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Yang F, Zhang X, Li S, Yu X, Liu S. Immobilization-free and label-free electrochemical DNA biosensing based on target-stimulated release of redox reporter and its catalytic redox recycling. Bioelectrochemistry 2024; 158:108727. [PMID: 38728815 DOI: 10.1016/j.bioelechem.2024.108727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 05/05/2024] [Accepted: 05/06/2024] [Indexed: 05/12/2024]
Abstract
Herein, we demonstrate a simple, homogenous and label-free electrochemical biosensing system for sensitive nucleic acid detection based on target-responsive porous materials and nuclease-triggered target recycling amplification. The Fe(CN)63- reporter was firstly sealed into the pores of Fe3O4 nanoparticles by probe DNA. Target DNA recognition triggered the controllable release of Fe(CN)63- for the redox reaction with the electron mediator of methylene blue enriched in the dodecanethiol assembled electrode and thereby generating electrochemical signal. The exonuclease III (Exo III)-assisted target recycling and the catalytic redox recycling between Fe(CN)63- and methylene blue contributed for the enhanced signal response toward target recognition. The low detection limit toward target was obtained as 478 fM and 1.6 pM, respectively, by square wave voltammetry and cyclic voltammetry methods. It also possessed a well-discrimination ability toward mismatched strands and high tolerance to complex sample matrix. The coupling of bio-gated porous nanoparticles, nuclease-assisted target amplification and catalytic redox recycling afforded the sensing system with well-controllable signal responses, sensitive and selective DNA detection, and good stability, reusability and reproducibility. It thus opens a new avenue toward the development of simple but sensitive electrochemical biosensing platform.
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Affiliation(s)
- Fangfang Yang
- College of Chemistry and Chemical Engineering, Yantai University, 30 Qingquan Road, Yantai 264005, China
| | - Xiaolin Zhang
- College of Chemistry and Chemical Engineering, Yantai University, 30 Qingquan Road, Yantai 264005, China
| | - Shuang Li
- College of Chemistry and Chemical Engineering, Yantai University, 30 Qingquan Road, Yantai 264005, China
| | - Xiaoxiao Yu
- Shandong Marine Resource and Environment Research Institute, 216 Changjiang Road, Yantai 264006, China.
| | - Shufeng Liu
- College of Chemistry and Chemical Engineering, Yantai University, 30 Qingquan Road, Yantai 264005, China.
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Guan Y, Wang FP, Chen ZX, Yang YH, Yang T, Hu R. Ratiometrically homogeneous electrochemical biosensor based on the signal amplified strategy of dual DNA nanomachines for microRNA analysis. Talanta 2023; 254:124191. [PMID: 36525866 DOI: 10.1016/j.talanta.2022.124191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/24/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022]
Abstract
Precise and sensitive microRNA (miRNA) analysis is very significant for early disease diagnosis. In this work, a dual DNA nanomachines-based homogeneous electrochemical biosensor was constructed for the sensitively ratiometric detection of miRNA by a nicking enzyme (Nt.AlwI)-assisted cycling signal amplification strategy. The Co-based metal organic frameworks (Co-MOFs) and toluidine blue (TB) were employed as signal probes and internal reference probes, respectively. The introduction of internal reference probes can actually calibrate the interferent factors of the analytical system to improve the stability in detection procedure. In addition, with the help of the magnetic separation technique, the homogeneous electrochemical biosensor provides a more simpler way for the development of immobilization-free electrochemical miRNA biosensors, avoiding the complex modification procedure of traditional electrochemical biosensing interfaces. Consequently, taking advantages of this proposed dual DNA nanomachines-based homogeneous electrochemical biosensor, the highly sensitive and selective detection of miRNA-141 as model could be accomplished in ranging from 1 fM to 10 nM with detection limit of 0.46 fM. This strategy exhited good sensitivity and stability to integrate the nicking enzyme-powered dual DNA nanomachines with the ratiometric electrochemical output modes, which open new opportunities for the sensitive and reliable diagnosis of miRNA-related diseases.
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Affiliation(s)
- Yan Guan
- College of Chemistry and Chemical Engineering, Yunnan Normal University, Kunming, 650500, Yunnan, PR China
| | - Fu Peng Wang
- College of Chemistry and Chemical Engineering, Yunnan Normal University, Kunming, 650500, Yunnan, PR China
| | - Zhi Xiong Chen
- College of Chemistry and Chemical Engineering, Yunnan Normal University, Kunming, 650500, Yunnan, PR China
| | - Yun Hui Yang
- College of Chemistry and Chemical Engineering, Yunnan Normal University, Kunming, 650500, Yunnan, PR China
| | - Tong Yang
- College of Chemistry and Chemical Engineering, Yunnan Normal University, Kunming, 650500, Yunnan, PR China.
| | - Rong Hu
- College of Chemistry and Chemical Engineering, Yunnan Normal University, Kunming, 650500, Yunnan, PR China.
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Azeem MM, Shafa M, Aamir M, Zubair M, Souayeh B, Alam MW. Nucleotide detection mechanism and comparison based on low-dimensional materials: A review. Front Bioeng Biotechnol 2023; 11:1117871. [PMID: 36937765 PMCID: PMC10018150 DOI: 10.3389/fbioe.2023.1117871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/13/2023] [Indexed: 03/06/2023] Open
Abstract
The recent pandemic has led to the fabrication of new nucleic acid sensors that can detect infinitesimal limits immediately and effectively. Therefore, various techniques have been demonstrated using low-dimensional materials that exhibit ultrahigh detection and accuracy. Numerous detection approaches have been reported, and new methods for impulse sensing are being explored. All ongoing research converges at one unique point, that is, an impetus: the enhanced limit of detection of sensors. There are several reviews on the detection of viruses and other proteins related to disease control point of care; however, to the best of our knowledge, none summarizes the various nucleotide sensors and describes their limits of detection and mechanisms. To understand the far-reaching impact of this discipline, we briefly discussed conventional and nanomaterial-based sensors, and then proposed the feature prospects of these devices. Two types of sensing mechanisms were further divided into their sub-branches: polymerase chain reaction and photospectrometric-based sensors. The nanomaterial-based sensor was further subdivided into optical and electrical sensors. The optical sensors included fluorescence (FL), surface plasmon resonance (SPR), colorimetric, and surface-enhanced Raman scattering (SERS), while electrical sensors included electrochemical luminescence (ECL), microfluidic chip, and field-effect transistor (FET). A synopsis of sensing materials, mechanisms, detection limits, and ranges has been provided. The sensing mechanism and materials used were discussed for each category in terms of length, collectively forming a fusing platform to highlight the ultrahigh detection technique of nucleotide sensors. We discussed potential trends in improving the fabrication of nucleotide nanosensors based on low-dimensional materials. In this area, particular aspects, including sensitivity, detection mechanism, stability, and challenges, were addressed. The optimization of the sensing performance and selection of the best sensor were concluded. Recent trends in the atomic-scale simulation of the development of Deoxyribonucleic acid (DNA) sensors using 2D materials were highlighted. A critical overview of the challenges and opportunities of deoxyribonucleic acid sensors was explored, and progress made in deoxyribonucleic acid detection over the past decade with a family of deoxyribonucleic acid sensors was described. Areas in which further research is needed were included in the future scope.
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Affiliation(s)
- M. Mustafa Azeem
- Department of Civil, Architectural, and Environmental Engineering, Missouri University of Science and Technology, Rolla, MO, United States
- *Correspondence: M. Mustafa Azeem, ; Muhammad Aamir,
| | - Muhammad Shafa
- Yunnan Key Laboratory of Metal-Organic Molecular Materials and Devices, Kunming University, Kunming, Yunnan, China
| | - Muhammad Aamir
- Department of Basic Science, Deanship of Preparatory Year, King Faisal University, Hofuf, Saudi Arabia
- *Correspondence: M. Mustafa Azeem, ; Muhammad Aamir,
| | - Muhammad Zubair
- Mechanical and Nuclear Engineering Department, University of Sharjah, Sharjah, United Arab Emirates
| | - Basma Souayeh
- Department of Physics, College of Science, King Faisal University, Al Ahsa, Saudi Arabia
| | - Mir Waqas Alam
- Department of Physics, College of Science, King Faisal University, Al Ahsa, Saudi Arabia
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Recent progress in homogeneous electrochemical sensors and their designs and applications. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116712] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Huang T, Wang M, Hong N, Cui H, Fan Q, Wei G, Qin L, Zhang J, Fan H. An autonomous driven DNA walker-based electrochemical aptasensor for on-site detection of Ochratoxin A. Talanta 2022; 252:123785. [DOI: 10.1016/j.talanta.2022.123785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/22/2022] [Accepted: 07/25/2022] [Indexed: 11/17/2022]
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Ariffin EY, Zakariah EI, Ruslin F, Kassim M, Yamin BM, Heng LY, Hasbullah SA. Hexaferrocenium tri[hexa(isothiocyanato)iron(III)] trihydroxonium complex as a new DNA intercalator for electrochemical DNA biosensor. Sci Rep 2021; 11:7883. [PMID: 33846405 PMCID: PMC8041802 DOI: 10.1038/s41598-021-86939-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 03/17/2021] [Indexed: 11/09/2022] Open
Abstract
Ferrocene or ferrocenium has been widely studied in the field of organometallic complexes because of its stable thermodynamic, kinetic and redox properties. Novel hexaferrocenium tri[hexa(isothiocyanato)iron(III)]trihydroxonium (HexaFc) complex was the product from the reaction of ferrocene, maleic acid and ammonium thiocyanate and was confirmed by elemental analysis CHNS, FTIR and single crystal X-ray crystallography. In this study, HexaFc was used for the first time as an electroactive indicator for porcine DNA biosensor. The UV-Vis DNA titrations with this compound showed hypochromism and redshift at 250 nm with increasing DNA concentrations. The binding constant (Kb) for HexaFc complex towards CT-DNA (calf-thymus DNA) was 3.1 × 104 M-1, indicated intercalator behaviour of the complex. To test the usefulness of this complex for DNA biosensor application, a porcine DNA biosensor was constructed. The recognition probes were covalently immobilised onto silica nanospheres (SiNSs) via glutaraldehyde linker on a screen-printed electrode (SPE). After intercalation with the HexaFc complex, the response of the biosensor to the complementary porcine DNA was measured using differential pulse voltammetry. The DNA biosensor demonstrated a linear response range to the complementary porcine DNA from 1 × 10-6 to 1 × 10-3 µM (R2 = 0.9642) with a limit detection of 4.83 × 10-8 µM and the response was stable up to 23 days of storage at 4 °C with 86% of its initial response. The results indicated that HexaFc complex is a feasible indicator for the DNA hybridisation without the use of a chemical label for the detection of porcine DNA.
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Affiliation(s)
- Eda Yuhana Ariffin
- Department of Chemical Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), 43600, Bangi, Selangor Darul Ehsan, Malaysia
| | - Emma Izzati Zakariah
- Department of Chemical Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), 43600, Bangi, Selangor Darul Ehsan, Malaysia
| | - Farah Ruslin
- Department of Chemical Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), 43600, Bangi, Selangor Darul Ehsan, Malaysia
| | - Muhammad Kassim
- Department of Chemical Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), 43600, Bangi, Selangor Darul Ehsan, Malaysia
| | - Bohari M Yamin
- Department of Chemical Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), 43600, Bangi, Selangor Darul Ehsan, Malaysia
| | - Lee Yook Heng
- Department of Chemical Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), 43600, Bangi, Selangor Darul Ehsan, Malaysia
| | - Siti Aishah Hasbullah
- Department of Chemical Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), 43600, Bangi, Selangor Darul Ehsan, Malaysia.
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