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Gao Y, Wang Y. Interplay of graphene-DNA interactions: Unveiling sensing potential of graphene materials. APPLIED PHYSICS REVIEWS 2024; 11:011306. [PMID: 38784221 PMCID: PMC11115426 DOI: 10.1063/5.0171364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Graphene-based materials and DNA probes/nanostructures have emerged as building blocks for constructing powerful biosensors. Graphene-based materials possess exceptional properties, including two-dimensional atomically flat basal planes for biomolecule binding. DNA probes serve as excellent selective probes, exhibiting specific recognition capabilities toward diverse target analytes. Meanwhile, DNA nanostructures function as placement scaffolds, enabling the precise organization of molecular species at nanoscale and the positioning of complex biomolecular assays. The interplay of DNA probes/nanostructures and graphene-based materials has fostered the creation of intricate hybrid materials with user-defined architectures. This advancement has resulted in significant progress in developing novel biosensors for detecting DNA, RNA, small molecules, and proteins, as well as for DNA sequencing. Consequently, a profound understanding of the interactions between DNA and graphene-based materials is key to developing these biological devices. In this review, we systematically discussed the current comprehension of the interaction between DNA probes and graphene-based materials, and elucidated the latest advancements in DNA probe-graphene-based biosensors. Additionally, we concisely summarized recent research endeavors involving the deposition of DNA nanostructures on graphene-based materials and explored imminent biosensing applications by seamlessly integrating DNA nanostructures with graphene-based materials. Finally, we delineated the primary challenges and provided prospective insights into this rapidly developing field. We envision that this review will aid researchers in understanding the interactions between DNA and graphene-based materials, gaining deeper insight into the biosensing mechanisms of DNA-graphene-based biosensors, and designing novel biosensors for desired applications.
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Affiliation(s)
- Yanjing Gao
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Yichun Wang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
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Shang X, Yan Y, Li J, Zhou X, Xiang X, Huang R, Li X, Ma C, Nie X. A turn-on fluorescent strategy for alkaline phosphatase detection based on enzyme-assisted signal amplification. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 286:121939. [PMID: 36219964 DOI: 10.1016/j.saa.2022.121939] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 09/09/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
As a representative biochemical indicator, alkaline phosphatase (ALP) is of great importance in indicating and diagnosing clinical diseases. Herein, we developed a signal-on fluorescence sensing method for sensitive ALP activity detection based on the enzyme-assisted target recycling (EATR) technique. In this method, a two-step signal amplification process is designed. In the presence of ALP, the 3' phosphate group of an ss-DNA is removed explicitly by ALP, thus releasing free 3'-OH. Terminal deoxynucleotidyl transferase (TdT) can subsequently extend this substrate to generate poly(A) tails, converting the trace-level ALP information into multiple sequences and achieving the first-time amplification. A poly(T) Taqman probe labeled with FAM and BHQ1 provides the second one under the assistance of T7 exonuclease (T7 Exo) through alternate hybridization and degradation of ds-DNA regions. The previously quenched fluorescence is recovered due to the departure of FAM/BHQ1 during the cleavage of T7 Exo. Thus, taking advantage of template-free TdT-mediated polymerization and T7 Exo-based EATR, this strategy shows a sensitive LOD at 0.0074 U/L (S/N = 3) and a linear range of 0.01-8 U/L between ALP concentration and fluorescence intensity. To further verify the specificity and accuracy in practical application, we challenged it in a set of co-existing interference and biological environments and have gained satisfying results. The proposed method successfully quantified the ALP levels in clinical human serum samples, suggesting its applicability in practical application. Moreover, we have used this method to investigate the inhibition effects of Na3VO4. Above all, the proposed assay is sensitive, facile, and cost-effective for ALP determining, holding a promising perspective and excellent potential in clinical diagnosis and drug screening.
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Affiliation(s)
- Xueling Shang
- Department of Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha 410013, China
| | - Ying Yan
- School of Life Sciences, Central South University, Changsha 410013, China
| | - Jian Li
- Department of Blood Transfusion, The Third Xiangya Hospital, Central South University, Changsha 410013, China
| | - Xi Zhou
- School of Life Sciences, Central South University, Changsha 410013, China
| | - Xinying Xiang
- School of Life Sciences, Central South University, Changsha 410013, China
| | - Rong Huang
- Department of Blood Transfusion, The Third Xiangya Hospital, Central South University, Changsha 410013, China
| | - Xisheng Li
- Department of Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha 410013, China
| | - Changbei Ma
- School of Life Sciences, Central South University, Changsha 410013, China.
| | - Xinmin Nie
- Department of Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha 410013, China; Hunan Engineering Technology Research Center of Optoelectronic Health Detection, Changsha 410013, China.
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Yang X, Liu X, Kang Q, Qi Y, Du Y, Xiang H. A novel DNA detection using spherical identification probe and strand displacement reaction-initiated silver nanocluster switch. ANAL SCI 2023; 39:275-284. [PMID: 36607557 PMCID: PMC9816546 DOI: 10.1007/s44211-022-00243-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/23/2022] [Indexed: 01/07/2023]
Abstract
Herein, we developed a novel fluorescent assay using spherical identification probes and toehold-mediated strand displacement reaction-initiated silver nanoclusters (AgNCs) "on-off" signal switch. In this strategy, the target was captured by the spherical probes to induce the activity of exonuclease III (Exo III), catalyzing the cyclic cleavage of substrates to produce a mass of trigger strands. After magnetic bead separation, the intermediates in the supernatant activated downstream toehold-mediated strand displacement reaction to change the structure of silver nanocluster templates, leading to fluorescence intensity reduction. Furthermore, it is demonstrated that the application of spherical identification probes could reduce the signal leakage and the limit of detection. In addition, AgNCs with perfect optical property were ingeniously combined to realize signal output, which reduced the cost and time of synthesis. Under the optimal conditions, the sensing method displayed a good linear range from 250 pM to 25 nM with a detectable minimum concentration of 250 pM. And the practical application potential in complex biological matrices was also evaluated. Considering these advantages, this constructed strategy opens a new path for nucleic acid detection with better performance. A simple, label- and hairpin-free fluorescent system based on spherical identification probe and toehold-mediated strand displacement reaction-initiated silver nanoclusters (AgNCs) "on-off" signal switch was successfully constructed to detect target DNA.
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Affiliation(s)
- Xiaoyan Yang
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016 People’s Republic of China
| | - Xiaoyu Liu
- Department of Clinical Laboratory, Guang’an People’ Hospital, Guang’an, People’s Republic of China
| | - Qi Kang
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016 People’s Republic of China
| | - Yinxiao Qi
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016 People’s Republic of China
| | - Yumin Du
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016 People’s Republic of China
| | - Hua Xiang
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, People's Republic of China.
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Wang W, Gao Y, Wang W, Zhang J, Li Q, Wu ZS. Ultrasensitive Electrochemical Detection of cancer-Related Point Mutations Based on Surface-Initiated Three-Dimensionally Self-Assembled DNA Nanostructures from Only Two Palindromic Probes. Anal Chem 2021; 94:1029-1036. [PMID: 34932325 DOI: 10.1021/acs.analchem.1c03991] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Sensitive and selective detection of proto-oncogenes, especially recognition of point mutation, is of great importance in cancer diagnosis. Here, a ligation-mediated technique is demonstrated for the construction of an intertwined three-dimensional DNA nanosheet (3D SDN) on an electrode surface from only two palindromic hairpin probes (HP1 and HP2), creating a powerful electrochemical biosensor (E-biosensor) for the detection of the p53 gene. First, a capturing probe (CP) is immobilized on an electrode surface via Au-S chemistry, forming an electrochemical sensing interface. In the presence of the target p53 (T), the triggering probe is covalently linked to CP by a ligase. Moreover, target hybridization/ligation/dehybridization process is repeated, amplifying the target hybridization event and increasing the content of surface-confined triggering fragments. As a result, HP1 is opened and in turn interacts with HP2, forming intertwined 3D SDN where HP1 and HP2 are alternately arranged in parallel. Common hybridization and interaction between palindromic fragments are responsible for the assembly in the horizontal and vertical directions, respectively. An electrochemical indicator, methylene blue (MB), can be inserted into 3D SDN, generating a strong electrochemical signal. Utilizing the 3D SDN-based E-biosensor, the target DNA is detected down to 3 fM with a linear response range from 10 fM to 10 nM. Single point mutations are reliably identified even in fetal bovine serum and cellular homogenate. Because of the several advantages of simple design, good universality, inexpensive instrumentation, high assay specificity, and sensitivity, the 3D SDN-based E-biosensor is expected to provide a potential platform for screening point mutation required by early clinical diagnostics and medical research.
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Affiliation(s)
- Weijun Wang
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 305108, China
| | - Yansha Gao
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 305108, China
| | - Wenqing Wang
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 305108, China
| | - Jingjing Zhang
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 305108, China
| | - Qian Li
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 305108, China
| | - Zai-Sheng Wu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 305108, China
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Ma K, Li X, Xu B, Tian W. Label-free bioassay with graphene oxide-based fluorescent aptasensors: A review. Anal Chim Acta 2021; 1188:338859. [PMID: 34794573 DOI: 10.1016/j.aca.2021.338859] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/15/2021] [Accepted: 07/16/2021] [Indexed: 12/12/2022]
Abstract
Bioassays using a fluorophore and DNA aptamer have been extensively developed due to the ultrasensitivity of fluorophores and recognition ability of DNA aptamers. Conventional fluorescent aptamer-based sensors (aptasensors) require chemical labeling between the fluorophore and aptamer and is technologically impracical for various sensing and assay applications. A simple "mix and go" strategy has been introduced that uses label-free technology as a platform for sensor development. The biosensors comprise a fluorophore, a ssDNA aptamer, and eco-friendly graphene oxide (GO). In the absence of the sensor target, GO quenches the fluorescence of the fluorophore and single-strand DNA aptamer complex. When the target is added, the DNA aptamer conformationally turns into a duplex, G-quadruplexe, or other secondary structure. This structure change leads to release of GO by the fluorophore-aptamer-target complex, generating dramatic fluorescence recovery and amplification. With this sensing method, the DNA aptamer does not need to be chemically labeled. Therefore, flexible fluorophore indicators and ssDNA aptamers can be used in this label-free aptasensing strategy. In this review, we discuss various unlabeled fluorophores, including synthetic small molecular fluorophores and genetically encoded fluorescent proteins, as indicators for generating GO-based fluorescent DNA aptasensors for label-free bioassay.
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Affiliation(s)
- Ke Ma
- Center of AIE Research, College of Materials Science and Engineering, Shenzhen University, Shenzhen, 518060, PR China
| | - Xing Li
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, PR China.
| | - Bin Xu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, PR China
| | - Wenjing Tian
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, PR China
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Wu H, Wang H, Wu J, Han G, Liu Y, Zou P. A novel fluorescent aptasensor based on exonuclease-assisted triple recycling amplification for sensitive and label-free detection of aflatoxin B1. JOURNAL OF HAZARDOUS MATERIALS 2021; 415:125584. [PMID: 33743380 DOI: 10.1016/j.jhazmat.2021.125584] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/26/2021] [Accepted: 03/02/2021] [Indexed: 06/12/2023]
Abstract
Aflatoxins are the most toxic type of mycotoxins, which may cause serious carcinogenesis, teratogenesis, and mutagenesis to humans and animals. In this work, we demonstrate a novel label-free fluorescent aptasensor based on exonuclease-assisted triple recycling amplification for the sensitive detection of aflatoxin B1 (AFB1). With the close cooperation of T7 exonuclease and three elaborately designed hairpin probes, the target AFB1 can perform three consecutive cycles of amplification reactions. In this process, each hairpin probe is fully utilized, and the target AFB1, the secondary target and the tertiary target are recycled, thereby achieving a high amplification. Interestingly and importantly, the secondary and tertiary targets generated by amplification are also excellent DNA template sequences for silver nanoclusters (AgNCs). In the presence of NaBH4 and AgNO3, a great number of DNA-AgNCs are synthesized, thereby producing a strong fluorescent signal. Under optimal conditions, the developed aptasensor exhibited high sensitivity to AFB1 with a low detection limit of 0.19 pg mL-1 and a wide dynamic range of 1 × 10-6-1 μg mL-1. In addition, the aptasensor also performed well in the determination of AFB1 in real samples.
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Affiliation(s)
- Hao Wu
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China.
| | - Hongyong Wang
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China
| | - Jun Wu
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China
| | - Guoqing Han
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China
| | - Yaling Liu
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China.
| | - Pei Zou
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China; Jiangsu Kanion Pharmaceutical CO. LTD, Lianyungang 222001, China; State Key Laboratory of New-tech for Chinese Medicine Pharmaceutical Process, Lianyungang 222001, China.
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Zhao Y, Li L, Ma R, Wang L, Yan X, Qi X, Wang S, Mao X. A competitive colorimetric aptasensor transduced by hybridization chain reaction-facilitated catalysis of AuNPs nanozyme for highly sensitive detection of saxitoxin. Anal Chim Acta 2021; 1173:338710. [PMID: 34172145 DOI: 10.1016/j.aca.2021.338710] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/25/2021] [Accepted: 05/26/2021] [Indexed: 12/14/2022]
Abstract
Saxitoxin (STX) is a small molecule toxin (Mw. ca. 299 g/mol) with high acute toxicity, and it has urgent need of facile analytical methods. Herein, a competitive colorimetric aptasensor was developed for highly sensitive detection of STX. An anti-STX aptamer was hybridized with a complementary strand on the magnetic beads and was competitively bound by STX. The supernatant containing the aptamer binding to STX was obtained by magnetic separation, which could trigger hybridization chain reaction (HCR) to generate rigid double stranded DNAs (dsDNAs) with sticky end and variable length. These HCR-dsDNAs were found to be able to facilitate significant enhancement on the peroxidase-like catalytic capability of AuNPs nanozyme towards 3,3,5,5-tetramethylbenzidine (TMB). The concentration of STX was responded in a "turn on" mode, based on the amplified colorimetric transduction thereof. The aptasensor realized high sensitivity, with a limit of detection (LOD) as low as 42.46 pM. Moreover, a wide linear detection range of 78.13-2500 pM, good selectivity, as well as good recovery rates of 106.2-113.5% when analyzing STX in real shellfish samples were obtained. This strategy could be referred to develop robust aptasensors for simple and highly sensitive detection of other small molecules and toxins.
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Affiliation(s)
- Yinglin Zhao
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China
| | - Ling Li
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China
| | - Rui Ma
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China
| | - Lele Wang
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China
| | - Xiaochen Yan
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China
| | - Xiaoyan Qi
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China
| | - Sai Wang
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China.
| | - Xiangzhao Mao
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
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Chen S, Huang Y, Yang Y, Luo F, Zhao Q, Chen G. Ultrasensitive Fe 3+ ion detection based on pH-insensitive fluorescent graphene nanosensors in strong acid and neutral media. NEW J CHEM 2021. [DOI: 10.1039/d0nj06201d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Schematic illustration of the preparation of FRGO and the detection of Fe3+ ions in strong acid and neutral media.
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Affiliation(s)
- Songlin Chen
- College of Materials Science and Engineering
- Huaqiao University
- Xiamen 361021
- P. R. China
| | - Yajing Huang
- College of Materials Science and Engineering
- Huaqiao University
- Xiamen 361021
- P. R. China
| | - Yang Yang
- College of Materials Science and Engineering
- Huaqiao University
- Xiamen 361021
- P. R. China
| | - Fanghua Luo
- College of Materials Science and Engineering
- Huaqiao University
- Xiamen 361021
- P. R. China
| | - Qinghua Zhao
- College of Materials Science and Engineering
- Huaqiao University
- Xiamen 361021
- P. R. China
- Graphene Powder & Composite Research Center of Fujian Province
| | - Guohua Chen
- College of Materials Science and Engineering
- Huaqiao University
- Xiamen 361021
- P. R. China
- Graphene Powder & Composite Research Center of Fujian Province
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