1
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Lak A, Wang Y, Kolbeck PJ, Pauer C, Chowdhury MS, Cassani M, Ludwig F, Viereck T, Selbach F, Tinnefeld P, Schilling M, Liedl T, Tavacoli J, Lipfert J. Cooperative dynamics of DNA-grafted magnetic nanoparticles optimize magnetic biosensing and coupling to DNA origami. NANOSCALE 2024; 16:7678-7689. [PMID: 38533617 DOI: 10.1039/d3nr06253h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
Magnetic nanoparticles (MNPs) provide new opportunities for enzyme-free biosensing of nucleic acid biomarkers and magnetic actuation by patterning on DNA origami, yet how the DNA grafting density affects their dynamics and accessibility remains poorly understood. Here, we performed surface functionalization of MNPs with single-stranded DNA (ssDNA) via click chemistry with a tunable grafting density, which enables the encapsulation of single MNPs inside a functional polymeric layer. We used several complementary methods to show that particle translational and rotational dynamics exhibit a sigmoidal dependence on the ssDNA grafting density. At low densities, ssDNA strands adopt a coiled conformation that results in minor alterations to particle dynamics, while at high densities, they organize into polymer brushes that collectively influence particle dynamics. Intermediate ssDNA densities, where the dynamics are most sensitive to changes, show the highest magnetic biosensing sensitivity for the detection of target nucleic acids. Finally, we demonstrate that MNPs with high ssDNA grafting densities are required to efficiently couple to DNA origami. Our results establish ssDNA grafting density as a critical parameter for the functionalization of MNPs for magnetic biosensing and functionalization of DNA nanostructures.
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Affiliation(s)
- Aidin Lak
- Institute for Electrical Measurement Science and Fundamental Electrical Engineering and Laboratory for Emerging Nanometrology (LENA), Hans-Sommer-Str. 66, Braunschweig, 38106, Germany.
| | - Yihao Wang
- Institute for Electrical Measurement Science and Fundamental Electrical Engineering and Laboratory for Emerging Nanometrology (LENA), Hans-Sommer-Str. 66, Braunschweig, 38106, Germany.
| | - Pauline J Kolbeck
- Soft Condensed Matter and Biophysics, Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, The Netherlands
- Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, The Netherlands
| | - Christoph Pauer
- Soft Condensed Matter and Biophysics, Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, The Netherlands
| | - Mohammad Suman Chowdhury
- Institute for Electrical Measurement Science and Fundamental Electrical Engineering and Laboratory for Emerging Nanometrology (LENA), Hans-Sommer-Str. 66, Braunschweig, 38106, Germany.
| | - Marco Cassani
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | - Frank Ludwig
- Institute for Electrical Measurement Science and Fundamental Electrical Engineering and Laboratory for Emerging Nanometrology (LENA), Hans-Sommer-Str. 66, Braunschweig, 38106, Germany.
| | - Thilo Viereck
- Institute for Electrical Measurement Science and Fundamental Electrical Engineering and Laboratory for Emerging Nanometrology (LENA), Hans-Sommer-Str. 66, Braunschweig, 38106, Germany.
| | - Florian Selbach
- Department of Chemistry and Center for NanoScience, LMU Munich, 81377 Munich, Germany
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience, LMU Munich, 81377 Munich, Germany
| | - Meinhard Schilling
- Institute for Electrical Measurement Science and Fundamental Electrical Engineering and Laboratory for Emerging Nanometrology (LENA), Hans-Sommer-Str. 66, Braunschweig, 38106, Germany.
| | - Tim Liedl
- Soft Condensed Matter and Biophysics, Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, The Netherlands
| | - Joe Tavacoli
- Soft Condensed Matter and Biophysics, Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, The Netherlands
| | - Jan Lipfert
- Soft Condensed Matter and Biophysics, Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, The Netherlands
- Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, The Netherlands
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2
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El-Sherif DM, Abouzid M, Gaballah MS, Ahmed AA, Adeel M, Sheta SM. New approach in SARS-CoV-2 surveillance using biosensor technology: a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:1677-1695. [PMID: 34689274 PMCID: PMC8541810 DOI: 10.1007/s11356-021-17096-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/13/2021] [Indexed: 05/14/2023]
Abstract
Biosensors are analytical tools that transform the bio-signal into an observable response. Biosensors are effective for early detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection because they target viral antigens to assess clinical development and provide information on the severity and critical trends of infection. The biosensors are capable of being on-site, fast, and extremely sensitive to the target viral antigen, opening the door for early detection of SARS-CoV-2. They can screen individuals in hospitals, airports, and other crowded locations. Microfluidics and nanotechnology are promising cornerstones for the development of biosensor-based techniques. Recently, due to high selectivity, simplicity, low cost, and reliability, the production of biosensor instruments have attracted considerable interest. This review article precisely provides the extensive scientific advancement and intensive look of basic principles and implementation of biosensors in SARS-CoV-2 surveillance, especially for human health. In this review, the importance of biosensors including Optical, Electrochemical, Piezoelectric, Microfluidic, Paper-based biosensors, Immunosensors, and Nano-Biosensors in the detection of SARS-CoV-2 has been underscored. Smartphone biosensors and calorimetric strips that target antibodies or antigens should be developed immediately to combat the rapidly spreading SARS-CoV-2. Wearable biosensors can constantly monitor patients, which is a highly desired feature of biosensors. Finally, we summarized the literature, outlined new approaches and future directions in diagnosing SARS-CoV-2 by biosensor-based techniques.
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Affiliation(s)
- Dina M El-Sherif
- National Institute of Oceanography and Fisheries, NIOF, Cairo, Egypt.
| | - Mohamed Abouzid
- Department of Physical Pharmacy and Pharmacokinetics, Faculty of Pharmacy, Poznan University of Medical Sciences, 60-781, Poznan, Poland.
| | - Mohamed S Gaballah
- National Institute of Oceanography and Fisheries, NIOF, Cairo, Egypt
- College of Engineering, Key Laboratory for Clean Renewable Energy Utilization Technology, Ministry of Agriculture), China Agricultural University, Beijing, 100083, People's Republic of China
| | - Alhassan Ali Ahmed
- Department of Bioinformatics and Computational Biology, Poznan University of Medical Sciences, Poznan, Poland
| | - Muhammad Adeel
- BNU-HKUST Laboratory of Green Innovation, Advanced Institute of Natural Sciences, Beijing Normal University Zhuhai Subcampus, 18 Jinfeng Road, Tangjiawan, Zhuhai, Guangdong, China
| | - Sheta M Sheta
- Inorganic Chemistry Department, National Research Centre, 33 El-Behouth St., Dokki, Giza, 12622, Egypt
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3
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Usha SP, Manoharan H, Deshmukh R, Álvarez-Diduk R, Calucho E, Sai VVR, Merkoçi A. Attomolar analyte sensing techniques (AttoSens): a review on a decade of progress on chemical and biosensing nanoplatforms. Chem Soc Rev 2021; 50:13012-13089. [PMID: 34673860 DOI: 10.1039/d1cs00137j] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Detecting the ultra-low abundance of analytes in real-life samples, such as biological fluids, water, soil, and food, requires the design and development of high-performance biosensing modalities. The breakthrough efforts from the scientific community have led to the realization of sensing technologies that measure the analyte's ultra-trace level, with relevant sensitivity, selectivity, response time, and sampling efficiency, referred to as Attomolar Analyte Sensing Techniques (AttoSens) in this review. In an AttoSens platform, 1 aM detection corresponds to the quantification of 60 target analyte molecules in 100 μL of sample volume. Herein, we review the approaches listed for various sensor probe design, and their sensing strategies that paved the way for the detection of attomolar (aM: 10-18 M) concentration of analytes. A summary of the technological advances made by the diverse AttoSens trends from the past decade is presented.
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Affiliation(s)
- Sruthi Prasood Usha
- Biomedical Engineering, Department of Applied Mechanics, Indian Institute of Technology Madras (IITM), India.
| | - Hariharan Manoharan
- Biomedical Engineering, Department of Applied Mechanics, Indian Institute of Technology Madras (IITM), India.
| | - Rehan Deshmukh
- Biomedical Engineering, Department of Applied Mechanics, Indian Institute of Technology Madras (IITM), India.
| | - Ruslan Álvarez-Diduk
- Nanobioelectronics & Biosensors Group, Institut Català de Nanociència i Nanotecnologia (ICN2), Campus UAB, Barcelona, Spain.
| | - Enric Calucho
- Nanobioelectronics & Biosensors Group, Institut Català de Nanociència i Nanotecnologia (ICN2), Campus UAB, Barcelona, Spain.
| | - V V R Sai
- Biomedical Engineering, Department of Applied Mechanics, Indian Institute of Technology Madras (IITM), India.
| | - Arben Merkoçi
- Nanobioelectronics & Biosensors Group, Institut Català de Nanociència i Nanotecnologia (ICN2), Campus UAB, Barcelona, Spain. .,ICREA, Institució Catalana de Recercai Estudis Avançats, Barcelona, Spain
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4
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Fu J, Li J, Chen J, Li Y, Liu J, Su X, Shi S. Ultra-specific nucleic acid testing by target-activated nucleases. Crit Rev Biotechnol 2021; 42:1061-1078. [PMID: 34706599 DOI: 10.1080/07388551.2021.1983757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Specific and sensitive detection of nucleic acids is essential to clinical diagnostics and biotechnological applications. Currently, amplification steps are necessary for most detection methods due to the low concentration of nucleic acid targets in real samples. Although amplification renders high sensitivity, poor specificity is prevalent because of the lack of highly accurate precise strategies, resulting in significant false positives and false negatives. Nucleases exhibit high catalytic activity for nucleic acid cleavage which is regulated in a programmable manner. This review focuses on the latest progress in nucleic acid testing methods based on the target-activated nucleases. It summarizes the property of enzymes such as CRISPR/Cas, Argonautes, and some gene-editing irrelevant nucleases, which have been leveraged to create highly specific and sensitive nucleic acid testing tools. We elaborate on recent advances in the field of nuclease-mediated DNA recognition techniques for nucleic acid detection, and discuss its future applications and challenges in molecular diagnostics.
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Affiliation(s)
- Jinyu Fu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Junjie Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Jing Chen
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yabei Li
- Department of Neurosurgery, People's Hospital of Shijiazhuang, Shijiazhuang, China
| | - Jiajia Liu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Xin Su
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Shuobo Shi
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
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5
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Bhalla N, Pan Y, Yang Z, Payam AF. Opportunities and Challenges for Biosensors and Nanoscale Analytical Tools for Pandemics: COVID-19. ACS NANO 2020; 14:7783-7807. [PMID: 32551559 PMCID: PMC7319134 DOI: 10.1021/acsnano.0c04421] [Citation(s) in RCA: 210] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 06/18/2020] [Indexed: 05/05/2023]
Abstract
Biosensors and nanoscale analytical tools have shown huge growth in literature in the past 20 years, with a large number of reports on the topic of 'ultrasensitive', 'cost-effective', and 'early detection' tools with a potential of 'mass-production' cited on the web of science. Yet none of these tools are commercially available in the market or practically viable for mass production and use in pandemic diseases such as coronavirus disease 2019 (COVID-19). In this context, we review the technological challenges and opportunities of current bio/chemical sensors and analytical tools by critically analyzing the bottlenecks which have hindered the implementation of advanced sensing technologies in pandemic diseases. We also describe in brief COVID-19 by comparing it with other pandemic strains such as that of severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) for the identification of features that enable biosensing. Moreover, we discuss visualization and characterization tools that can potentially be used not only for sensing applications but also to assist in speeding up the drug discovery and vaccine development process. Furthermore, we discuss the emerging monitoring mechanism, namely wastewater-based epidemiology, for early warning of the outbreak, focusing on sensors for rapid and on-site analysis of SARS-CoV2 in sewage. To conclude, we provide holistic insights into challenges associated with the quick translation of sensing technologies, policies, ethical issues, technology adoption, and an overall outlook of the role of the sensing technologies in pandemics.
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Affiliation(s)
- Nikhil Bhalla
- Nanotechnology
and Integrated Bioengineering Centre (NIBEC), School of Engineering, Ulster University, Shore Road, BT37
0QB Jordanstown, Northern Ireland, United Kingdom
- Healthcare
Technology Hub, Ulster University, Shore Road, BT37 0QB Jordanstown, Northern
Ireland, United Kingdom
| | - Yuwei Pan
- Cranfield
Water Science Institute, Cranfield University, Cranfield, Bedfordshire MK43 0AL, United Kingdom
| | - Zhugen Yang
- Cranfield
Water Science Institute, Cranfield University, Cranfield, Bedfordshire MK43 0AL, United Kingdom
| | - Amir Farokh Payam
- Nanotechnology
and Integrated Bioengineering Centre (NIBEC), School of Engineering, Ulster University, Shore Road, BT37
0QB Jordanstown, Northern Ireland, United Kingdom
- Healthcare
Technology Hub, Ulster University, Shore Road, BT37 0QB Jordanstown, Northern
Ireland, United Kingdom
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6
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Nucleic acid amplification free biosensors for pathogen detection. Biosens Bioelectron 2020; 153:112049. [DOI: 10.1016/j.bios.2020.112049] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/21/2020] [Accepted: 01/23/2020] [Indexed: 12/11/2022]
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7
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Sosa-Acosta JR, Iriarte-Mesa C, Ortega GA, Díaz-García AM. DNA–Iron Oxide Nanoparticles Conjugates: Functional Magnetic Nanoplatforms in Biomedical Applications. Top Curr Chem (Cham) 2020; 378:13. [DOI: 10.1007/s41061-019-0277-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 12/20/2019] [Indexed: 02/08/2023]
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8
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Single-Step FRET-Based Detection of Femtomoles DNA. SENSORS 2019; 19:s19163495. [PMID: 31405068 PMCID: PMC6719117 DOI: 10.3390/s19163495] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/02/2019] [Accepted: 08/05/2019] [Indexed: 12/11/2022]
Abstract
Sensitive detection of nucleic acids and identification of single nucleotide polymorphism (SNP) is crucial in diagnosis of genetic diseases. Many strategies have been developed for detection and analysis of DNA, including fluorescence, electrical, optical, and mechanical methods. Recent advances in fluorescence resonance energy transfer (FRET)-based sensing have provided a new avenue for sensitive and quantitative detection of various types of biomolecules in simple, rapid, and recyclable platforms. Here, we report single-step FRET-based DNA sensors designed to work via a toehold-mediated strand displacement (TMSD) process, leading to a distinct change in the FRET efficiency upon target binding. Using single-molecule FRET (smFRET), we show that these sensors can be regenerated in situ, and they allow detection of femtomoles DNA without the need for target amplification while still using a dramatically small sample size (fewer than three orders of magnitude compared to the typical sample size of bulk fluorescence). In addition, these single-molecule sensors exhibit a dynamic range of approximately two orders of magnitude. Using one of the sensors, we demonstrate that the single-base mismatch sequence can be discriminated from a fully matched DNA target, showing a high specificity of the method. These sensors with simple and recyclable design, sensitive detection of DNA, and the ability to discriminate single-base mismatch sequences may find applications in quantitative analysis of nucleic acid biomarkers.
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9
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Shlyapnikov YM, Malakhova EA, Shlyapnikova EA. Rapid Amplification-Free Microarray-Based Ultrasensitive Detection of DNA. Anal Chem 2019; 91:11209-11214. [DOI: 10.1021/acs.analchem.9b02149] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yuri M. Shlyapnikov
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow
Region, 142290, Russia
| | - Ekaterina A. Malakhova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow
Region, 142290, Russia
| | - Elena A. Shlyapnikova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow
Region, 142290, Russia
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10
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Masud MK, Na J, Younus M, Hossain MSA, Bando Y, Shiddiky MJA, Yamauchi Y. Superparamagnetic nanoarchitectures for disease-specific biomarker detection. Chem Soc Rev 2019; 48:5717-5751. [DOI: 10.1039/c9cs00174c] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Synthesis, bio-functionalization, and multifunctional activities of superparamagnetic-nanostructures have been extensively reviewed with a particular emphasis on their uses in a range of disease-specific biomarker detection and associated challenges.
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Affiliation(s)
- Mostafa Kamal Masud
- Australian Institute for Bioengineering and Nanotechnology (AIBN)
- The University of Queensland
- Brisbane
- Australia
- Department of Biochemistry & Molecular Biology
| | - Jongbeom Na
- Australian Institute for Bioengineering and Nanotechnology (AIBN)
- The University of Queensland
- Brisbane
- Australia
- International Center for Materials Nanoarchitechtonics (MANA)
| | - Muhammad Younus
- Department of Chemistry
- School of Physical Sciences
- Shahjalal University of Science & Technology
- Sylhet 3114
- Bangladesh
| | - Md. Shahriar A. Hossain
- Australian Institute for Bioengineering and Nanotechnology (AIBN)
- The University of Queensland
- Brisbane
- Australia
- School of Mechanical and Mining Engineering
| | - Yoshio Bando
- International Center for Materials Nanoarchitechtonics (MANA)
- National Institute for Materials Science (NIMS)
- Ibaraki 305-0044
- Japan
- Institute of Molecular Plus
| | - Muhammad J. A. Shiddiky
- School of Environment and Sciences and Queensland Micro- and Nanotechnology Centre (QMMC)
- Griffith University
- QLD 4111
- Australia
| | - Yusuke Yamauchi
- Australian Institute for Bioengineering and Nanotechnology (AIBN)
- The University of Queensland
- Brisbane
- Australia
- International Center for Materials Nanoarchitechtonics (MANA)
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11
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Mejía-Salazar JR, Camacho SA, Constantino CJL, Oliveira ON. New trends in plasmonic (bio)sensing. AN ACAD BRAS CIENC 2018; 90:779-801. [PMID: 29742207 DOI: 10.1590/0001-3765201820170571] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 10/04/2017] [Indexed: 11/22/2022] Open
Abstract
The strong enhancement and localization of electromagnetic field in plasmonic systems have found applications in many areas, which include sensing and biosensing. In this paper, an overview will be provided of the use of plasmonic phenomena in sensors and biosensors with emphasis on two main topics. The first is related to possible ways to enhance the performance of sensors and biosensors based on surface plasmon resonance (SPR), where examples are given of functionalized magnetic nanoparticles, magnetoplasmonic effects and use of metamaterials for SPR sensing. The other topic is focused on surface-enhanced Raman scattering (SERS) for sensing, for which uniform, flexible, and reproducible SERS substrates have been produced. With such recent developments, there is the prospect of improving sensitivity and lowering the limit of detection in order to overcome the limitations inherent in ultrasensitive detection of chemical and biological analytes, especially at single molecule levels.
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12
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Hybrid Magnetic-DNA Directed Immobilisation Approach for Efficient Protein Capture and Detection on Microfluidic Platforms. Sci Rep 2017; 7:194. [PMID: 28298637 PMCID: PMC5427967 DOI: 10.1038/s41598-017-00268-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 02/14/2017] [Indexed: 01/17/2023] Open
Abstract
In this study, a hybrid magnetic-DNA directed immobilisation approach is presented to enhance protein capture and detection on a microfluidic platform. DNA-modified magnetic nanoparticles are added in a solution to capture fluorescently labelled immunocomplexes to be detected optically. A magnetic set-up composed of cubic permanent magnets and a microchannel was designed and implemented based on finite element analysis results to efficiently concentrate the nanoparticles only over a defined area of the microchannel as the sensing zone. This in turn, led to the fluorescence emission localisation and the searching area reduction. Also, compared to processes in which the immunocomplex is formed directly on the surface, the proposed approach provides a lower steric hindrance, higher mass transfer, lower equilibrium time, and more surface concentration of the captured targets leading to a faster and more sensitive detection. As a proof-of-concept, the set-up is capable of detecting prostate-specific membrane antigen with concentrations down to 0.7 nM. Our findings suggest that the approach holds a great promise for applications in clinical assays and disease diagnosis.
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13
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Santos GM, Zhao F, Zeng J, Li M, Shih WC. Label-free, zeptomole cancer biomarker detection by surface-enhanced fluorescence on nanoporous gold disk plasmonic nanoparticles. JOURNAL OF BIOPHOTONICS 2015; 8:855-63. [PMID: 25727212 DOI: 10.1002/jbio.201400134] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 01/22/2015] [Accepted: 02/05/2015] [Indexed: 05/21/2023]
Abstract
We experimentally demonstrate a label-free biosensor for the ERBB2 cancer gene DNA target based on the distance-dependent detection of surface-enhanced fluorescence (SEF) on nanoporous gold disk (NPGD) plasmonic nanoparticles. We achieve detection of 2.4 zeptomole of DNA target on the NPGD substrate with an upper concentration detection limit of 1 nM. Without the use of molecular spacers, the NPGD substrate as an SEF platform was shown to provide higher net fluorescence for visible and NIR fluorophores compared to glass and non-porous gold substrates. The enhanced fluorescence signals in patterned nanoporous gold nanoparticles make NPGD a viable material for further reducing detection limits for biomolecular targets used in clinical assays. With patterned nanoporous gold disk (NPGD) plasmonic nanoparticles, a label-free biosensor that makes use of distance-dependent detection of surface-enhanced fluorescence (SEF) is constructed and tested for zeptomole detection of ERBB2 cancer gene DNA targets.
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Affiliation(s)
- Greggy M Santos
- Department of Electrical and Computer Engineering, University of Houston, 4800 Calhoun Road, Houston, Texas, 77204, USA
| | - Fusheng Zhao
- Department of Electrical and Computer Engineering, University of Houston, 4800 Calhoun Road, Houston, Texas, 77204, USA
| | - Jianbo Zeng
- Department of Electrical and Computer Engineering, University of Houston, 4800 Calhoun Road, Houston, Texas, 77204, USA
| | - Ming Li
- Department of Electrical and Computer Engineering, University of Houston, 4800 Calhoun Road, Houston, Texas, 77204, USA
| | - Wei-Chuan Shih
- Department of Electrical and Computer Engineering, University of Houston, 4800 Calhoun Road, Houston, Texas, 77204, USA.
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14
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Cannon B, Kachroo AH, Jarmoskaite I, Jayaram M, Russell R. Hexapeptides that inhibit processing of branched DNA structures induce a dynamic ensemble of Holliday junction conformations. J Biol Chem 2015; 290:22734-46. [PMID: 26209636 PMCID: PMC4566245 DOI: 10.1074/jbc.m115.663930] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 07/23/2015] [Indexed: 11/06/2022] Open
Abstract
Holliday junctions are critical intermediates in DNA recombination, repair, and restart of blocked replication. Hexapeptides have been identified that bind to junctions and inhibit various junction-processing enzymes, and these peptides confer anti-microbial and anti-tumor properties. Earlier studies suggested that inhibition results from stabilization of peptide-bound Holliday junctions in the square planar conformation. Here, we use single molecule fluorescence resonance energy transfer (smFRET) and two model junctions, which are AT- or GC-rich at the branch points, to show that binding of the peptide KWWCRW induces a dynamic ensemble of junction conformations that differs from both the square planar and stacked X conformations. The specific features of the conformational distributions differ for the two peptide-bound junctions, but both junctions display greatly decreased Mg(2+) dependence and increased conformational fluctuations. The smFRET results, complemented by gel mobility shift and small angle x-ray scattering analyses, reveal structural effects of peptides and highlight the sensitivity of smFRET for analyzing complex mixtures of DNA structures. The peptide-induced conformational dynamics suggest multiple stacking arrangements of aromatic amino acids with the nucleobases at the junction core. This conformational heterogeneity may inhibit DNA processing by increasing the population of inactive junction conformations, thereby preventing the binding of processing enzymes and/or resulting in their premature dissociation.
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Affiliation(s)
- Brian Cannon
- From the Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712
| | - Aashiq H Kachroo
- From the Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712
| | - Inga Jarmoskaite
- From the Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712
| | - Makkuni Jayaram
- From the Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712
| | - Rick Russell
- From the Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712
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15
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Mavrogiannopoulou E, Petrou PS, Koukouvinos G, Yannoukakos D, Siafaka-Kapadai A, Fornal K, Awsiuk K, Budkowski A, Kakabakos SE. Improved DNA microarray detection sensitivity through immobilization of preformed in solution streptavidin/biotinylated oligonucleotide conjugates. Colloids Surf B Biointerfaces 2015; 128:464-472. [PMID: 25805150 DOI: 10.1016/j.colsurfb.2015.02.045] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 02/24/2015] [Accepted: 02/25/2015] [Indexed: 11/18/2022]
Abstract
A novel immobilization approach involving binding of preformed streptavidin/biotinylated oligonucleotide conjugates onto surfaces coated with biotinylated bovine serum albumin is presented. Microarrays prepared according to the proposed method were compared, in terms of detection sensitivity and specificity, with other immobilization schemes employing coupling of biotinylated oligonucleotides onto directly adsorbed surface streptavidin, or sequential coupling of streptavidin and biotinylated oligonucleotides onto a layer of adsorbed biotinylated bovine serum albumin. A comparison was performed employing biotinylated oligonucleotides corresponding to wild- and mutant-type sequences of seven single point mutations of the BRCA1 gene. With respect to the other immobilization protocols, the proposed oligonucleotide immobilization approach offered the highest hybridization signals (at least 5 times higher) and permitted more elaborative washings, thus providing considerably higher discrimination between complimentary and non-complementary DNA sequences for all mutations tested. In addition, the hybridization kinetics were significantly enhanced compared to two other immobilization protocols, permitting PCR sample analysis in less than 40 min. Thus, the proposed oligonucleotide immobilization approach offered improved detection sensitivity and discrimination ability along with considerably reduced analysis time, and it is expected to find wide application in DNA mutation detection.
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Affiliation(s)
- E Mavrogiannopoulou
- Immunoassay/Immunosensors Lab, Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, NCSR "Demokritos", GR-15310 Aghia Paraskevi, Greece
| | - P S Petrou
- Immunoassay/Immunosensors Lab, Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, NCSR "Demokritos", GR-15310 Aghia Paraskevi, Greece
| | - G Koukouvinos
- Immunoassay/Immunosensors Lab, Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, NCSR "Demokritos", GR-15310 Aghia Paraskevi, Greece
| | - D Yannoukakos
- Molecular Diagnostics Lab, Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, NCSR "Demokritos", GR-15310 Aghia Paraskevi, Greece
| | - A Siafaka-Kapadai
- Biochemistry Lab, Department of Chemistry, University of Athens, GR-15771 Panepistimiopolis, Athens, Greece
| | - K Fornal
- M. Smoluchowski Institute of Physics, Jagiellonian University, Reymonta 4, 30-059 Kraków, Poland
| | - K Awsiuk
- M. Smoluchowski Institute of Physics, Jagiellonian University, Reymonta 4, 30-059 Kraków, Poland
| | - A Budkowski
- M. Smoluchowski Institute of Physics, Jagiellonian University, Reymonta 4, 30-059 Kraków, Poland
| | - S E Kakabakos
- Immunoassay/Immunosensors Lab, Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, NCSR "Demokritos", GR-15310 Aghia Paraskevi, Greece.
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Li B, Lai H, Wei Y, Wang X, Chen Y, Zou M, Duan Y. Competitive immunoassay combined with magnetic separation and pulsed LIF system for cefalexin detection. RSC Adv 2014. [DOI: 10.1039/c4ra08105f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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17
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Qiu W, Xu H, Takalkar S, Gurung AS, Liu B, Zheng Y, Guo Z, Baloda M, Baryeh K, Liu G. Carbon nanotube-based lateral flow biosensor for sensitive and rapid detection of DNA sequence. Biosens Bioelectron 2014; 64:367-72. [PMID: 25262062 DOI: 10.1016/j.bios.2014.09.028] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Revised: 09/04/2014] [Accepted: 09/14/2014] [Indexed: 01/31/2023]
Abstract
In this article, we describe a carbon nanotube (CNT)-based lateral flow biosensor (LFB) for rapid and sensitive detection of DNA sequence. Amine-modified DNA detection probe was covalently immobilized on the shortened multi-walled carbon nanotubes (MWCNTs) via diimide-activated amidation between the carboxyl groups on the CNT surface and amine groups on the detection DNA probes. Sandwich-type DNA hybridization reactions were performed on the LFB and the captured MWCNTs on test zone and control zone of LFB produced the characteristic black bands, enabling visual detection of DNA sequences. Combining the advantages of lateral flow chromatographic separation with unique physical properties of MWCNT (large surface area), the optimized LFB was capable of detecting of 0.1 nM target DNA without instrumentation. Quantitative detection could be realized by recording the intensity of the test line with the Image J software, and the detection limit of 40 pM was obtained. This detection limit is 12.5 times lower than that of gold nanoparticle (GNP)-based LFB (0.5 nM, Mao et al. Anal. Chem. 2009, 81, 1660-1668). Another important feature is that the preparation of MWCNT-DNA conjugates was robust and the use of MWCNT labels avoided the aggregation of conjugates and tedious preparation time, which were often met in the traditional GNP-based nucleic acid LFB. The applications of MWCNT-based LFB can be extended to visually detect protein biomarkers using MWCNT-antibody conjugates. The MWCNT-based LFB thus open a new door to prepare a new generation of LFB, and shows great promise for in-field and point-of-care diagnosis of genetic diseases and for the detection of infectious agents.
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Affiliation(s)
- Wanwei Qiu
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, PR China; Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58105, United States
| | - Hui Xu
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, PR China; Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58105, United States
| | - Sunitha Takalkar
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58105, United States
| | - Anant S Gurung
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58105, United States
| | - Bin Liu
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, PR China.
| | - Yafeng Zheng
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, PR China; Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58105, United States
| | - Zebin Guo
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, PR China; Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58105, United States
| | - Meenu Baloda
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58105, United States
| | - Kwaku Baryeh
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58105, United States
| | - Guodong Liu
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, PR China; Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58105, United States.
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