1
|
Nguyen TNP, Nguyen SH, Tran MT. Disposable impedance sensors based on novel hybrid MoS2 nanosheets and microparticles to detect Escherichia Coli DNA. PLoS One 2024; 19:e0299272. [PMID: 38422053 PMCID: PMC10903914 DOI: 10.1371/journal.pone.0299272] [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: 11/22/2023] [Accepted: 02/06/2024] [Indexed: 03/02/2024] Open
Abstract
The rapid and accurate detection of pathogenic bacteria is essential for food safety and public health. Conventional detection techniques, such as nucleic acid sequence-based amplification and polymerase chain reaction, are time-consuming and require specialized equipment and trained personnel. Here, we present quick, disposable impedance sensors based on the novel hybrid MoS2 nanomaterial for detecting Escherichia coli DNA. Our results indicate that the proposed sensors operate linearly between 10- 20 and 10-15 M concentrations, achieving an impressive detection limit of 10-20 M with the highest sensitivity observed at a 0.325 nM probe concentration sensor. Furthermore, the electrochemical impedance spectroscopy biosensors exhibited potential selectivity for Escherichia coli DNA over Bacillus subtilis and Vibrio proteolyticus DNA sequences. The findings offer a promising avenue for efficient and precise DNA detection, with potential implications for broader biotechnology and medical diagnostics applications.
Collapse
Affiliation(s)
- Tien Ngoc Phuc Nguyen
- College of Engineering and Computer Science, VinUniversity, Hanoi, Vietnam
- VinUni-Illinois Smart Health Center, VinUniversity, Hanoi, Vietnam
| | - Son Hai Nguyen
- School of Mechanical Engineering, Hanoi University of Science and Technology, Hanoi, Vietnam
| | - Mai Thi Tran
- College of Engineering and Computer Science, VinUniversity, Hanoi, Vietnam
- VinUni-Illinois Smart Health Center, VinUniversity, Hanoi, Vietnam
| |
Collapse
|
2
|
Zhang Z, Zhang L, Liu Y, Hu C, Liu Q. Sensitive DNA Detection using a Branched DNA as a Sensor Coupled with Hybridization Chain Reaction. ChemistrySelect 2022. [DOI: 10.1002/slct.202201891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Zhikun Zhang
- School of Chemical and Pharmaceutical Engineering Hebei University of Science and Technology Shijiazhuang 050018 China
| | - Liu Zhang
- School of Chemical and Pharmaceutical Engineering Hebei University of Science and Technology Shijiazhuang 050018 China
| | - Yumin Liu
- School of Chemical and Pharmaceutical Engineering Hebei University of Science and Technology Shijiazhuang 050018 China
| | - Cuixia Hu
- School of Chemical and Pharmaceutical Engineering Hebei University of Science and Technology Shijiazhuang 050018 China
| | - Qingju Liu
- Beijing Research Center for Agriculture Standards and Testing Beijing Academy of Agriculture and Forestry Sciences Beijing 100097 China
| |
Collapse
|
3
|
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: 14] [Impact Index Per Article: 4.7] [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.
Collapse
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
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Cao Y, Zheng Z, Monbouquette HG. Nucleic acid amplification-free detection of DNA and RNA at ultralow concentration. Curr Opin Biotechnol 2021; 71:145-150. [PMID: 34375812 DOI: 10.1016/j.copbio.2021.07.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 07/14/2021] [Accepted: 07/18/2021] [Indexed: 02/04/2023]
Abstract
The broad spectrum of approaches for nucleic acid amplification-free detection of DNA and RNA at single-digit attomolar (10-18 M) concentration and lower is reviewed. These low concentrations correspond roughly to the most clinically desirable detection range for pathogen-specific nucleic acid as well as the detection limits of commercially available, nucleic acid amplification tests based primarily on polymerase chain reaction (PCR). The need for more rapid and inexpensive, yet still highly accurate tests, has become evident during the pandemic. It is expected that publication of reports describing improved tests will accelerate soon, and this review covers the wide variety of detection methods based on both optical and electrical measurements that have been conceived over recent years, enabled generally by the advent of nanotechnology.
Collapse
Affiliation(s)
- Yan Cao
- Chemical and Biomolecular Engineering Department, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Zhenrong Zheng
- Chemical and Biomolecular Engineering Department, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Harold G Monbouquette
- Chemical and Biomolecular Engineering Department, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| |
Collapse
|
6
|
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]
|
7
|
Koo B, Yorita AM, Schmidt JJ, Monbouquette HG. Amplification-free, sequence-specific 16S rRNA detection at 1 aM. LAB ON A CHIP 2018; 18:2291-2299. [PMID: 29987290 DOI: 10.1039/c8lc00452h] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A nucleic acid amplification-free, optics-free platform has been demonstrated for sequence-specific detection of Escherichia coli (E. coli) 16S rRNA at 1 aM (10-18 M) against a 106-fold (1 pM) background of Pseudomonas putida (P. putida) RNA. This work was driven by the need for simple, rapid, and low cost means for species-specific bacterial detection at low concentration. Our simple, conductometric sensing device functioned by detecting blockage of a nanopore fabricated in a sub-micron-thick glass membrane. Upon sequence-specific binding of target 16S rRNA, otherwise charge-neutral, PNA oligonucleotide probe-polystyrene bead conjugates become electrophoretically mobile and are driven to the glass nanopore of lesser diameter, which is blocked, thereby generating a large, sustained and readily observable step decrease in ionic current. No false positive signals were observed with P. putida RNA when this device was configured to detect E. coli 16S rRNA. Also, when a universal PNA probe complementary to the 16S rRNA of both E. coli and P. putida was conjugated to beads, a positive response to rRNA of both bacterial species was observed. Finally, the device readily detected E. coli at 10 CFU mL-1 in a 1 mL sample, also against a million-fold background of viable P. putida. These results suggest that this new device may serve as the basis for small, portable, low power, and low-cost systems for rapid detection of specific bacterial species in clinical samples, food, and water.
Collapse
Affiliation(s)
- Bonhye Koo
- Chemical and Biomolecular Engineering Department, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | | | | | | |
Collapse
|
8
|
Kuralay F, Dükar N, Bayramlı Y. Poly-L-lysine Coated Surfaces for Ultrasensitive Nucleic Acid Detection. ELECTROANAL 2018; 30:1556-1565. [PMID: 32313411 PMCID: PMC7163579 DOI: 10.1002/elan.201800153] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 05/01/2018] [Indexed: 01/28/2023]
Abstract
Poly-L-lysine is one of the biocompatible polymers having amino and carboxyl groups in its structure. This attractive feature of poly-L-lysine makes it very convenient for bioactive molecule attachment. This study details the preparation of poly-L-lysine-based pencil graphite electrodes (PLL/PGEs) and use of the coated electrodes for direct ultrasensitive DNA hybridization detection. In the first part of this study, poly-L-lysine coated electrodes were prepared using L-lysine as the monomer by cyclic voltammetry (CV) with different cyclic scans. The effect of these cyclic scans during the electropolymerization was investigated. Coated electrodes were characterized by cyclic voltammetry, electrochemical impedance spectroscopy (EIS) and scanning electron microscopy (SEM). Then, one-pot preparation of poly-L-lysine composites with graphene (GN) and multi-walled carbon nanotubes (MWCNTs) onto the pencil graphite electrodes were achieved. Electrochemical responses of these 3 electrodes were compared. After all, electrochemical DNA hybridization was performed using the poly-L-lysine-based electrodes prepared at optimum polymerization condition. The PLL/PGE coated electrode presented a good linear response in the target concentration range of 1.0×10-13 to 1.0×10-6 with a detection limit of 2.25×10-14 using differential pulse voltammetry as the detection method. We believe that poly-L-lysine-based surfaces will be useful for further clinical applications.
Collapse
Affiliation(s)
- Filiz Kuralay
- Department of Chemistry, Faculty of Arts and SciencesOrdu University52200OrduTurkeyPhone: +90-452-2345010/1680Fax: +90-452-2339149
| | - Nilgün Dükar
- Department of Chemistry, Faculty of Arts and SciencesOrdu University52200OrduTurkeyPhone: +90-452-2345010/1680Fax: +90-452-2339149
| | - Yaşar Bayramlı
- Department of Chemistry, Faculty of Arts and SciencesOrdu University52200OrduTurkeyPhone: +90-452-2345010/1680Fax: +90-452-2339149
- Espiye Vocational SchoolGiresun University28200GiresunTurkey
| |
Collapse
|
9
|
Jin X, Zhou L, Zhu B, Jiang X, Zhu N. Silver-dendrimer nanocomposites as oligonucleotide labels for electrochemical stripping detection of DNA hybridization. Biosens Bioelectron 2018; 107:237-243. [PMID: 29477124 DOI: 10.1016/j.bios.2018.02.033] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 01/30/2018] [Accepted: 02/12/2018] [Indexed: 01/07/2023]
Abstract
Silver-dendrimer nanocomposites were synthesized and used as oligonucleotide labels for electrochemical stripping detection of DNA hybridization. The synthesized silver-dendrimer nanocomposites were characterized by UV-vis spectrophotometry, X-ray photoelectron spectroscopy (XPS) and transmission electron microscopy (TEM). Ratios of silver/dendrimer were optimized in order to obtain stable nanocomposites with maximal silver loading in the interior of a polymeric shell. The silver-dendrimer nanocomposites were attached to sequence-known DNA probes specific to colitoxin, and used to detect probe hybridization by dissolution of the silver nanoparticles in the interior of dendrimer in a diluted nitric acid, followed by measurement of Ag+ ions by anodic stripping voltammetry (ASV). Use of differential pulse voltammetry for the stripping step, along with optimization of the ASV conditions, enabled a detection limit of 0.78 pM. The present strategy, in combination with dendrimer-encapsulated copper labeled oligonucleotides probe reported previously, could potentially be used to detect single or multiple DNA targets in one sample.
Collapse
Affiliation(s)
- Xin Jin
- Department of Chemistry, College of Life and Environment Sciences, Shanghai Normal University, Guilin Road 100, Shanghai 200234, China
| | - Ling Zhou
- Department of Chemistry, College of Life and Environment Sciences, Shanghai Normal University, Guilin Road 100, Shanghai 200234, China
| | - Bo Zhu
- Department of Chemistry, College of Life and Environment Sciences, Shanghai Normal University, Guilin Road 100, Shanghai 200234, China
| | - Xue Jiang
- Department of Chemistry, College of Life and Environment Sciences, Shanghai Normal University, Guilin Road 100, Shanghai 200234, China
| | - Ningning Zhu
- Department of Chemistry, College of Life and Environment Sciences, Shanghai Normal University, Guilin Road 100, Shanghai 200234, China.
| |
Collapse
|