of Medicine, Durham, NC 27710, USA
| | - Joseph Rich
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA.
| | - Jianping Xia
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA.
| | - Kyeri Kim
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA.
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA.
- Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27708, USA
| | - Chenglong Zhao
- Department of Physics, University of Dayton, 300 College Park, Dayton, Ohio 45469, USA.
- Department of Electro-Optics and Photonics, University of Dayton, 300 College Park, Dayton, Ohio 45469, USA
| | - Tony Jun Huang
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA.
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23
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Xiong Y, Huang Q, Canady TD, Barya P, Liu S, Arogundade OH, Race CM, Che C, Wang X, Zhou L, Wang X, Kohli M, Smith AM, Cunningham BT. Photonic crystal enhanced fluorescence emission and blinking suppression for single quantum dot digital resolution biosensing. Nat Commun 2022; 13:4647. [PMID: 35941132 PMCID: PMC9360002 DOI: 10.1038/s41467-022-32387-w] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 07/29/2022] [Indexed: 12/21/2022] Open
Abstract
While nanoscale quantum emitters are effective tags for measuring biomolecular interactions, their utilities for applications that demand single-unit observations are limited by the requirements for large numerical aperture (NA) objectives, fluorescence intermittency, and poor photon collection efficiency resulted from omnidirectional emission. Here, we report a nearly 3000-fold signal enhancement achieved through multiplicative effects of enhanced excitation, highly directional extraction, quantum efficiency improvement, and blinking suppression through a photonic crystal (PC) surface. The approach achieves single quantum dot (QD) sensitivity with high signal-to-noise ratio, even when using a low-NA lens and an inexpensive optical setup. The blinking suppression capability of the PC improves the QDs on-time from 15% to 85% ameliorating signal intermittency. We developed an assay for cancer-associated miRNA biomarkers with single-molecule resolution, single-base mutation selectivity, and 10-attomolar detection limit. Additionally, we observed differential surface motion trajectories of QDs when their surface attachment stringency is altered by changing a single base in a cancer-specific miRNA sequence.
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Affiliation(s)
- Yanyu Xiong
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Qinglan Huang
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Taylor D Canady
- Holonyak 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
| | - Priyash Barya
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Shengyan Liu
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Opeyemi H Arogundade
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Caitlin M Race
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Congnyu Che
- Holonyak 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
| | - Xiaojing Wang
- Holonyak 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
| | - Lifeng Zhou
- Holonyak 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
| | - Xing Wang
- Holonyak 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 Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Manish Kohli
- Department of Oncology, Huntsman Cancer Institute, Salt Lake City, UT, 84112, USA
| | - Andrew M Smith
- Holonyak 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
- Carle Illinois College of Medicine, Urbana, IL, 61801, USA
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Cancer Center at Illinois, Urbana, IL, 61801, USA
| | - Brian T Cunningham
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Holonyak 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 Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Cancer Center at Illinois, Urbana, IL, 61801, USA.
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24
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Role of Nano-miRNAs in Diagnostics and Therapeutics. Int J Mol Sci 2022; 23:ijms23126836. [PMID: 35743278 PMCID: PMC9223810 DOI: 10.3390/ijms23126836] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/15/2022] [Accepted: 06/17/2022] [Indexed: 12/26/2022] Open
Abstract
MicroRNAs (miRNA) are key regulators of gene expression, controlling different biological processes such as cellular development, differentiation, proliferation, metabolism, and apoptosis. The relationships between miRNA expression and the onset and progression of different diseases, such as tumours, cardiovascular and rheumatic diseases, and neurological disorders, are well known. A nanotechnology-based approach could match miRNA delivery and detection to move beyond the proof-of-concept stage. Different kinds of nanotechnologies can have a major impact on the diagnosis and treatment of miRNA-related diseases such as cancer. Developing novel methodologies aimed at clinical practice represents a big challenge for the early diagnosis of specific diseases. Within this context, nanotechnology represents a wide emerging area at the forefront of research over the last two decades, whose potential has yet to be fully attained. Nanomedicine, derived from nanotechnology, can exploit the unique properties of nanometer-sized particles for diagnostic and therapeutic purposes. Through nanomedicine, specific treatment to counteract only cancer-cell proliferation will be improved, while leaving healthy cells intact. In this review, we dissect the properties of different nanocarriers and their roles in the early detection and treatment of cancer.
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25
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Zhao B, Wang W, Li N, Garcia-Lezana T, Che C, Wang X, Losic B, Villanueva A, Cunningham BT. Digital-resolution and highly sensitive detection of multiple exosomal small RNAs by DNA toehold probe-based photonic resonator absorption microscopy. Talanta 2022; 241:123256. [PMID: 35085990 PMCID: PMC8857068 DOI: 10.1016/j.talanta.2022.123256] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/16/2022] [Accepted: 01/20/2022] [Indexed: 11/19/2022]
Abstract
Small noncoding RNAs (snRNA) have been emerging as promising diagnostic biomarkers for detecting early stage cancer. Currently existing methods for snRNA detection, including northern blot, reverse transcription-polymerase chain reaction, microarrays and RNA-Seq, are limited to time-consuming, low sensitivity, expensive instrumentation or complex analysis of data. Herein, we present a rapid quantitative analysis of multiple liver cancer-associated exosomal snRNA by a nucleic acid toehold probe-based photonic resonator absorption microscopy (PRAM) assay, with digital resolution and high sensitivity. The assay relies on the use of three toehold probe-encoded gold nanoparticles (AuNPs) and addressable photonic crystal (PC) sensing chips. The presence of target snRNA will initiate toehold-mediated strand displacement reactions that trigger the capture of gold particles onto the PC surface, which is subsequently imaged by PRAM for digital counting of detected snRNA molecules. We achieved highly sensitive and selective detection of three snRNA targets in buffer with a 30 min assay protocol, with detection limits of 4.56 fM, 4.68 fM and 0.69 pM. Having confirmed our assay's performance for detection of snRNA targets spiked into exosomal RNA extracts, we demonstrated its capability for quantitative detection of the same targets from patient blood plasma samples. The approach offers a rapid, simple workflow that operates at room temperature with a single step without enzymatic amplification, while the detection instrument can be implemented as a low-cost portable system for point of care environments.
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Affiliation(s)
- Bin Zhao
- Carl R. Woese Institute for Genomic Biology, 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
| | - Weijing Wang
- 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
- Nick Holonyak, Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Teresa Garcia-Lezana
- Division of Liver Diseases, Division of Hematology / Medical Oncology, Tisch Cancer Institute, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Congnyu Che
- 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
| | - Xiaojing Wang
- Nick Holonyak, Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Bojan Losic
- Division of Liver Diseases, Division of Hematology / Medical Oncology, Tisch Cancer Institute, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Augusto Villanueva
- Division of Liver Diseases, Division of Hematology / Medical Oncology, Tisch Cancer Institute, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Brian T Cunningham
- Carl R. Woese Institute for Genomic Biology, 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; Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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26
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Joshi N, Shukla S, Narayan RJ. Novel photonic methods for diagnosis of SARS-CoV-2 infection. TRANSLATIONAL BIOPHOTONICS 2022; 4:e202200001. [PMID: 35602265 PMCID: PMC9111306 DOI: 10.1002/tbio.202200001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/27/2022] [Accepted: 03/02/2022] [Indexed: 11/08/2022] Open
Abstract
The COVID-19 pandemic that began in March 2020 continues in many countries. The ongoing pandemic makes early diagnosis a crucial part of efforts to prevent the spread of SARS-CoV-2 infections. As such, the development of a rapid, reliable, and low-cost technique with increased sensitivity for detection of SARS-CoV-2 is an important priority of the scientific community. At present, nucleic acid-based techniques are primarily used as the reference approach for the detection of SARS-CoV-2 infection. However, in several cases, false positive results have been observed with these techniques. Due to the drawbacks associated with existing techniques, the development of new techniques for the diagnosis of COVID-19 is an important research activity. We provide an overview of novel diagnostic methods for SARS-CoV-2 diagnosis that integrate photonic technology with artificial intelligence. Recent developments in emerging diagnostic techniques based on the principles of advanced molecular spectroscopy and microscopy are considered.
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Affiliation(s)
- Naveen Joshi
- Department of Materials Science and EngineeringNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Shubhangi Shukla
- Joint Department of Biomedical EngineeringNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Roger J. Narayan
- Joint Department of Biomedical EngineeringNorth Carolina State UniversityRaleighNorth CarolinaUSA
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27
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Che C, Xue R, Li N, Gupta P, Wang X, Zhao B, Singamaneni S, Nie S, Cunningham BT. Accelerated Digital Biodetection Using Magneto-plasmonic Nanoparticle-Coupled Photonic Resonator Absorption Microscopy. ACS NANO 2022; 16:2345-2354. [PMID: 35040633 DOI: 10.1021/acsnano.1c08569] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Rapid, ultrasensitive, and selective quantification of circulating microRNA (miRNA) biomarkers in body fluids is increasingly deployed in early cancer diagnosis, prognosis, and therapy monitoring. While nanoparticle tags enable detection of nucleic acid or protein biomarkers with digital resolution and subfemtomolar detection limits without enzymatic amplification, the response time of these assays is typically dominated by diffusion-limited transport of the analytes or nanotags to the biosensor surface. Here, we present a magnetic activate capture and digital counting (mAC+DC) approach that utilizes magneto-plasmonic nanoparticles (MPNPs) to accelerate single-molecule sensing, demonstrated by miRNA detection via toehold-mediated strand displacement. Spiky Fe3O4@Au MPNPs with immobilized target-specific probes are "activated" by binding with miRNA targets, followed by magnetically driven transport through the bulk fluid toward nanoparticle capture probes on a photonic crystal (PC). By spectrally matching the localized surface plasmon resonance of the MPNPs to the PC-guided resonance, each captured MPNP locally quenches the PC reflection efficiency, thus enabling captured MPNPs to be individually visualized with high contrast for counting. We demonstrate quantification of the miR-375 cancer biomarker directly from unprocessed human serum with a 1 min response time, a detection limit of 61.9 aM, a broad dynamic range (100 aM to 10 pM), and a single-base mismatch selectivity. The approach is well-suited for minimally invasive biomarker quantification, enabling potential applications in point-of-care testing with short sample-to-answer time.
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Affiliation(s)
- Congnyu Che
- Department of Bioengineering, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
- Nick Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
| | - Ruiyang Xue
- Department of Materials Science and Engineering, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
| | - Nantao Li
- Nick Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
- Department of Electrical and Computer Engineering, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
| | - Prashant Gupta
- Department of Mechanical Engineering and Materials Science, Institute of Materials Science and Engineering, Washington University in St. Louis, St Louis, Missouri 63031, United States
| | - Xiaojing Wang
- Nick Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
| | - Bin Zhao
- Nick Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
| | - Srikanth Singamaneni
- Department of Mechanical Engineering and Materials Science, Institute of Materials Science and Engineering, Washington University in St. Louis, St Louis, Missouri 63031, United States
| | - Shuming Nie
- Department of Bioengineering, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
- Department of Materials Science and Engineering, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
- Department of Electrical and Computer Engineering, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
| | - Brian T Cunningham
- Department of Bioengineering, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
- Nick Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
- Department of Electrical and Computer Engineering, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
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28
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Li N, Zhao B, Stavins R, Peinetti AS, Chauhan N, Bashir R, Cunningham BT, King WP, Lu Y, Wang X, Valera E. Overcoming the limitations of COVID-19 diagnostics with nanostructures, nucleic acid engineering, and additive manufacturing. CURRENT OPINION IN SOLID STATE & MATERIALS SCIENCE 2022; 26:100966. [PMID: 34840515 PMCID: PMC8604633 DOI: 10.1016/j.cossms.2021.100966] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 11/05/2021] [Accepted: 11/09/2021] [Indexed: 05/04/2023]
Abstract
The COVID-19 pandemic revealed fundamental limitations in the current model for infectious disease diagnosis and serology, based upon complex assay workflows, laboratory-based instrumentation, and expensive materials for managing samples and reagents. The lengthy time delays required to obtain test results, the high cost of gold-standard PCR tests, and poor sensitivity of rapid point-of-care tests contributed directly to society's inability to efficiently identify COVID-19-positive individuals for quarantine, which in turn continues to impact return to normal activities throughout the economy. Over the past year, enormous resources have been invested to develop more effective rapid tests and laboratory tests with greater throughput, yet the vast majority of engineering and chemistry approaches are merely incremental improvements to existing methods for nucleic acid amplification, lateral flow test strips, and enzymatic amplification assays for protein-based biomarkers. Meanwhile, widespread commercial availability of new test kits continues to be hampered by the cost and time required to develop single-use disposable microfluidic plastic cartridges manufactured by injection molding. Through development of novel technologies for sensitive, selective, rapid, and robust viral detection and more efficient approaches for scalable manufacturing of microfluidic devices, we can be much better prepared for future management of infectious pathogen outbreaks. Here, we describe how photonic metamaterials, graphene nanomaterials, designer DNA nanostructures, and polymers amenable to scalable additive manufacturing are being applied towards overcoming the fundamental limitations of currently dominant COVID-19 diagnostic approaches. In this paper, we review how several distinct classes of nanomaterials and nanochemistry enable simple assay workflows, high sensitivity, inexpensive instrumentation, point-of-care sample-to-answer virus diagnosis, and rapidly scaled manufacturing.
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Affiliation(s)
- Nantao Li
- Carle Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, United States
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, United States
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, United States
| | - Bin Zhao
- Carle Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, United States
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, United States
| | - Robert Stavins
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, United States
| | - Ana Sol Peinetti
- Department of Chemistry, University of Illinois at Urbana-Champaign, United States
| | - Neha Chauhan
- Carle Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, United States
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, United States
| | - Rashid Bashir
- Carle Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, United States
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, United States
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, United States
- Department of Bioengineering, University of Illinois at Urbana-Champaign, United States
| | - Brian T Cunningham
- Carle Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, United States
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, United States
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, United States
- Department of Bioengineering, University of Illinois at Urbana-Champaign, United States
| | - William P King
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, United States
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, United States
| | - Yi Lu
- Carle Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, United States
| | - Xing Wang
- Carle Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, United States
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, United States
| | - Enrique Valera
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, United States
- Department of Bioengineering, University of Illinois at Urbana-Champaign, United States
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29
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Xiong Y, Li N, Che C, Wang W, Barya P, Liu W, Liu L, Wang X, Wu S, Hu H, Cunningham BT. Microscopies Enabled by Photonic Metamaterials. SENSORS (BASEL, SWITZERLAND) 2022; 22:1086. [PMID: 35161831 PMCID: PMC8840465 DOI: 10.3390/s22031086] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 01/23/2022] [Accepted: 01/26/2022] [Indexed: 11/16/2022]
Abstract
In recent years, the biosensor research community has made rapid progress in the development of nanostructured materials capable of amplifying the interaction between light and biological matter. A common objective is to concentrate the electromagnetic energy associated with light into nanometer-scale volumes that, in many cases, can extend below the conventional Abbé diffraction limit. Dating back to the first application of surface plasmon resonance (SPR) for label-free detection of biomolecular interactions, resonant optical structures, including waveguides, ring resonators, and photonic crystals, have proven to be effective conduits for a wide range of optical enhancement effects that include enhanced excitation of photon emitters (such as quantum dots, organic dyes, and fluorescent proteins), enhanced extraction from photon emitters, enhanced optical absorption, and enhanced optical scattering (such as from Raman-scatterers and nanoparticles). The application of photonic metamaterials as a means for enhancing contrast in microscopy is a recent technological development. Through their ability to generate surface-localized and resonantly enhanced electromagnetic fields, photonic metamaterials are an effective surface for magnifying absorption, photon emission, and scattering associated with biological materials while an imaging system records spatial and temporal patterns. By replacing the conventional glass microscope slide with a photonic metamaterial, new forms of contrast and enhanced signal-to-noise are obtained for applications that include cancer diagnostics, infectious disease diagnostics, cell membrane imaging, biomolecular interaction analysis, and drug discovery. This paper will review the current state of the art in which photonic metamaterial surfaces are utilized in the context of microscopy.
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Affiliation(s)
- Yanyu Xiong
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Champaign, IL 61822, USA; (Y.X.); (N.L.); (P.B.); (W.L.); (L.L.)
- Holonyak Micro and Nanotechnology Laboratory, Champaign, IL 61822, USA; (C.C.); (W.W.); (X.W.)
| | - Nantao Li
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Champaign, IL 61822, USA; (Y.X.); (N.L.); (P.B.); (W.L.); (L.L.)
- Holonyak Micro and Nanotechnology Laboratory, Champaign, IL 61822, USA; (C.C.); (W.W.); (X.W.)
| | - Congnyu Che
- Holonyak Micro and Nanotechnology Laboratory, Champaign, IL 61822, USA; (C.C.); (W.W.); (X.W.)
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Champaign, IL 61822, USA
| | - Weijing Wang
- Holonyak Micro and Nanotechnology Laboratory, Champaign, IL 61822, USA; (C.C.); (W.W.); (X.W.)
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Champaign, IL 61822, USA
| | - Priyash Barya
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Champaign, IL 61822, USA; (Y.X.); (N.L.); (P.B.); (W.L.); (L.L.)
- Holonyak Micro and Nanotechnology Laboratory, Champaign, IL 61822, USA; (C.C.); (W.W.); (X.W.)
| | - Weinan Liu
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Champaign, IL 61822, USA; (Y.X.); (N.L.); (P.B.); (W.L.); (L.L.)
- Holonyak Micro and Nanotechnology Laboratory, Champaign, IL 61822, USA; (C.C.); (W.W.); (X.W.)
| | - Leyang Liu
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Champaign, IL 61822, USA; (Y.X.); (N.L.); (P.B.); (W.L.); (L.L.)
- Holonyak Micro and Nanotechnology Laboratory, Champaign, IL 61822, USA; (C.C.); (W.W.); (X.W.)
| | - Xiaojing Wang
- Holonyak Micro and Nanotechnology Laboratory, Champaign, IL 61822, USA; (C.C.); (W.W.); (X.W.)
- Carl R. Woese Institute for Genomic Biology, Urbana, IL 61801, USA
| | - Shaoxiong Wu
- Zhejiang University-University of Illinois at Urbana-Champaign Institute, International Campus, Zhejiang University, Haining 314400, China; (S.W.); (H.H.)
| | - Huan Hu
- Zhejiang University-University of Illinois at Urbana-Champaign Institute, International Campus, Zhejiang University, Haining 314400, China; (S.W.); (H.H.)
- State Key Laboratory of Fluid Power & Mechatronic Systems, Zhejiang University, Hangzhou 310027, China
| | - Brian T. Cunningham
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Champaign, IL 61822, USA; (Y.X.); (N.L.); (P.B.); (W.L.); (L.L.)
- Holonyak Micro and Nanotechnology Laboratory, Champaign, IL 61822, USA; (C.C.); (W.W.); (X.W.)
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Champaign, IL 61822, USA
- Carl R. Woese Institute for Genomic Biology, Urbana, IL 61801, USA
- Cancer Center at Illinois, Urbana, IL 61801, USA
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30
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Zhang J, Hou M, Chen G, Mao H, Chen W, Wang W, Chen J. An electrochemical biosensor based on DNA “nano-bridge” for amplified detection of exosomal microRNAs. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2021.04.056] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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31
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Ghosh S, Li N, Xiong Y, Ju YG, Rathslag MP, Onal EG, Falkiewicz E, Kohli M, Cunningham BT. A compact photonic resonator absorption microscope for point of care digital resolution nucleic acid molecular diagnostics. BIOMEDICAL OPTICS EXPRESS 2021; 12:4637-4650. [PMID: 34513214 PMCID: PMC8407813 DOI: 10.1364/boe.427475] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/24/2021] [Accepted: 06/27/2021] [Indexed: 05/05/2023]
Abstract
Rapid, sensitive, and selective detection of nucleic acid biomarkers for health diagnostic applications becomes feasible for point of care scenarios when the detection instrument is inexpensive, simple, and robust. Here, we report the design, implementation, and characterization of a point of care instrument for photonic resonator absorption microscopy (PRAM) that takes advantage of resonant optical coupling between plasmonic gold nanoparticle tags and a photonic crystal (PC) surface. Matching the PC resonant wavelength to the gold nanoparticle's surface plasmon wavelength generates localized and efficient quenching of the PC resonant reflection intensity, resulting in the ability to clearly detect and count individual gold nanoparticles when they are captured on the PC surface. Surface-captured nanoparticles are observed by illuminating the PC at normal incidence with polarized light from a low-intensity red LED, and recording of PC reflected intensity on an inexpensive CMOS image sensor. A contrast limited adaptive histogram equalization (CLAHE) image processing algorithm was applied to derive counts of captured nanoparticles. The instrument is utilized in the context of an activate capture + digital counting (AC + DC) assay for a specific miRNA sequence, using nucleic acid toehold probes applied to gold nano-urchin (AuNU) nanoparticles to achieve 160 aM detection limits in a 30 min. assay.
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Affiliation(s)
- Shreya Ghosh
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- S. G. and N. L. contributed equally to this work
| | - Nantao Li
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- S. G. and N. L. contributed equally to this work
| | - Yanyu Xiong
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Young-Gu Ju
- Department of Physics Education, Kyungpook National University, 80 Daehak-ro, Sangyeok-dong, Buk-gu, Daegu, Republic of Korea
| | - Michael P Rathslag
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ege G Onal
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Erika Falkiewicz
- School of Integrative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Manish Kohli
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Brian T Cunningham
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Electrical and Computer Engineering, 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, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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32
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Plasmonic Biosensors for Single-Molecule Biomedical Analysis. BIOSENSORS-BASEL 2021; 11:bios11040123. [PMID: 33921010 PMCID: PMC8071374 DOI: 10.3390/bios11040123] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/18/2021] [Accepted: 04/13/2021] [Indexed: 11/16/2022]
Abstract
The rapid spread of epidemic diseases (i.e., coronavirus disease 2019 (COVID-19)) has contributed to focus global attention on the diagnosis of medical conditions by ultrasensitive detection methods. To overcome this challenge, increasing efforts have been driven towards the development of single-molecule analytical platforms. In this context, recent progress in plasmonic biosensing has enabled the design of novel detection strategies capable of targeting individual molecules while evaluating their binding affinity and biological interactions. This review compiles the latest advances in plasmonic technologies for monitoring clinically relevant biomarkers at the single-molecule level. Functional applications are discussed according to plasmonic sensing modes based on either nanoapertures or nanoparticle approaches. A special focus was devoted to new analytical developments involving a wide variety of analytes (e.g., proteins, living cells, nucleic acids and viruses). The utility of plasmonic-based single-molecule analysis for personalized medicine, considering technological limitations and future prospects, is also overviewed.
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Zhao B, Che C, Wang W, Li N, Cunningham BT. Single-step, wash-free digital immunoassay for rapid quantitative analysis of serological antibody against SARS-CoV-2 by photonic resonator absorption microscopy. Talanta 2021; 225:122004. [PMID: 33592744 PMCID: PMC7833826 DOI: 10.1016/j.talanta.2020.122004] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 02/06/2023]
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the cause of Coronavirus Disease 2019 (COVID-19), poses extraordinary threats and complex challenges to global public health. Quantitative measurement of SARS-CoV-2 antibody titer plays an important role in understanding the patient-to-patient variability of immune response, assessing the efficacy of vaccines, and identifying donors for blood transfusion therapy. There is an urgent and ever-increasing demand for serological COVID-19 antibody tests that are highly sensitive, quantitative, rapid, simple, minimally invasive, and inexpensive. In this work, we developed a single-step, wash-free immunoassay for rapid and highly sensitive quantitative analysis of serological human IgG against SARS-CoV-2 which requires only a single droplet of serum. By simply incubating 4 μL human serum samples with antibody-functionalized gold nanoparticles, a photonic crystal optical biosensor coated with the recombinant spike protein serves as a sensing platform for the formation of sandwich immunocomplex through specific antigen-antibody interactions, upon which the detected IgG molecules can be counted with digital precision. We demonstrated a single-step 15-min assay capable of detecting as low as 100 pg mL-1 human COVID-19 IgG in serum samples. The calculated limit of detecting (LOD) and limit of quantification (LOQ) is 26.7 ± 7.7 and 32.0 ± 8.9 pg mL-1, respectively. This work represents the first utilization of the Activate Capture + Digital Counting (AC + DC)-based immunoassay for rapid and quantitative analysis of serological COVID-19 antibody, demonstrating a route toward point-of-care testing, using a portable detection instrument. On the basis of the sandwich immunoassay principle, the biosensing platform can be extended for the multiplexed detection of antigens, additional IgGs, cytokines, and other protein biomarkers.
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Affiliation(s)
- Bin Zhao
- Carl R. Woese Institute for Genomic Biology, 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
| | - Congnyu Che
- 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
| | - Weijing Wang
- 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
- Nick Holonyak, Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Brian T Cunningham
- Carl R. Woese Institute for Genomic Biology, 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; Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Cancer Center at Illinois, Urbana, IL, 61801, USA.
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Yan H, Li Y, Cheng S, Zeng Y. Advances in Analytical Technologies for Extracellular Vesicles. Anal Chem 2021; 93:4739-4774. [PMID: 33635060 DOI: 10.1021/acs.analchem.1c00693] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- He Yan
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Yutao Li
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Shibo Cheng
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Yong Zeng
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States.,University of Florida Health Cancer Center, Gainesville, Florida 32610, United States
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Tian T, Shu B, Jiang Y, Ye M, Liu L, Guo Z, Han Z, Wang Z, Zhou X. An Ultralocalized Cas13a Assay Enables Universal and Nucleic Acid Amplification-Free Single-Molecule RNA Diagnostics. ACS NANO 2021; 15:1167-1178. [PMID: 33498106 DOI: 10.1021/acsnano.0c08165] [Citation(s) in RCA: 207] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Existing methods for RNA diagnostics, such as reverse transcription PCR (RT-PCR), mainly rely on nucleic acid amplification (NAA) and RT processes, which are known to introduce substantial issues, including amplification bias, cross-contamination, and sample loss. To address these problems, we introduce a confinement effect-inspired Cas13a assay for single-molecule RNA diagnostics, eliminating the need for NAA and RT. This assay involves confining the RNA-triggered Cas13a catalysis system in cell-like-sized reactors to enhance local concentrations of target and reporter simultaneously, via droplet microfluidics. It achieves >10 000-fold enhancement in sensitivity when compared to the bulk Cas13a assay and enables absolute digital single-molecule RNA quantitation. We experimentally demonstrate its broad applicability for precisely counting microRNAs, 16S rRNAs, and SARS-CoV-2 RNA from synthetic sequences to clinical samples with excellent accuracy. Notably, this direct RNA diagnostic technology enables detecting a wide range of RNA molecules at the single-molecule level. Moreover, its simplicity, universality, and excellent quantification capability might render it to be a dominant rival to RT-qPCR.
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Affiliation(s)
- Tian Tian
- School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Bowen Shu
- Department of Laboratory Medicine, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou 510180, China
- Clinical Molecular Medicine and Molecular Diagnosis Key Laboratory of Guangdong Province, Guangzhou 510180, China
| | - Yongzhong Jiang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
- Hubei Provincial Center for Disease Control and Prevention, Wuhan 430079, China
| | - Miaomiao Ye
- Hubei Provincial Center for Disease Control and Prevention, Wuhan 430079, China
| | - Lei Liu
- Institute for Brain Research and Rehabilitation, Guangdong Key Laboratory of Mental Health and Cognitive Science, Center for Studies of Psychological Application, South China Normal University, Guangzhou 510631, China
| | - Zhonghui Guo
- Department of Clinical Laboratory Medicine, Central Hospital of Panyu District, Guangzhou 511400, China
| | - Zeping Han
- Department of Clinical Laboratory Medicine, Central Hospital of Panyu District, Guangzhou 511400, China
| | - Zhang Wang
- Institute of Ecological Science, School of Life Sciences, South China Normal University, Guangzhou 510180, China
| | - Xiaoming Zhou
- School of Life Sciences, South China Normal University, Guangzhou 510631, China
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Li F, Li G, Cao S, Liu B, Ren X, Kang N, Qiu F. Target-triggered entropy-driven amplification system-templated silver nanoclusters for multiplexed microRNA analysis. Biosens Bioelectron 2021; 172:112757. [PMID: 33129074 DOI: 10.1016/j.bios.2020.112757] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 10/09/2020] [Accepted: 10/21/2020] [Indexed: 10/23/2022]
Abstract
MicroRNAs (miRNAs) are important biomarkers for the diagnosis, prognosis, and treatment of human diseases. Sensitive and selective detection of multiple miRNAs simultaneously will greatly facilitate the early and accurate diagnosis of cancers. Herein, a novel entropy-driven amplification system-templated silver nanoclusters sensing platform was developed for the multiplexed analysis of tumor-associated miRNAs. The sensing platform was constructed by coupling target-triggered entropy-driven catalysis with luminescence adjustable DNA-templated silver nanoclusters (Ag NCs). In the presence of target miRNA, the sensing platform initiates the branch migration and strand displacement of the complex, which has a six-base cytosine loop for stabilizing the luminous Ag NCs. The target is cyclically generated for new catalysis while turning off the fluorescence of Ag NCs; this is accompanied by a significantly amplified optical readout. In this study, two different complex-stabilized Ag NCs systems were proposed, the yellow-emitting Ag NCs and red-emitting Ag NCs biosensors enabled the analysis of miRNA-141 and miRNA-155 with detection limits of 6.1 pM and 8.7 pM, respectively. Impressively, owing to the excellent selectivity, flexibility, and narrow-band excitation of the platform, the multiplexed synchronous detection of miRNA-141 and miRNA-155 were achieved in buffer, biological cell lysates and human serum samples with satisfactory results. The simple, flexible, and convenient strategy provides a powerful tool for multiple biomarkers analysis and related clinical applications.
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Affiliation(s)
- Fengyun Li
- School of Chinese Materia Medica, State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin, 301617, PR China
| | - Gen Li
- School of Chinese Materia Medica, State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin, 301617, PR China
| | - Shijie Cao
- Tianjin Key Laboratory of TCM Chemistry and Analysis, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin, 301617, PR China
| | - Boshi Liu
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin, 301617, PR China
| | - Xiaoliang Ren
- School of Chinese Materia Medica, State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin, 301617, PR China
| | - Ning Kang
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin, 301617, PR China
| | - Feng Qiu
- School of Chinese Materia Medica, State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin, 301617, PR China.
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Dell'Olio F, Su J, Huser T, Sottile V, Cortés-Hernández LE, Alix-Panabières C. Photonic technologies for liquid biopsies: recent advances and open research challenges. LASER & PHOTONICS REVIEWS 2021; 15:2000255. [PMID: 35360260 PMCID: PMC8966629 DOI: 10.1002/lpor.202000255] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Indexed: 05/15/2023]
Abstract
The recent development of sophisticated techniques capable of detecting extremely low concentrations of circulating tumor biomarkers in accessible body fluids, such as blood or urine, could contribute to a paradigm shift in cancer diagnosis and treatment. By applying such techniques, clinicians can carry out liquid biopsies, providing information on tumor presence, evolution, and response to therapy. The implementation of biosensing platforms for liquid biopsies is particularly complex because this application domain demands high selectivity/specificity and challenging limit-of-detection (LoD) values. The interest in photonics as an enabling technology for liquid biopsies is growing owing to the well-known advantages of photonic biosensors over competing technologies in terms of compactness, immunity to external disturbance, and ultra-high spatial resolution. Some encouraging experimental results in the field of photonic devices and systems for liquid biopsy have already been achieved by using fluorescent labels and label-free techniques and by exploiting super-resolution microscopy, surface plasmon resonance, surface-enhanced Raman scattering, and whispering gallery mode resonators. This paper critically reviews the current state-of-the-art, starting from the requirements imposed by the detection of the most common circulating biomarkers. Open research challenges are considered together with competing technologies, and the most promising paths of improvement are discussed for future applications.
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Affiliation(s)
- Francesco Dell'Olio
- Department of Electrical and Information Engineering, Polytechnic University of Bari, 70125, Italy
| | - Judith Su
- Department of Biomedical Engineering, College of Optical Sciences, and BIO5 Institute, University of Arizona, 85721, USA
| | - Thomas Huser
- Biomolecular Photonics, Department of Physics, University of Bielefeld, 33615 Germany
| | - Virginie Sottile
- Department of Molecular Medicine, University of Pavia, 27100, Italy
| | | | - Catherine Alix-Panabières
- Laboratory of Rare Human Circulating Cells (LCCRH), University Medical Center of Montpellier, 34093 CEDEX 5, France
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38
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Huang Q, Li N, Zhang H, Che C, Sun F, Xiong Y, Canady TD, Cunningham BT. Critical Review: digital resolution biomolecular sensing for diagnostics and life science research. LAB ON A CHIP 2020; 20:2816-2840. [PMID: 32700698 PMCID: PMC7485136 DOI: 10.1039/d0lc00506a] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
One of the frontiers in the field of biosensors is the ability to quantify specific target molecules with enough precision to count individual units in a test sample, and to observe the characteristics of individual biomolecular interactions. Technologies that enable observation of molecules with "digital precision" have applications for in vitro diagnostics with ultra-sensitive limits of detection, characterization of biomolecular binding kinetics with a greater degree of precision, and gaining deeper insights into biological processes through quantification of molecules in complex specimens that would otherwise be unobservable. In this review, we seek to capture the current state-of-the-art in the field of digital resolution biosensing. We describe the capabilities of commercially available technology platforms, as well as capabilities that have been described in published literature. We highlight approaches that utilize enzymatic amplification, nanoparticle tags, chemical tags, as well as label-free biosensing methods.
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Affiliation(s)
- Qinglan Huang
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 208 North Wright Street, Urbana, IL 61801
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Nantao Li
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 208 North Wright Street, Urbana, IL 61801
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Hanyuan Zhang
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Congnyu Che
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- Department of Bioengineering, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Fu Sun
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 208 North Wright Street, Urbana, IL 61801
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Yanyu Xiong
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 208 North Wright Street, Urbana, IL 61801
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Taylor D. Canady
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Brian T. Cunningham
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 208 North Wright Street, Urbana, IL 61801
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- Department of Bioengineering, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- Illinois Cancer Center, University of Illinois at Urbana-Champaign Urbana, IL 61801
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Yuan X, Yang C, He Q, Chen J, Yu D, Li J, Zhai S, Qin Z, Du K, Chu Z, Qin P. Current and Perspective Diagnostic Techniques for COVID-19. ACS Infect Dis 2020; 6:1998-2016. [PMID: 32677821 PMCID: PMC7409380 DOI: 10.1021/acsinfecdis.0c00365] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Indexed: 02/08/2023]
Abstract
Since late December 2019, the coronavirus pandemic (COVID-19; previously known as 2019-nCoV) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been surging rapidly around the world. With more than 1,700,000 confirmed cases, the world faces an unprecedented economic, social, and health impact. The early, rapid, sensitive, and accurate diagnosis of viral infection provides rapid responses for public health surveillance, prevention, and control of contagious diffusion. More than 30% of the confirmed cases are asymptomatic, and the high false-negative rate (FNR) of a single assay requires the development of novel diagnostic techniques, combinative approaches, sampling from different locations, and consecutive detection. The recurrence of discharged patients indicates the need for long-term monitoring and tracking. Diagnostic and therapeutic methods are evolving with a deeper understanding of virus pathology and the potential for relapse. In this Review, a comprehensive summary and comparison of different SARS-CoV-2 diagnostic methods are provided for researchers and clinicians to develop appropriate strategies for the timely and effective detection of SARS-CoV-2. The survey of current biosensors and diagnostic devices for viral nucleic acids, proteins, and particles and chest tomography will provide insight into the development of novel perspective techniques for the diagnosis of COVID-19.
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Affiliation(s)
- Xi Yuan
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong 518055, China
| | - Chengming Yang
- Southern
University of Science and Technology Hospital, Shenzhen, Guangdong 518055, China
| | - Qian He
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong 518055, China
| | - Junhu Chen
- National
Institute of Parasitic Diseases, Chinese
Center for Disease Control and Prevention, Shanghai 200025, China
| | - Dongmei Yu
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong 518055, China
- Department
of Mechanics and Aerospace Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Jie Li
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong 518055, China
- Kunming
Dog Base of Police Security, Ministry of Public Security, Kunming, Yunnan 650204, China
| | - Shiyao Zhai
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong 518055, China
| | - Zhifeng Qin
- Animal &
Plant Inspection and Quarantine Technology Center, Shenzhen Customs District People’s Republic of China, Shenzhen, Guangdong 518045, China
| | - Ke Du
- Department
of Mechanical Engineering, Rochester Institute
of Technology, Rochester, New York 14623, United States
| | - Zhenhai Chu
- Southern
University of Science and Technology Hospital, Shenzhen, Guangdong 518055, China
| | - Peiwu Qin
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong 518055, China
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Jin G, Bachman H, Naquin TD, Rufo J, Hou S, Tian Z, Zhao C, Huang TJ. Acoustofluidic Scanning Nanoscope with High Resolution and Large Field of View. ACS NANO 2020; 14:8624-8633. [PMID: 32574033 PMCID: PMC7438315 DOI: 10.1021/acsnano.0c03009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Optical imaging with nanoscale resolution and a large field of view is highly desirable in many research areas. Unfortunately, it is challenging to achieve these two features simultaneously while using a conventional microscope. An objective lens with a low numerical aperture (NA) has a large field of view but poor resolution. In contrast, a high NA objective lens will have a higher resolution but reduced field of view. In an effort to close the gap between these trade-offs, we introduce an acoustofluidic scanning nanoscope (AS-nanoscope) that can simultaneously achieve high resolution with a large field of view. The AS-nanoscope relies on acoustofluidic-assisted scanning of multiple microsized particles. A scanned 2D image is then compiled by processing the microparticle images using an automated big-data image algorithm. The AS-nanoscope has the potential to be integrated into a conventional microscope or could serve as a stand-alone instrument for a wide range of applications where both high resolution and large field of view are required.
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Affiliation(s)
- Geonsoo Jin
- Department of Mechanical Engineering and Material Science, Duke University, Durham, North Carolina 27708, United States
| | - Hunter Bachman
- Department of Mechanical Engineering and Material Science, Duke University, Durham, North Carolina 27708, United States
| | - Ty Downing Naquin
- Department of Mechanical Engineering and Material Science, Duke University, Durham, North Carolina 27708, United States
| | - Joseph Rufo
- Department of Mechanical Engineering and Material Science, Duke University, Durham, North Carolina 27708, United States
| | - Serena Hou
- Department of Mechanical Engineering and Material Science, Duke University, Durham, North Carolina 27708, United States
| | - Zhenhua Tian
- Department of Mechanical Engineering and Material Science, Duke University, Durham, North Carolina 27708, United States
| | - Chenglong Zhao
- Department of Physics, University of Dayton, 300 College Park, Dayton, Ohio 45469, United States
- Department of Electro-Optics and Photonics, University of Dayton, 300 College Park, Dayton, Ohio 45469, United States
| | - Tony Jun Huang
- Department of Mechanical Engineering and Material Science, Duke University, Durham, North Carolina 27708, United States
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Zou L, Wu Z, Liu X, Zheng Y, Mei W, Wang Q, Yang X, Wang K. DNA Hydrogelation-Enhanced Imaging Ellipsometry for Sensing Exosomal microRNAs with a Tunable Detection Range. Anal Chem 2020; 92:11953-11959. [DOI: 10.1021/acs.analchem.0c02345] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Liyuan Zou
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, People’s Republic of China
| | - Zhaoxing Wu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, People’s Republic of China
| | - Xiaofeng Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, People’s Republic of China
| | - Yan Zheng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, People’s Republic of China
| | - Wenjing Mei
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, People’s Republic of China
| | - Qing Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, People’s Republic of China
| | - Xiaohai Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, People’s Republic of China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, People’s Republic of China
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Akkilic N, Geschwindner S, Höök F. Single-molecule biosensors: Recent advances and applications. Biosens Bioelectron 2019; 151:111944. [PMID: 31999573 DOI: 10.1016/j.bios.2019.111944] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/26/2019] [Accepted: 11/29/2019] [Indexed: 02/07/2023]
Abstract
Single-molecule biosensors serve the unmet need for real time detection of individual biological molecules in the molecular crowd with high specificity and accuracy, uncovering unique properties of individual molecules which are hidden when measured using ensemble averaging methods. Measuring a signal generated by an individual molecule or its interaction with biological partners is not only crucial for early diagnosis of various diseases such as cancer and to follow medical treatments but also offers a great potential for future point-of-care devices and personalized medicine. This review summarizes and discusses recent advances in nanosensors for both in vitro and in vivo detection of biological molecules offering single-molecule sensitivity. In the first part, we focus on label-free platforms, including electrochemical, plasmonic, SERS-based and spectroelectrochemical biosensors. We review fluorescent single-molecule biosensors in the second part, highlighting nanoparticle-amplified assays, digital platforms and the utilization of CRISPR technology. We finally discuss recent advances in the emerging nanosensor technology of important biological species as well as future perspectives of these sensors.
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Affiliation(s)
- Namik Akkilic
- Structure, Biophysics and Fragment-based Lead Generation, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden.
| | - Stefan Geschwindner
- Structure, Biophysics and Fragment-based Lead Generation, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Fredrik Höök
- Department of Applied Physics, Division of Biological Physics, Chalmers University of Technology, Gothenburg, Sweden.
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Che C, Li N, Long KD, Aguirre MÁ, Canady TD, Huang Q, Demirci U, Cunningham BT. Activate capture and digital counting (AC + DC) assay for protein biomarker detection integrated with a self-powered microfluidic cartridge. LAB ON A CHIP 2019; 19:3943-3953. [PMID: 31641717 PMCID: PMC11483904 DOI: 10.1039/c9lc00728h] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
We demonstrate a rapid, 2-step, and ultrasensitive assay approach for quantification of target protein molecules from a single droplet test sample. The assay is comprised of antibody-conjugated gold nanoparticles (AuNPs) that are "activated" when they are mixed with the test sample and bind their targets. The resulting liquid is passed through a microfluidic channel with a photonic crystal (PC) biosensor that is functionalized with secondary antibodies to the target biomarker, so that only activated AuNPs are captured. Utilizing recently demonstrated hybrid optical coupling between the plasmon resonance of the AuNP and the resonance of the PC, each captured AuNP efficiently quenches the resonant reflection of the PC, thus enabling the captured AuNPs to be digitally counted with high signal-to-noise. To achieve a 2-step assay process that is performed on a single droplet test sample without washing steps or active pump elements, controlled single-pass flow rate is obtained with an absorbing paper pad waste reservoir embedded in a microfluidic cartridge. We use the activate capture and digital counting (AC + DC) approach to demonstrate HIV-1 capsid antigen p24 detection from a 40 μL spiked-in human serum sample at a one thousand-fold dynamic range (1-103 pg mL-1) with only a 35-minute process that is compatible with point-of-care (POC) analysis. The AC + DC approach allows for ultrasensitive and ultrafast biomolecule detection, with potential applications in infectious disease diagnostics and early stage disease monitoring.
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Affiliation(s)
- Congnyu Che
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 208 North Wright Street, Urbana, IL 61801, USA.
| | - Nantao Li
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 208 North Wright Street, Urbana, IL 61801, USA
| | - Kenneth D Long
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 208 North Wright Street, Urbana, IL 61801, USA.
| | - Miguel Ángel Aguirre
- Department of Analytical Chemistry and Food Science and University Institute of Materials, Faculty of Science, University of Alicante, P.O. Box 99, 03080 Alicante, Spain
| | - Taylor D Canady
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, USA
| | - Qinglan Huang
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 208 North Wright Street, Urbana, IL 61801, USA
| | - Utkan Demirci
- Bio-Acoustic MEMS in Medicine (BAMM) Laboratory, Canary Center at Stanford for Cancer Early Detection, Department of Radiology School of Medicine Stanford University, Palo Alto, CA 94304, USA
| | - Brian T Cunningham
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 208 North Wright Street, Urbana, IL 61801, USA. and Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 208 North Wright Street, Urbana, IL 61801, USA and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, USA
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44
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Garcia-Fernandez E, Gonzalez-Garcia MC, Pernagallo S, Ruedas-Rama MJ, Fara MA, López-Delgado FJ, Dear JW, Ilyine H, Ress C, Díaz-Mochón JJ, Orte A. miR-122 direct detection in human serum by time-gated fluorescence imaging. Chem Commun (Camb) 2019; 55:14958-14961. [PMID: 31774422 DOI: 10.1039/c9cc08069d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A simple method for direct detection of microRNAs (miRs) in human serum without the use of polymerase amplification is presented, achieving low miR-122 concentrations and importantly, discerning effectively single-base sequence mutations. The method is based on the capture of target miRs with synthetic peptide nucleic acid oligomers, dynamic chemical labelling, separation with quaternary amine microplatforms and detection using time-gated fluorescence imaging.
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Affiliation(s)
- Emilio Garcia-Fernandez
- Departamento de Fisicoquimica. Unidad de Excelencia de Química aplicada a Biomedicina y Medioambiente, Facultad de Farmacia, Universidad de Granada, Campus de Cartuja s/n, 18071-Granada, Spain.
| | - M Carmen Gonzalez-Garcia
- Departamento de Fisicoquimica. Unidad de Excelencia de Química aplicada a Biomedicina y Medioambiente, Facultad de Farmacia, Universidad de Granada, Campus de Cartuja s/n, 18071-Granada, Spain.
| | - Salvatore Pernagallo
- DestiNA Genomica S.L., Parque Tecnológico Ciencias de la Salud (PTS), Av. de la Innovación 1, Edificio BIC, Armilla, Granada, Spain and DestiNA Genomics Ltd, 7-11 Melville St, Edinburgh EH3 7PE, UK
| | - Maria J Ruedas-Rama
- Departamento de Fisicoquimica. Unidad de Excelencia de Química aplicada a Biomedicina y Medioambiente, Facultad de Farmacia, Universidad de Granada, Campus de Cartuja s/n, 18071-Granada, Spain.
| | - Mario A Fara
- DestiNA Genomica S.L., Parque Tecnológico Ciencias de la Salud (PTS), Av. de la Innovación 1, Edificio BIC, Armilla, Granada, Spain
| | - Francisco J López-Delgado
- DestiNA Genomica S.L., Parque Tecnológico Ciencias de la Salud (PTS), Av. de la Innovación 1, Edificio BIC, Armilla, Granada, Spain
| | - James W Dear
- Centre for Cardiovascular Science, University of Edinburgh, The Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Hugh Ilyine
- DestiNA Genomics Ltd, 7-11 Melville St, Edinburgh EH3 7PE, UK
| | - Cristina Ress
- Optoi Microelectronics, Via Vienna n°8, Trento, 38121 Gardolo, Italy
| | - Juan J Díaz-Mochón
- DestiNA Genomica S.L., Parque Tecnológico Ciencias de la Salud (PTS), Av. de la Innovación 1, Edificio BIC, Armilla, Granada, Spain and GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, Av. de la Ilustración, 114, 18016-Granada, Spain and Departamento de Quimica Farmaceutica y Organica, Facultad de Farmacia, Universidad de Granada, Campus de Cartuja s/n, 18071-Granada, Spain
| | - Angel Orte
- Departamento de Fisicoquimica. Unidad de Excelencia de Química aplicada a Biomedicina y Medioambiente, Facultad de Farmacia, Universidad de Granada, Campus de Cartuja s/n, 18071-Granada, Spain.
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