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Mishra M, Ahmed R, Das DK, Pramanik DD, Dash SK, Pramanik A. Recent Advancements in the Application of Circulating Tumor DNA as Biomarkers for Early Detection of Cancers. ACS Biomater Sci Eng 2024; 10:4740-4756. [PMID: 38950521 PMCID: PMC11322919 DOI: 10.1021/acsbiomaterials.4c00606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 05/24/2024] [Accepted: 06/21/2024] [Indexed: 07/03/2024]
Abstract
Early detection of cancer is vital for increasing patient survivability chances. The three major techniques used to diagnose cancers are instrumental examination, tissue biopsy, and tumor biomarker detection. Circulating tumor DNA (ctDNA) has gained much attention in recent years due to advantages over traditional technology, such as high sensitivity, high specificity, and noninvasive nature. Through the mechanism of apoptosis, necrosis, and circulating exosome release in tumor cells, ctDNA can spread throughout the circulatory system and carry modifications such as methylations, mutations, gene rearrangements, and microsatellite instability. Traditional gene-detection technology struggles to achieve real-time, low-cost, and portable ctDNA measurement, whereas electrochemical biosensors offer low cost, high specificity alongside sensitivity, and portability for the detection of ctDNA. Therefore, this review focuses on describing the recent advancements in ctDNA biomarkers for various cancer types and biosensor developments for real-time, noninvasive, and rapid ctDNA detection. Further in the review, ctDNA sensors are also discussed in regards to their selections of probes for receptors based on the electrode surface recognition elements.
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Affiliation(s)
- Mahima Mishra
- Amity Institute
of Biotechnology, Amity University, Noida 201301, India
| | - Rubai Ahmed
- Department of Physiology, University of Gour Banga, Malda-732103, West Bengal, India
| | - Deepak Kumar Das
- Department
of Chemistry and Nanoscience, GLA University, Mathura, 281406 Uttar Pradesh, India
| | | | - Sandeep Kumar Dash
- Department of Physiology, University of Gour Banga, Malda-732103, West Bengal, India
| | - Arindam Pramanik
- Amity Institute
of Biotechnology, Amity University, Noida 201301, India
- School of Medicine, University of Leeds, Leeds LS53RL, United Kingdom
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Wu X, Cui J, Sun Q, Wang X, Chen J, Liu Y, Chen JH, Jiang D, Zhou Z, Zhou H. Organic photoelectrochemical transistor based on cascaded DNA network structure modulated ZnIn 2S 4/MXene Schottky junction for sensitive ATP detection. Talanta 2024; 274:125992. [PMID: 38552479 DOI: 10.1016/j.talanta.2024.125992] [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: 01/09/2024] [Revised: 03/20/2024] [Accepted: 03/23/2024] [Indexed: 05/04/2024]
Abstract
Organic photoelectrochemical transistor (OPECT) biosensor is now appearing in perspective of public, which characterized by amplified the grating electrode potential by ion transport. In this study, the DNA network formed by the hybridization chain reaction (HCR) detects the target adenosine triphosphate (ATP) by adjusting the surface potential of the new heterojunction of ZnIn2S4/MXene. The formation of DNA network amplifies the detection signal of ATP. Significantly, OPECT biosensor could further amplify the signal, which calculated the gain achieved 103, which is consistent with the gain signal of the previously reported OPECT biosensor. Furthermore, the OPECT biosensor achieved a highly sensitivity detection of the target ATP, which the linear detection range is 0.03 pM-30 nM, and the detection limit is 0.03 pM, and illustrated a high selectivity to ATP. The proposed OPECT biosensor achieved signal amplification by adjusting the surface potential of ZnIn2S4/MXene through cascade DNA network, which provides a new direction for the detection of biomolecules.
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Affiliation(s)
- Xiaodi Wu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Jiayi Cui
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Qihao Sun
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Xue Wang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Jiahe Chen
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Yue Liu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Jia-Hao Chen
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Degang Jiang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Zhongmin Zhou
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China.
| | - Hong Zhou
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China.
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Ma Z, Xu J, Hou W, Lei Z, Li T, Shen W, Yu H, Liu C, Zhang J, Tang S. Detection of Single Nucleotide Polymorphisms of Circulating Tumor DNA by Strand Displacement Amplification Coupled with Liquid Chromatography. Anal Chem 2024; 96:5195-5204. [PMID: 38520334 DOI: 10.1021/acs.analchem.3c05500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2024]
Abstract
The detection of multiple single nucleotide polymorphisms (SNPs) of circulating tumor DNA (ctDNA) is still a great challenge. In this study, we designed enzyme-assisted nucleic acid strand displacement amplification combined with high-performance liquid chromatography (HPLC) for the simultaneous detection of three ctDNA SNPs. First, the trace ctDNA could be hybridized to the specially designed template strand, which initiated the strand displacement nucleic acid amplification process under the synergistic action of DNA polymerase and restriction endonuclease. Then, the targets would be replaced with G-quadruplex fluorescent probes with different tail lengths. Finally, the HPLC-fluorescence assay enabled the separation and quantification of multiple signals. Notably, this method can simultaneously detect both the wild type (WT) and mutant type (MT) of multiple ctDNA SNPs. Within a linear range of 0.1 fM-0.1 nM, the detection limits of BRAF V600E-WT, EGFR T790M-WT, and KRAS 134A-WT and BRAF V600E-MT, EGFR T790M-MT, and KRAS 134A-MT were 29, 31, and 11 aM and 22, 29, and 33 aM, respectively. By using this method, the mutation rates of multiple ctDNA SNPs in blood samples from patients with lung or breast cancer can be obtained in a simple way, providing a convenient and highly sensitive analytical assay for the early screening and monitoring of lung cancer.
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Affiliation(s)
- Ziyu Ma
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu, P. R. China
| | - Junjie Xu
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu, P. R. China
| | - Weilin Hou
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu, P. R. China
| | - Zi Lei
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu, P. R. China
| | - Tingting Li
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu, P. R. China
| | - Wei Shen
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu, P. R. China
| | - Hui Yu
- Department of Thoracic Surgery, Affiliated Hospital of Jiangsu University, No. 438, Jiefang Road, Zhenjiang 212000, Jiangsu, P. R. China
| | - Chang Liu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu, P. R. China
| | - Jinghui Zhang
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu, P. R. China
| | - Sheng Tang
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu, P. R. China
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, P. R. China
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Wang K, Lin X, Zhang M, Yang M, Shi X, Xie M, Luo Y. ACEK Biosensor for the Minute-Scale Quantification of Breast Cancer ctDNA. SENSORS (BASEL, SWITZERLAND) 2024; 24:547. [PMID: 38257640 PMCID: PMC10818266 DOI: 10.3390/s24020547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/05/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024]
Abstract
Circulating tumor DNA (ctDNA) appears as a valuable liquid biopsy biomarker in the early diagnosis, treatment, and prognosis of cancer. Here, a biosensing method derived from the AC electrokinetics (ACEK) effect was constructed in this study for the simple, efficient, and rapid method of detection of ctDNA. In the proof-of-concept experiment, ctDNA from the PIK3CA E542K mutant in breast cancer was quantified by detecting a normalized capacitance change rate using a forked-finger gold electrode as the sensing electrode in combination with the ACEK effect. We compared two formats for the construction of the approach by employing varied immobilization strategies; one is to immobilize the DNA capture probe on the electrode surface by Au-S bonding, while the other immobilizes the probe on a self-assembled membrane on the electrode surface by amide bonding. Both formats demonstrated ultrafast detection speed by completing the ctDNA quantification within 1 min and a linear range of 10 fM-10 pM was observed. Meanwhile, the immobilization via the self-assembled membrane yielded improved stability, sensitivity, and specificity than its Au-S bonding counterpart. A detection limit of 1.94 fM was eventually achieved using the optimized approach. This research provides a label-free and minute-scale universal method for the detection of various malignant tumors. The ctDNA biosensors based on the ACEK effect improved according to the probe type or electrode structure and have potential applications in tumor drug efficacy prediction, drug resistance monitoring, screening of high-risk groups, differential diagnosis, monitoring of tiny residual lesions, and prognosis determination.
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Affiliation(s)
- Ke Wang
- Key Laboratory of Optoelectronic Technology and Systems of Ministry of Education of China, Chongqing University, Chongqing 400044, China; (K.W.); (M.Z.); (M.Y.); (X.S.); (M.X.)
| | - Xiaogang Lin
- Key Laboratory of Optoelectronic Technology and Systems of Ministry of Education of China, Chongqing University, Chongqing 400044, China; (K.W.); (M.Z.); (M.Y.); (X.S.); (M.X.)
| | - Maoxiao Zhang
- Key Laboratory of Optoelectronic Technology and Systems of Ministry of Education of China, Chongqing University, Chongqing 400044, China; (K.W.); (M.Z.); (M.Y.); (X.S.); (M.X.)
| | - Mengjie Yang
- Key Laboratory of Optoelectronic Technology and Systems of Ministry of Education of China, Chongqing University, Chongqing 400044, China; (K.W.); (M.Z.); (M.Y.); (X.S.); (M.X.)
| | - Xiang Shi
- Key Laboratory of Optoelectronic Technology and Systems of Ministry of Education of China, Chongqing University, Chongqing 400044, China; (K.W.); (M.Z.); (M.Y.); (X.S.); (M.X.)
| | - Mingna Xie
- Key Laboratory of Optoelectronic Technology and Systems of Ministry of Education of China, Chongqing University, Chongqing 400044, China; (K.W.); (M.Z.); (M.Y.); (X.S.); (M.X.)
| | - Yang Luo
- Center of Smart Laboratory and Molecular Medicine, NHC Key Laboratory of Birth Defects and Reproductive Health, School of Medicine, Chongqing University, Chongqing 400044, China
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Qi J, Qi Q, Zhou Z, Wu Y, Cai A, Wu J, Chen B, Wang Q, Chen L, Wang F. PER-CRISPR/Cas14a system-based electrochemical biosensor for the detection of ctDNA EGFR L858R. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 16:51-61. [PMID: 38058174 DOI: 10.1039/d3ay01615c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
The detection of epidermal growth factor receptor (EGFR) mutation L858R in circulating tumor DNA (ctDNA) is beneficial for the clinical diagnosis and personalized therapy of non-small cell lung cancer (NSCLC). Herein, for the first time, the combination of the primer exchange reaction (PER) and clustered regularly interspaced short palindromic repeats (CRISPR) and its associated nucleases (Cas) 14a was used in electrochemical biosensor construction for the detection of ctDNA EGFR L858R. EGFR L858R, as the target, induced the isothermal amplification of the PER reaction, and then the CRISPR/Cas14a system was activated; subsequently, the substrate ssDNA-MB was cleaved and the electron on the surface of the gold electrode transferred, resulting in the fluctuation of the electrochemical redox signal on the electrode surface, whereas the electrochemical signal will be stable when EGFR L858R is absent. Therefore, the concentration of EGFR L858R can be quantified by electrochemical signal analysis. The low detection limit is 0.34 fM and the dynamic detection range is from 1 fM to 1 μM in this work. The PER-CRISPR/Cas14a electrochemical biosensor greatly improved the analytical sensitivity. In addition, this platform also exhibited excellent specificity, reproducibility, stability and good recovery. This study provides an efficient and novel strategy for the detection of ctDNA EGFR L858R, which has great potential for application in the diagnosis and treatment of NSCLC.
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Affiliation(s)
- Jing Qi
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China.
| | - Qianyi Qi
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China.
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China
| | - Zhou Zhou
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China.
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China
| | - Yixuan Wu
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China.
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China
| | - Aiting Cai
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China.
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China
| | - Jinran Wu
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China.
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China
| | - Bairong Chen
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China.
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China
| | - Qingxiang Wang
- College of Chemistry and Environment, Minnan Normal University, Zhangzhou 363000, China
- Nantong Institute of Liver Diseases, Nantong Third People's Hospital Affiliated Nantong Hospital 3 of Nantong University, Nantong 226006, China.
| | - Lin Chen
- Nantong Institute of Liver Diseases, Nantong Third People's Hospital Affiliated Nantong Hospital 3 of Nantong University, Nantong 226006, China.
| | - Feng Wang
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China.
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China
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Alexandrou G, Mantikas KT, Allsopp R, Yapeter CA, Jahin M, Melnick T, Ali S, Coombes RC, Toumazou C, Shaw JA, Kalofonou M. The Evolution of Affordable Technologies in Liquid Biopsy Diagnostics: The Key to Clinical Implementation. Cancers (Basel) 2023; 15:5434. [PMID: 38001698 PMCID: PMC10670715 DOI: 10.3390/cancers15225434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/01/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
Cancer remains a leading cause of death worldwide, despite many advances in diagnosis and treatment. Precision medicine has been a key area of focus, with research providing insights and progress in helping to lower cancer mortality through better patient stratification for therapies and more precise diagnostic techniques. However, unequal access to cancer care is still a global concern, with many patients having limited access to diagnostic tests and treatment regimens. Noninvasive liquid biopsy (LB) technology can determine tumour-specific molecular alterations in peripheral samples. This allows clinicians to infer knowledge at a DNA or cellular level, which can be used to screen individuals with high cancer risk, personalize treatments, monitor treatment response, and detect metastasis early. As scientific understanding of cancer pathology increases, LB technologies that utilize circulating tumour DNA (ctDNA) and circulating tumour cells (CTCs) have evolved over the course of research. These technologies incorporate tumour-specific markers into molecular testing platforms. For clinical translation and maximum patient benefit at a wider scale, the accuracy, accessibility, and affordability of LB tests need to be prioritized and compared with gold standard methodologies in current use. In this review, we highlight the range of technologies in LB diagnostics and discuss the future prospects of LB through the anticipated evolution of current technologies and the integration of emerging and novel ones. This could potentially allow a more cost-effective model of cancer care to be widely adopted.
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Affiliation(s)
- George Alexandrou
- Centre For Bio-Inspired Technology, Department of Electrical & Electronic Engineering, Imperial College London, London SW7 2BT, UK; (K.-T.M.); (C.A.Y.); (M.J.); (T.M.); (C.T.)
| | - Katerina-Theresa Mantikas
- Centre For Bio-Inspired Technology, Department of Electrical & Electronic Engineering, Imperial College London, London SW7 2BT, UK; (K.-T.M.); (C.A.Y.); (M.J.); (T.M.); (C.T.)
| | - Rebecca Allsopp
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, Leicester LE2 7LX, UK; (R.A.); (J.A.S.)
| | - Calista Adele Yapeter
- Centre For Bio-Inspired Technology, Department of Electrical & Electronic Engineering, Imperial College London, London SW7 2BT, UK; (K.-T.M.); (C.A.Y.); (M.J.); (T.M.); (C.T.)
| | - Myesha Jahin
- Centre For Bio-Inspired Technology, Department of Electrical & Electronic Engineering, Imperial College London, London SW7 2BT, UK; (K.-T.M.); (C.A.Y.); (M.J.); (T.M.); (C.T.)
| | - Taryn Melnick
- Centre For Bio-Inspired Technology, Department of Electrical & Electronic Engineering, Imperial College London, London SW7 2BT, UK; (K.-T.M.); (C.A.Y.); (M.J.); (T.M.); (C.T.)
| | - Simak Ali
- Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK; (S.A.); (R.C.C.)
| | - R. Charles Coombes
- Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK; (S.A.); (R.C.C.)
| | - Christofer Toumazou
- Centre For Bio-Inspired Technology, Department of Electrical & Electronic Engineering, Imperial College London, London SW7 2BT, UK; (K.-T.M.); (C.A.Y.); (M.J.); (T.M.); (C.T.)
| | - Jacqueline A. Shaw
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, Leicester LE2 7LX, UK; (R.A.); (J.A.S.)
| | - Melpomeni Kalofonou
- Centre For Bio-Inspired Technology, Department of Electrical & Electronic Engineering, Imperial College London, London SW7 2BT, UK; (K.-T.M.); (C.A.Y.); (M.J.); (T.M.); (C.T.)
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Jiang L, Lin X, Chen F, Qin X, Yan Y, Ren L, Yu H, Chang L, Wang Y. Current research status of tumor cell biomarker detection. MICROSYSTEMS & NANOENGINEERING 2023; 9:123. [PMID: 37811123 PMCID: PMC10556054 DOI: 10.1038/s41378-023-00581-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 06/26/2023] [Accepted: 07/23/2023] [Indexed: 10/10/2023]
Abstract
With the annual increases in the morbidity and mortality rates of tumors, the use of biomarkers for early diagnosis and real-time monitoring of tumor cells is of great importance. Biomarkers used for tumor cell detection in body fluids include circulating tumor cells, nucleic acids, protein markers, and extracellular vesicles. Among them, circulating tumor cells, circulating tumor DNA, and exosomes have high potential for the prediction, diagnosis, and prognosis of tumor diseases due to the large amount of valuable information on tumor characteristics and evolution; in addition, in situ monitoring of telomerase and miRNA in living cells has been the topic of extensive research to understand tumor development in real time. Various techniques, such as enzyme-linked immunosorbent assays, immunoblotting, and mass spectrometry, have been widely used for the detection of these markers. Among them, the detection of tumor cell markers in body fluids based on electrochemical biosensors and fluorescence signal analysis is highly preferred because of its high sensitivity, rapid detection and portable operation. Herein, we summarize recent research progress in the detection of tumor cell biomarkers in body fluids using electrochemical and fluorescence biosensors, outline the current research status of in situ fluorescence monitoring and the analysis of tumor markers in living cells, and discuss the technical challenges for their practical clinical application to provide a reference for the development of new tumor marker detection methods.
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Affiliation(s)
- Liying Jiang
- School of Electrical and Information Engineering, Zhengzhou University of Light Industry, Zhengzhou, 450002 China
- Academy for Quantum Science and Technology, Zhengzhou University of Light Industry, Zhengzhou, 450002 China
| | - Xinyi Lin
- School of Electrical and Information Engineering, Zhengzhou University of Light Industry, Zhengzhou, 450002 China
| | - Fenghua Chen
- School of Electrical and Information Engineering, Zhengzhou University of Light Industry, Zhengzhou, 450002 China
| | - Xiaoyun Qin
- School of Electrical and Information Engineering, Zhengzhou University of Light Industry, Zhengzhou, 450002 China
| | - Yanxia Yan
- School of Electrical and Information Engineering, Zhengzhou University of Light Industry, Zhengzhou, 450002 China
| | - Linjiao Ren
- School of Electrical and Information Engineering, Zhengzhou University of Light Industry, Zhengzhou, 450002 China
| | - Hongyu Yu
- Department of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Lingqian Chang
- key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083 China
| | - Yang Wang
- key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083 China
- School of Engineering Medicine, Beihang University, Beijing, 100083 China
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Yang X, Huang Y, Yang S, Tang M, Liu J, Shen J, Fa H, Huo D, Hou C, Yang M. A label-free fluorescent sensor for rapid and sensitive detection of ctDNA based on fluorescent PDA nanoparticles. Analyst 2023; 148:4885-4896. [PMID: 37650747 DOI: 10.1039/d3an01169k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Technological advances in the detection of circulating tumor DNA (ctDNA) have made new options available for diagnosis, classification, biological studies, and treatment selection. However, effective and practical methods for analyzing this emerging class of biomarkers are still lacking. In this work, a fluorescent biosensor was designed for the label-free detection of ctDNA (EGFR 19 del for non-small cell lung cancer, NSCLC). The biosensor was based on the fact that MnO2 nanosheets (MnO2 NSs) have stronger affinity towards single-stranded DNA (ssDNA), as compared with double-stranded DNA (dsDNA). As a high-performance nanoenzyme, MnO2 NSs could oxidize dopamine (DA) into fluorescent polydopamine nanoparticles (FL-PDA NPs), which could be used as a fluorescence signal. The probe ssDNA could be adsorbed on the surface of MnO2 NSs through π-π stacking, and the active site would be masked, causing a lower fluorescence. After the targets were recognized by probe ssDNA to form dsDNA, its affinity for MnO2 NSs decreased and the active site recovered, causing a restored fluorescence. It was verified that Mn ions, •OH radicals and electron transfer were the important factors in the catalytic oxidation of DA. Under the optimal experimental conditions, this biosensor exhibited a detection limit of 380 pM and a linear range of 25-125 nM, providing reliable readout in a short time (45 min). This sensor exhibited outstanding specificity, stability and reproducibility. In addition, this sensor was applied to the detection of ctDNA in serum samples and cell lysates. It is demonstrated that FL-PDA NPs can be used as a fluorescence signal for easy, rapid and label-free detection of ctDNA without any other amplification strategies, and the proposed strategy has great potential for biomarker detection in the field of liquid biopsy.
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Affiliation(s)
- Xiao Yang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, PR China.
| | - Yang Huang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, PR China.
| | - Siyi Yang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, PR China.
| | - Miao Tang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, PR China.
| | - Juan Liu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, PR China.
| | - Jinhui Shen
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, PR China.
| | - Huanbao Fa
- College of Chemistry and Chemical Engineering, Chongqing University, Chongqing 400044, PR China
| | - Danqun Huo
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, PR China.
- College of Bioengineering, Chongqing University, Chongqing 400044, PR China
| | - Changjun Hou
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, PR China.
- College of Bioengineering, Chongqing University, Chongqing 400044, PR China
| | - Mei Yang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, PR China.
- College of Bioengineering, Chongqing University, Chongqing 400044, PR China
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Tan K, Chen L, Cao D, Xiao W, Lv Q, Zou L. A rapid and highly sensitive ctDNA detection platform based on locked nucleic acid-assisted catalytic hairpin assembly circuits. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:4548-4554. [PMID: 37642516 DOI: 10.1039/d3ay01150j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
As a promising biomarker of liquid biopsy, circulating tumor DNA (ctDNA) plays a paramount role in the early diagnosis of noninvasive cancer. The isothermal catalytic hairpin assembly (CHA) strategy has great potential for in vitro detection of ctDNA in low abundance. However, a traditional CHA strategy for ctDNA detection at the earlier stages of cancer remains extremely challenging, as annoying signal leakage from the 'breathing' phenomenon and nuclease degradation occur. Herein, we report a locked nucleic acid (LNA)-incorporated CHA circuit for the rapid and sensitive detection of target ctDNA. The target ctDNA intelligently catalyzed LNA-modified hairpins H1 and H2via a range of toehold-mediated strand displacement processes, leading to the continuous generation of an H1-H2 hybrid for the amplified fluorescence signal. In comparison to conventional CHA circuits, the stronger binding affinity of LNA-DNA bases greatly inhibited the breathing effect, which endowed it with greater thermodynamic stability and resistance to nuclease degradation in the LNA-assisted CHA system, thus achieving a high signal gain. The developed CHA circuit demonstrated excellent performance during target ctDNA detection, with a linear range from 10 pM to 5 nM, and its target detection limit was reached at 3.3 pM. Moreover, this LNA-assisted CHA system was successfully applied to the analysis of target ctDNA in clinical serum samples of breast cancer patients. This updated CHA system provides a general and robust platform for the sensitive detection of biomarkers of interest, thus facilitating the accurate identification and diagnosis of cancers.
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Affiliation(s)
- Kaiyue Tan
- Institute of Biological and Medical Engineering, Guangdong Academy of Sciences & National Engineering Research Center for Healthcare Devices, Guangzhou 510632, China.
- Guangdong Engineering Technology Research Center for Diagnosis and Rehabilitation of Dementia, Guangzhou 510500, China
- Guangdong Key Lab of Medical Electronic Instruments and Polymer Material Products, Guangzhou 510632, China
| | - Longsheng Chen
- Institute of Biological and Medical Engineering, Guangdong Academy of Sciences & National Engineering Research Center for Healthcare Devices, Guangzhou 510632, China.
- Guangdong Engineering Technology Research Center for Diagnosis and Rehabilitation of Dementia, Guangzhou 510500, China
- Guangdong Key Lab of Medical Electronic Instruments and Polymer Material Products, Guangzhou 510632, China
| | - Donglin Cao
- Department of Laboratory Medicine, Guangdong Provincial Key Laboratory of Point-of-care Testing (POCT), Guangdong Second Provincial General Hospital, Guangzhou 510500, China
| | - Wei Xiao
- Department of Laboratory Medicine, Guangdong Provincial Key Laboratory of Point-of-care Testing (POCT), Guangdong Second Provincial General Hospital, Guangzhou 510500, China
| | - Qian Lv
- Institute of Biological and Medical Engineering, Guangdong Academy of Sciences & National Engineering Research Center for Healthcare Devices, Guangzhou 510632, China.
- Guangdong Engineering Technology Research Center for Diagnosis and Rehabilitation of Dementia, Guangzhou 510500, China
- Guangdong Key Lab of Medical Electronic Instruments and Polymer Material Products, Guangzhou 510632, China
| | - Lili Zou
- Institute of Biological and Medical Engineering, Guangdong Academy of Sciences & National Engineering Research Center for Healthcare Devices, Guangzhou 510632, China.
- Guangdong Engineering Technology Research Center for Diagnosis and Rehabilitation of Dementia, Guangzhou 510500, China
- Guangdong Key Lab of Medical Electronic Instruments and Polymer Material Products, Guangzhou 510632, China
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10
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Wu X, Ju T, Li Z, Li J, Zhai X, Han K. Target-independent hybridization chain reaction-fluorescence resonance energy transfer for sensitive assay of ctDNA based on Cas12a. Anal Chim Acta 2023; 1261:341170. [PMID: 37147050 DOI: 10.1016/j.aca.2023.341170] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/13/2023] [Accepted: 03/31/2023] [Indexed: 05/07/2023]
Abstract
Circulating tumor DNA (ctDNA) is a noninvasive biomarker which offer valuable information for cancer diagnosis and prognosis. In this study, a target-independent fluorescent signal system, Hybridization chain reaction-Fluorescence resonance energy transfer (HCR-FRET) system, is designed and optimized. Combined with CRISPR/Cas12a system, a fluorescent biosensing protocol was developed for sensing assay of T790 M. When the target is absent, the initiator remains intact, opens the fuel hairpins and triggers the following HCR-FRET. At presence of the target, the Cas12a/crRNA binary complex specifically recognizes the target, and the Cas12a trans-cleavage activity is activated. As a result, the initiator is cleaved and subsequent HCR responses and FRET processes are attenuated. This method showed detection range from 1 pM to 400 pM with a detection limit of 316 fM. The target independent property of the HCR-FRET system endows this protocol a promising potential to transplant to the assay of other DNA target in parallel.
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Affiliation(s)
- Xuelan Wu
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China; CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science, Suzhou, 215163, China
| | - Ting Ju
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China; CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science, Suzhou, 215163, China
| | - Zeyang Li
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science, Suzhou, 215163, China
| | - Jingwen Li
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China; CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science, Suzhou, 215163, China
| | - Xingwei Zhai
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science, Suzhou, 215163, China
| | - Kun Han
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China; CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science, Suzhou, 215163, China.
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11
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Li M, Luo N, Liao X, Zou L. Proximity hybridization-regulated CRISPR/Cas12a-based dual signal amplification strategy for sensitive detection of circulating tumor DNA. Talanta 2023; 257:124395. [PMID: 36858011 DOI: 10.1016/j.talanta.2023.124395] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 02/20/2023] [Accepted: 02/23/2023] [Indexed: 02/27/2023]
Abstract
Circulating tumor DNA (ctDNA) is regarded as an ideal candidate biomarker for the non-invasive diagnosis of cancer. However, the lack of convenient and reliable detection methods for ctDNA restricts its clinical application. Herein, we developed a dual signal amplification strategy for sensitive detection of ctDNA based on hybridization chain reaction (HCR) and proximity hybridization-regulated CRISPR/Cas12a. The ctDNA initiates HCR through the continuous hybridization of two hairpin probes (H1 and H2), yielding long nicked double-stranded DNA nanowires composed of numerous split segments, which are successively connected to activate the trans-cleavage activity of CRISPR/Cas12a. In this case, the doubly labeled single-stranded DNA reporter can be cleaved to produce a strong fluorescent signal. Owing to the dual amplification of HCR and CRISPR/Cas12a, this strategy exhibits high sensitivity toward ctDNA with a low detection limit of 5.43 fM. Moreover, the proposed method was successfully applied for ctDNA detection in serum samples with satisfactory results, which has great potential in the clinical diagnosis of cancer.
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Affiliation(s)
- Mengyan Li
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China
| | - Nian Luo
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China
| | - Xiaofei Liao
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China
| | - Li Zou
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China; Key Specialty of Clinical Pharmacy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, 510699, PR China.
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12
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Yang LY, Xu XW, Lin Y, Ye CL, Liu WQ, Liu ZJ, Zhong GX, Xu YF, Lin XH, Chen JY. Nucleic Acid Amplification by Template-Dominated Click Chemistry for Ultrasensitive DNA/RNA Detection on an Electrochemical Readout Platform. Anal Chem 2023; 95:5331-5339. [PMID: 36926822 DOI: 10.1021/acs.analchem.2c05421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
As an enzyme-free exponential nucleic acid amplification method, the click chemistry-mediated ligation chain reaction (ccLCR) has shown great prospects in the molecular diagnosis. However, the current optics-based ccLCR is challenged by remarkable nonspecific amplification, severely hindering its future application. This study demonstrated that the severe nonspecific amplification was generated probably due to high random collision in the high DNA probe concentration (μM level). To solve this hurdle, a nucleic acid template-dominated ccLCR was constructed using nM-level DNA probes and read on an electrochemical platform (cc-eLCR). Under the optimal conditions, the proposed cc-eLCR detected a low-level nucleic acid target (1 fM) with a single-base resolution. Furthermore, this assay was applied to detect the target of interest in cell extracts with a satisfactory result. The proposed cc-eLCR offers huge possibility for click chemistry-mediated enzyme-free exponential nucleic acid amplification in the application of medical diagnosis and biomedical research.
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Affiliation(s)
- Liang-Yong Yang
- The Central Laboratory, Fujian Key Laboratory of Precision Medicine for Cancer, Key Laboratory of Radiation Biology of Fujian Higher Education Institutions, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China.,Department of Pharmaceutical Analysis, Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Faculty of Pharmacy, Fujian Medical University, Fuzhou 350122, China
| | - Xiong-Wei Xu
- The Central Laboratory, Fujian Key Laboratory of Precision Medicine for Cancer, Key Laboratory of Radiation Biology of Fujian Higher Education Institutions, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
| | - Yan Lin
- The Central Laboratory, Fujian Key Laboratory of Precision Medicine for Cancer, Key Laboratory of Radiation Biology of Fujian Higher Education Institutions, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
| | - Chen-Liu Ye
- Department of Pharmacy, Longyan First Affiliated Hospital of Fujian Medical University, Longyan 364000, China
| | - Wei-Qiang Liu
- The Central Laboratory, Fujian Key Laboratory of Precision Medicine for Cancer, Key Laboratory of Radiation Biology of Fujian Higher Education Institutions, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
| | - Zhou-Jie Liu
- The Central Laboratory, Fujian Key Laboratory of Precision Medicine for Cancer, Key Laboratory of Radiation Biology of Fujian Higher Education Institutions, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
| | - Guang-Xian Zhong
- Department of Rehabilitation Medicine, School of Health, Fujian Medical University, Fuzhou 350122, China
| | - Yan-Fang Xu
- Department of Nephrology, the Central Laboratory, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
| | - Xin-Hua Lin
- Department of Pharmaceutical Analysis, Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Faculty of Pharmacy, Fujian Medical University, Fuzhou 350122, China
| | - Jin-Yuan Chen
- The Central Laboratory, Fujian Key Laboratory of Precision Medicine for Cancer, Key Laboratory of Radiation Biology of Fujian Higher Education Institutions, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
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13
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Electrochemical biosensors for analysis of DNA point mutations in cancer research. Anal Bioanal Chem 2023; 415:1065-1085. [PMID: 36289102 DOI: 10.1007/s00216-022-04388-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/11/2022] [Accepted: 10/14/2022] [Indexed: 02/07/2023]
Abstract
Cancer is a genetic disease induced by mutations in DNA, in particular point mutations in important driver genes that lead to protein malfunctioning and ultimately to tumorigenesis. Screening for the most common DNA point mutations, especially in such genes as TP53, BRCA1 and BRCA2, EGFR, KRAS, or BRAF, is crucial to determine predisposition risk for cancer or to predict response to therapy. In this review, we briefly depict how these genes are involved in cancer, followed by a description of the most common techniques routinely applied for their analysis, including high-throughput next-generation sequencing technology and less expensive low-throughput options, such as real-time PCR, restriction fragment length polymorphism, or high resolution melting analysis. We then introduce benefits of electrochemical biosensors as interesting alternatives to the standard methods in terms of cost, speed, and simplicity. We describe most common strategies involved in electrochemical biosensing of point mutations, relying mostly on PCR or isothermal amplification techniques, and critically discuss major challenges and obstacles that, until now, prevented their more widespread application in clinical settings.
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14
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Pan A, Truong TN, Su YH, Dao DY. Circulating Biomarkers for the Early Diagnosis and Management of Hepatocellular Carcinoma with Potential Application in Resource-Limited Settings. Diagnostics (Basel) 2023; 13:diagnostics13040676. [PMID: 36832164 PMCID: PMC9954913 DOI: 10.3390/diagnostics13040676] [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: 12/10/2022] [Revised: 02/02/2023] [Accepted: 02/07/2023] [Indexed: 02/15/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is among the world's third most lethal cancers. In resource-limited settings (RLS), up to 70% of HCCs are diagnosed with limited curative treatments at an advanced symptomatic stage. Even when HCC is detected early and resection surgery is offered, the post-operative recurrence rate after resection exceeds 70% in five years, of which about 50% occur within two years of surgery. There are no specific biomarkers addressing the surveillance of HCC recurrence due to the limited sensitivity of the available methods. The primary goal in the early diagnosis and management of HCC is to cure disease and improve survival, respectively. Circulating biomarkers can be used as screening, diagnostic, prognostic, and predictive biomarkers to achieve the primary goal of HCC. In this review, we highlighted key circulating blood- or urine-based HCC biomarkers and considered their potential applications in resource-limited settings, where the unmet medical needs of HCC are disproportionately highly significant.
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Affiliation(s)
- Annabelle Pan
- School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Thai N. Truong
- Department of Internal Medicine, Campus in Thanh Hoa, Hanoi Medical University, Thanh Hoa 40000, Vietnam
| | - Ying-Hsiu Su
- Department of Translational Medical Science, The Baruch S. Blumberg Institute, Doylestown, PA 18902, USA
| | - Doan Y Dao
- School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- Center of Excellence for Liver Disease in Vietnam, Johns Hopkins University of Medicine, Baltimore, MD 21205, USA
- Correspondence:
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15
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Wang W, Ge Q, Zhao X. Enzyme-free isothermal amplification strategy for the detection of tumor-associated biomarkers: A review. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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16
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Jin F, Liu M, Xu D. Web hybrid chain reaction enhanced fluorescent magnetic bead array for digital nucleic acid detection. Talanta 2023; 253:123968. [PMID: 36209644 DOI: 10.1016/j.talanta.2022.123968] [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: 06/29/2022] [Revised: 09/20/2022] [Accepted: 09/23/2022] [Indexed: 12/13/2022]
Abstract
The detection of biomarkers at low concentrations is important in clinical diagnostic analyses and has attracted continuous research. In this work, absolute quantification of hepatitis B virus (HBV) DNA was achieved using magnetic beads with isothermal, enzyme-free DNA nanostructure for fluorescence amplification. Firstly, the DNA-functionalized bead captured the target nucleic acid in the form of sandwich hybridization, and the individual target lighted up the entire bead by isothermal web hybridization chain reaction (wHCR). After the microarray scanning, the target nucleic acids can be digitally quantified based on the Poisson statistics. Therefore, the fluorescent bead assay enabled precise detection of HBV DNA down to 5 fM level without external calibration curves. Moreover, this method not only specifically distinguished single-base mismatched sequences, but also obtained the quantitative detection of HBV DNA in serum samples. Unlike routine digital detection usually combined with complex compartment partitioning operations, the amplification structure immobilized on beads can be conducted in microcentrifuge tubes with a volume of microliter scale. This work expands the application of magnetic beads in the digital quantitative detection via enzyme-free and isothermal method.
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Affiliation(s)
- Furui Jin
- State Key Laboratory of Analytical Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, No 163, Xianlin Avenue, Nanjing, 210023, China
| | - Min Liu
- State Key Laboratory of Analytical Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, No 163, Xianlin Avenue, Nanjing, 210023, China
| | - Danke Xu
- State Key Laboratory of Analytical Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, No 163, Xianlin Avenue, Nanjing, 210023, China.
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17
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Azeem MM, Shafa M, Aamir M, Zubair M, Souayeh B, Alam MW. Nucleotide detection mechanism and comparison based on low-dimensional materials: A review. Front Bioeng Biotechnol 2023; 11:1117871. [PMID: 36937765 PMCID: PMC10018150 DOI: 10.3389/fbioe.2023.1117871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/13/2023] [Indexed: 03/06/2023] Open
Abstract
The recent pandemic has led to the fabrication of new nucleic acid sensors that can detect infinitesimal limits immediately and effectively. Therefore, various techniques have been demonstrated using low-dimensional materials that exhibit ultrahigh detection and accuracy. Numerous detection approaches have been reported, and new methods for impulse sensing are being explored. All ongoing research converges at one unique point, that is, an impetus: the enhanced limit of detection of sensors. There are several reviews on the detection of viruses and other proteins related to disease control point of care; however, to the best of our knowledge, none summarizes the various nucleotide sensors and describes their limits of detection and mechanisms. To understand the far-reaching impact of this discipline, we briefly discussed conventional and nanomaterial-based sensors, and then proposed the feature prospects of these devices. Two types of sensing mechanisms were further divided into their sub-branches: polymerase chain reaction and photospectrometric-based sensors. The nanomaterial-based sensor was further subdivided into optical and electrical sensors. The optical sensors included fluorescence (FL), surface plasmon resonance (SPR), colorimetric, and surface-enhanced Raman scattering (SERS), while electrical sensors included electrochemical luminescence (ECL), microfluidic chip, and field-effect transistor (FET). A synopsis of sensing materials, mechanisms, detection limits, and ranges has been provided. The sensing mechanism and materials used were discussed for each category in terms of length, collectively forming a fusing platform to highlight the ultrahigh detection technique of nucleotide sensors. We discussed potential trends in improving the fabrication of nucleotide nanosensors based on low-dimensional materials. In this area, particular aspects, including sensitivity, detection mechanism, stability, and challenges, were addressed. The optimization of the sensing performance and selection of the best sensor were concluded. Recent trends in the atomic-scale simulation of the development of Deoxyribonucleic acid (DNA) sensors using 2D materials were highlighted. A critical overview of the challenges and opportunities of deoxyribonucleic acid sensors was explored, and progress made in deoxyribonucleic acid detection over the past decade with a family of deoxyribonucleic acid sensors was described. Areas in which further research is needed were included in the future scope.
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Affiliation(s)
- M. Mustafa Azeem
- Department of Civil, Architectural, and Environmental Engineering, Missouri University of Science and Technology, Rolla, MO, United States
- *Correspondence: M. Mustafa Azeem, ; Muhammad Aamir,
| | - Muhammad Shafa
- Yunnan Key Laboratory of Metal-Organic Molecular Materials and Devices, Kunming University, Kunming, Yunnan, China
| | - Muhammad Aamir
- Department of Basic Science, Deanship of Preparatory Year, King Faisal University, Hofuf, Saudi Arabia
- *Correspondence: M. Mustafa Azeem, ; Muhammad Aamir,
| | - Muhammad Zubair
- Mechanical and Nuclear Engineering Department, University of Sharjah, Sharjah, United Arab Emirates
| | - Basma Souayeh
- Department of Physics, College of Science, King Faisal University, Al Ahsa, Saudi Arabia
| | - Mir Waqas Alam
- Department of Physics, College of Science, King Faisal University, Al Ahsa, Saudi Arabia
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18
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Singh S, Podder PS, Russo M, Henry C, Cinti S. Tailored point-of-care biosensors for liquid biopsy in the field of oncology. LAB ON A CHIP 2022; 23:44-61. [PMID: 36321747 DOI: 10.1039/d2lc00666a] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
In the field of cancer detection, technologies to analyze tumors using biomarkers circulating in fluids such as blood have developed rapidly based on liquid biopsy. A proactive approach to early cancer detection can lead to more effective treatments with minimal side effects and better long-term patient survival. However, early detection of cancer is hindered by the existing limitations of conventional cancer diagnostic methods. To enable early diagnosis and regular monitoring and improve automation, the development of integrated point-of-care (POC) and biosensors is needed. This is expected to fundamentally change the diagnosis, management, and monitoring of response to treatment of cancer. POC-based techniques will provide a way to avoid complications that occur after invasive tissue biopsy, such as bleeding, infection, and pain. The aim of this study is to provide a comprehensive view of biosensors and their clinical relevance in oncology for the detection of biomarkers with liquid biopsies of proteins, miRNA, ctDNA, exosomes, and cancer cells. The preceding discussion also illustrates the changing landscape of liquid biopsy-based cancer diagnosis through nanomaterials, machine learning, artificial intelligence, wearable devices, and sensors, many of which apply POC design principles. With the advent of sensitive, selective, and timely detection of cancer, we see the field of POC technology for cancer detection and treatment undergoing a positive paradigm shift in the foreseeable future.
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Affiliation(s)
- Sima Singh
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy.
| | - Pritam Saha Podder
- Department of Pharmacy, Jahangirnagar University, Savar, Dhaka-1342, Bangladesh
| | - Matt Russo
- Department of Chemistry, Colorado State University, Fort Collins, CO, 80523-1872, USA
| | - Charles Henry
- Department of Chemistry, Colorado State University, Fort Collins, CO, 80523-1872, USA
| | - Stefano Cinti
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy.
- BAT Center-Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology, University of Napoli Federico II, 80055 Naples, Italy
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19
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Cai A, Yang L, Kang X, Liu J, Wang F, Ji H, Wang Q, Wu M, Li G, Zhou X, Qin Y, Wu L. Target Recognition- and HCR Amplification-Induced In Situ Electrochemical Signal Probe Synthesis Strategy for Trace ctDNA Analysis. BIOSENSORS 2022; 12:bios12110989. [PMID: 36354498 PMCID: PMC9688549 DOI: 10.3390/bios12110989] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/03/2022] [Accepted: 11/06/2022] [Indexed: 05/31/2023]
Abstract
An electrochemical-DNA (E-DNA) sensor was constructed by using DNA metallization to produce an electrochemical signal reporter in situ and hybridization chain reaction (HCR) as signal amplification strategy. The cyclic voltammetry (CV) technique was used to characterize the electrochemical solid-state Ag/AgCl process. Moreover, the enzyme cleavage technique was introduced to reduce background signals and further improve recognition accuracy. On the basis of these techniques, the as-prepared E-DNA sensor exhibited superior sensing performance for trace ctDNA analysis with a detection range of 0.5 fM to 10 pM and a detection limit of 7 aM. The proposed E-DNA sensor also displayed excellent selectivity, satisfied repeatability and stability, and had good recovery, all of which supports its potential applications for future clinical sample analysis.
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Affiliation(s)
- Aiting Cai
- School of Public Health, Nantong University, No.9 Seyuan Road, Nantong 226019, China
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China
| | - Luxia Yang
- School of Public Health, Nantong University, No.9 Seyuan Road, Nantong 226019, China
| | - Xiaoxia Kang
- School of Public Health, Nantong University, No.9 Seyuan Road, Nantong 226019, China
| | - Jinxia Liu
- School of Public Health, Nantong University, No.9 Seyuan Road, Nantong 226019, China
| | - Feng Wang
- School of Public Health, Nantong University, No.9 Seyuan Road, Nantong 226019, China
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China
| | - Haiwei Ji
- School of Public Health, Nantong University, No.9 Seyuan Road, Nantong 226019, China
| | - Qi Wang
- School of Public Health, Nantong University, No.9 Seyuan Road, Nantong 226019, China
| | - Mingmin Wu
- School of Public Health, Nantong University, No.9 Seyuan Road, Nantong 226019, China
| | - Guo Li
- School of Public Health, Nantong University, No.9 Seyuan Road, Nantong 226019, China
| | - Xiaobo Zhou
- School of Public Health, Nantong University, No.9 Seyuan Road, Nantong 226019, China
| | - Yuling Qin
- School of Public Health, Nantong University, No.9 Seyuan Road, Nantong 226019, China
| | - Li Wu
- School of Public Health, Nantong University, No.9 Seyuan Road, Nantong 226019, China
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20
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Liu J, Yang S, Shen J, Fa H, Hou C, Yang M. Conductive metal-organic framework based label-free electrochemical detection of circulating tumor DNA. Mikrochim Acta 2022; 189:391. [PMID: 36138259 DOI: 10.1007/s00604-022-05482-4] [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: 04/25/2022] [Accepted: 08/29/2022] [Indexed: 11/29/2022]
Abstract
An ultrasensitive electrochemical biosensor was designed for the rapid label-free detection of circulating tumor DNA (ctDNA, EGFR 19 Dels for non-small cell lung cancer, NSCLC). We linked the highly conjugated tricatecholate, 2,3,6,7,10,11-hexahydroxytriphenylene (HHTP) with Ni(II) ions into the two-dimensional porous conductive metal-organic frameworks (MOFs), which is termed Ni-catecholates (Ni-CAT). Then, the AuNPs/Ni-catecholates/carbon black/polarized pencil graphite electrode (AuNPs/Ni-CAT/CB/PPGE) was obtained by electrodeposition of AuNPs on the surface of PPGE modified with Ni-CAT/CB composite materials. The AuNPs/Ni-CAT/CB/PPGE were used for label-less detection of ctDNA, with a total detection time of only 30 min. Under optimal detection conditions, the AuNPs/Ni-CAT/CB/PPGE sensor exhibited excellent detection performance with good linear response to ctDNA over a wide concentration range and the detection limit down to the femtomolar level. The sensor was applied to the determination of ctDNA in serum samples with high sensitivity. This simple, efficient, and expeditious method has practical value in liquid biopsy of ctDNA and has potential for development in early detection, treatment, and prognosis of tumors. Herein, an ultrasensitive electrochemical biosensor was designed for the rapid label-free detection of ctDNA (EGFR 19 Dels for non-small cell lung cancer, NSCLC). We linked the highly conjugated tricatecholate, 2,3,6,7,10,11-hexahydroxytriphenylene (HHTP) with Ni(II) ions into the two-dimensional porous conductive metal-organic frameworks (MOFs), which is termed as Ni-catecholates (Ni-CAT). Then, the AuNPs/Ni-catecholates/carbon black/polarized pencil graphite electrode (AuNPs/Ni-CAT/CB/PPGE) was obtained by electrodeposition of AuNPs on the surface of PPGE modified with Ni-CAT/CB composite materials. The AuNPs/Ni-CAT/CB/PPGEs were used for label-less detection of ctDNA, with a total detection time of only 30 min. Under optimal detection conditions, the AuNPs/Ni-CAT/CB/PPGE sensor exhibited excellent detection performance with good linear response to ctDNA in the concentration range of 1 × 10-15 M to 1 × 10-6 M and with a detection limit as low as 0.32 fM. The sensor was applied for determination of ctDNA in serum samples and gave high sensitivity. This simple, efficient and expeditious method has practical value in liquid biopsy of ctDNA and has potential for development in early detection, treatment and prognosis of tumors.
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Affiliation(s)
- Juan Liu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, People's Republic of China
| | - Siyi Yang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, People's Republic of China
| | - Jinhui Shen
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, People's Republic of China
| | - Huanbao Fa
- College of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 400044, People's Republic of China
| | - Changjun Hou
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, People's Republic of China. .,College of Bioengineering, Chongqing University, Chongqing, 400044, People's Republic of China.
| | - Mei Yang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, People's Republic of China. .,College of Bioengineering, Chongqing University, Chongqing, 400044, People's Republic of China.
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21
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Li L, Zhang YN, Zheng W, Li X, Zhao Y. Optical fiber SPR biosensor based on gold nanoparticle amplification for DNA hybridization detection. Talanta 2022; 247:123599. [DOI: 10.1016/j.talanta.2022.123599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 03/28/2022] [Accepted: 05/25/2022] [Indexed: 01/08/2023]
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22
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Cui Z, Li D, Yang W, Fan K, Liu H, Wen F, Li L, Dong L, Wang G, Wu W. An electrochemical biosensor based on few-layer MoS 2 nanosheets for highly sensitive detection of tumor marker ctDNA. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:1956-1962. [PMID: 35531866 DOI: 10.1039/d2ay00467d] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
An electrochemical biosensor based on few-layer molybdenum disulfide (MoS2) nanosheets was fabricated for the highly sensitive detection of tumor marker circulating tumor DNA (ctDNA) in this paper. The MoS2 nanosheets with few layers were prepared by the shear stripping. Compared with the mechanical stripping method and the lithium ion intercalation method, this method is simpler to operate, and the prepared MoS2 nanosheets had good electrochemical activity. The biosensing platform was fabricated based on the discriminative affinity of MoS2 nanosheets towards single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA). Methylene blue (MB) was used as the signal molecule. The results showed that the detection of ctDNA by this sensor showed an excellent linear relationship in the concentration range of 1.0 × 10-7 M to 1.0 × 10-16 M, and the detection limit was 2.5 × 10-18 M. In addition, this sensor exhibited outstanding stability and specificity. This strategy provides an alternative approach for ctDNA detection and an effective sensing strategy for future in vitro cancer diagnosis by label-free detection.
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Affiliation(s)
- Zhilian Cui
- Ministry of Education Engineering Research Center of Smart Microsensors and Microsystems, Hangzhou Dianzi University, Hangzhou, 310018, China.
- School of Electronics and Information, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Dujuan Li
- Ministry of Education Engineering Research Center of Smart Microsensors and Microsystems, Hangzhou Dianzi University, Hangzhou, 310018, China.
- School of Electronics and Information, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Weihuang Yang
- Ministry of Education Engineering Research Center of Smart Microsensors and Microsystems, Hangzhou Dianzi University, Hangzhou, 310018, China.
- School of Electronics and Information, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Kai Fan
- School of Automation, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Hongying Liu
- School of Automation, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Fei Wen
- Ministry of Education Engineering Research Center of Smart Microsensors and Microsystems, Hangzhou Dianzi University, Hangzhou, 310018, China.
- School of Electronics and Information, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Lili Li
- Ministry of Education Engineering Research Center of Smart Microsensors and Microsystems, Hangzhou Dianzi University, Hangzhou, 310018, China.
- School of Electronics and Information, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Linxi Dong
- Ministry of Education Engineering Research Center of Smart Microsensors and Microsystems, Hangzhou Dianzi University, Hangzhou, 310018, China.
- School of Electronics and Information, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Gaofeng Wang
- Ministry of Education Engineering Research Center of Smart Microsensors and Microsystems, Hangzhou Dianzi University, Hangzhou, 310018, China.
- School of Electronics and Information, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Wei Wu
- Ministry of Education Engineering Research Center of Smart Microsensors and Microsystems, Hangzhou Dianzi University, Hangzhou, 310018, China.
- School of Electronics and Information, Hangzhou Dianzi University, Hangzhou, 310018, China
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23
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Wang D, Zhou H, Shi Y, Sun W. A FEN 1-assisted swing arm DNA walker for electrochemical detection of ctDNA by target recycling cascade amplification. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:1922-1927. [PMID: 35527509 DOI: 10.1039/d2ay00364c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A flap endonuclease 1 (FEN 1)-assisted swing arm DNA walker was constructed to achieve the signal amplification detection of ctDNA. The MB-labeled hairpin DNA was designed as the track and a long swing-arm DNA strand as the capture probe. The introduction of ctDNA unlocked a helper hairpin DNA, which could be captured to form the DNA duplex walker with the capture probe, and also activated the catalyst hairpin assembly. The DNA duplex walker opened the hairpin track and formed a three-base overlapping DNA structure, which was recognized and cleaved by FEN 1. Driven by the FEN 1 and the high reaction temperature, the DNA walker was initiated to hybridize with the track DNA and release multiple MB-labeled flaps for signal amplification. Owing to the excellent amplification capacity of the target recycling-induced DNA walker and programmed catalysis hairpin assembly, the one-step biosensor showed a linear detection range from 1 fM to 100 pM with a detection limit of 0.33 fM. Moreover, the sensitive detection of ctDNA in serum samples was verified, suggesting its potential application in liquid biopsy for clinical diagnosis.
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Affiliation(s)
- Dongmei Wang
- School of Laboratory Medicine, Wannan Medical College, Wuhu, 241000, P. R. China.
| | - Huan Zhou
- School of Laboratory Medicine, Wannan Medical College, Wuhu, 241000, P. R. China.
| | - Yundong Shi
- School of Laboratory Medicine, Wannan Medical College, Wuhu, 241000, P. R. China.
| | - Wanjun Sun
- School of Laboratory Medicine, Wannan Medical College, Wuhu, 241000, P. R. China.
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24
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Liu S, Yang Y, Shi M, Shi H, Mao D, Mao X, Zhang Y. Smartphone-Based Pure DNAzyme Hydrogel Platform for Visible and Portable Colorimetric Detection of Cell-Free DNA. ACS Sens 2022; 7:658-665. [PMID: 35107259 DOI: 10.1021/acssensors.1c02662] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cell-free DNA (cfDNA), as a tumor marker, is of great importance for the diagnosis of cancer and targeted therapy. However, the need for huge analytical instruments for cfDNA analysis has restricted its practical applications, especially in rural areas and third-world countries. Herein, a portable and visual smartphone-based DNAzyme hydrogel platform is developed for cfDNA detection. The target cfDNA triggers rolling circle amplification to produce a G-quadruplex-comprised DNA hydrogel with an horseradish peroxidase (HRP)-like catalytic function, which further catalyzes the chromogenic substrate to generate a visible output signal. Notably, the naked-eye detection of cfDNA can be realized by the macroscale visibility and catalytic ability of the DNA hydrogel. The linear range of the DNAzyme hydrogel platform for cfDNA detection is 0.1 pM-1500 nM with a detection limit of 0.042 pM. Moreover, this platform is exploited for the detection of cfDNA in spiked human serum with favorable sensitivity and recovery. Therefore, the DNAzyme hydrogel platform provides highly promising potential for testing other nucleic acid biomarkers.
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Affiliation(s)
- Shaowei Liu
- Key Laboratory of Aqueous Environment Protection and Pollution Control of Yangtze River in Anhui of Anhui Provincial Education Department, College of Resources and Environment, Anqing Normal University, Anqing 246011, China
| | - Yumeng Yang
- College of Chemistry and Chemical Engineering, Anqing Normal University, Anqing 246011, China
| | - Mengqin Shi
- Key Laboratory of Aqueous Environment Protection and Pollution Control of Yangtze River in Anhui of Anhui Provincial Education Department, College of Resources and Environment, Anqing Normal University, Anqing 246011, China
| | - Hai Shi
- The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Dongsheng Mao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Xiaoxia Mao
- Key Laboratory of Aqueous Environment Protection and Pollution Control of Yangtze River in Anhui of Anhui Provincial Education Department, College of Resources and Environment, Anqing Normal University, Anqing 246011, China
| | - Yuanguang Zhang
- Key Laboratory of Aqueous Environment Protection and Pollution Control of Yangtze River in Anhui of Anhui Provincial Education Department, College of Resources and Environment, Anqing Normal University, Anqing 246011, China
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25
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Rapid Multiplex Strip Test for the Detection of Circulating Tumor DNA Mutations for Liquid Biopsy Applications. BIOSENSORS 2022; 12:bios12020097. [PMID: 35200357 PMCID: PMC8869478 DOI: 10.3390/bios12020097] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/26/2022] [Accepted: 02/01/2022] [Indexed: 01/16/2023]
Abstract
In the era of personalized medicine, molecular profiling of patient tumors has become the standard practice, especially for patients with advanced disease. Activating point mutations of the KRAS proto-oncogene are clinically relevant for many types of cancer, including colorectal cancer (CRC). While several approaches have been developed for tumor genotyping, liquid biopsy has been gaining much attention in the clinical setting. Analysis of circulating tumor DNA for genetic alterations has been challenging, and many methodologies with both advantages and disadvantages have been developed. We here developed a gold nanoparticle-based rapid strip test that has been applied for the first time for the multiplex detection of KRAS mutations in circulating tumor DNA (ctDNA) of CRC patients. The method involved ctDNA isolation, PCR-amplification of the KRAS gene, multiplex primer extension (PEXT) reaction, and detection with a multiplex strip test. We have optimized the efficiency and specificity of the multiplex strip test in synthetic DNA targets, in colorectal cancer cell lines, in tissue samples, and in blood-derived ctDNA from patients with advanced colorectal cancer. The proposed strip test achieved rapid and easy multiplex detection (normal allele and three major single-point mutations) of the clinically relevant KRAS mutations in ctDNA in blood samples of CRC patients with high specificity and repeatability. This multiplex strip test represents a minimally invasive, rapid, low-cost, and promising diagnostic tool for the detection of clinically relevant mutations in cancer patients.
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26
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Azzouz A, Hejji L, Kim KH, Kukkar D, Souhail B, Bhardwaj N, Brown RJC, Zhang W. Advances in surface plasmon resonance-based biosensor technologies for cancer biomarker detection. Biosens Bioelectron 2022; 197:113767. [PMID: 34768064 DOI: 10.1016/j.bios.2021.113767] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 10/21/2021] [Accepted: 10/31/2021] [Indexed: 01/25/2023]
Abstract
Surface plasmon resonance approach is a highly useful option to offer optical and label-free detection of target bioanalytes with numerous advantages (e.g., low-cost fabrication, appreciable sensitivity, label-free detection, and outstanding accuracy). As such, it allows early diagnosis of cancer biomarkers to monitor tumor progression and to prevent the recurrence of oncogenic tumors. This work highlights the recent progress in SPR biosensing technology for the diagnosis of various cancer types (e.g., lung, breast, prostate, and ovarian). Further, the performance of various SPR biosensors is also evaluated in terms of the basic quality assurance criteria (e.g., limit of detection (LOD), selectivity, sensor response time, and reusability). Finally, the limitations and future challenges associated with SPR biosensors are also discussed with respect to cancer biomarker detection.
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Affiliation(s)
- Abdelmonaim Azzouz
- Department of Chemistry, Faculty of Science, University of Abdelmalek Essaadi, B.P. 2121, M'Hannech II, 93002, Tétouan, Morocco
| | - Lamia Hejji
- Department of Chemistry, Faculty of Science, University of Abdelmalek Essaadi, B.P. 2121, M'Hannech II, 93002, Tétouan, Morocco
| | - Ki-Hyun Kim
- Department of Civil and Environmental Engineering, Hanyang University, 222 Wangsimni-Ro, Seoul, 04763, South Korea.
| | - Deepak Kukkar
- Department of Nanotechnology, Sri Guru Granth Sahib World University, Fatehgarh Sahib, 140406, Punjab, India
| | - Badredine Souhail
- Department of Chemistry, Faculty of Science, University of Abdelmalek Essaadi, B.P. 2121, M'Hannech II, 93002, Tétouan, Morocco
| | - Neha Bhardwaj
- Department of Biotechnology, University Institute of Engineering Technology (UIET), Panjab University, Chandigarh, India
| | - Richard J C Brown
- Environment Department, National Physical Laboratory, Teddington, TW11 0LW, UK
| | - Wei Zhang
- School of Ecology and Environmental Science, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan, 450001, PR China
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27
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Abouali H, Hosseini SA, Purcell E, Nagrath S, Poudineh M. Recent Advances in Device Engineering and Computational Analysis for Characterization of Cell-Released Cancer Biomarkers. Cancers (Basel) 2022; 14:288. [PMID: 35053452 PMCID: PMC8774172 DOI: 10.3390/cancers14020288] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/21/2021] [Accepted: 01/04/2022] [Indexed: 02/04/2023] Open
Abstract
During cancer progression, tumors shed different biomarkers into the bloodstream, including circulating tumor cells (CTCs), extracellular vesicles (EVs), circulating cell-free DNA (cfDNA), and circulating tumor DNA (ctDNA). The analysis of these biomarkers in the blood, known as 'liquid biopsy' (LB), is a promising approach for early cancer detection and treatment monitoring, and more recently, as a means for cancer therapy. Previous reviews have discussed the role of CTCs and ctDNA in cancer progression; however, ctDNA and EVs are rapidly evolving with technological advancements and computational analysis and are the subject of enormous recent studies in cancer biomarkers. In this review, first, we introduce these cell-released cancer biomarkers and briefly discuss their clinical significance in cancer diagnosis and treatment monitoring. Second, we present conventional and novel approaches for the isolation, profiling, and characterization of these markers. We then investigate the mathematical and in silico models that are developed to investigate the function of ctDNA and EVs in cancer progression. We convey our views on what is needed to pave the way to translate the emerging technologies and models into the clinic and make the case that optimized next-generation techniques and models are needed to precisely evaluate the clinical relevance of these LB markers.
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Affiliation(s)
- Hesam Abouali
- Department of Electrical and Computer Engineering, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (H.A.); (S.A.H.)
| | - Seied Ali Hosseini
- Department of Electrical and Computer Engineering, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (H.A.); (S.A.H.)
| | - Emma Purcell
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109-2800, USA; (E.P.); (S.N.)
| | - Sunitha Nagrath
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109-2800, USA; (E.P.); (S.N.)
| | - Mahla Poudineh
- Department of Electrical and Computer Engineering, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (H.A.); (S.A.H.)
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28
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Zhao H, Niu Z, Chen K, Chen L, Wang Z, Lan M, Shi J, Huang W. A novel sandwich-type electrochemical biosensor enabling sensitive detection of circulating tumor DNA. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106783] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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29
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Dual-signal amplification electrochemical sensing for the sensitive detection of uranyl ion based on gold nanoparticles and hybridization chain reaction-assisted synthesis of silver nanoclusters. Anal Chim Acta 2021; 1184:338986. [PMID: 34625249 DOI: 10.1016/j.aca.2021.338986] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 08/19/2021] [Accepted: 08/21/2021] [Indexed: 11/20/2022]
Abstract
Herein, a dual-signal amplification electrochemical sensing has been proposed for the ultrasensitive detection of uranyl ions (UO22+) by integration of gold nanoparticles (AuNPs) and hybridization chain reaction (HCR)-assisted synthesis of silver nanoclusters (AgNCs). In this sensing platform, AuNPs are used as an ideal signal amplification carrier, aiming at increasing the loads of UO22+-specific DNAzyme on the gold electrode. In the presence of UO22+, UO22+-specific DNAzyme can be activated, leading to the cleavage of substrate strands (S-DNA). Then, HCR is triggered to produce long dsDNA through hybridization the probe with the ssDNA on the electrode surface. As a result, an amplified electrochemical response can be detected by inserting a large amount of AgNCs generated in situ using dsDNA as template. Featured with amplification efficiency, good specificity and high sensitivity, the strategy could quantitatively detect UO22+ down to 6.2 pM with a linear calibration range from 20 pM to 5000 pM. The proposed sensing platform has been also successfully demonstrated the practical application of detecting UO22+, indicating that the developed method has the potential applications and can open up a new avenue for highly sensitive detection of UO22+ in environmental monitoring.
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30
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Yang X, Liao M, Zhang H, Gong J, Yang F, Xu M, Tremblay PL, Zhang T. An electrochemiluminescence resonance energy transfer biosensor for the detection of circulating tumor DNA from blood plasma. iScience 2021; 24:103019. [PMID: 34522862 PMCID: PMC8426273 DOI: 10.1016/j.isci.2021.103019] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/02/2021] [Accepted: 08/18/2021] [Indexed: 01/14/2023] Open
Abstract
A liquid biopsy is a noninvasive approach for detecting double-stranded circulating tumor DNA (ctDNA) of 90-320 nucleotides in blood plasma from patients with cancer. Most techniques employed for ctDNA detection are time consuming and require expensive DNA purification kits. Electrochemiluminescence resonance energy transfer (ECL-RET) biosensors exhibit high sensitivity, a wide response range, and are promising for straightforward sensing applications. Until now, ECL-RET biosensors have been designed for sensing short single-stranded oligonucleotides of less than 45 nucleotides. In this work, an ECL-RET biosensor comprising graphitic carbon nitride quantum dots was assessed for the amplification-free detection in the blood plasma of DNA molecules coding for the EGFR L858R mutation, which is associated with non-small-cell lung cancer. Following a low-cost pre-treatment, the highly specific ECL-RET biosensor quantified double-stranded EGFR L858R DNA of 159 nucleotides diluted into the blood within a linear range of 0.01 fM to 1 pM, demonstrating its potential for noninvasive biopsies.
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Affiliation(s)
- Xidong Yang
- School of Chemistry, Chemical Engineering, and Life Science, Wuhan University of Technology, Wuhan 430070, PR China
- Shaoxing Institute for Advanced Research, Wuhan University of Technology, Shaoxing 312300, PR China
| | - Meiyan Liao
- Department of Radiology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Hanfei Zhang
- Department of Radiology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - JinBo Gong
- School of Chemistry, Chemical Engineering, and Life Science, Wuhan University of Technology, Wuhan 430070, PR China
| | - Fan Yang
- School of Chemistry, Chemical Engineering, and Life Science, Wuhan University of Technology, Wuhan 430070, PR China
| | - Mengying Xu
- School of Chemistry, Chemical Engineering, and Life Science, Wuhan University of Technology, Wuhan 430070, PR China
- Shaoxing Institute for Advanced Research, Wuhan University of Technology, Shaoxing 312300, PR China
| | - Pier-Luc Tremblay
- School of Chemistry, Chemical Engineering, and Life Science, Wuhan University of Technology, Wuhan 430070, PR China
- Shaoxing Institute for Advanced Research, Wuhan University of Technology, Shaoxing 312300, PR China
- State Key Laboratory of Silicate Materials for Architectures, Wuhan University of Technology, Wuhan 430070, PR China
| | - Tian Zhang
- School of Chemistry, Chemical Engineering, and Life Science, Wuhan University of Technology, Wuhan 430070, PR China
- Shaoxing Institute for Advanced Research, Wuhan University of Technology, Shaoxing 312300, PR China
- State Key Laboratory of Silicate Materials for Architectures, Wuhan University of Technology, Wuhan 430070, PR China
- School of Materials Science and Engineering, Wuhan University of Technology, Wuhan 430070, PR China
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31
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Gong P, Wang Y, Zhou X, Wang S, Zhang Y, Zhao Y, Nguyen LV, Ebendorff-Heidepriem H, Peng L, Warren-Smith SC, Li X. In Situ Temperature-Compensated DNA Hybridization Detection Using a Dual-Channel Optical Fiber Sensor. Anal Chem 2021; 93:10561-10567. [PMID: 34291916 DOI: 10.1021/acs.analchem.1c01660] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A multifunction, high-sensitivity, and temperature-compensated optical fiber DNA hybridization sensor combining surface plasmon resonance (SPR) and Mach-Zehnder interference (MZI) has been designed and implemented. We demonstrate, for the first time to our knowledge, the dual-parameter measurement of temperature and refractive index (RI) by simultaneously using SPR and MZI in a simple single-mode fiber (SMF)-no-core fiber (NCF)-SMF structure. The experimental results show RI sensitivities of 930 and 1899 nm/RIU and temperature sensitivities of 0.4 and -1.4 nm/°C for the MZI and SPR, respectively. We demonstrate a sensitivity matrix used to simultaneously detect both parameters, solving the problem of temperature interference of RI variation-based biosensors. In addition, the sensor can also distinguish biological binding events by detecting the localized RI changes at the fiber's surface. We realize label-free sensing of DNA hybridization detection by immobilizing probe DNA (pDNA) onto the fiber as the probe to capture complementary DNA (cDNA). The experimental results show that the sensor can qualitatively detect cDNA after temperature compensation, and the limit of detection (LOD) of the sensor reaches 80 nM. The proposed sensor has advantages of high sensitivity, real time, low cost, temperature compensation, and low detection limit and is suitable for in situ monitoring, high-precision sensing of DNA molecules, and other related fields, such as gene diagnosis, kinship judgment, environmental monitoring, and so on.
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Affiliation(s)
- Pengqi Gong
- College of Information Science and Engineering, Northeastern University, Shenyang, Liaoning 110819, China
| | - Yiming Wang
- No. 120 High School of Shenyang, Shenyang, Liaoning 110031, China
| | - Xue Zhou
- College of Information Science and Engineering, Northeastern University, Shenyang, Liaoning 110819, China
| | - Shankun Wang
- College of Information Science and Engineering, Northeastern University, Shenyang, Liaoning 110819, China
| | - Yanan Zhang
- College of Information Science and Engineering, Northeastern University, Shenyang, Liaoning 110819, China
| | - Yong Zhao
- College of Information Science and Engineering, Northeastern University, Shenyang, Liaoning 110819, China.,Hebei Key Laboratory of Micro-Nano Precision Optical Sensing and Measurement Technology, Qinhuangdao, Hebei 066004, China
| | - Linh Viet Nguyen
- Institute for Photonics and Advanced Sensing and School of Physical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Heike Ebendorff-Heidepriem
- Institute for Photonics and Advanced Sensing and School of Physical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Lu Peng
- Institute for Photonics and Advanced Sensing and School of Physical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Stephen C Warren-Smith
- Institute for Photonics and Advanced Sensing and School of Physical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia.,Future Industries Institute, University of South Australia, Mawson Lakes, South Australia 5095, Australia
| | - Xuegang Li
- College of Information Science and Engineering, Northeastern University, Shenyang, Liaoning 110819, China
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32
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The mechanism and improvements to the isothermal amplification of nucleic acids, at a glance. Anal Biochem 2021; 631:114260. [PMID: 34023274 DOI: 10.1016/j.ab.2021.114260] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 05/15/2021] [Accepted: 05/18/2021] [Indexed: 01/08/2023]
Abstract
A comparative review of the most common isothermal methods is provided. In the last two decades, the challenge of using isothermal amplification systems as an alternate to the most extensive and long-standing nucleic acids-amplifying method-the polymerase chain reaction-has arisen. The main advantage of isothermal amplification is no requirement for expensive laboratory equipment for thermal cycling. Considerable efforts have been made to improve the current techniques of nucleic acid amplification and the development of new approaches based on the main drawbacks of each method. The most important and challenging goal was to achieve a low-cost, straightforward system that is rapid, specific, accurate, and sensitive.
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33
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Chen C, He R, Zhang Z, Chen Y. Dual-recognition-based determination of ctDNA via the clamping function of peptide nucleic acid and terminal protection of small-molecule-linked DNA. Analyst 2021; 145:7603-7608. [PMID: 32990694 DOI: 10.1039/d0an01305f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A new dual-recognition fluorescent biosensor for circulating tumor DNA (ctDNA) detection has been developed, which combines the clamping function of peptide nucleic acid (PNA) and terminal protection of small-molecule-linked DNA (TPSMLD). Taking the tumor-specific E542K mutation and methylation of the PIK3CA gene as the target ctDNA, a low detection limit of 0.3161 pM ctDNA is achieved with good selectivity. This study not only offers a sensitive, selective and accurate ctDNA detection method, but can also be used to detect the target in complex biological samples.
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Affiliation(s)
- Chaohui Chen
- Institute for Interdisciplinary Research, Jianghan University, Wuhan 430056, P. R. China.
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34
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Deng Y, Cao G, Chen X, Yang M, Huo D, Hou C. Ultrasensitive detection of gene-PIK3CA H1047R mutation based on cascaded strand displacement amplification and trans-cleavage ability of CRISPR/Cas12a. Talanta 2021; 232:122415. [PMID: 34074403 DOI: 10.1016/j.talanta.2021.122415] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 03/22/2021] [Accepted: 04/07/2021] [Indexed: 01/22/2023]
Abstract
Low abundance gene-PIK3CAH1047R mutation detection is crucial for the clinical diagnosis and treatment of breast cancer. Here, a fluorescent biosensor which combines cascaded strand displacement amplification (C-SDA) and trans-cleavage ability of CRISPR/Cas12a was established to ultra-sensitively detect gene-PIK3CAH1047R mutation. The mutated gene-PIK3CAH1047R can combine with complementary sequence to form an intact recognition site for endonuclease FspI. Mediated by FspI, it breaks at the mutation site to produce DNA fragment to trigger SDA or C-SDA. Then, the fluorescent biosensors based on SDA-CRISPR/Cas12a or C-SDA-CRISPR/Cas12a were constructed. Compared with biosensor based on SDA-CRISPR/Cas12a (5 pM), the minimum detection of the biosensor based on C-SDA-CRISPR/Cas12a is reduced two orders of magnitude (50 fM). In range of 0.001%-50%, we achieved the ultrasensitive detection of gene-PIK3CAH1047R mutation low to 0.001%. Besides, the proposed biosensor works well in human serum samples, showing its application potential in low-abundance gene-PIK3CAH1047R mutation detection.
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Affiliation(s)
- Yuanyi Deng
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, PR China
| | - Gaihua Cao
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, PR China
| | - Xiaolong Chen
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, PR China
| | - Mei Yang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, PR China
| | - Danqun Huo
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, PR China; Chongqing Key Laboratory of Bio-perception & Intelligent Information Processing, School of Microelectronics and Communication Engineering, Chongqing University, Chongqing, 400044, PR China.
| | - Changjun Hou
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, PR China; Chongqing Key Laboratory of Bio-perception & Intelligent Information Processing, School of Microelectronics and Communication Engineering, Chongqing University, Chongqing, 400044, PR China.
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Liquid biopsy genotyping by a simple lateral flow strip assay with visual detection. Anal Chim Acta 2021; 1163:338470. [PMID: 34024417 DOI: 10.1016/j.aca.2021.338470] [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: 02/23/2021] [Revised: 03/24/2021] [Accepted: 03/29/2021] [Indexed: 12/19/2022]
Abstract
Liquid biopsy, as a minimally invasive method that allows real-time monitoring of the tumor genome, represents a competing approach for cancer diagnosis, prognosis and therapy decision making. Liquid biopsy in cancer patients mainly includes analysis of circulating tumor cells (CTC) and cell-free circulating tumor DNA (ctDNA). ctDNA is the tumor-derived fraction of the cell-free DNA present in the blood. ctDNA is detected based on cancer-specific genomic aberrations (mainly mutations) and represents a challenging analyte due to high fragmentation and low concentration. Several methodologies have been developed for ctDNA analysis in cancer patients but many of these technologies are too time-intensive, complicated and expensive for implementation in diagnostic testing. Herein, we developed a novel lateral flow strip assay for mutational analysis of ctDNA in blood samples and visual detection that is based on gold nanoparticles as reporters. As a model, common single-point mutations of the KRAS gene, related to colorectal cancer (CRC), have been selected for method development. The proposed DNA biosensor has been successfully applied for the detection of three KRAS mutations (KRAS G12D/A/V), along with the wild-type KRAS gene in synthetic DNA targets, cancer cell lines and cfDNA from blood samples of healthy individuals and CRC patients. The main advantages of the proposed lateral flow assay are simplicity, rapid analysis time (∼10 min) and visual detection without the requirement of special instrumentation. The assay is also cost-effective with high detectability, specificity and reproducibility and has the potential to be used as a portable and universal device. In conclusion, the proposed assay offers a rapid diagnostic strip test for visual genotyping, as an alternative approach for liquid biopsy applications.
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Chen D, Wu Y, Hoque S, Tilley RD, Gooding JJ. Rapid and ultrasensitive electrochemical detection of circulating tumor DNA by hybridization on the network of gold-coated magnetic nanoparticles. Chem Sci 2021; 12:5196-5201. [PMID: 34163756 PMCID: PMC8179593 DOI: 10.1039/d1sc01044a] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 02/26/2021] [Indexed: 12/12/2022] Open
Abstract
An accurate and robust method for quantifying the levels of circulating tumor DNA (ctDNA) is vital if this potential biomarker is to be used for the early diagnosis of cancer. The analysis of ctDNA presents unique challenges because of its short half-life and ultralow abundance in early stage cancers. Here we develop an ultrasensitive electrochemical biosensor for rapid detection of ctDNA in whole blood. The sensing of ctDNA is based on hybridization on a network of probe DNA modified gold-coated magnetic nanoparticles (DNA-Au@MNPs). This DNA-Au@MNPs biosensor can selectively detect short- and long-strand DNA targets. It has a broad dynamic range (2 aM to 20 nM) for 22 nucleotide DNA target with an ultralow detection limit of 3.3 aM. For 101 nucleotide ctDNA target, a dynamic range from 200 aM to 20 nM was achieved with a detection limit of 5 fM. This DNA-Au@MNPs based sensor provides a promising method to achieve 20 min response time and minimally invasive cancer early diagnosis.
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Affiliation(s)
- Dongfei Chen
- School of Chemistry, The University of New South Wales Sydney NSW 2052 Australia
- Australian Centre for NanoMedicine, The University of New South Wales Sydney NSW 2052 Australia
- The ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales Sydney NSW 2052 Australia
| | - Yanfang Wu
- School of Chemistry, The University of New South Wales Sydney NSW 2052 Australia
- Australian Centre for NanoMedicine, The University of New South Wales Sydney NSW 2052 Australia
- The ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales Sydney NSW 2052 Australia
| | - Sharmin Hoque
- School of Chemistry, The University of New South Wales Sydney NSW 2052 Australia
- Australian Centre for NanoMedicine, The University of New South Wales Sydney NSW 2052 Australia
- The ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales Sydney NSW 2052 Australia
| | - Richard D Tilley
- School of Chemistry, The University of New South Wales Sydney NSW 2052 Australia
- Australian Centre for NanoMedicine, The University of New South Wales Sydney NSW 2052 Australia
- Electron Microscope Unit, Mark Wainwright Analytical Centre, The University of New South Wales Sydney NSW 2052 Australia
| | - J Justin Gooding
- School of Chemistry, The University of New South Wales Sydney NSW 2052 Australia
- Australian Centre for NanoMedicine, The University of New South Wales Sydney NSW 2052 Australia
- The ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales Sydney NSW 2052 Australia
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Borum RM, Jokerst JV. Hybridizing clinical translatability with enzyme-free DNA signal amplifiers: recent advances in nucleic acid detection and imaging. Biomater Sci 2021; 9:347-366. [PMID: 32734995 PMCID: PMC7855509 DOI: 10.1039/d0bm00931h] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Nucleic acids have become viable prognostic and diagnostic biomarkers for a diverse class of diseases, particularly cancer. However, the low femtomolar to attomolar concentration of nucleic acids in human samples require sensors with excellent detection capabilities; many past and current platforms fall short or are economically difficult. Strand-mediated signal amplifiers such as hybridization chain reaction (HCR) and catalytic hairpin assembly (CHA) are superior methods for detecting trace amounts of biomolecules because one target molecule triggers the continuous production of synthetic double-helical DNA. This cascade event is highly discriminatory to the target via sequence specificity, and it can be coupled with fluorescence, electrochemistry, magnetic moment, and electrochemiluminescence for signal reporting. Here, we review recent advances in enhancing the sensing abilities in HCR and CHA for improved live-cell imaging efficiency, lowered limit of detection, and optimized multiplexity. We further outline the potential for clinical translatability of HCR and CHA by summarizing progress in employing these two tools for in vivo imaging, human sample testing, and sensing-treating dualities. We finally discuss their future prospects and suggest clinically-relevant experiments to supplement further related research.
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Affiliation(s)
- Raina M Borum
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA.
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38
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Li Z, Zou S, Wu S, Miao X, Ma DL. Polymerase chain reaction-based ultrasensitive detection of HBV DNA via G-quadruplex selective iridium(III) complex luminescent probe. Talanta 2021; 221:121661. [DOI: 10.1016/j.talanta.2020.121661] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 09/07/2020] [Accepted: 09/09/2020] [Indexed: 12/20/2022]
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Zeng N, Guo Y, Xiang J. A Pterin-FAM-TAMRA Tri-color Fluorescence Biosensor to Detect the Level of KRAS Point Mutation. ANAL SCI 2020; 36:1529-1533. [PMID: 32830162 DOI: 10.2116/analsci.20p265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Monitoring the changes in the level of KRAS point mutation (the concentration fraction of the KRAS point mutated DNA to the total DNA) in clinical treatment progress can guide and greatly improve the personalized therapy and therapeutic evaluation of patients with cancer. In this work, based on FRET fluorescence quenching and apyrimidinic site-induced guanine/pterin specific binding, we developed a pterin-FAM-TAMRA tri-color fluorescence sensing system to assess the level of KRAS point mutation in one step. The responses from TAMRA displayed good and similar linear correlations in the range from 60 nM to 2 μM for all four types of DNA, resulting in a common linear equation related to the T-DNA concentration (NΔFTAMRA = 2.908cT-DNA + 0.364). Meanwhile, the responses from pterin showed excellent selectivity to W-DNA and an excellent linear correlation to the W-DNA in the concentration range from 60 nM to 1 μM (NΔFpterin = -0.364cgDNA-G + 0.034). This biosensor has an effective concentration range for detecting KRAS point mutations. Especially, because the apyrimidinic site-induced guanine/pterin binding is selective for the detection of wild-type DNA, the sensing system can be applied for clinical mutation level detection of all kinds of KRAS point mutations (G → A, G → C and G → T) in blood samples, which is crucial for the personalized therapy and therapeutic evaluation of patients with most KRAS-related cancer types.
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Affiliation(s)
- Ni Zeng
- College of Chemistry and Chemical Engineering, Central South University
| | - Yaxin Guo
- College of Chemistry and Chemical Engineering, Central South University
| | - Juan Xiang
- College of Chemistry and Chemical Engineering, Central South University
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40
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Zeng Z, Zhou R, Sun R, Zhang X, Cheng Z, Chen C, Zhu Q. Nonlinear hybridization chain reaction-based functional DNA nanostructure assembly for biosensing, bioimaging applications. Biosens Bioelectron 2020; 173:112814. [PMID: 33197767 DOI: 10.1016/j.bios.2020.112814] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/23/2020] [Accepted: 11/09/2020] [Indexed: 12/14/2022]
Abstract
Hybridization chain reaction (HCR) can be divided into two categories: linear HCR and nonlinear HCR. In traditional linear HCR, the relatively slow kinetics and less sufficient sensitivity largely limit its scope of application. In the nonlinear HCR system, under the trigger of the initiator, the judicious designed substrate sequences (hairpin or hairpin-free) will self-assembly to dendritic or branched DNA nanostructures with exponential growth kinetics. Given the advantages of its enzyme-free, high-order growth kinetic, high sensitivity, and simple operation, nonlinear HCR is regarded as a powerful signal amplifier for the detection of biomarkers by integrating with versatile sensing platforms in the past few decades. In this review, we describe the basic features of nonlinear HCR mechanism and classify the nonlinear HCR into several categories based on their self-assembly mechanisms: the branched HCR, dendritic HCR, hydrogel-based clamped HCR, and other types of HCR. Then, we summarize the recent development of nonlinear HCR in biosensing, such as nucleic acid, protein, enzyme activities, and cancer cell detection, etc., and we also review the current applications of nonlinear HCR in bioimaging (mRNA in situ imaging). We choose several representative works to further illustrate the analysis mechanisms via various detection platforms, such as fluorescence, electrochemical, colorimetric, etc. At last, we also review the challenges and further perspectives of nonlinear HCR in the use of bioanalysis.
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Affiliation(s)
- Zhuoer Zeng
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, 410013, Hunan, China.
| | - Rong Zhou
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, 410013, Hunan, China.
| | - Ruowei Sun
- Hunan Zaochen Nanorobot Co., Ltd, Liuyang, Hunan, China.
| | - Xun Zhang
- Hunan Zaochen Nanorobot Co., Ltd, Liuyang, Hunan, China.
| | - Zeneng Cheng
- 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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Feng D, Su J, He G, Xu Y, Wang C, Zheng M, Qian Q, Mi X. Electrochemical DNA Sensor for Sensitive BRCA1 Detection Based on DNA Tetrahedral-Structured Probe and Poly-Adenine Mediated Gold Nanoparticles. BIOSENSORS-BASEL 2020; 10:bios10070078. [PMID: 32698331 PMCID: PMC7400266 DOI: 10.3390/bios10070078] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 06/28/2020] [Accepted: 07/08/2020] [Indexed: 01/18/2023]
Abstract
BRCA1 is the biomarker for the early diagnosis of breast cancer. Detection of BRCA1 has great significance for the genetic analysis, early diagnosis and clinical treatment of breast cancer. In this work, we developed a simple electrochemical DNA sensor based on a DNA tetrahedral-structured probe (TSP) and poly-adenine (polyA) mediated gold nanoparticles (AuNPs) for the sensitive detection of BRCA1. A thiol-modified TSP was used as the scaffold on the surface of the screen-printed AuNPs electrode. The capture DNA (TSP) and reporter DNA were hybridized to the target DNA (BRCA1), respectively, to form the typical sandwich system. The nanocomposites of reporter DNA (polyA at the 5′ end) combined with AuNPs were employed for signal amplification which can capture multiple enzymes by the specificity between biotin and streptavidin. Measurements were completed in the electrochemical workstation by cyclic voltammetry and amperometry and we obtained the low limit of detection of 0.1 fM with the linear range from 1 fM to 1 nM. High sensitivity and good specificity of the proposed electrochemical DNA sensor showed potential applications in clinical early diagnosis for breast cancer.
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Affiliation(s)
- Dezhi Feng
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China; (D.F.); (G.H.); (Y.X.); (C.W.); (M.Z.); (Q.Q.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Su
- Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China;
| | - Guifang He
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China; (D.F.); (G.H.); (Y.X.); (C.W.); (M.Z.); (Q.Q.)
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Yi Xu
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China; (D.F.); (G.H.); (Y.X.); (C.W.); (M.Z.); (Q.Q.)
| | - Chenguang Wang
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China; (D.F.); (G.H.); (Y.X.); (C.W.); (M.Z.); (Q.Q.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mengmeng Zheng
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China; (D.F.); (G.H.); (Y.X.); (C.W.); (M.Z.); (Q.Q.)
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Qiuling Qian
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China; (D.F.); (G.H.); (Y.X.); (C.W.); (M.Z.); (Q.Q.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xianqiang Mi
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China; (D.F.); (G.H.); (Y.X.); (C.W.); (M.Z.); (Q.Q.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Functional Materials for Informatics, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China
- CAS Center for Excellence in Superconducting Electronics (CENSE), Shanghai 200050, China
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou 310024, China
- Correspondence:
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Wang J, Hua G, Li L, Li D, Wang F, Wu J, Ye Z, Zhou X, Ye S, Yang J, Zhang X, Ren L. Upconversion nanoparticle and gold nanocage satellite assemblies for sensitive ctDNA detection in serum. Analyst 2020; 145:5553-5562. [PMID: 32613211 DOI: 10.1039/d0an00701c] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A rapid molecular diagnostic technique targeting circulating tumor DNA (ctDNA) has become one of the most clinically significant liquid biopsy methods for non-invasive and timely diagnosis of cancer. Herein, a sensitive detection system of ctDNA based on a fluorescence resonance energy transfer (FRET) system using upconversion nanoparticles (UCNPs) and gold nanocages (AuNCs) was constructed. Through the doping of Yb and Tm ions, the excitation and emission wavelengths of UCNPs were adjusted to 980 nm and 806 nm, respectively. Subsequently, UCNPs and AuNCs with the corresponding wavelength absorption were linked by complementary pairing of surface-modified DNA to form near-infrared fluorescent nanoprobes (NIR probes). Targeting DNA mutation recognition and signal transduction were realized by using NIR probes through the toehold-mediated strand displacement reaction. This method could detect a single point mutation of the KRAS gene with a wide detection range from 5 pM to 1000 pM and the limit of detection reached 6.30 pM. More importantly, the stable and highly specific NIR probes could be directly used in the serum environment without complicated pretreatment and amplification processes in advance. It could be envisioned that this specific and sensitive ctDNA detection strategy has great potential in clinical diagnosis and monitoring of diverse malignant tumors.
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Affiliation(s)
- Jiawei Wang
- Key Laboratory of Biomedical Engineering of Fujian Province University/Research Center of Biomedical Engineering of Xiamen, Department of Biomaterials, College of Materials, Xiamen University, Xiamen 361005, P.R. China.
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