1
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Huang Q, Wang K, Wang Y. Highly sensitive miRNA-21 detection with enzyme-free cascade amplification biosensor. Talanta 2024; 273:125928. [PMID: 38508125 DOI: 10.1016/j.talanta.2024.125928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/17/2024] [Accepted: 03/14/2024] [Indexed: 03/22/2024]
Abstract
In this study, we present an enzyme-free fluorescence biosensor for the highly sensitive detection of miRNA-21, a crucial biomarker in clinical diagnosis. Our innovative approach combines catalytic hairpin assembly (CHA) and entropy-driven amplification into a cascade amplification strategy. MicroRNA initiates the catalytic hairpin assembly reaction, liberating the trigger region needed for the entropy-driven amplification reaction. This triggers a series of strand displacement reactions, resulting in the separation of the fluorescence resonance energy transfer pair and an amplified fluorescence signal from FAM. Our cascade amplification strategy achieves ultra-sensitive microRNA detection, with an impressive limit of detection (LOD) of 1.3 fM, approximately 100-fold lower than CHA alone. Additionally, we successfully applied this biosensor for microRNA quantification in human serum and cell lysates, demonstrating its practicality and potential for early diagnosis.
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Affiliation(s)
- Qiuyan Huang
- School of Chemistry and Enviromental Engineering, Changchun University of Science and Technology, Changchun, 130022, China
| | - Kun Wang
- Department of Physics, New York University, New York, NY, 10003, USA
| | - Yuan Wang
- School of Chemistry and Enviromental Engineering, Changchun University of Science and Technology, Changchun, 130022, China.
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2
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Liu J, Guo J, Li G, Zou L. Cascade signal amplification strategy for the electrochemical aptasensing of nucleic acid: Combination of dual-output toehold-mediated DNA strand displacement, DNA walker and Exo III. Anal Chim Acta 2024; 1297:342370. [PMID: 38438228 DOI: 10.1016/j.aca.2024.342370] [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: 11/22/2023] [Revised: 01/27/2024] [Accepted: 02/10/2024] [Indexed: 03/06/2024]
Abstract
BACKGROUND Sensitive and selective analysis of low content nucleic acid sequences plays an important role in pathogen analysis, disease diagnosis and biomedicine. The electrochemical biosensor based on toehold-mediated strand displacement reaction (TMSD) is highly attractive in nucleic acid detection due to their improved sensitivity and rapid response. But the traditional TMSD carried out on the electrode always with low displacement efficiency and complicated electrode operation, resulting in compromised sensing performance. There is a great need to construct a novel TMSD based electrochemical detection strategy to overcome such challenges in nucleic acid detecting. RESULT Herein, a triple signal amplification electrochemical aptasensor was developed for ultrasensitive detection of CYFRA21-1 DNA. The dual-output toehold mediated strand displacement reaction (dTMSD) can convert one input to two strands output within one strand displacement cycle. So that it possesses a higher efficiency for improving the sensitivity in comparison with the single-output TMSD. And the fuel strand was configured with a tail to realize successive DNA circuits through self-propelling as a DNA walker. All the above processes were carried out on magnetic beads, which is conducive to achieving effective sample purification and minimizing the background signals. Besides, Exonuclease III was further amplified signal. As a result, through the cascade use of above three technologies, the proposed biosensing strategy realized sensitive detection of target DNA with a low detection limit of 0.35 fM (S/N = 3) and wide linear range (0.5 fM-500 pM). SIGNIFICANCE The proposed novel dTMSD combining multiple signal amplification strategies for electrochemical detection of CYFRA21-1 DNA with easy operation not only possesses excellent sensitivity and selectivity, but also has potential application value for monitoring DNA in serum. Meanwhile, the development of highly sensitive and specific CYFRA21-1 DNA detection methods is very important for the prevention and treatment of lung cancer.
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Affiliation(s)
- Jinzhi Liu
- College of Chemistry, Green Catalysis Center, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Jiaxin Guo
- College of Chemistry, Green Catalysis Center, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Gaiping Li
- College of Chemistry, Green Catalysis Center, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Lina Zou
- College of Chemistry, Green Catalysis Center, Zhengzhou University, Zhengzhou, 450001, PR China.
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3
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Tajadini H, Cornelissen JJLM, Zadegan R, Ravan H. An approach for state differentiation in nucleic acid circuits: Application to diagnostic DNA computing. Anal Chim Acta 2024; 1294:342266. [PMID: 38336407 DOI: 10.1016/j.aca.2024.342266] [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: 09/09/2023] [Revised: 01/13/2024] [Accepted: 01/16/2024] [Indexed: 02/12/2024]
Abstract
BACKGROUND Differentiating between different states in nucleic acid circuits is crucial for various biological applications. One approach, there is a requirement for complicated sequential summation, which can be excessive for practical purposes. By selectively labeling biologically significant states, this study tackles the issue and presents a more cost-effective and streamlined solution. The challenge is to efficiently distinguish between different states in a nucleic acid circuit. RESULTS An innovative method is introduced in this study to distinguish between states in a nucleic acid circuit, emphasizing the biologically relevant ones. The circuit comprises four DNA logic gates and two detection modules, one for determining fetal gender and the other for diagnosing X-linked genetic disorders. The primary module generates a G-quadruplex DNAzyme when activated by specific biomarkers, which leads to a distinct colorimetric signal. The secondary module responds to hemophilia and choroideremia biomarkers, generating one or two DNAzymes. The absence of female fetus indicators results in no DNAzyme or color change. The circuit can differentiate various fetal states by producing one to four active DNAzymes in response to male fetus biomarkers. A single-color solution for state differentiation is provided by this approach, which promises significant advancements in DNA computing and diagnostic applications. SIGNIFICANCE The innovative approach used in this study to distinguish states in nucleic acid circuits holds great significance. By selectively labeling biologically relevant states, circuit design is simplified and complexity is reduced. This advancement enables cost-effective and efficient diagnostic applications and contributes to DNA computing, providing a valuable solution to a fundamental problem.
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Affiliation(s)
- Hanie Tajadini
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Jeroen J L M Cornelissen
- Department of Molecules & Materials, MESA+ Institute for Nanotechnology, University of Twente, Enschede, AE, 7500, the Netherlands
| | - Reza Zadegan
- Department of Nanoengineering, Joint School of Nanoscience and Nanoengineering, North Carolina A&T State University, Greensboro, NC, USA
| | - Hadi Ravan
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran; Department of Molecules & Materials, MESA+ Institute for Nanotechnology, University of Twente, Enschede, AE, 7500, the Netherlands.
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4
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Li D, Huang Q, Wang K. Exonuclease III-propelled DNAzyme walker: an electrochemical strategy for microRNA diagnostics. Mikrochim Acta 2024; 191:173. [PMID: 38436735 DOI: 10.1007/s00604-024-06208-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 01/09/2024] [Indexed: 03/05/2024]
Abstract
MicroRNA detection is crucial for early infectious disease diagnosis and rapid cancer screening. However, conventional techniques like reverse transcription-quantitative polymerase chain reaction, requiring specialized training and intricate procedures, are less suitable for point-of-care analyses. To address this, we've developed a straightforward amplifier based on an exonuclease III (exo III)-propelled DNAzyme walker for sensitive and selective microRNA detection. This amplifier employs a specially designed hairpin probe with two exposed segments for strand recognition. Once the target microRNA is identified by the hairpin's extended single-strand DNA, exo III initiates its digestion, allowing microRNA regeneration and subsequent hairpin probe digestion cycles. This cyclical process produces a significant amount of DNAzyme, leading to a marked reduction in electrochemical signals. The biosensor exhibits a detection range from 10 fM to 100 pM and achieves a detection limit of 5 fM (3σ criterion). Importantly, by integrating an "And logic gate," our system gains the capacity for simultaneous diagnosis of multiple microRNAs, enhancing its applicability in RNA-based disease diagnostics.
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Affiliation(s)
- Dengke Li
- Department of Rehabilitation Medicine, the Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huaian, 223300, China.
| | - Qiuyan Huang
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Kun Wang
- Department of Physics, New York University, New York, NY, 10003, USA
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5
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Xu J, Liu Y, Li Y, Liu Y, Huang KJ. Smartphone-Assisted Flexible Electrochemical Sensor Platform by a Homology DNA Nanomanager Tailored for Multiple Cancer Markers Field Inspection. Anal Chem 2023; 95:13305-13312. [PMID: 37608571 DOI: 10.1021/acs.analchem.3c02481] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
In this work, an ingenious sensor technology was established by integrating the EBFCs on a flexible paper strip carrier (PE) that was used for simultaneous detection of tumor markers in complex samples. Adopting high performance ultrathin graphdiyne (U-GDY) as the substrate can increase the enzyme load, accelerate the electron transfer rate, and significantly enhance the detection sensitivity. A homologous DNA nanomanager strategy cleverly uses signal switches to recycle and amplify target miRNAs, while the smartphone receives real-time instantaneous current values to realize multivariate detection. Electrochemical data show that the detection limits (LODs) of miRNA-21 and miRNA-155 are 0.09 and 0.15 fM in the wide concentration range. The results confirm that the tailored sensor platform provides a strategy for the early cancer diagnosis and lays the foundation for the construction of a flexible wearable platform.
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Affiliation(s)
- Jing Xu
- College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang 464000, China
| | - Yinbing Liu
- College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang 464000, China
| | - Yujin Li
- College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang 464000, China
| | - Yilin Liu
- College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang 464000, China
| | - Ke-Jing Huang
- Education Department of Guangxi Zhuang Autonomous Region, Key Laboratory of Applied Analytical Chemistry, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning 530006, China
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6
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Li Z, Xu H, Zhang Z, Miao X. DNA tetrahedral scaffold-corbelled 3D DNAzyme walker for electrochemiluminescent aflatoxin B 1 detection. Food Chem 2023; 407:135049. [PMID: 36493494 DOI: 10.1016/j.foodchem.2022.135049] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 11/24/2022]
Abstract
The reaction efficiency of surface-based DNA walker can directly affect the properties of a biosensor. Herein, three-dimensional (3D) DNAzyme walker were first fixed on the top of DNA tetrahedral scaffold to improve the immobilization efficiency. Ferrocene (Fc) that labeled at substrate strand ends effectively quenched the electrochemiluminescence (ECL) signal of Ru(bpy)2(cpaphen)2+, yielding the sensor in a "signal-off" state. Upon the addition of aflatoxin B1 (AFB1), 3D DNAzyme walker was activated and fueled by Na+, accordingly releasing Fc and recovering the ECL signal of Ru(bpy)2(cpaphen)2+. Due to the high movement efficiency of such 3D DNAzyme walker, ultrasensitive detection of AFB1 was achieved in the range of 1.0 fg mL-1-10 ng mL-1, with a detection limit of 0.58 fg mL-1. Moreover, satisfactory results were obtained while detecting AFB1 in corn and peanut samples, suggesting it has a potential application in food safety analysis.
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Affiliation(s)
- Zongbing Li
- School of Life Science, Jiangsu Normal University, Xuzhou 221116, PR China
| | - Huanwen Xu
- School of Life Science, Jiangsu Normal University, Xuzhou 221116, PR China
| | - Zifeng Zhang
- School of Life Science, Jiangsu Normal University, Xuzhou 221116, PR China.
| | - Xiangmin Miao
- School of Life Science, Jiangsu Normal University, Xuzhou 221116, PR China.
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7
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Wang MY, Jing WJ, Wang LJ, Jia LP, Ma RN, Zhang W, Shang L, Li XJ, Xue QW, Wang HS. Electrochemiluminescence detection of miRNA-21 based on dual signal amplification strategies: Duplex-specific nuclease -mediated target recycle and nicking endonuclease-driven 3D DNA nanomachine. Biosens Bioelectron 2023; 226:115116. [PMID: 36753989 DOI: 10.1016/j.bios.2023.115116] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/15/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023]
Abstract
DNA nanomachines have shown potential application in the construction of various biosensors. Here, an electrochemiluminescence biosensor for the sensitive detection of miRNA-21 were reported based on three-dimensional (3D) DNA nanomachine and duplex-specific nuclease (DSN)-mediated target recycle amplification strategy. First, the bipedal DNA walkers were obtained by DSN-mediated digestion reaction initiated by target miRNA-21.3D DNA tracks were prepared by modifying Fe3O4 magnetic beads (MBs) with ferrocene-labeled DNA (Fc-DNA). The produced DNA walkers autonomously moved along 3D DNA tracks powered by nicking endonuclease. During the movement, ferrocene-labeled DNA was cleaved, resulting in large amounts of Fc-labeled DNA fragments away from the MBs surface. Finally, the liberated Fc-labeled DNA fragments were dropped on the C-g-C3N4 modified electrode surface, leading to the quenching of C-g-C3N4 electrochemiluminescence (ECL). Benefiting from the dual amplification strategy of 3D DNA nanomachine and DSN-mediated target recycling, the developed ECL biosensor exhibited an excellent performance for miRNA-21 detection with a wide linear range of 10 fM to 10 nM and a low detection limit of 1.0 fM. This work offers a new thought for the application of DNA walkers in the construction of various biosensors.
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Affiliation(s)
- Ming-Yue Wang
- College of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, 252000, China
| | - Wen-Jie Jing
- College of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, 252000, China
| | - Li-Juan Wang
- No. 3 Middle School of Liaocheng, Liaocheng, Shandong Province, 252000, China
| | - Li-Ping Jia
- College of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, 252000, China.
| | - Rong-Na Ma
- College of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, 252000, China
| | - Wei Zhang
- College of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, 252000, China
| | - Lei Shang
- College of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, 252000, China
| | - Xiao-Jian Li
- College of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, 252000, China
| | - Qing-Wang Xue
- College of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, 252000, China
| | - Huai-Sheng Wang
- College of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, 252000, China.
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8
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Cao X, Chen C, Zhu Q. Biosensors based on functional nucleic acids and isothermal amplification techniques. Talanta 2023; 253:123977. [PMID: 36201957 DOI: 10.1016/j.talanta.2022.123977] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/20/2022] [Accepted: 09/27/2022] [Indexed: 12/13/2022]
Abstract
In the past few years, with the in-depth research of functional nucleic acids and isothermal amplification techniques, their applications in the field of biosensing have attracted great interest. Since functional nucleic acids have excellent flexibility and convenience in their structural design, they have significant advantages as recognition elements in biosensing. At the same time, isothermal amplification techniques have higher amplification efficiency, so the combination of functional nucleic acids and isothermal amplification techniques can greatly promote the widespread application of biosensors. For the purpose of further improving the performance of biosensors, this review introduces several widely used functional nucleic acids and isothermal amplification techniques, as well as their classification, basic principles, application characteristics, and summarizes their important applications in the field of biosensing. We hope to provide some references for the design and construction of new tactics to enhance the detection sensitivity and detection range of biosensing.
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Affiliation(s)
- Xiuen Cao
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, 410013, Hunan, China.
| | - Chuanpin Chen
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, 410013, Hunan, China.
| | - Qubo Zhu
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, 410013, Hunan, China.
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9
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Bahri M, Amin Elaguech M, Nasraoui S, Djebbi K, Kanoun O, Qin P, Tlili C, Wang D. Laser-Induced Graphene Electrodes for Highly Sensitive Detection of DNA Hybridization via Consecutive Cytosines (polyC)-DNA-based Electrochemical Biosensors. Microchem J 2022. [DOI: 10.1016/j.microc.2022.108208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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10
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A reagentless electrochemical DNA sensor based on a self‐powered DNA machine. ELECTROANAL 2022. [DOI: 10.1002/elan.202200330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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11
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Zhang B, Lv L, Ma X, Xie L, Lin M, Chen H, He B. Au@ZnNi-MOF labeled electrochemical aptasensor for detection of enrofloxacin based on AuPt@h-CeO2/MoS2 and DNAzyme-driven DNA walker triple amplification signal strategy. Biosens Bioelectron 2022; 210:114296. [DOI: 10.1016/j.bios.2022.114296] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/11/2022] [Accepted: 04/18/2022] [Indexed: 11/30/2022]
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12
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He S, Yang Y, Xu Z, Ling H, Wang Y, Wan L, Huang N, Ye Q, Liu Y. Development of Enzyme-Free DNA Amplifier Based on Chain Reaction Principle. Acta Biomater 2022; 149:213-219. [PMID: 35811071 DOI: 10.1016/j.actbio.2022.06.047] [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: 04/18/2022] [Revised: 06/27/2022] [Accepted: 06/30/2022] [Indexed: 11/01/2022]
Abstract
Enzyme-free DNA amplifiers can amplify the signal of nucleic acid molecules. They can be applied to DNA molecular operation and nucleic acid detection. The reaction speed is the core index to evaluate DNA amplifiers. In this study, we designed a DNA amplifier based on an enzyme-free chain reaction. This DNA amplifier can release one more signal molecule in each round of reaction and trigger the next round, which significantly improved reaction speed. Moreover, because the amplifier used a stable DNA structure, the reaction can occur at room temperature. To integrate the amplifier into other DNA molecular operations, we performed the amplification reaction in a microfluidic chip module. The results showed that the amplifier can realize real-time signal feedback at a proper input molecule concentration and reach the endpoint in 40 s, even at a low relative concentration. To apply the amplifier for nucleic acid detection, we also used a conventional fluorescent polymerase chain reaction instrument for the reaction. The results showed that the amplifier specifically detected trace DNA single-stranded molecules. To solve the leakage problem of existing amplifiers, we designed a DNA molecule as the chain reaction's inhibitor, which was crucial in controlling the reaction speed and preventing leakage. STATEMENT OF SIGNIFICANCE: Traditional amplifier strategies of enzyme-free DNA amplifiers relied on a constant number of cycling molecules to catalyze the amplifier molecules' changing structure and release fluorescent signals, which lead low reaction speed. Based on an enzyme-free chain reaction, we designed a DNA amplifier which can release one more cycling molecule in each loop and trigger the next loop and significantly improve reaction speed in this study. Our analysis on microfluidic chip module and PCR instrument verifies high sensitivity and selectivity. And this strategy of DNA amplifier realizes the control of reaction and prevents leakage. We believe that this automated amplification strategy could have great applications in vivo signal detection, imaging, and signal molecule translation.
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Affiliation(s)
- Songlin He
- School of Medicine, Nankai University, Tianjin 300071, China; Institute of Orthopedics, the First Medical Center, Chinese PLA General Hospital, Beijing Key Lab of Regenerative Medicine in Orthopedics, Key Laboratory of Musculoskeletal Trauma & War Injuries PLA, No. 28 Fuxing Road, Haidian District, Beijing 100853, China
| | - Yongkang Yang
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Ziheng Xu
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Hongkun Ling
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Yu Wang
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Li Wan
- School of Medicine, Nankai University, Tianjin 300071, China; Nankai University Eye Institute, Nankai University, Tianjin 300071, China
| | - Ningning Huang
- Key Laboratory of Weak-Light Nonlinear Photonics, Ministry of Education, School of Physics and TEDA Applied Physics, Nankai University, Tianjin 300071, China
| | - Qing Ye
- Key Laboratory of Weak-Light Nonlinear Photonics, Ministry of Education, School of Physics and TEDA Applied Physics, Nankai University, Tianjin 300071, China; Nankai University Eye Institute, Nankai University, Tianjin 300071, China.
| | - Yin Liu
- School of Medicine, Nankai University, Tianjin 300071, China; Nankai University Eye Institute, Nankai University, Tianjin 300071, China.
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13
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An electrochemical DNA sensor based on an integrated and automated DNA Walker. Bioelectrochemistry 2022; 147:108198. [DOI: 10.1016/j.bioelechem.2022.108198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 06/25/2022] [Accepted: 06/26/2022] [Indexed: 11/22/2022]
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14
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Piranej S, Bazrafshan A, Salaita K. Chemical-to-mechanical molecular computation using DNA-based motors with onboard logic. NATURE NANOTECHNOLOGY 2022; 17:514-523. [PMID: 35347272 PMCID: PMC9119907 DOI: 10.1038/s41565-022-01080-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 01/13/2022] [Indexed: 05/15/2023]
Abstract
DNA has become the biomolecule of choice for molecular computation that may one day complement conventional silicon-based processors. In general, DNA computation is conducted in individual tubes, is slow in generating chemical outputs in response to chemical inputs and requires fluorescence readout. Here, we introduce a new paradigm for DNA computation where the chemical input is processed and transduced into a mechanical output using dynamic DNA-based motors operating far from equilibrium. We show that DNA-based motors with onboard logic (DMOLs) can perform Boolean functions (NOT, YES, AND and OR) with 15 min readout times. Because DMOLs are micrometre-sized, massive arrays of DMOLs that are identical or uniquely encoded by size and refractive index can be multiplexed and perform motor-to-motor communication on the same chip. Finally, DMOL computational outputs can be detected using a conventional smartphone camera, thus transducing chemical information into the electronic domain in a facile manner, suggesting potential applications.
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Affiliation(s)
- Selma Piranej
- Department of Chemistry, Emory University, Atlanta, GA, USA
| | | | - Khalid Salaita
- Department of Chemistry, Emory University, Atlanta, GA, USA.
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA.
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15
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Zhao LD, Yang X, Zhong X, zhuo Y. Advances in Electrochemiluminescence Biosensors Based on DNA Walkers. Chempluschem 2022; 87:e202200070. [DOI: 10.1002/cplu.202200070] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/19/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Li-Dan Zhao
- Southwest University College of Chemistry and Chemical Engineering CHINA
| | - Xia Yang
- Southwest University College of Chemistry and Chemical Engineering CHINA
| | - Xia Zhong
- Southwest University College of Chemistry and Chemical Engineering CHINA
| | - ying zhuo
- Southwest University College of Chemistry and Chemical Engineering No.2 Tiansheng RoadBeiBei District 400715 Chongqing CHINA
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16
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Batasheva S, Fakhrullin R. Sequence Does Not Matter: The Biomedical Applications of DNA-Based Coatings and Cores. Int J Mol Sci 2021; 22:ijms222312884. [PMID: 34884687 PMCID: PMC8658021 DOI: 10.3390/ijms222312884] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/21/2021] [Accepted: 11/24/2021] [Indexed: 12/20/2022] Open
Abstract
Biomedical applications of DNA are diverse but are usually associated with specific recognition of target nucleotide sequences or proteins and with gene delivery for therapeutic or biotechnological purposes. However, other aspects of DNA functionalities, like its nontoxicity, biodegradability, polyelectrolyte nature, stability, thermo-responsivity and charge transfer ability that are rather independent of its sequence, have recently become highly appreciated in material science and biomedicine. Whereas the latest achievements in structural DNA nanotechnology associated with DNA sequence recognition and Watson–Crick base pairing between complementary nucleotides are regularly reviewed, the recent uses of DNA as a raw material in biomedicine have not been summarized. This review paper describes the main biomedical applications of DNA that do not involve any synthesis or extraction of oligo- or polynucleotides with specified sequences. These sequence-independent applications currently include some types of drug delivery systems, biocompatible coatings, fire retardant and antimicrobial coatings and biosensors. The reinforcement of DNA properties by DNA complexation with nanoparticles is also described as a field of further research.
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17
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Liu L, Liu P, Ga L, Ai J. Advances in Applications of Molecular Logic Gates. ACS OMEGA 2021; 6:30189-30204. [PMID: 34805654 PMCID: PMC8600522 DOI: 10.1021/acsomega.1c02912] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 10/05/2021] [Indexed: 05/21/2023]
Abstract
Logic gates are devices that can perform Boolean logic operations and are the basic components of integrated circuits for information processing and storage. In recent years, molecular logic gates are gradually replacing traditional silicon-based electronic computers with their significant advantages and are used in research in water quality monitoring, heavy metal ion detection, disease diagnosis and treatment, food safety detection, and biological sensors. Logic gates at the molecular level have broad development prospects and huge development potential. In this review, the development and application of logic gates in various fields are used as the entry point to discuss the research progress of logic gates and logic circuits. At the same time, the application of logic gates in quite a few emerging fields is briefly summarized and predicted.
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Affiliation(s)
- Lijun Liu
- College
of Chemistry and Environmental Science, Inner Mongolian Key Laboratory
for Enviromental Chemistry, Inner Mongolia
Normal University, 81 Zhaowudalu, Hohhot 010022, People’s Republic of China
| | - Pingping Liu
- College
of Chemistry and Environmental Science, Inner Mongolian Key Laboratory
for Enviromental Chemistry, Inner Mongolia
Normal University, 81 Zhaowudalu, Hohhot 010022, People’s Republic of China
| | - Lu Ga
- College
of Pharmacy, Inner Mongolia Medical University, Jinchuankaifaqu, Hohhot 010110, People’s Republic of China
| | - Jun Ai
- College
of Chemistry and Environmental Science, Inner Mongolian Key Laboratory
for Enviromental Chemistry, Inner Mongolia
Normal University, 81 Zhaowudalu, Hohhot 010022, People’s Republic of China
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18
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Zhai F, Guan Y, Zhu B, Chen S, He R. Intraparticle and Interparticle Transferable DNA Walker Supported by DNA Micelles for Rapid Detection of MicroRNA. Anal Chem 2021; 93:12346-12352. [PMID: 34469684 DOI: 10.1021/acs.analchem.1c02104] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Synthetic DNA walkers are artificially designed DNA self-assemblies with the capability of performing quasi-mechanical movement at the micro/nanoscale and have shown extensive promise in biosensing, intracellular imaging, and drug delivery. However, DNA walkers are usually constructed by covalently or coordinately binding DNA strands specifically to hard surfaces, thereby greatly limiting their movement efficiency. Herein, we report an intraparticle and interparticle transferable DNA walker (dynamic micelle-supported DNA walker, DM-walker) constructed by immobilizing walking tracks and walking arms onto the corona of DNA micelles according to the principle of Watson-Crick base pairing. The DNAzyme-powered walking arm can drive the intraparticle and interparticle movements of the DM-walker due to the fact that the dynamic structure of the DNA micelle helps overcome the spatial barrier between the arms and tracks in the system, resulting in high walking efficiency. Moreover, the whole DM-walker can be constructed by self-assembly, getting rid of the tedious process and low efficiency of fixing DNA strands on hard surfaces. Taking miRNA-10b as a model target, the DM-walker demonstrates high walking efficiency (reaction duration of 20 min) and high sensitivity (LOD of 87 pM). The proposed DM-walker provides an avenue to develop novel DNA walkers on dynamic interfaces and holds great potential in clinical diagnosis.
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Affiliation(s)
- Fuheng Zhai
- Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Yufei Guan
- Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Binbing Zhu
- Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Shuai Chen
- Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Ronghuan He
- Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China
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19
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Dou B, Zhou H, Hong Y, Zhao L, Wang P. Cross-triggered and cascaded recycling amplification system for electrochemical detection of circulating microRNA in human serum. Chem Commun (Camb) 2021; 57:7116-7119. [PMID: 34179904 DOI: 10.1039/d1cc02060a] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A cross-triggered and cascaded recycling amplification system was developed for electrochemical sensing of microRNA 122 based on the DNAzyme/multicomponent nucleic acid enzyme cleavage technique and a dumbbell-shaped probe. The linear range and detection limit were obtained to be 1 fM-100 pM and 0.34 fM, respectively. Compared with some reported studies, the proposed system can achieve the selective detection of endogenous miRNA in liver injury patients and healthy human serums with the advantages of high sensitivity, low cost, and easy manipulation, which are significant for disease diagnosis as well as the fundamental research of molecular biology.
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Affiliation(s)
- Baoting Dou
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, China.
| | - Hui Zhou
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, China.
| | - Yajun Hong
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, China.
| | - Liming Zhao
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, China.
| | - Po Wang
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, China.
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20
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Zhang B, Tian P, Zhu H, Xie L, Dai P, He B. Ultrasensitive detection of PCB77 based on Exonuclease III-powered DNA walking machine. JOURNAL OF HAZARDOUS MATERIALS 2021; 416:125831. [PMID: 33878649 DOI: 10.1016/j.jhazmat.2021.125831] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 03/01/2021] [Accepted: 04/03/2021] [Indexed: 06/12/2023]
Abstract
In view of the urgent need to determine polychlorinated biphenyls (PCBs) in the environment, we report a simple and sensitive electrochemical aptasensor to detect 3,3',4,4'-tetrachlorobiphenyl (PCB77) based on Exonuclease III-powered Deoxyribonucleic Acid (DNA) walking machine using poly (diallyldimethylammonium chloride) (PDDA), which was functionalized hollow porous graphitic carbon nitride/ Ni-Co hollow nanoboxes/ Au-Pd-Pt nanoflowers composite material. Upon the addition of PCB77, the specific binding between PCB77 and the aptamer (Apt) could trigger the Exo III-assisted cyclic amplification process and release unlocking probes to deblock the Swing arm/Blocker duplex. Finally, the hybridized hairpin 3 (HP3), a short oligonucleotide, was left on the electrode via Exo III digestion of hybridized HP2, and thus a strong methylene blue (MB) signal was obtained. As expected, the proposed aptasensor exhibits exceptional PCB77 detection performances with a very low detection limit of 5.13 pg/L and a wide linear range of 0.01-100 ng/L based on the calibration curve. Moreover, the aptasensor presents a high level of selectivity and stability, with an acceptable degree of reproducibility. The results of this study have indicated that the proposed aptasensor has great potential application prospects, as demonstrated by its successful use in real environmental water samples.
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Affiliation(s)
- Baozhong Zhang
- School of Environmental Engineering, Henan University of Technology, Lianhua Road 100#, Zhengzhou 450001, Henan Province, People's Republic of China.
| | - Panpan Tian
- School of Environmental Engineering, Henan University of Technology, Lianhua Road 100#, Zhengzhou 450001, Henan Province, People's Republic of China; School of Chemistry and Chemical Engineering, Henan University of Technology, Lianhua Road 100#, Zhengzhou 450001, Henan Province, People's Republic of China
| | - Huina Zhu
- School of Environmental Engineering, Henan University of Technology, Lianhua Road 100#, Zhengzhou 450001, Henan Province, People's Republic of China
| | - Lingling Xie
- School of Environmental Engineering, Henan University of Technology, Lianhua Road 100#, Zhengzhou 450001, Henan Province, People's Republic of China
| | - Pengbo Dai
- School of Environmental Engineering, Henan University of Technology, Lianhua Road 100#, Zhengzhou 450001, Henan Province, People's Republic of China
| | - Baoshan He
- School of Food Science and Technology, Henan University of Technology, Lianhua Road 100#, Zhengzhou 450001, Henan Province, People's Republic of China.
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21
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Saha U, Todi K, Malhotra BD. Emerging DNA-based multifunctional nano-biomaterials towards electrochemical sensing applications. NANOSCALE 2021; 13:10305-10319. [PMID: 34086027 DOI: 10.1039/d1nr02409d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
DNA is known to be ubiquitous in nature as it is the controlling unit for genetic information storage in most living organisms. Lately, there has been a surge in studies relating to the use of DNA as a biomaterial for various biomedical applications such as biosensing, therapeutics, and drug delivery. The role of DNA as a bioreceptor in biosensors has been known for a long time. DNA-based biosensors are gradually evolving into highly sophisticated and sensitive molecular devices. The current realization of DNA-based biosensors embraces the unique structural and functional properties of DNA in the form of a biopolymer. The interesting properties of DNA, such as self-assembly, programmability, catalytic activity, dynamic behavior, and precise molecular recognition, have led to the emergence of innovative DNA assembly based electrochemical biosensors. This review article aims to cover the recent progress in the field of DNA-based electrochemical (EC) biosensors. It commences with an introduction to electrochemical biosensors and elucidates the advantages of integrating DNA-based materials into them. Besides this, we discuss the principles of EC biosensors based on different types of DNA-based materials. The article concludes by highlighting the outlook and importance of this interesting field for biomedical developments.
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Affiliation(s)
- Udiptya Saha
- Nanobioelectronics Laboratory, Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, New Delhi 110042, India.
| | - Keshav Todi
- Nanobioelectronics Laboratory, Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, New Delhi 110042, India.
| | - Bansi D Malhotra
- Nanobioelectronics Laboratory, Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, New Delhi 110042, India.
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22
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Hydrazone ligation assisted DNAzyme walking nanomachine coupled with CRISPR-Cas12a for lipopolysaccharide analysis. Anal Chim Acta 2021; 1174:338747. [PMID: 34247734 DOI: 10.1016/j.aca.2021.338747] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/24/2021] [Accepted: 06/06/2021] [Indexed: 12/26/2022]
Abstract
In this work, hydrazone ligation assisted DNAzyme walking nanomachine is explored to couple with CRISPR-Cas12a trans-cleavage. Hydrazone ligation with high efficiency can mediate signal input which can be induced by target binding, thereby regulating the performance of DNAzyme walking nanomachine. The product strand from DNAzyme walking nanomachine can further activate the trans-cleavage of Cas12a. So, cascade signal amplification can be achieved to enhance the sensitivity for target detection. Subsequently, hydrazone ligation assisted DNAzyme walking nanomachine coupled with CRISPR-Cas12a has been further developed as a biosensor to analyze lipopolysaccharides. The developed biosensor exhibits a linear range from 0.05 ng/mL to 106 ng/mL and a lowest limit of detection of 7.31 fg/mL. This research provides a new mode for the signal output of DNAzyme walking nanomachine, so as to sensitively analyze different biomolecules.
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23
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Wei M, Yue S, Liu Y. An amplified electrochemical aptasensor for ochratoxin A based on DNAzyme-mediated DNA walker. J Electroanal Chem (Lausanne) 2021. [DOI: 10.1016/j.jelechem.2021.115269] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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24
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Broadwater DWB, Cook AW, Kim HD. First passage time study of DNA strand displacement. Biophys J 2021; 120:2400-2412. [PMID: 33894217 DOI: 10.1016/j.bpj.2021.01.043] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 12/18/2020] [Accepted: 01/12/2021] [Indexed: 12/15/2022] Open
Abstract
DNA strand displacement, in which a single-stranded nucleic acid invades a DNA duplex, is pervasive in genomic processes and DNA engineering applications. The kinetics of strand displacement have been studied in bulk; however, the kinetics of the underlying strand exchange were obfuscated by a slow bimolecular association step. Here, we use a novel single-molecule fluorescence resonance energy transfer approach termed the "fission" assay to obtain the full distribution of first passage times of unimolecular strand displacement. At a frame time of 4.4 ms, the first passage time distribution for a 14-nucleotide displacement domain exhibited a nearly monotonic decay with little delay. Among the eight different sequences we tested, the mean displacement time was on average 35 ms and varied by up to a factor of 13. The measured displacement kinetics also varied between complementary invaders and between RNA and DNA invaders of the same base sequence, except for T → U substitution. However, displacement times were largely insensitive to the monovalent salt concentration in the range of 0.25-1 M. Using a one-dimensional random walk model, we infer that the single-step displacement time is in the range of ∼30-300 μs, depending on the base identity. The framework presented here is broadly applicable to the kinetic analysis of multistep processes investigated at the single-molecule level.
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Affiliation(s)
- D W Bo Broadwater
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia
| | - Alexander W Cook
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia
| | - Harold D Kim
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia.
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25
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Zhao S, Yu L, Yang S, Tang X, Chang K, Chen M. Boolean logic gate based on DNA strand displacement for biosensing: current and emerging strategies. NANOSCALE HORIZONS 2021; 6:298-310. [PMID: 33877218 DOI: 10.1039/d0nh00587h] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
DNA computers are considered one of the most prominent next-generation molecular computers that perform Boolean logic using DNA elements. DNA-based Boolean logic gates, especially DNA strand displacement-based logic gates (SDLGs), have shown tremendous potential in biosensing since they can perform the logic analysis of multi-targets simultaneously. Moreover, SDLG biosensors generate a unique output in the form of YES/NO, which is contrary to the quantitative measurement used in common biosensors. In this review, the recent achievements of SDLG biosensing strategies are summarized. Initially, the development and mechanisms of Boolean logic gates, strand-displacement reaction, and SDLGs are introduced. Afterwards, the diversified input and output of SDLG biosensors are elaborated. Then, the state-of-the-art SDLG biosensors are reviewed in the classification of different signal-amplification methods, such as rolling circle amplification, catalytic hairpin assembly, strand-displacement amplification, DNA molecular machines, and DNAzymes. Most importantly, limitations and future trends are discussed. The technology reviewed here is a promising tool for multi-input analysis and lays a foundation for intelligent diagnostics.
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Affiliation(s)
- Shuang Zhao
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University, 30 Gaotanyan, Shapingba District, Chongqing 400038, China.
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26
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Wang Y, Song W, Zhao H, Ma X, Yang S, Qiao X, Sheng Q, Yue T. DNA walker-assisted aptasensor for highly sensitive determination of Ochratoxin A. Biosens Bioelectron 2021; 182:113171. [PMID: 33773380 DOI: 10.1016/j.bios.2021.113171] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/03/2021] [Accepted: 03/13/2021] [Indexed: 02/07/2023]
Abstract
Ochratoxin A (OTA), a toxic secondary metabolite produced via various fungus, poses a serious threat to the health of human beings and animals. In this paper, an aptasensor for OTA detection based on gold nanoparticles decorated molybdenum oxide (AuNPs-MoOx) nanocomposites, hybridization chain reaction (HCR) and a restriction endonuclease (Nb.BbvCI)-aided walker DNA machine was successfully constructed. In this electrochemical platform, the HCR was also used to embed more electrical signal molecules of methylene blue (MB) on silver nanoparticles (AgNPs) to achieve signal amplification. Under the optimum conditions, after adding OTA and Nb.BbvCI in turn and responding adequately under appropriate conditions, aptamer-DNA (6-DNA) carries the OTA away from the electrode surface, and walker DNA was hybridized autonomously with 5-DNA, releasing a large amount of 5'-DNA with the help of Nb.BBVCI. Finally, the electrochemical signal obtained by differential pulse voltammetry (DPV) was weakened. As an artificial and popular signal amplification technique, the DNA walking machine greatly improved the sensitivity. The proposed biosensor exhibited excellent analytical performance in the range of 0.01-10000 pg mL-1 with a detection limit as low as 3.3 fg mL-1. Furthermore, direct comparison with ultraperformance liquid chromatography (UPLC) indicates excellent agreement to actual samples such as apple juice, orange juice, red wine and serum.
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Affiliation(s)
- Yahui Wang
- College of Chemistry & Materials Science/Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education/Shaanxi Provincial Key Laboratory of Electroanalytical Chemistry, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Wei Song
- College of Food Science and Technology, Northwest University, Laboratory of Nutritional and Healthy Food-Individuation Manufacturing Engineering/Research Center of Food Safety Risk Assessment and Control, Xi'an, Shaanxi, 710069, China
| | - Haiyan Zhao
- College of Chemistry & Materials Science/Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education/Shaanxi Provincial Key Laboratory of Electroanalytical Chemistry, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Xin Ma
- College of Food Science and Technology, Northwest University, Laboratory of Nutritional and Healthy Food-Individuation Manufacturing Engineering/Research Center of Food Safety Risk Assessment and Control, Xi'an, Shaanxi, 710069, China
| | - Shuying Yang
- College of Food Science and Technology, Northwest University, Laboratory of Nutritional and Healthy Food-Individuation Manufacturing Engineering/Research Center of Food Safety Risk Assessment and Control, Xi'an, Shaanxi, 710069, China
| | - Xiujuan Qiao
- College of Chemistry & Materials Science/Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education/Shaanxi Provincial Key Laboratory of Electroanalytical Chemistry, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Qinglin Sheng
- College of Food Science and Technology, Northwest University, Laboratory of Nutritional and Healthy Food-Individuation Manufacturing Engineering/Research Center of Food Safety Risk Assessment and Control, Xi'an, Shaanxi, 710069, China; College of Chemistry & Materials Science/Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education/Shaanxi Provincial Key Laboratory of Electroanalytical Chemistry, Northwest University, Xi'an, Shaanxi, 710069, China.
| | - Tianli Yue
- College of Food Science and Technology, Northwest University, Laboratory of Nutritional and Healthy Food-Individuation Manufacturing Engineering/Research Center of Food Safety Risk Assessment and Control, Xi'an, Shaanxi, 710069, China
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27
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Liao N, Pan MC, Wang L, Yang F, Yuan R, Zhuo Y. Swing Arm Location-Controllable DNA Walker for Electrochemiluminescence Biosensing. Anal Chem 2021; 93:4051-4058. [PMID: 33587601 DOI: 10.1021/acs.analchem.0c05051] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Here, we described a novel swing arm location-controllable DNA walker based on the DNA tetrahedral nanostructures (DTNs) for nucleic acid detection using the polycyclic aromatic hydrocarbon (PAH) microcrystals (TAPE-Pe MCs) consisting of the nonplanar molecular tetrakis(4-aminophenyl)ethene (TAPE) and planar molecular perylene (Pe) as electrochemiluminescence (ECL) luminophores. Specifically, the swing arm strands and track strands were fixed simultaneously on the DTNs to obtain the location-controllable DNA walker, which possessed an improved reaction efficiency compared to that of a fixed swing arm-based DNA walker due to the quantitative and orderly swing arm on the DTNs. On the other hand, the Pe microcrystals doped by TAPE molecules could decrease the π-π stacking of Pe molecules for the ECL efficiency enhancement, achieving a blue-shifted and intense ECL emission. Therefore, we defined this enhanced and blue-shifted ECL phenomenon as "inhibition of conjugation-driven ECL (IC-ECL)". To prove these principles, a location-controllable DNA walker-based ECL biosensor was developed with microRNA let-7a as target molecules. The ECL biosensor achieved a low detection limit of 4.92 fM within a wide linear range from 10 fM to 100 nM. This approach offers a new insight for ECL efficiency increase and location-controllable strategies with improved reaction efficiency, demonstrating potential in diagnostic analysis.
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Affiliation(s)
- Ni Liao
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China.,College of Biological and Chemical Engineering, Panzhihua University, Panzhihua 617000, China
| | - Mei-Chen Pan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Li Wang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Fan Yang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Ying Zhuo
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
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28
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Wang Y, Wang Y, Liu S, Sun W, Zhang M, Jiang L, Li M, Yu J, Huang J. Toehold-mediated DNA strand displacement-driven super-fast tripedal DNA walker for ultrasensitive and label-free electrochemical detection of ochratoxin A. Anal Chim Acta 2020; 1143:21-30. [PMID: 33384119 DOI: 10.1016/j.aca.2020.11.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/28/2020] [Accepted: 11/13/2020] [Indexed: 11/18/2022]
Abstract
DNA walkers, as intelligent artificial DNA nanomachines, have been widely used as efficient nucleic acid amplification tools that the detection sensitivity can be improved by incorporating DNA walkers into DNA biosensors. Nevertheless, since the premature release or flameout in a region of locally exhausted substrate, the walking efficiency of DNA walkers remains unsatisfactory. In this work, we design a smart tripedal DNA walker that is formed by target-initiated catalyzed hairpin assembly (CHA), which can move along the DNA duplex tracks on electrode driven by toehold-mediated DNA strand displacement (TMSD) for transduction and amplification of electrochemical signals. Emphatically, this flexible tripedal DNA walker is capable of walking freely along the tracks with unconstrained walking range. Moreover, the design of multi-legged walker can weaken the derailment of leg DNA and shorten the moving time on electrode, ensuring the processive walking with high efficiency. Additionally, the persistent walking of tripedal walker is driven by cascading TMSD, which eliminates the defects of high cost and instability of enzyme-assisted amplification technology. Therefore, the tripedal DNA walker-based electrochemical biosensor has enormous potential for the applications of OTA detection, and reveals a new avenue for food safety analysis and clinical diagnosis.
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Affiliation(s)
- Yeru Wang
- School of Biological Sciences and Technology, University of Jinan, Jinan, 250022, PR China
| | - Yu Wang
- School of Biological Sciences and Technology, University of Jinan, Jinan, 250022, PR China
| | - Su Liu
- School of Water Conservancy and Environment, University of Jinan, Jinan, 250022, PR China
| | - Wenyu Sun
- School of Biological Sciences and Technology, University of Jinan, Jinan, 250022, PR China
| | - Manru Zhang
- School of Water Conservancy and Environment, University of Jinan, Jinan, 250022, PR China
| | - Long Jiang
- School of Water Conservancy and Environment, University of Jinan, Jinan, 250022, PR China
| | - Minghan Li
- School of Biological Sciences and Technology, University of Jinan, Jinan, 250022, PR China
| | - Jinghua Yu
- Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, PR China
| | - Jiadong Huang
- School of Biological Sciences and Technology, University of Jinan, Jinan, 250022, PR China; Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, PR China.
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29
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Su S, Ma J, Xu Y, Pan H, Zhu D, Chao J, Weng L, Wang L. Electrochemical Analysis of Target-Induced Hairpin-Mediated Aptamer Sensors. ACS APPLIED MATERIALS & INTERFACES 2020; 12:48133-48139. [PMID: 32955243 DOI: 10.1021/acsami.0c12897] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The state of probe DNA at the biosensing interface greatly affects the detection performance of electrochemical DNA biosensors. Herein, we constructed a target-induced hairpin-mediated biosensing interface to study the effect of probe DNA on the analytical performance of adenosine triphosphate aptamer (ATPA) and adenosine triphosphate (ATP) detection. Moreover, we also explored the electrochemical contribution of the coexisting hairpin and double-stranded DNA (dsDNA) to this sensing interface. Experimental results suggested that the molecular recognition ability and detection performance of the biosensing interface were majorly dependent on the surface density of methylene blue (MB)-labeled probe hairpin DNA and partly affected by the spatial state of the formed dsDNA. When the surface density of hairpin DNA was moderate (5.72 pmol cm-2), this sensing interface determined as low as 0.74 fM ATPA and 5.04 pM ATP with high selectivity and excellent regeneration, respectively. Furthermore, we calculated that the formed dsDNA had a 31.87% contribution in the total electrochemical signal for 10 pM ATPA detection. Based on the above results, we designed an XOR logic gate based on the biosensing interface for ATPA and ATP detection.
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Affiliation(s)
- Shao Su
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Jianfeng Ma
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Yongqiang Xu
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Hemeng Pan
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Dan Zhu
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Jie Chao
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Lixing Weng
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
- College of Geography and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Lianhui Wang
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
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30
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Mao J, Chen X, Xu H, Xu X. DNAzyme-driven DNA walker biosensor for amplified electrochemical detection of T4 polynucleotide kinase activity and inhibition. J Electroanal Chem (Lausanne) 2020. [DOI: 10.1016/j.jelechem.2020.114470] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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A molecular device: A DNA molecular lock driven by the nicking enzymes. Comput Struct Biotechnol J 2020; 18:2107-2116. [PMID: 32913580 PMCID: PMC7451616 DOI: 10.1016/j.csbj.2020.08.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 07/28/2020] [Accepted: 08/01/2020] [Indexed: 11/22/2022] Open
Abstract
As people are placing more and more importance on information security, how to realize the protection of information has become a hotspot of current research. As a security device, DNA molecular locks have great potential to realize information protection at the molecular level. However, building a highly secure molecular lock is still a serious challenge. Therefore, taking advantage of the DNA strand displacement and enzyme control technology, we constructed a molecular lock with a self-destructive mechanism. This molecular lock is mainly composed of logic circuits and takes nicking enzymes as inputs. To build this molecular lock, we first constructed a series of cascade circuits, including a YES–YES cascade circuit and a YES–AND cascade circuit. Then, an Inhibit logic gate was constructed to explore the inhibitory properties between different combinations of two nicking enzymes. Finally, using the characteristics of mutual inhibition between several enzymes, a DNA molecular lock driven by three nicking enzymes was constructed. In this molecular device, only the correct sequence of nicking enzymes can be input to ensure the normal operation of the molecular lock. Once the wrong password is entered, the device will be destroyed and cannot be recovered, which effectively prevents intruders from cracking the lock through exhaustive methods. The molecular lock has the function of simulating an electronic keyboard, which can realize the protection of information at the molecular level, and provides a new implementation method for building more advanced and complex molecular devices.
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Wu N, Wang K, Wang YT, Chen ML, Chen XW, Yang T, Wang JH. Three-Dimensional DNA Nanomachine Biosensor by Integrating DNA Walker and Rolling Machine Cascade Amplification for Ultrasensitive Detection of Cancer-Related Gene. Anal Chem 2020; 92:11111-11118. [PMID: 32646212 DOI: 10.1021/acs.analchem.0c01074] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Stochastic DNA walkers capable of traversing on three-dimensional (3D) tracks have received great deal of attention. However, DNA walker-based biosensors exhibit limited amplification efficiency because of their slow walking kinetics and low processivity. Herein, by taking advantage of the high processivity of a DNA rolling machine, a sensitive ratiometric DNA nanomachine biosensor is designed. The biosensor is constructed with hairpin-loaded Au nanoparticles (NPs) (hpDNA@AuNPs) as a DNA walker and AgNCs-decorated magnetic NPs (AgNCs@MNPs) as a DNA rolling machine. In the presence of target DNA, exonuclease III (Exo III)-powered DNA walker is activated to accomplish first-stage amplification via a burnt-bridge mechanism, generating a great deal of toehold-loaded AuNPs (Toehold@AuNPs) to hybridize with magnetic nanoparticles loaded with silver-nanoclusters-labeled DNA (AgNCs@MNPs) with the assistance of Exo III. These trigger rapid rolling of AuNPs on the AgNCs@MNPs surface and release free AgNCs, converting the biological signal into a mass spectrometric signal ratio (107Ag/197Au) with detection by ICP-MS. A linear range of 0.5-500 fmol L-1 is achieved with a detection limit of 119 amol L-1 for the p53 gene. The practical applicability of the biosensor has been demonstrated in the accurate assay of the p53 gene in the human blood.
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Affiliation(s)
- Na Wu
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Kun Wang
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Yi-Ting Wang
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Ming-Li Chen
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Xu-Wei Chen
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Ting Yang
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Jian-Hua Wang
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China
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Chen Z, Liu X, Liu D, Li F, Wang L, Liu S. Ultrasensitive Electrochemical DNA Biosensor Fabrication by Coupling an Integral Multifunctional Zirconia-Reduced Graphene Oxide-Thionine Nanocomposite and Exonuclease I-Assisted Cleavage. Front Chem 2020; 8:521. [PMID: 32733846 PMCID: PMC7363972 DOI: 10.3389/fchem.2020.00521] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/19/2020] [Indexed: 12/17/2022] Open
Abstract
In this work, a simple but sensitive electrochemical DNA biosensor for nucleic acid detection was developed by taking advantage of exonuclease (Exo) I-assisted cleavage for background reduction and zirconia-reduced graphene oxide-thionine (ZrO2-rGO-Thi) nanocomposite for integral DNA recognition, signal amplification, and reporting. The ZrO2-rGO nanocomposite was obtained by a one-step hydrothermal synthesis method. Then, thionine was adsorbed onto the rGO surface, via π-π stacking, as an excellent electrochemical probe. The biosensor fabrication is very simple, with probe DNA immobilization and hybridization recognition with the target nucleic acid. Then, the ZrO2-rGO-Thi nanocomposite was captured onto an electrode via the multicoordinative interaction of ZrO2 with the phosphate group on the DNA skeleton. The adsorbed abundant thionine molecules onto the ZrO2-rGO nanocomposite facilitated an amplified electrochemical response related with the target DNA. Since upon the interaction of the ZrO2-rGO-Thi nanocomposite with the probe DNA an immobilized electrode may also occur, an Exo I-assisted cleavage was combined to remove the unhybridized probe DNA for background reduction. With the current proposed strategy, the target DNA related with P53 gene could be sensitively assayed, with a wide linear detection range from 100 fM to 10 nM and an attractive low detection limit of 24 fM. Also, the developed DNA biosensor could differentiate the mismatched targets from complementary target DNA. Therefore, it offers a simple but effective biosensor fabrication strategy and is anticipated to show potential for applications in bioanalysis and medical diagnosis.
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Affiliation(s)
- Zhiqiang Chen
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Xueqian Liu
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Dengren Liu
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Fang Li
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Li Wang
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Shufeng Liu
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, China
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Hu Y, Wang Y, Yan J, Wen N, Xiong H, Cai S, He Q, Peng D, Liu Z, Liu Y. Dynamic DNA Assemblies in Biomedical Applications. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2000557. [PMID: 32714763 PMCID: PMC7375253 DOI: 10.1002/advs.202000557] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 04/07/2020] [Indexed: 05/13/2023]
Abstract
Deoxyribonucleic acid (DNA) has been widely used to construct homogeneous structures with increasing complexity for biological and biomedical applications due to their powerful functionalities. Especially, dynamic DNA assemblies (DDAs) have demonstrated the ability to simulate molecular motions and fluctuations in bionic systems. DDAs, including DNA robots, DNA probes, DNA nanochannels, DNA templates, etc., can perform structural transformations or predictable behaviors in response to corresponding stimuli and show potential in the fields of single molecule sensing, drug delivery, molecular assembly, etc. A wave of exploration of the principles in designing and usage of DDAs has occurred, however, knowledge on these concepts is still limited. Although some previous reviews have been reported, systematic and detailed reviews are rare. To achieve a better understanding of the mechanisms in DDAs, herein, the recent progress on the fundamental principles regarding DDAs and their applications are summarized. The relative assembly principles and computer-aided software for their designing are introduced. The advantages and disadvantages of each software are discussed. The motional mechanisms of the DDAs are classified into exogenous and endogenous stimuli-triggered responses. The special dynamic behaviors of DDAs in biomedical applications are also summarized. Moreover, the current challenges and future directions of DDAs are proposed.
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Affiliation(s)
- Yaqin Hu
- Department of Pharmaceutical EngineeringCollege of Chemistry and Chemical EngineeringCentral South UniversityChangshaHunan410083P. R. China
| | - Ying Wang
- Department of Pharmaceutical EngineeringCollege of Chemistry and Chemical EngineeringCentral South UniversityChangshaHunan410083P. R. China
| | - Jianhua Yan
- Xiangya School of Pharmaceutical SciencesCentral South UniversityChangshaHunan410013P. R. China
| | - Nachuan Wen
- Department of Pharmaceutical EngineeringCollege of Chemistry and Chemical EngineeringCentral South UniversityChangshaHunan410083P. R. China
| | - Hongjie Xiong
- Xiangya School of Pharmaceutical SciencesCentral South UniversityChangshaHunan410013P. R. China
| | - Shundong Cai
- Xiangya School of Pharmaceutical SciencesCentral South UniversityChangshaHunan410013P. R. China
| | - Qunye He
- Xiangya School of Pharmaceutical SciencesCentral South UniversityChangshaHunan410013P. R. China
| | - Dongming Peng
- Department of Medicinal ChemistrySchool of PharmacyHunan University of Chinese MedicineChangshaHunan410013P. R. China
| | - Zhenbao Liu
- Xiangya School of Pharmaceutical SciencesCentral South UniversityChangshaHunan410013P. R. China
- Molecular Imaging Research Center of Central South UniversityChangshaHunan410013P. R. China
| | - Yanfei Liu
- Department of Pharmaceutical EngineeringCollege of Chemistry and Chemical EngineeringCentral South UniversityChangshaHunan410083P. R. China
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Yin Z, Cui H, Shu Q, Jin C, Lin Y, Su J, Huang H, Liao F, Ma G, Hong N, Jiang Y, Fan H. Multi-signal amplification electrochemical DNA biosensor based on exonuclease III and tetraferrocene. J Mater Chem B 2020; 8:4143-4150. [PMID: 32270173 DOI: 10.1039/d0tb00204f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Homogeneous electrochemical DNA biosensors' unique qualities have been of great interest to researchers, mainly due to their high recognition efficiency in solutions. However, the processes of introducing additional markers and extra operations to obtain a signal are tedious and time consuming, which limits their overall potential applications. Herein, a novel tetraferrocene was synthesized and used as a homogeneous electrochemical DNA biosensor probe label. It contains four ferrocene units, which provide greater signaling potential compared to monoferrocene. Furthermore, the target DNA triggers the digestion of the double hairpin DNA probe with the aid of exonuclease III, promoting short single stranded DNA probe formation. With the combination of the incorporated tetraferrocene labeled short DNA probe strands and graphene's ability to adsorb single stranded DNA, the hybridization process can produce an electrode signal provided by tetraferrocene. A low detection limit of 8.2 fM toward target DNA with excellent selectivity was achieved. The proposed sensing system avoids tedious and time-consuming steps of DNA modification, making the experimental processes simpler and convenient. The advantages of high sensitivity, selectivity and simple operation make this strategy applicable to DNA detection.
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Affiliation(s)
- Zhaojiang Yin
- The Affiliated Hospital, Department of Pharmacy, JiangXi University of Traditional Chinese Medicine, JiangXi 330004, China.
| | - Hanfeng Cui
- The Affiliated Hospital, Department of Pharmacy, JiangXi University of Traditional Chinese Medicine, JiangXi 330004, China.
| | - Qingxia Shu
- The Affiliated Hospital, Department of Pharmacy, JiangXi University of Traditional Chinese Medicine, JiangXi 330004, China.
| | - Chen Jin
- The Affiliated Hospital, Department of Pharmacy, JiangXi University of Traditional Chinese Medicine, JiangXi 330004, China.
| | - Yan Lin
- The Affiliated Hospital, Department of Pharmacy, JiangXi University of Traditional Chinese Medicine, JiangXi 330004, China.
| | - Jia Su
- South University of Science and Technology of China, Shenzhen 518055, China
| | - HuiLian Huang
- The Affiliated Hospital, Department of Pharmacy, JiangXi University of Traditional Chinese Medicine, JiangXi 330004, China.
| | - Fusheng Liao
- The Affiliated Hospital, Department of Pharmacy, JiangXi University of Traditional Chinese Medicine, JiangXi 330004, China.
| | - Guangqiang Ma
- The Affiliated Hospital, Department of Pharmacy, JiangXi University of Traditional Chinese Medicine, JiangXi 330004, China.
| | - Nian Hong
- The Affiliated Hospital, Department of Pharmacy, JiangXi University of Traditional Chinese Medicine, JiangXi 330004, China.
| | - Yunfeng Jiang
- The Affiliated Hospital, Department of Pharmacy, JiangXi University of Traditional Chinese Medicine, JiangXi 330004, China.
| | - Hao Fan
- The Affiliated Hospital, Department of Pharmacy, JiangXi University of Traditional Chinese Medicine, JiangXi 330004, China.
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36
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Oishi M, Saito K. Simple Single-Legged DNA Walkers at Diffusion-Limited Nanointerfaces of Gold Nanoparticles Driven by a DNA Circuit Mechanism. ACS NANO 2020; 14:3477-3489. [PMID: 32053345 DOI: 10.1021/acsnano.9b09581] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We designed and prepared a single-legged DNA walker that relies on the creation of a simple diffusion-limited nanointerface on a gold nanoparticle (DNA/PEG(+)-GNP) track co-modified with fluorescence-labeled hairpin DNA and poly(ethylene glycol) (PEG) containing a positively charged amino group at one end. The movement of our single-legged DNA walker is driven by an enzyme-free DNA circuit mechanism through cascading toehold mediated DNA displacement reactions (TMDRs) using fuel hairpin DNAs. The acceleration of TMDRs was observed for the DNA/PEG(+)-GNP track through electrostatic interaction between the positively charged track and negatively charged DNAs, resulting in the acceleration of the DNA circuit and amplification of the fluorescence signal. Furthermore, the DNA/PEG(+)-GNP track allowed autonomous and persistent movement of a walker DNA strand on the same GNP track, because the intraparticle DNA circuit occurred preferentially by preventing diffusion of the negatively charged free walker DNA strand from near the positively charged tracks into solution through electrostatic interaction. Based on comparative study of kinetics of TMDRs and DNA walking behaviors, it is to be noted that the DNA/PEG(+)-GNP track showed the fastest DNA circuit reaction (walking rate) and the largest number of steps taken by the walker DNA strand compared to other GNP tracks with varying nanointerfaces that differ in terms of their type of charges (no and negative charges), density of positive charges, and number of hairpin DNAs per GNP track. These facts reveal that the positive charges on the GNP track play an important role in the acceleration of the DNA circuit, as well as the successful walking motion of the single-legged DNA strand. By using the fluorescence signal amplification functions, our single-legged DNA walker could be applied directly and successfully to enzyme-free miRNA-detection systems. The miRNA-detection system provided higher discrimination of other mismatched miRNAs and higher sensitivity (the lowest LOD: 4.0 pM) when compared to other miRNA-detection systems based on other GNP tracks without positive charges. Unlike existing single-legged DNA walkers, our single-legged DNA walkers do not require complex processes, such as immobilization of the walker DNA strand on the tracks and precise adjustment of the sequence of walker DNA. Therefore, our strategy, based on the creation of diffusion-limited nanointerfaces, has enormous potential for the applications of single-legged DNA walkers to biosensors, bioimaging, and computing.
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Affiliation(s)
- Motoi Oishi
- Division of Materials Science, Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8573, Japan
| | - Kosuke Saito
- Division of Materials Science, Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8573, Japan
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37
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Li D, Xu Y, Fan L, Shen B, Ding X, Yuan R, Li X, Chen W. Target-driven rolling walker based electrochemical biosensor for ultrasensitive detection of circulating tumor DNA using doxorubicin@tetrahedron-Au tags. Biosens Bioelectron 2020; 148:111826. [DOI: 10.1016/j.bios.2019.111826] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/05/2019] [Accepted: 10/25/2019] [Indexed: 12/12/2022]
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38
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Chen J, Luo Z, Sun C, Huang Z, Zhou C, Yin S, Duan Y, Li Y. Research progress of DNA walker and its recent applications in biosensor. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.115626] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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39
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Zhou X, Zhang W, Wang Z, Han J, Xie G, Chen S. Ultrasensitive aptasensing of insulin based on hollow porous C 3N 4/S 2O 82-/AuPtAg ECL ternary system and DNA walker amplification. Biosens Bioelectron 2019; 148:111795. [PMID: 31665673 DOI: 10.1016/j.bios.2019.111795] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/16/2019] [Accepted: 10/17/2019] [Indexed: 11/29/2022]
Abstract
In this work, a high-efficiency electrochemiluminescence (ECL) ternary system was constructed for ultrasensitive assay of insulin based on hollow porous graphitic carbon nitride (HP-C3N4) as novel luminophore, S2O82- as coreactant and tri-metallic AuPtAg as coreaction accelerator. Specifically, in comparison with C3N4-based bulk nanomaterials, the as-prepared HP-C3N4 exhibits high luminous efficiency though decreased inner filter effect and minimized inactive ECL emitter. Noteworthy, tri-metallic AuPtAg, possessing the superiority of Au, Pt and Ag, was first used as coreaction accelerator to significantly enhance ECL intensity of HP-C3N4 and S2O82-. As a consequence, with the resultant ECL ternary (HP-C3N4/S2O82-/AuPtAg) system as aptasensing platform, a high-intense initial ECL signal was achieved. Subsequently, ferrocene-labeled quenching probe (Fc-HP2) as ECL quencher was used to quench the initial signal and achieve the low-background noise. Eventually, in the presence of insulin, the target-induced triple-helix molecular switch and Nb.BbvCI-assisted DNA walker amplification were executed to recover a strong ECL signal by releasing Fc-HP2 from the electrode surface. As expected, the constructed aptasensor presents an excellent sensitivity and selectivity for detecting insulin range from 0.05 pg mL-1 to 100 ng mL-1 with a detection limit of 17 fg mL-1. This work provides a new avenue for developing highly efficient HP-C3N4 based ECL ternary system as well as ultrasensitive ECL aptasensors for bioanalysis.
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Affiliation(s)
- Xumei Zhou
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, Shaanxi, 710127, PR China
| | - Wen Zhang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, Shaanxi, 710127, PR China
| | - Zhen Wang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, Shaanxi, 710127, PR China
| | - Jing Han
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, Shaanxi, 710127, PR China.
| | - Gang Xie
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, Shaanxi, 710127, PR China
| | - Sanping Chen
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, Shaanxi, 710127, PR China.
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Jahanban-Esfahlan R, Seidi K, Jahanban-Esfahlan A, Jaymand M, Alizadeh E, Majdi H, Najjar R, Javaheri T, Zare P. Static DNA Nanostructures For Cancer Theranostics: Recent Progress In Design And Applications. Nanotechnol Sci Appl 2019; 12:25-46. [PMID: 31686793 PMCID: PMC6800557 DOI: 10.2147/nsa.s227193] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 09/13/2019] [Indexed: 12/13/2022] Open
Abstract
Among the various nano/biomaterials used in cancer treatment, the beauty and benefits of DNA nanocomposites are outstanding. The specificity and programmability of the base pairing of DNA strands, together with their ability to conjugate with different types of functionalities have realized unsurpassed potential for the production of two- and three-dimensional nano-sized structures in any shape, size, surface chemistry and functionality. This review aims to provide an insight into the diversity of static DNA nanodevices, including DNA origami, DNA polyhedra, DNA origami arrays and bioreactors, DNA nanoswitch, DNA nanoflower, hydrogel and dendrimer as young but promising platforms for cancer theranostics. The utility and potential of the individual formats in biomedical science and especially in cancer therapy will be discussed.
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Affiliation(s)
- Rana Jahanban-Esfahlan
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz9841, Iran
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz9841, Iran
| | - Khaled Seidi
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz9841, Iran
| | | | - Mehdi Jaymand
- Nano Drug Delivery Research Center (NDDRC), Kermanshah University of Medical Sciences, Kermanshah9883, Iran
| | - Effat Alizadeh
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz9841, Iran
| | - Hasan Majdi
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz9841, Iran
| | - Reza Najjar
- Polymer Research Laboratory, Faculty of Chemistry, University of Tabriz, Tabriz9841, Iran
| | - Tahereh Javaheri
- Ludwig Boltzmann Institute for Cancer Research, Vienna1090, Austria
| | - Peyman Zare
- Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw01-938, Poland
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41
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Kogikoski S, Paschoalino WJ, Cantelli L, Silva W, Kubota LT. Electrochemical sensing based on DNA nanotechnology. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.06.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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42
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Abstract
Specific nucleic acid detection in vitro or in vivo has become increasingly important in the discovery of genetic diseases, diagnosing pathogen infection and monitoring disease treatment. One challenge, however, is that the amount of target nucleic acid in specimens is limited. Furthermore, direct sensing methods are also unable to provide sufficient sensitivity and specificity. Fortunately, due to advances in nanotechnology and nanomaterials, nanotechnology-based bioassays have emerged as powerful and promising approaches providing ultra-high sensitivity and specificity in nucleic acid detection. This chapter presents an overview of strategies used in the development and integration of nanotechnology for nucleic acid detection, including optical and electrical detection methods, and nucleic acid assistant recycling amplification strategies. Recent 5 years representative examples are reviewed to demonstrate the proof-of-concept with promising applications for DNA/RNA detection and the underlying mechanism for detection of DNA/RNA with the higher sensitivity and selectivity. Furthermore, a brief discussion of common unresolved issues and future trends in this field is provided both from fundamental and practical point of view.
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Affiliation(s)
- Hong Zhou
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi, China
| | - Jing Liu
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi, China
| | - Jing-Juan Xu
- Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China.
| | - Shusheng Zhang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi, China.
| | - Hong-Yuan Chen
- Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
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43
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Ma X, Miao P. Silver nanoparticle@DNA tetrahedron-based colorimetric detection of HIV-related DNA with cascade strand displacement amplification. J Mater Chem B 2019; 7:2608-2612. [PMID: 32254992 DOI: 10.1039/c9tb00274j] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
DNA tetrahedron-modified silver nanoparticles (AgNPs) were achieved via amino-silver chemistry for the first time and were applied as a colorimetric biosensor for detecting HIV-related DNA. Target DNA initiated strand displacement polymerization and nicking endonuclease-aided cycles were involved to link DNA tetrahedron-modified AgNPs, reporting colorimetric responses. This developed method showed excellent specificity and sensitivity. A wide linear range from 1 to 15 000 nM was achieved with a limit of detection of 0.84 nM. Moreover, it was successfully applied to determine DNA in blood serum samples.
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Affiliation(s)
- Xiaoyi Ma
- University of Science and Technology of China, Hefei 230026, China.
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44
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Wang S, Ji Y, Fu H, Ju H, Lei J. A rolling circle amplification-assisted DNA walker triggered by multiple DNAzyme cores for highly sensitive electrochemical biosensing. Analyst 2019; 144:691-697. [DOI: 10.1039/c8an01892h] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A DNA walker triggered by multiple DNAzyme cores was constructed with the assistance of rolling circle amplification for electrochemical biosensing.
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Affiliation(s)
- Sina Wang
- State Key Laboratory of Analytical Chemistry for Life Science
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210023
- China
| | - Yuhang Ji
- State Key Laboratory of Analytical Chemistry for Life Science
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210023
- China
| | - Haomin Fu
- State Key Laboratory of Analytical Chemistry for Life Science
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210023
- China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210023
- China
| | - Jianping Lei
- State Key Laboratory of Analytical Chemistry for Life Science
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210023
- China
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45
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Qin P, Yao L, Xu J, Liu G, Chen W. Smart engineering of a dual-DNA machine with a high signal-to-noise ratio for one-pot robust and sensitive miRNA signaling. Chem Commun (Camb) 2019; 55:14367-14370. [DOI: 10.1039/c9cc07442b] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A target triggered dual-DNA machine composed of RCA and SDA was developed for robust and one-pot determination of miRNA.
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Affiliation(s)
- Panzhu Qin
- Engineering Research Center of Bioprocess
- MOE
- School of Food and Biological Engineering
- Hefei University of Technology
- Hefei
| | - Li Yao
- Engineering Research Center of Bioprocess
- MOE
- School of Food and Biological Engineering
- Hefei University of Technology
- Hefei
| | - Jianguo Xu
- Engineering Research Center of Bioprocess
- MOE
- School of Food and Biological Engineering
- Hefei University of Technology
- Hefei
| | - Guodong Liu
- Department of Chemistry and Biochemistry
- North Dakota State University
- Fargo
- USA
- Research Center for Biomedical and Health Science
| | - Wei Chen
- Engineering Research Center of Bioprocess
- MOE
- School of Food and Biological Engineering
- Hefei University of Technology
- Hefei
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46
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Wang K, Zhai FH, He MQ, Wang J, Yu YL, He RH. A simple enzyme-assisted cascade amplification strategy for ultrasensitive and label-free detection of DNA. Anal Bioanal Chem 2018; 411:4569-4576. [DOI: 10.1007/s00216-018-1422-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 09/19/2018] [Accepted: 10/05/2018] [Indexed: 02/07/2023]
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47
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Li Y, Wang GA, Mason SD, Yang X, Yu Z, Tang Y, Li F. Simulation-guided engineering of an enzyme-powered three dimensional DNA nanomachine for discriminating single nucleotide variants. Chem Sci 2018; 9:6434-6439. [PMID: 30310573 PMCID: PMC6115701 DOI: 10.1039/c8sc02761g] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 06/30/2018] [Indexed: 12/15/2022] Open
Abstract
Single nucleotide variants (SNVs) are important both clinically and biologically because of their profound biological consequences. Herein, we engineered a nicking endonuclease-powered three dimensional (3D) DNA nanomachine for discriminating SNVs with high sensitivity and specificity. Particularly, we performed a simulation-guided tuning of sequence designs to achieve the optimal trade-off between device efficiency and specificity. We also introduced an auxiliary probe, a molecular fuel capable of tuning the device in solution via noncovalent catalysis. Collectively, our device produced discrimination factors comparable with commonly used molecular probes but improved the assay sensitivity by ∼100 times. Our results also demonstrate that rationally designed DNA probes through computer simulation can be used to quantitatively improve the design and operation of complexed molecular devices and sensors.
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Affiliation(s)
- Yongya Li
- Department of Chemistry , Centre for Biotechnology , Brock University , 1812 Sir Isaac Brock Way , St. Catharines , Ontario L2S 3A1 , Canada .
| | - Guan A Wang
- Department of Chemistry , Centre for Biotechnology , Brock University , 1812 Sir Isaac Brock Way , St. Catharines , Ontario L2S 3A1 , Canada .
| | - Sean D Mason
- Department of Chemistry , Centre for Biotechnology , Brock University , 1812 Sir Isaac Brock Way , St. Catharines , Ontario L2S 3A1 , Canada .
| | - Xiaolong Yang
- Department of Chemistry , Centre for Biotechnology , Brock University , 1812 Sir Isaac Brock Way , St. Catharines , Ontario L2S 3A1 , Canada .
| | - Zechen Yu
- Department of Chemistry , Centre for Biotechnology , Brock University , 1812 Sir Isaac Brock Way , St. Catharines , Ontario L2S 3A1 , Canada .
| | - Yanan Tang
- Department of Chemistry , Centre for Biotechnology , Brock University , 1812 Sir Isaac Brock Way , St. Catharines , Ontario L2S 3A1 , Canada .
- College of Chemistry , Sichuan University , 29 Wangjiang Road , Chengdu , Sichuan , China 610064
| | - Feng Li
- Department of Chemistry , Centre for Biotechnology , Brock University , 1812 Sir Isaac Brock Way , St. Catharines , Ontario L2S 3A1 , Canada .
- College of Chemistry , Sichuan University , 29 Wangjiang Road , Chengdu , Sichuan , China 610064
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48
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Zeng R, Su L, Luo Z, Zhang L, Lu M, Tang D. Ultrasensitive and label-free electrochemical aptasensor of kanamycin coupling with hybridization chain reaction and strand-displacement amplification. Anal Chim Acta 2018; 1038:21-28. [PMID: 30278904 DOI: 10.1016/j.aca.2018.07.010] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 06/29/2018] [Accepted: 07/04/2018] [Indexed: 12/17/2022]
Abstract
This work reports the proof-of-concept of an ultrasensitive label-free electrochemical aptasensor for Kanamycin (Kana) detection coupling strand-displacement amplification (SDA) with hybridization chain reaction (HCR). In the presence of target Kana, the analyte triggers conformational change of hairpin HP1 (HP1) and two-staged SDA to produce short single-stranded DNA (S1) with the aid of KF polymerase and nicking endonuclease. Meanwhile, the as-produced S1 hybridizes with the immobilized hairpin HP2 (HP2) on the electrode to open the hairpin, thereby resulting in the formation of DNA duplex. Thereafter, DNA duplex is selectively digested by Exo III accompanying S1 recycling. The residual single-stranded probe (S2) on the electrode opens another two hairpins in sequence and propagates a chain reaction of hybridization events between two alternating hairpins (H1 and H2) to form a long nicked double-helix. Upon addition of redox-active methylene blue (MB), numerous indicators are intercalated into the grooves of double-helix DNA polymers, each of which produces an electrochemical signal within the applied potentials. Under optimum conditions, the SDA/HCR-based electrochemical aptasensor exhibits a high sensitivity for detection of Kana down to 36 fM with a linear range from 0.05 to 200 pM. Additionally, the as-prepared aptasensor is successfully employed to determinate the Kana in animal derived food (milk). With the advantages of high sensitivity, label-free strategy and excellent selectivity, the developed aptasensor possesses great potential application value in food-safety analysis field.
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Affiliation(s)
- Ruijin Zeng
- Key Laboratory of Analysis and Detection for Food Safety (Ministry of Education and Fujian Province), Institute of Nanomedicine and Nanobiosensing, Department of Chemistry, Fuzhou University, Fuzhou 350108, PR China
| | - Lingshan Su
- Key Laboratory of Analysis and Detection for Food Safety (Ministry of Education and Fujian Province), Institute of Nanomedicine and Nanobiosensing, Department of Chemistry, Fuzhou University, Fuzhou 350108, PR China
| | - Zhongbin Luo
- Key Laboratory of Analysis and Detection for Food Safety (Ministry of Education and Fujian Province), Institute of Nanomedicine and Nanobiosensing, Department of Chemistry, Fuzhou University, Fuzhou 350108, PR China
| | - Lijia Zhang
- Key Laboratory of Analysis and Detection for Food Safety (Ministry of Education and Fujian Province), Institute of Nanomedicine and Nanobiosensing, Department of Chemistry, Fuzhou University, Fuzhou 350108, PR China
| | - Minghua Lu
- Institute of Environmental and Analytical Science, School of Chemistry and Chemical Engineering, Henan University, Kaifeng 475004, Henan, PR China.
| | - Dianping Tang
- Key Laboratory of Analysis and Detection for Food Safety (Ministry of Education and Fujian Province), Institute of Nanomedicine and Nanobiosensing, Department of Chemistry, Fuzhou University, Fuzhou 350108, PR China.
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49
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Wang K, Feng M, He MQ, Zhai FH, Dai Y, He RH, Yu YL. DNA-fueled target recycling-induced two-leg DNA walker for amplified electrochemical detection of nucleic acid. Talanta 2018; 188:685-690. [PMID: 30029432 DOI: 10.1016/j.talanta.2018.06.049] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/11/2018] [Accepted: 06/13/2018] [Indexed: 12/13/2022]
Abstract
Taking advantage of the homogeneous and heterogeneous electrochemical biosensors, a simple, sensitive, and selective electrochemical biosensor is constructed by combining entropy-driven amplification (EDA) with DNA walker. This electrochemical biosensor realizes the biorecognition and EDA operation in homogeneous solution, which is beneficial to improve the recognition and amplification efficiency. A two-leg DNA walker generated by EDA can walk on the surface of gold electrode for cleaving the immobilized substrate DNA and releasing the electroactive labels, giving rise to a significant decrease of the electrochemical signal. The immobilization of the electroactive labels ensures the reproducibility and reliability of the biosensor. The present cascade amplification assay can be applied to detect target DNA with a detection limit of 0.29 fM, and base mutations can be easily distinguished. Moreover, the proposed electrochemical biosensor shows a satisfactory performance for the detection of target DNA in human serum. Thus, the novel electrochemical biosensor holds promising potential for a future application in disease diagnosis.
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Affiliation(s)
- Kun Wang
- Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Min Feng
- The first Affiliated Hospital of Dalian Medical University, Dalian 116011, China
| | - Meng-Qi He
- Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Fu-Heng Zhai
- Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Yu Dai
- Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Rong-Huan He
- Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China.
| | - Yong-Liang Yu
- Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China.
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50
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Cui Y, Han X, An R, Zhou G, Komiyama M, Liang X. Cyclization of secondarily structured oligonucleotides to single-stranded rings by using Taq DNA ligase at high temperatures. RSC Adv 2018; 8:18972-18979. [PMID: 35539641 PMCID: PMC9080623 DOI: 10.1039/c8ra02804d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 05/10/2018] [Indexed: 11/21/2022] Open
Abstract
Single-stranded DNA rings play important roles in nanoarchitectures, molecular machines, DNA detection, etc. Although T4 DNA ligase has been widely employed to cyclize single-stranded oligonucleotides into rings, the cyclization efficiency is very low when the oligonucleotides (l-DNAs) take complicated secondary structures at ambient temperatures. In the present study, this problem has been solved by using Thermus aquaticus DNA ligase (Taq DNA ligase) at higher temperatures (65 and 70 °C) where the secondary structures are less stable or completely destroyed. This method is based on our new finding that this ligase successfully functions even when the splint strand is short and forms no stable duplex with l-DNA (at least in the absence of the enzyme). In order to increase the efficiency of cyclization, various operation factors (lengths and sequences of splint, as well as the size of the DNA ring) have been investigated. Based on these results, DNA rings have been successfully synthesized from secondarily structured oligonucleotides in high yields and high selectivity. The present methodology is applicable to the preparation of versatile DNA rings involving complicated secondary structures, which should show novel properties and greatly widen the scope of DNA-based nanotechnology. We have achieved the efficient preparation of single-stranded DNA rings from secondarily structured oligonucleotides.![]()
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Affiliation(s)
- Yixiao Cui
- College of Food Science and Engineering
- Ocean University of China
- Qingdao 266003
- China
| | - Xutiange Han
- College of Food Science and Engineering
- Ocean University of China
- Qingdao 266003
- China
| | - Ran An
- College of Food Science and Engineering
- Ocean University of China
- Qingdao 266003
- China
- Laboratory for Marine Drugs and Bioproducts
| | - Guangqing Zhou
- College of Food Science and Engineering
- Ocean University of China
- Qingdao 266003
- China
| | - Makoto Komiyama
- College of Food Science and Engineering
- Ocean University of China
- Qingdao 266003
- China
- National Institute for Materials Science (NIMS)
| | - Xingguo Liang
- College of Food Science and Engineering
- Ocean University of China
- Qingdao 266003
- China
- Laboratory for Marine Drugs and Bioproducts
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