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Adil O, Eddington SB, Gagnon KT, Shamsi MH. Microprobes for Label-Free Detection of Short Tandem Repeats: An Insight into Alleviating Secondary Structure Effects. Anal Chem 2023; 95:13528-13536. [PMID: 37651633 DOI: 10.1021/acs.analchem.3c01886] [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: 09/02/2023]
Abstract
Overgrowth of short tandem repeat sequences in our genes can cause various neurodegenerative disorders. Such repeat sequences are ideal targets for the label-free electrochemical detection of such potential expansions. However, their length- and sequence-dependent secondary structures may interfere with the interfacial charge transfer of a detection platform, making them complex targets. In addition, the gene contains sporadic repeats that may result in false-positive signals. Therefore, it is necessary to design a platform capable of mitigating these effects and ultimately enhancing the specificity of tandem repeats. Here, we analyzed three different backbones of nucleic acid microprobes [DNA, peptide nucleic acid, and lock-nucleic acid (LNA)] to detect in vitro transcribed RNA carrying CAG repeats, which are associated with Huntington's disease, based on the charge-transfer resistance of the interface. We found that the LNA microprobe can distinguish lengths down to the attomolar concentration level and alleviate the effect of secondary structures and sporadic repeats in the sequence, thus distinguishing the "tandem repeats" specifically. Additionally, the control experiments conducted with and without Mg2+ demonstrated the LNA microprobe to perform better in the presence of the divalent cation. The results suggest that the LNA-based platform may eventually lead to the development of a reliable and straightforward biosensor for genetic neurodegenerative disorders.
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Affiliation(s)
- Omair Adil
- School of Chemical and Biomolecular Sciences, 1245 Lincoln Dr, Southern Illinois University at Carbondale, Carbondale, Illinois 62901, United States
| | - Seth B Eddington
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27101, United States
| | - Keith T Gagnon
- School of Chemical and Biomolecular Sciences, 1245 Lincoln Dr, Southern Illinois University at Carbondale, Carbondale, Illinois 62901, United States
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27101, United States
| | - Mohtashim H Shamsi
- School of Chemical and Biomolecular Sciences, 1245 Lincoln Dr, Southern Illinois University at Carbondale, Carbondale, Illinois 62901, United States
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Asefifeyzabadi N, Durocher G, Tshilenge KT, Alam T, Ellerby LM, Shamsi MH. PNA microprobe for label-free detection of expanded trinucleotide repeats. RSC Adv 2022; 12:7757-7761. [PMID: 35424746 PMCID: PMC8982460 DOI: 10.1039/d2ra00230b] [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: 01/12/2022] [Accepted: 03/03/2022] [Indexed: 11/28/2022] Open
Abstract
We present a PNA microprobe sensing platform to detect trinucleotide repeat mutation by electrochemical impedance spectroscopy. The microprobe platform discriminated Huntington's disease-associated CAG repeats in cell-derived total RNA with S/N 1 : 3. This sensitive, label-free, and PCR-free detection strategy may be employed in the future to develop biosensing platforms for the detection of a plethora of repeat expansion disorders.
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Affiliation(s)
- Narges Asefifeyzabadi
- School of Chemical and Biomolecular Sciences, 1245 Lincoln Dr, Southern Illinois University at Carbondale IL 62901 USA
| | - Grace Durocher
- School of Chemical and Biomolecular Sciences, 1245 Lincoln Dr, Southern Illinois University at Carbondale IL 62901 USA
| | | | - Tanimul Alam
- The Buck Institute for Research on Aging 8001 Redwood Blvd Novato CA 94945 USA
| | - Lisa M Ellerby
- The Buck Institute for Research on Aging 8001 Redwood Blvd Novato CA 94945 USA
| | - Mohtashim H Shamsi
- School of Chemical and Biomolecular Sciences, 1245 Lincoln Dr, Southern Illinois University at Carbondale IL 62901 USA
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3
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Wannapob R, Chuaychob S, Fujita M, Maeda M. Electrochemical Impedimetric Study of Non-Watson-Crick Base Pairs of DNA. ANAL SCI 2021; 37:765-771. [PMID: 33487601 DOI: 10.2116/analsci.20scp21] [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: 11/23/2022]
Abstract
Electrochemical impedance spectroscopy (EIS) was used to detect non-Watson-Crick base pairs of DNA. Thiol-modified DNA as a probe and mercaptohexanol (MCH) were co-immobilized to form a DNA/MCH mixed self-assembled monolayer on a gold electrode surface and then hybridized with complementary DNAs. The DNA layers were measured by the EIS method and interpreted by equivalent circuits. Every terminal base mismatch of the DNA duplex brought about an increase in the charge-transfer resistance (Rct), unlike the case with a fully matched DNA duplex. The value of Rct was highly sensitive to the number of base mismatches for both unpaired and overhang DNA at the terminal. For internal base mismatches, however, no significant increase in Rct was observed. These experimental results proved that the charge transfer of redox molecules to the electrode surface is largely hindered by an end fraying motion due to base unpairing and dangling overhang. EIS was able to detect these steric properties of DNA strands. Furthermore, an electrode modified with G-quadruplex (G4) DNA demonstrated the influences of bulkiness and loop structure on the accessibility of the redox probe to the electrode.
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Affiliation(s)
| | - Surachada Chuaychob
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research.,Graduate School of Frontier Sciences, The University of Tokyo
| | - Masahiro Fujita
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research
| | - Mizuo Maeda
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research.,Graduate School of Frontier Sciences, The University of Tokyo
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Asefifeyzabadi N, Alkhaldi R, Qamar AZ, Pater AA, Patwardhan M, Gagnon KT, Talapatra S, Shamsi MH. Label-free Electrochemical Detection of CGG Repeats on Inkjet Printable 2D Layers of MoS 2. ACS APPLIED MATERIALS & INTERFACES 2020; 12:52156-52165. [PMID: 33151065 DOI: 10.1021/acsami.0c14912] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Flexible and ultrasensitive biosensing platforms capable of detecting a large number of trinucleotide repeats (TNRs) are crucial for future technology development needed to combat a variety of genetic disorders. For example, trinucleotide CGG repeat expansions in the FMR1 gene can cause Fragile X syndrome (FXS) and Fragile X-associated tremor/ataxia syndrome (FXTAS). Current state-of-the-art technologies to detect repeat sequences are expensive, while relying on complicated procedures, and prone to false negatives. We reasoned that two-dimensional (2D) molybdenum sulfide (MoS2) surfaces may be useful for label-free electrochemical detection of CGG repeats due to its high affinity for guanine bases. Here, we developed a low-cost and sensitive wax-on-plastic electrochemical sensor using 2D MoS2 ink for the detection of CGG repeats. The ink containing few-layered MoS2 nanosheets was prepared and characterized using optical, electrical, electrochemical, and electron microscopic methods. The devices were characterized by electron microscopic and electrochemical methods. Repetitive CGG DNA was adsorbed on a MoS2 surface in a high cationic strength environment and the electrocatalytic current of the CGG/MoS2 interface was recorded using a soluble Fe(CN)6-3/-4 redox probe by differential pulse voltammetry (DPV). The dynamic range for the detection of prehybridized duplexes ranged from 1 aM to 100 nM with a 3.0 aM limit of detection. A detection range of 100 fM to 1 nM was recorded for surface hybridization events. Using this method, we were able to observe selectivity of MoS2 for CGG repeats and distinguish nonpathogenic from disease-associated repeat lengths. The detection of CGG repeat sequences on inkjet printable 2D MoS2 surfaces is a forward step toward developing chip-based rapid and label-free sensors for the detection of repeat expansion sequences.
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Affiliation(s)
- Narges Asefifeyzabadi
- Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois 62901, United States
| | - Rana Alkhaldi
- Department of Physics, Southern Illinois University, Carbondale, Illinois 62901, United States
| | - Ahmad Z Qamar
- Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois 62901, United States
| | - Adrian A Pater
- Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois 62901, United States
| | - Meera Patwardhan
- Department of Chemistry, Kalamazoo College, Kalamazoo, Michigan 62901, United States
| | - Keith T Gagnon
- Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois 62901, United States
- Department of Biochemistry and Molecular Biology, School of Medicine, Southern Illinois University, Carbondale, Illinois 62901, United States
| | - Saikat Talapatra
- Department of Physics, Southern Illinois University, Carbondale, Illinois 62901, United States
| | - Mohtashim H Shamsi
- Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois 62901, United States
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Asefifeyzabadi N, Taki M, Funneman M, Song T, Shamsi MH. Unique sequence-dependent properties of trinucleotide repeat monolayers: electrochemical, electrical, and topographic characterization. J Mater Chem B 2020; 8:5225-5233. [DOI: 10.1039/d0tb00507j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The sequence-dependent properties of the surface-assembled trinucleotide repeat interface on a gold surface were explored by electrochemical methods and surface probe microscopy.
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Affiliation(s)
- Narges Asefifeyzabadi
- Department of Chemistry & Biochemistry
- 1245 Lincoln Dr
- Southern Illinois University at Carbondale
- USA
| | - Motahareh Taki
- Department of Chemistry & Biochemistry
- 1245 Lincoln Dr
- Southern Illinois University at Carbondale
- USA
| | - Madison Funneman
- Department of Chemistry & Biochemistry
- 1245 Lincoln Dr
- Southern Illinois University at Carbondale
- USA
| | - Tingjie Song
- Department of Chemistry
- University of Illinois at Urbana-Champaign
- USA
| | - Mohtashim Hassan Shamsi
- Department of Chemistry & Biochemistry
- 1245 Lincoln Dr
- Southern Illinois University at Carbondale
- USA
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Lahiri H, Banerjee S, Mukhopadhyay R. Free-Energy-Based Gene Mutation Detection Using LNA Probes. ACS Sens 2019; 4:2688-2696. [PMID: 31549503 DOI: 10.1021/acssensors.9b01115] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We have developed a label-free approach for direct detection of gene mutations using free-energy values that are derived from single-molecule force spectroscopy (SMFS)-based nucleic acid unbinding experiments. From the duplex unbinding force values acquired by SMFS, the force-loading-rate-independent Gibbs free-energy values were derived using Jarzinsky's equality treatment. Because it provides molecule-by-molecule information, this approach is a major shift compared to the earlier reports on label-free detection of DNA sequences, which are mostly based on ensemble level data. We tested our approach in the disease model framework of multiple drug-resistant tuberculosis using the nuclease-resistant and conformationally rigid locked nucleic acid probes that are a robust and efficient alternative to the DNA probes. All of the major mutations in Mycobacterium tuberculosis (MTB), as relevant to MTB's resistance to the first-line anti-TB drugs rifampicin and isoniazid, could be identified, and the wild type could be discriminated from the most prevalent mutation and the most prevalent mutation from the less occurring ones. Our approach could also identify DNA sequences (45 mer), having overhang stretches at different positions with respect to the complementary stretch. Probably for the first time, the findings show that free-energy-based detection of gene mutations is possible at molecular resolution.
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Affiliation(s)
- Hiya Lahiri
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata 700 032, India
| | - Siddhartha Banerjee
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata 700 032, India
| | - Rupa Mukhopadhyay
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata 700 032, India
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7
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Taki M, Rohilla KJ, Barton M, Funneman M, Benzabeh N, Naphade S, Ellerby LM, Gagnon KT, Shamsi MH. Novel probes for label-free detection of neurodegenerative GGGGCC repeats associated with amyotrophic lateral sclerosis. Anal Bioanal Chem 2019; 411:6995-7003. [PMID: 31435686 PMCID: PMC7433021 DOI: 10.1007/s00216-019-02075-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/18/2019] [Accepted: 08/06/2019] [Indexed: 01/28/2023]
Abstract
DNA repeat expansion sequences cause a myriad of neurological diseases when they expand beyond a critical threshold. Previous electrochemical approaches focused on the detection of trinucleotide repeats (CAG, CGG, and GAA) and relied on labeling of the probe and/or target strands or enzyme-linked assays. However, detection of expanded GC-rich sequences is challenging because they are prone to forming secondary structures such as cruciforms and quadruplexes. Here, we present label-free detection of hexanucleotide GGGGCC repeat sequences, which cause the leading genetic form of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS). The approach relies on capturing targets by surface-bound oligonucleotide probes with a different number of complementary repeats, which proportionately translates the length of the target strands into charge transfer resistance (RCT) signal measured by electrochemical impedance spectroscopy. The probe carrying three tandem repeats transduces the number of repeats into RCT with a 3× higher calibration sensitivity and detection limit. Chronocoulometric measurements show a decrease in surface density with increasing repeat length, which is opposite of the impedance trend. This implies that the length of the target itself can contribute to amplification of the impedance signal independent of the surface density. Moreover, the probe can distinguish between a control and patient sequences while remaining insensitive to non-specific Huntington's disease (CAG) repeats in the presence of a complementary target. This label-free strategy might be applied to detect the length of other neurodegenerative repeat sequences using short probes with a few complementary repeats. Graphical abstract Short oligomeric probes with multiple complementary repeats detect long neurodegenerative targets with high sensitivity and transduce into higher impedance signal.
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Affiliation(s)
- Motahareh Taki
- Department of Chemistry & Biochemistry, Southern Illinois University, 1245 Lincoln Dr, Carbondale, IL, 62901, USA
| | - Kushal J Rohilla
- Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL, 62901, USA
| | - Maria Barton
- Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL, 62901, USA
| | - Madison Funneman
- Department of Chemistry & Biochemistry, Southern Illinois University, 1245 Lincoln Dr, Carbondale, IL, 62901, USA
| | - Najiyah Benzabeh
- Department of Chemistry & Biochemistry, Southern Illinois University, 1245 Lincoln Dr, Carbondale, IL, 62901, USA
| | - Swati Naphade
- The Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, CA, 94945, USA
| | - Lisa M Ellerby
- The Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, CA, 94945, USA
| | - Keith T Gagnon
- Department of Chemistry & Biochemistry, Southern Illinois University, 1245 Lincoln Dr, Carbondale, IL, 62901, USA
- Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL, 62901, USA
| | - Mohtashim H Shamsi
- Department of Chemistry & Biochemistry, Southern Illinois University, 1245 Lincoln Dr, Carbondale, IL, 62901, USA.
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Ultrasensitive Electrochemical Detection of Clostridium perfringens DNA Based Morphology-Dependent DNA Adsorption Properties of CeO₂ Nanorods in Dairy Products. SENSORS 2018; 18:s18061878. [PMID: 29890646 PMCID: PMC6022109 DOI: 10.3390/s18061878] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 06/04/2018] [Accepted: 06/06/2018] [Indexed: 01/04/2023]
Abstract
Foodborne pathogens such as Clostridium perfringens can cause diverse illnesses and seriously threaten to human health, yet far less attention has been given to detecting these pathogenic bacteria. Herein, two morphologies of nanoceria were synthesized via adjusting the concentration of NaOH, and CeO₂ nanorod has been utilized as sensing material to achieve sensitive and selective detection of C. perfringens DNA sequence due to its strong adsorption ability towards DNA compared to nanoparticle. The DNA probe was tightly immobilized on CeO₂/chitosan modified electrode surface via metal coordination, and the DNA surface density was 2.51 × 10−10 mol/cm². Under optimal experimental conditions, the electrochemical impedance biosensor displays favorable selectivity toward target DNA in comparison with base-mismatched and non-complementary DNA. The dynamic linear range of the proposed biosensor for detecting oligonucleotide sequence of Clostridium perfringens was from 1.0 × 10−14 to 1.0 × 10−7 mol/L. The detection limit was 7.06 × 10−15 mol/L. In comparison, differential pulse voltammetry (DPV) method quantified the target DNA with a detection limit of 1.95 × 10−15 mol/L. Moreover, the DNA biosensor could detect C. perfringens extracted DNA in dairy products and provided a potential application in food quality control.
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Corrigan D, Schulze H, Ciani I, Henihan G, Mount A, Bachmann T. Improving performance of a rapid electrochemical MRSA assay: Optimisation of assay conditions to achieve enhanced discrimination of clinically important DNA sequences under ambient conditions. J Electroanal Chem (Lausanne) 2017. [DOI: 10.1016/j.jelechem.2016.12.050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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10
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Thipmanee O, Numnuam A, Limbut W, Buranachai C, Kanatharana P, Vilaivan T, Hirankarn N, Thavarungkul P. Enhancing capacitive DNA biosensor performance by target overhang with application on screening test of HLA-B*58:01 and HLA-B*57:01 genes. Biosens Bioelectron 2016; 82:99-104. [PMID: 27054813 DOI: 10.1016/j.bios.2016.03.065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 03/12/2016] [Accepted: 03/24/2016] [Indexed: 10/22/2022]
Abstract
A highly sensitive label-free DNA biosensor based on PNA probes immobilized on a gold electrode was used to detect a hybridization event. The effect of a target DNA overhang on the hybridization efficiency was shown to enhance the detected signal and allowed detection at a very low concentration. The sensors performances were investigated with a complementary target that had the same length as the probe, and the signal was compared to the target DNAs with different lengths and overhangs. A longer target DNA overhang was found to provide a better response. When the overhang was on the electrode side the signal enhancement was greater than when the overhang was on the solution side due to the increased thickness of the sensing surface, hence produced a larger capacitance change. Using conformationally constrained acpcPNA probes, double stranded DNA was detected sensitively and specifically without any denaturing step. When two acpcPNA probes were applied for the screening test for the double stranded HLA-B*58:01 and HLA-B*57:01 genes that are highly similar, the method differentiated the two genes in all samples. Both purified and unpurified PCR products gave comparable results. This method would be potentially useful as a rapid screening test without the need for purification and denaturation of the PCR products.
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Affiliation(s)
- Orawan Thipmanee
- Trace Analysis and Biosensor Research Center, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand; Center of Excellence for Innovation in Chemistry, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand; Department of Chemistry, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand
| | - Apon Numnuam
- Trace Analysis and Biosensor Research Center, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand; Center of Excellence for Innovation in Chemistry, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand; Department of Chemistry, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand
| | - Warakorn Limbut
- Trace Analysis and Biosensor Research Center, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand; Center of Excellence for Innovation in Chemistry, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand; Department of Applied Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand
| | - Chittanon Buranachai
- Trace Analysis and Biosensor Research Center, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand; Department of Physics, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand
| | - Proespichaya Kanatharana
- Trace Analysis and Biosensor Research Center, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand; Center of Excellence for Innovation in Chemistry, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand; Department of Chemistry, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Nattiya Hirankarn
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; Center of Excellence in Immunology and Immune-Mediated Diseases, Chulalongkorn University, Bangkok 10330, Thailand.
| | - Panote Thavarungkul
- Trace Analysis and Biosensor Research Center, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand; Center of Excellence for Innovation in Chemistry, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand; Department of Physics, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand.
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Rafiee-Pour HA, Behpour M, Keshavarz M. A novel label-free electrochemical miRNA biosensor using methylene blue as redox indicator: application to breast cancer biomarker miRNA-21. Biosens Bioelectron 2016; 77:202-7. [DOI: 10.1016/j.bios.2015.09.025] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 09/03/2015] [Accepted: 09/10/2015] [Indexed: 11/28/2022]
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12
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Noor MO, Hrovat D, Moazami-Goudarzi M, Espie GS, Krull UJ. Ratiometric fluorescence transduction by hybridization after isothermal amplification for determination of zeptomole quantities of oligonucleotide biomarkers with a paper-based platform and camera-based detection. Anal Chim Acta 2015; 885:156-65. [PMID: 26231901 DOI: 10.1016/j.aca.2015.05.026] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 05/08/2015] [Accepted: 05/14/2015] [Indexed: 11/27/2022]
Abstract
Paper is a promising platform for the development of decentralized diagnostic assays owing to the low cost and ease of use of paper-based analytical devices (PADs). It can be challenging to detect on PADs very low concentrations of nucleic acid biomarkers of lengths as used in clinical assays. Herein we report the use of thermophilic helicase-dependent amplification (tHDA) in combination with a paper-based platform for fluorescence detection of probe-target hybridization. Paper substrates were patterned using wax printing. The cellulosic fibers were chemically derivatized with imidazole groups for the assembly of the transduction interface that consisted of immobilized quantum dot (QD)-probe oligonucleotide conjugates. Green-emitting QDs (gQDs) served as donors with Cy3 as the acceptor dye in a fluorescence resonance energy transfer (FRET)-based transduction method. After probe-target hybridization, a further hybridization event with a reporter sequence brought the Cy3 acceptor dye in close proximity to the surface of immobilized gQDs, triggering a FRET sensitized emission that served as an analytical signal. Ratiometric detection was evaluated using both an epifluorescence microscope and a low-cost iPad camera as detectors. Addition of the tHDA method for target amplification to produce sequences of ∼100 base length allowed for the detection of zmol quantities of nucleic acid targets using the two detection platforms. The ratiometric QD-FRET transduction method not only offered improved assay precision, but also lowered the limit of detection of the assay when compared with the non-ratiometric QD-FRET transduction method. The selectivity of the hybridization assays was demonstrated by the detection of single nucleotide polymorphism.
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Affiliation(s)
- M Omair Noor
- Chemical Sensors Group, Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
| | - David Hrovat
- Chemical Sensors Group, Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
| | - Maryam Moazami-Goudarzi
- Department of Cell and Systems Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
| | - George S Espie
- Department of Cell and Systems Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada; Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
| | - Ulrich J Krull
- Chemical Sensors Group, Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada.
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Rackus DG, Shamsi MH, Wheeler AR. Electrochemistry, biosensors and microfluidics: a convergence of fields. Chem Soc Rev 2015; 44:5320-40. [PMID: 25962356 DOI: 10.1039/c4cs00369a] [Citation(s) in RCA: 188] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Electrochemistry, biosensors and microfluidics are popular research topics that have attracted widespread attention from chemists, biologists, physicists, and engineers. Here, we introduce the basic concepts and recent histories of electrochemistry, biosensors, and microfluidics, and describe how they are combining to form new application-areas, including so-called "point-of-care" systems in which measurements traditionally performed in a laboratory are moved into the field. We propose that this review can serve both as a useful starting-point for researchers who are new to these topics, as well as being a compendium of the current state-of-the art for experts in these evolving areas.
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Affiliation(s)
- Darius G Rackus
- Department of Chemistry, University of Toronto, 80 St. George St., Toronto, ON M5S 3H6, Canada.
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14
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Nowicka AM, Fau M, Rapecki T, Donten M. Polypyrrole-Au Nanoparticles Composite as Suitable Platform for DNA Biosensor with Electrochemical Impedance Spectroscopy Detection. Electrochim Acta 2014. [DOI: 10.1016/j.electacta.2014.03.187] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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15
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Kowalczyk A, Fau M, Karbarz M, Donten M, Stojek Z, Nowicka AM. Hydrogel with chains functionalized with carboxyl groups as universal 3D platform in DNA biosensors. Biosens Bioelectron 2014; 54:222-8. [DOI: 10.1016/j.bios.2013.11.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 11/04/2013] [Accepted: 11/05/2013] [Indexed: 11/28/2022]
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16
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Labib M, Ghobadloo SM, Khan N, Kolpashchikov DM, Berezovski MV. Four-Way Junction Formation Promoting Ultrasensitive Electrochemical Detection of MicroRNA. Anal Chem 2013; 85:9422-7. [DOI: 10.1021/ac402416z] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Mahmoud Labib
- Department
of Chemistry, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Shahrokh M. Ghobadloo
- Department
of Chemistry, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Nasrin Khan
- Department
of Chemistry, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Dmitry M. Kolpashchikov
- Department
of Chemistry, University of Central Florida, 4000 Central Blvd, Orlando, Florida 32816, United States
- The
Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida 32816, United States
| | - Maxim V. Berezovski
- Department
of Chemistry, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
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Howell C, Hamoudi H, Zharnikov M. Thymine/adenine diblock-oligonucleotide monolayers and hybrid brushes on gold: a spectroscopic study. Biointerphases 2013; 8:6. [PMID: 24706119 DOI: 10.1186/1559-4106-8-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 02/13/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The establishment of spectroscopic analysis techniques for complex, surface-bound biological systems is an important step toward the further application of these powerful experimental tools to new questions in biology and medicine. METHODS We use a combination of the complementary spectroscopic techniques of X-ray photoelectron spectroscopy, Infrared reflection-absorption spectroscopy, and near-edge x-ray absorption fine structure spectroscopy to monitor the composition and molecular orientation in adenine/thymine diblock oligonucleotide films and their hybridized brushes on gold. RESULTS We demonstrate that the surface-bound probe molecules, consisting of a binding adenine block, d(A), and a sensing thymine block, d(T), deviate from the ideal L-shape model due to the internal intra- and intermolecular hybridization. This effect becomes more pronounced with increasing length of the d(A) block. Nevertheless, these films were found to hybridize well with the complementary target d(A) strands, especially if they were treated in advance to reduce internal interaction between the molecules. In spite of the structural complexity of these films, the hybridization efficiency correlated well with the potential accessibility of the sensing d(T) blocks, defined by their lateral spacing. CONCLUSIONS These findings are a good demonstration of the strength of multi-technique spectroscopic analysis when applied to assemblies of biological molecules intrinsically prone to complex interactions.
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Affiliation(s)
- Caitlin Howell
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany,
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18
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Shamsi MH, Kraatz HB. Electrochemical signature of mismatch in overhang DNA films: a scanning electrochemical microscopic study. Analyst 2013; 138:3538-43. [DOI: 10.1039/c3an36810f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Alam MN, Shamsi MH, Kraatz HB. Scanning positional variations in single-nucleotide polymorphism of DNA: an electrochemical study. Analyst 2012; 137:4220-5. [DOI: 10.1039/c2an35420a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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20
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Yu ZG, Lai RY. A reagentless and reusable electrochemical DNA sensor based on target hybridization-induced stem-loop probe formation. Chem Commun (Camb) 2012; 48:10523-5. [DOI: 10.1039/c2cc35985e] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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21
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Huy TQ, Hanh NTH, Thuy NT, Chung PV, Nga PT, Tuan MA. A novel biosensor based on serum antibody immobilization for rapid detection of viral antigens. Talanta 2011; 86:271-7. [PMID: 22063541 PMCID: PMC7111752 DOI: 10.1016/j.talanta.2011.09.012] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Revised: 09/09/2011] [Accepted: 09/09/2011] [Indexed: 11/18/2022]
Abstract
In this paper, we represent a label-free biosensor based on immobilization of serum antibodies for rapid detection of viral antigens. Human serum containing specific antibodies against Japanese encephalitis virus (JEV) was immobilized on a silanized surface of an interdigitated sensor via protein A/glutaraldehyde for electrical detection of JEV antigens. The effective immobilization of serum antibodies on the sensor surface was verified by Fourier transform infrared spectrometry and fluorescence microscopy. The signal of the biosensor obtained by the differential voltage converted from the change into non-Faradic impedance resulting from the specific binding of JEV antigens on the surface of the sensor. The detection analyzed indicates that the detection range of this biosensor is 1-10 μg/ml JEV antigens, with a detection limit of 0.75 μg/ml and that stable signals are measured in about 20 min. This study presents a useful biosensor with a high selectivity for rapid and simple detection of JEV antigens, and it also proposes the biosensor as a future diagnostic tool for rapid and direct detection of viral antigens in clinical samples for preliminary pathogenic screenings in the case of possible outbreaks.
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Affiliation(s)
- Tran Quang Huy
- National Institute of Hygiene and Epidemiology (NIHE), 1 Yersin Street, Hanoi, Viet Nam.
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