1
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Wang KH, Chen YY, Wang CH, Hsu KF, Chau LK, Wang SC, Chen YL. Ultrasensitive amplification-free detection of circulating miRNA via droplet-based processing of SERS tag-miRNA-magnetic nanoparticle sandwich nanocomplexes on a paper-based electrowetting-on-dielectric platform. Analyst 2024; 149:1981-1987. [PMID: 38226658 DOI: 10.1039/d3an01429k] [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: 01/17/2024]
Abstract
MicroRNAs (miRNAs) have emerged as a promising class of biomarkers for early detection of various cancers, including ovarian cancer. However, quantifying miRNAs in human blood samples is challenging owing to the issues of sensitivity and specificity. In this study, hsa-miR-200a-3p of the miR-200a sub-family, which is a biomarker of ovarian cancer, was used as the analyte to demonstrate the analytical capability of an integrated biosensing platform using an extremely sensitive surface-enhanced Raman scattering (SERS) nanotag-nanoaggregate-embedded beads (NAEBs), magnetic nanoparticles (MNPs), a pair of highly specific locked nucleic acid (LNA) probes, and a semi-automated paper-based electrowetting-on-dielectric (pEWOD) device to provide labor-less and thorough sample cleanup and recovery. A sandwich approach where NAEBs are modified by one LNA-1 probe and MNPs are modified by another LNA-2 probe was applied. Then, the target analyte miRNA-200a-3p was introduced to form a sandwich nanocomplex through hybridization with the pair of LNA probes. The pEWOD device was used to achieve short cleanup time and good recovery of the nanocomplex, bringing the total analysis time to less than 30 min. The detection limit of this approach can reach 0.26 fM through SERS detection. The versatility of this method without the need for RNA extraction from clinical samples is expected to have good potential in detecting other miRNAs.
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Affiliation(s)
- Kai-Hao Wang
- Department of Chemistry and Biochemistry and Center for Nano Bio-Detection, National Chung Cheng University, Chia-Yi 62102, Taiwan.
| | - Yuan-Yu Chen
- Department of Chemistry and Biochemistry and Center for Nano Bio-Detection, National Chung Cheng University, Chia-Yi 62102, Taiwan.
| | - Chih-Hsien Wang
- Department of Chemistry and Biochemistry and Center for Nano Bio-Detection, National Chung Cheng University, Chia-Yi 62102, Taiwan.
| | - Keng-Fu Hsu
- Department of Obstetrics and Gynecology, National Cheng Kung University Hospital, Tainan 70101, Taiwan
| | - Lai-Kwan Chau
- Department of Chemistry and Biochemistry and Center for Nano Bio-Detection, National Chung Cheng University, Chia-Yi 62102, Taiwan.
| | - Shau-Chun Wang
- Department of Chemistry and Biochemistry and Center for Nano Bio-Detection, National Chung Cheng University, Chia-Yi 62102, Taiwan.
| | - Yuh-Ling Chen
- Institute of Oral Medicine, National Cheng Kung University, Tainan 70101, Taiwan.
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2
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Paul T, Palaniyandi K, Gnanasampanthapandian D. Therapeutic Approaches to Increase the Survival Rate of Cancer Patients in the Younger and Older Population. Curr Aging Sci 2024; 17:16-30. [PMID: 38062658 DOI: 10.2174/0118746098241507231127114248] [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: 01/25/2023] [Revised: 06/25/2023] [Accepted: 09/22/2023] [Indexed: 05/18/2024]
Abstract
Various developments have been observed in the treatment of cancer patients, such as higher survival rates and better treatment outcomes. However, expecting similar outcomes in older patients remains a challenge. The main reason for this conclusion is the exclusion of older people from clinical trials for cancer drugs, as well as other factors, such as comorbidity, side effects, age-related frailties and their willingness to undergo multiple treatments. However, the discovery of new techniques and drug combinations has led to a significant improvement in the survival of the elderly population after the onset of the disease. On the other hand, cancer treatments have not become more complex for the younger population when compared to the older population, as the younger population tends to respond well to treatment trials and their physiological conditions are stable in response to treatments. In summary, this review correlates recent cancer treatment strategies and the corresponding responses and survival outcomes of older and younger patients.
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Affiliation(s)
- Tharrun Paul
- Cancer Science Laboratory, Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203, Chengalpattu, India
| | - Kanagaraj Palaniyandi
- Cancer Science Laboratory, Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203, Chengalpattu, India
| | - Dhanavathy Gnanasampanthapandian
- Cancer Science Laboratory, Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203, Chengalpattu, India
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3
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Hosseini SA, Kardani A, Yaghoobi H. A comprehensive review of cancer therapies mediated by conjugated gold nanoparticles with nucleic acid. Int J Biol Macromol 2023; 253:127184. [PMID: 37797860 DOI: 10.1016/j.ijbiomac.2023.127184] [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: 08/02/2023] [Revised: 09/16/2023] [Accepted: 09/24/2023] [Indexed: 10/07/2023]
Abstract
Nucleic acids provide a promising therapeutic platform by targeting various cell signaling pathways involved in cancer and genetic disorders. However, maintaining optimal stability during delivery limits their utility. Nucleic acid delivery vehicles are generally categorized into biological and synthetic carriers. Regardless of the efficiency of biological vectors, such as viral vectors, issues related to their immunogenicity and carcinogenesis are very important and vital for clinical applications. On the other hand, synthetic vectors such as lipids or polymers, have been widely used for nucleic acid delivery. Despite their transfection efficiency, low storage stability, targeting inefficiency, and tracking limitations are among the limitations of the clinical application of these vectors. In the past decades, gold nanoparticles with unique properties have been shown to be highly efficient mineral vectors for overcoming these obstacles. In this review, we focus on gold nanoparticle-nucleic acid combinations and highlight their use in the treatment of various types of cancers. Furthermore, by stating the biological applications of these structures, we will discuss their clinical applications.
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Affiliation(s)
- Sayedeh Azimeh Hosseini
- Student Research Committee, Shahrekord University of Medical Sciences, Shahrekord, Iran; Department of Medical Biotechnology, School of Advanced Technology, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Arefeh Kardani
- Department of Medical Biotechnology, School of Advanced Technology, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Hajar Yaghoobi
- Clinical Biochemistry Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran.
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4
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Li R, Li F, Zhang Y, He Y, Wang Y, Wang F. Miniature Hierarchical DNA Hybridization Circuit for Amplified Multiplexed MicroRNA Imaging. Anal Chem 2023; 95:3848-3855. [PMID: 36745869 DOI: 10.1021/acs.analchem.2c05373] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Accurate diagnosis requires the development of multiple-guaranteed DNA circuits. Nevertheless, for reliable multiplexed molecular imaging, existing DNA circuits are limited by poor cell-delivering homogeneity due to their cumbersome and dispersive reactants. Herein, we developed a compact-yet-efficient hierarchical DNA hybridization (HDH) circuit for in situ simultaneous analysis of multiple miRNAs, which could be further exploited for specifically discriminating cancer cells from normal ones. By integrating the traditional hybridization chain reaction and catalytic hairpin assembly reactants into two highly organized hairpins, the HDH circuit is fitted with condensed components and multiple response domains, thus permitting the programmable multiple microRNA-guaranteed sequential activations and the localized cascaded signal amplification. The synergistic multi-recognition and amplification features of the HDH circuit facilitate the magnified detection of multiplex endogenous miRNAs in living cells. The in vitro and cellular imaging experimental results revealed that the HDH circuit displayed a reliable sensing performance with high selective cell-identification capacity. We anticipate that this compact design can provide a powerful toolkit for accurate diagnostics and pathological evolution.
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Affiliation(s)
- Ruomeng Li
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P.R. China
| | - Fengzhe Li
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P.R. China
| | - Yanping Zhang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P.R. China
| | - Yuqiu He
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P.R. China
| | - Yushi Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P.R. China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P.R. China.,Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan 430072, P.R. China
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5
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Overview of Optical Biosensors for Early Cancer Detection: Fundamentals, Applications and Future Perspectives. BIOLOGY 2023; 12:biology12020232. [PMID: 36829508 PMCID: PMC9953566 DOI: 10.3390/biology12020232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 02/05/2023]
Abstract
Conventional cancer detection and treatment methodologies are based on surgical, chemical and radiational processes, which are expensive, time consuming and painful. Therefore, great interest has been directed toward developing sensitive, inexpensive and rapid techniques for early cancer detection. Optical biosensors have advantages in terms of high sensitivity and being label free with a compact size. In this review paper, the state of the art of optical biosensors for early cancer detection is presented in detail. The basic idea, sensitivity analysis, advantages and limitations of the optical biosensors are discussed. This includes optical biosensors based on plasmonic waveguides, photonic crystal fibers, slot waveguides and metamaterials. Further, the traditional optical methods, such as the colorimetric technique, optical coherence tomography, surface-enhanced Raman spectroscopy and reflectometric interference spectroscopy, are addressed.
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6
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Oliveira MJ, Dalot A, Fortunato E, Martins R, Byrne HJ, Franco R, Águas H. Microfluidic SERS devices: brightening the future of bioanalysis. DISCOVER MATERIALS 2022; 2:12. [PMID: 36536830 PMCID: PMC9751519 DOI: 10.1007/s43939-022-00033-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
A new avenue has opened up for applications of surface-enhanced Raman spectroscopy (SERS) in the biomedical field, mainly due to the striking advantages offered by SERS tags. SERS tags provide indirect identification of analytes with rich and highly specific spectral fingerprint information, high sensitivity, and outstanding multiplexing potential, making them very useful in in vitro and in vivo assays. The recent and innovative advances in nanomaterial science, novel Raman reporters, and emerging bioconjugation protocols have helped develop ultra-bright SERS tags as powerful tools for multiplex SERS-based detection and diagnosis applications. Nevertheless, to translate SERS platforms to real-world problems, some challenges, especially for clinical applications, must be addressed. This review presents the current understanding of the factors influencing the quality of SERS tags and the strategies commonly employed to improve not only spectral quality but the specificity and reproducibility of the interaction of the analyte with the target ligand. It further explores some of the most common approaches which have emerged for coupling SERS with microfluidic technologies, for biomedical applications. The importance of understanding microfluidic production and characterisation to yield excellent device quality while ensuring high throughput production are emphasised and explored, after which, the challenges and approaches developed to fulfil the potential that SERS-based microfluidics have to offer are described.
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Affiliation(s)
- Maria João Oliveira
- CENIMAT|i3N, Department of Materials Science, School of Science and Technology, NOVA University Lisbon and, CEMOP/UNINOVA, Caparica, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO—Applied Molecular Biosciences Unit, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Ana Dalot
- CENIMAT|i3N, Department of Materials Science, School of Science and Technology, NOVA University Lisbon and, CEMOP/UNINOVA, Caparica, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO—Applied Molecular Biosciences Unit, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Elvira Fortunato
- CENIMAT|i3N, Department of Materials Science, School of Science and Technology, NOVA University Lisbon and, CEMOP/UNINOVA, Caparica, Portugal
| | - Rodrigo Martins
- CENIMAT|i3N, Department of Materials Science, School of Science and Technology, NOVA University Lisbon and, CEMOP/UNINOVA, Caparica, Portugal
| | - Hugh J. Byrne
- FOCAS Research Institute, Technological University Dublin, Camden Row, Dublin 8, Dublin, Ireland
| | - Ricardo Franco
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO—Applied Molecular Biosciences Unit, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Hugo Águas
- CENIMAT|i3N, Department of Materials Science, School of Science and Technology, NOVA University Lisbon and, CEMOP/UNINOVA, Caparica, Portugal
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7
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Zhang Z, Ma X, Zhu J, Yan R, Miao P. Roll-to-Roll DNA Nanomachine for Ultrasensitive Electrochemical Determination of miRNA. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:11130-11135. [PMID: 36045009 DOI: 10.1021/acs.langmuir.2c02102] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
MicroRNAs (miRNAs) are a family of endogenous noncoding RNAs with the functions of gene regulation, which serve as promising markers for a range of diseases such as diabetic foot ulcers, cancers, etc. In this work, we engineered a roll-to-roll DNA nanomachine for highly sensitive electrochemical detection of miRNA. A dumbbell-structured DNA probe could be transitioned to be wheel-structured conformation upon target recognition, which rolls around track strands on the surface of gold nanoparticles (AuNPs) in the presence of nicking endonuclease. The resulting single strands on AuNPs are activated for the second round of rolling at the DNA-modified electrode interface, leading to the variation of electrochemical responses. The roll-to-roll amplification behavior allows a wide detection range with a limit of detection as low as 10 aM. The practicability is also demonstrated by the application in human serum samples with satisfactory results. It is expected that the proposed electrochemical method offers a new paradigm to develop miRNA assays based on DNA nanotechnology.
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Affiliation(s)
- Zhenming Zhang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, P.R. China
- Department of Orthopedic Surgery, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Xin Ma
- Department of Orthopedic Surgery, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Jinwen Zhu
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, P.R. China
| | - Ruhong Yan
- Department of Clinical Laboratory, Suzhou Science & Technology Town Hospital, Nanjing Medical University, Suzhou 215153, P.R. China
| | - Peng Miao
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, P.R. China
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8
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Sivanathan PC, Ooi KS, Mohammad Haniff MAS, Ahmadipour M, Dee CF, Mokhtar NM, Hamzah AA, Chang EY. Lifting the Veil: Characteristics, Clinical Significance, and Application of β-2-Microglobulin as Biomarkers and Its Detection with Biosensors. ACS Biomater Sci Eng 2022; 8:3142-3161. [PMID: 35848712 DOI: 10.1021/acsbiomaterials.2c00036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Because β-2-microglobulin (β2M) is a surface protein that is present on most nucleated cells, it plays a key role in the human immune system and the kidney glomeruli to regulate homeostasis. The primary clinical significance of β2M is in dialysis-related amyloidosis, a complication of end-stage renal disease caused by a gradual accumulation of β2M in the blood. Therefore, the function of β2M in kidney-related diseases has been extensively studied to evaluate its glomerular and tubular functions. Because increased β2M shedding due to rapid cell turnover may indicate other underlying medical conditions, the possibility to use β2M as a versatile biomarker rose in prominence across multiple disciplines for various applications. Therefore, this work has reviewed the recent use of β2M to detect various diseases and its progress as a biomarker. While the use of state-of-the-art β2M detection requires sophisticated tools, high maintenance, and labor cost, this work also has reported the use of biosensor to quantify β2M over the past decade. It is hoped that a portable and highly efficient β2M biosensor device will soon be incorporated in point-of-care testing to provide safe, rapid, and reliable test results.
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Affiliation(s)
- P C Sivanathan
- Institute of Microengineering and Nanoelectronics, Universiti Kebangsaan Malaysia, 43600 Bangi, Malaysia
| | - Kai Shen Ooi
- Institute of Microengineering and Nanoelectronics, Universiti Kebangsaan Malaysia, 43600 Bangi, Malaysia.,Department of Paediatrics, Universiti Kebangsaan Malaysia Medical Centre, 56000 Kuala Lumpur, Malaysia
| | | | - Mohsen Ahmadipour
- Institute of Microengineering and Nanoelectronics, Universiti Kebangsaan Malaysia, 43600 Bangi, Malaysia
| | - Chang Fu Dee
- Institute of Microengineering and Nanoelectronics, Universiti Kebangsaan Malaysia, 43600 Bangi, Malaysia
| | - Norfilza Mohd Mokhtar
- Department of Physiology, Faculty of Medicine, Universiti Kebangsaan Malaysia, 56000 Kuala Lumpur, Malaysia
| | - Azrul Azlan Hamzah
- Institute of Microengineering and Nanoelectronics, Universiti Kebangsaan Malaysia, 43600 Bangi, Malaysia
| | - Edward Y Chang
- Department of Material Science and Engineering, International College of Semiconductor Technology, National Yang Ming Chiao Tung University, 30010 Hsinchu, Taiwan
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9
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Li X, Guo Z, Luo G, Miao P. Fluorescence DNA Switch for Highly Sensitive Detection of miRNA Amplified by Duplex-Specific Nuclease. SENSORS 2022; 22:s22093252. [PMID: 35590941 PMCID: PMC9104181 DOI: 10.3390/s22093252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/21/2022] [Accepted: 04/21/2022] [Indexed: 02/01/2023]
Abstract
DNA is a type of promising material for the construction of sensors owing to its sequence programmability to control the formation of certain structures. MicroRNA (miRNA) can be applied as promising biomarkers for the diagnosis of a range of diseases. Herein, a novel fluorescent sensing strategy for miRNA is proposed combining duplex-specific nuclease (DSN)-mediated amplification and dumbbell DNA structural switch. Gold nanoparticles (AuNPs) are employed, which provide a 3D reaction interface. They also act as effective fluorescence quenchers. The proposed sensor exhibits high sensitivity (sub-femtomolar level) with a wide dynamic range. In addition, excellent selectivity to distinguish homology sequences is achieved. It also performs satisfactorily in biological samples. Overall, this fluorescent sensor provides a powerful tool for the analysis of miRNA levels and can be applied for related biological studies and clinical diagnosis.
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Affiliation(s)
- Xiaoqiang Li
- School of Biomedical Engineering (Suzhou), University of Science and Technology of China, Hefei 230026, China;
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China; (Z.G.); (G.L.)
| | - Zhenzhen Guo
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China; (Z.G.); (G.L.)
- Ji Hua Laboratory, Foshan 528200, China
| | - Gangyin Luo
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China; (Z.G.); (G.L.)
| | - Peng Miao
- School of Biomedical Engineering (Suzhou), University of Science and Technology of China, Hefei 230026, China;
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China; (Z.G.); (G.L.)
- Correspondence:
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10
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Wang DD, Zhang J, Yu QQ, Zhang K, Chen TT, Chu X. Biomineralized Zeolitic Imidazolate Framework-8 Nanoparticles Enable Polymerase-Driven DNA Biocomputing for Reliable Cell Identification. Anal Chem 2022; 94:4794-4802. [PMID: 35266710 DOI: 10.1021/acs.analchem.1c05605] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Investigating multiple miRNA expression patterns in living cells by DNA logic biocomputing is a valuable strategy for diagnosis and biomedical studies. The introduction of protein enzymes in DNA logic biocomputing circuits not only expands the toolbox of nucleic acid assembly techniques, but also further improves the specificity of recognizing and processing of DNA input. Herein, a polymerase-driven primer exchange reaction, acting as the sensing module, is introduced into the biocomputing system and transduces the multiple miRNAs sensing event into the intermediate triggers for activating the subsequent processing module, which further performs signal readout through DNAzyme catalytic substrate cleavage reaction. By using biomineralized zeolitic imidazolate framework-8 nanoparticles (ZIF-8 NPs) to deliver all the components of the biocomputing system, including polymerase and DNA probes, we realized polymerase-driven DNA biocomputing operations in living cells, including AND and OR gates. The results exhibited that biomineralized ZIF-8 NPs can protect the loaded cargoes against the external environment and deliver them efficiently to the cytoplasm. The polymerase-driven DNA biocomputing system based on multiple miRNAs sensing can be used for reliable cell identification and may provide a promising platform for more accurate diagnosis and programmable therapeutics.
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Affiliation(s)
- Dan-Dan Wang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Juan Zhang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Qiao-Qin Yu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Ke Zhang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Ting-Ting Chen
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Xia Chu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
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11
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Yin X, Yao D, Lam MHW, Liang H. A facile biosynthesis strategy of plasmid DNA-derived nanowires for readable microRNA logic operations. J Mater Chem B 2022; 10:3055-3063. [DOI: 10.1039/d1tb02699b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Multiple microRNAs (miRNAs) logical assays have attracted wide attention recently, which can be applied to mimic and reveal cellular events at the molecular level. However, it remains challenging to develop...
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12
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Jin F, Xu D. A Cascaded DNA Circuit in Bead Arrays for Quantitative Single-Cell MicroRNA Analysis. Anal Chem 2021; 93:11617-11625. [PMID: 34375096 DOI: 10.1021/acs.analchem.1c02388] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Single-cell microRNA (miRNA) analysis helps people understand the causes of diseases and formulate new disease treatment strategies. However, miRNA from a single cell is usually very rare and requires signal amplification for accurate quantification. Here, to amplify the signal, we constructed the cascaded DNA circuits consisting of catalytic hairpin assembly and hybrid chain reaction into the bead array platform, on which the uniformly distributed beads were adopted for miRNA quantification. After exponential signal amplification, a consistent linear correlation between the percentage of fluorescent beads and the copy number of miRNA was detected. The proposed bead array can achieve ultrahigh sensitivity as low as 60 copies of miR-155 and high specificity for distinguishing single nucleotide differences. This method has been successfully applied to the quantitative detection of miRNA in a single cancer cell. The high sensitivity, programmability, and simple workflow of the bead array chip will give a huge advantage in basic and clinical research.
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Affiliation(s)
- Furui Jin
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, No 163, Xianlin Avenue, Nanjing 210023, P. R. China
| | - Danke Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, No 163, Xianlin Avenue, Nanjing 210023, P. R. China
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13
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Han Y, Qiu C, Li J, Gao F, Yuan Q, Tang Y, Niu W, Wang X, Gao X, Gao L. Metal Cluster-Based Electrochemical Biosensing System for Detecting Epithelial-to-Mesenchymal Transition. ACS Sens 2021; 6:2290-2298. [PMID: 34042418 DOI: 10.1021/acssensors.1c00339] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
N-cadherin serves as an important oncobiomarker of epithelial-to-mesenchymal transition (EMT) progression, which identifies invasion and metastasis of malignant tumor cells. Although many efforts have been devoted to quantitative detection of N-cadherin, efforts to analyzing the protein of interest at intact cellular levels are scarce. Herein, a metal cluster-based electrochemical biosensing system is developed to determine the expressing levels of N-cadherin during the EMT process of tumor cells. To be specific, a peptide with a unique sequence and function is designed as a reductant and an anchor to synthesize metal clusters in a precise manner. Consequently, peptide-modified metal clusters possess N-cadherin-targeting, photoluminescence, and electrocatalytic properties. Especially, the redox-active metal clusters function as both an electron-transfer mediator and an electronic conductor for enhanced electrochemical sensing. These favorable features enable them as a rapid, sensitive, and reliable whole-cell biosensor, which integrates the fluorescence and electrochemical signals. This cytosensor can accurately quantify the expression levels of N-cadherin on at least 5000 tumor cells. Further, the current signals of model cancer cells gradually increase with EMT progression, indicating tumor cell-type evolution. Our study represents the advanced bioprobe and analytical methods for accurate quantitation of a biomarker to identify tumor progression.
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Affiliation(s)
- Ying Han
- Department of Chemistry and Biology, Faculty of Environment and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Cuicui Qiu
- State Key Laboratory of Tribology, Tsinghua University, Beijing 100084, China
| | - Jiaojiao Li
- Department of Chemistry and Biology, Faculty of Environment and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Fuping Gao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Qing Yuan
- Department of Chemistry and Biology, Faculty of Environment and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Yuhua Tang
- Department of Chemistry and Biology, Faculty of Environment and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Wenchao Niu
- Department of Chemistry and Biology, Faculty of Environment and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Xiayan Wang
- Department of Chemistry and Biology, Faculty of Environment and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Xueyun Gao
- Department of Chemistry and Biology, Faculty of Environment and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Liang Gao
- Department of Chemistry and Biology, Faculty of Environment and Life Science, Beijing University of Technology, Beijing 100124, China
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14
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Highly Sensitive and Cost-Effective Portable Sensor for Early Gastric Carcinoma Diagnosis. SENSORS 2021; 21:s21082639. [PMID: 33918707 PMCID: PMC8069728 DOI: 10.3390/s21082639] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/23/2021] [Accepted: 03/25/2021] [Indexed: 11/17/2022]
Abstract
Facile and efficient early detection of cancer is a major challenge in healthcare. Herein we developed a novel sensor made from a polycarbonate (PC) membrane with nanopores, followed by sequence-specific Oligo RNA modification for early gastric carcinoma diagnosis. In this design, the gastric cancer antigen CA72-4 is specifically conjugated to the Oligo RNA, thereby inhibiting the electrical current through the PC membrane in a concentration-dependent manner. The device can determine the concentration of cancer antigen CA72-4 in the range from 4 to 14 U/mL, possessing a sensitivity of 7.029 µAU-1mLcm-2 with a linear regression (R2) of 0.965 and a lower detection limit of 4 U/mL. This device has integrated advantages including high specificity and sensitivity and being simple, portable, and cost effective, which collectively enables a giant leap for cancer screening technologies towards clinical use. This is the first report to use RNA aptamers to detect CA72-4 for gastric carcinoma diagnosis.
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15
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Li Z, Liu Q, Li Y, Yuan W, Y.Li F. One-step polymerized lanthanide-based polystyrene microsphere for sensitive lateral flow immunoassay. J RARE EARTH 2021. [DOI: 10.1016/j.jre.2020.06.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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16
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Chen L, Zhang Q, Liu W, Xiao H, Liu X, Fan L, Wang Y, Li H, Cao C. A facile thermometer-like electrophoresis titration biosensor for alternative miRNA assay via moving reaction boundary chip. Biosens Bioelectron 2021; 171:112676. [DOI: 10.1016/j.bios.2020.112676] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/14/2020] [Accepted: 10/01/2020] [Indexed: 01/07/2023]
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17
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Kariper IA, Üstündağ Z, Caglayan MO. A sensitive spectrophotometric ellipsometry based Aptasensor for the vascular endothelial growth factor detection. Talanta 2020; 225:121982. [PMID: 33592730 DOI: 10.1016/j.talanta.2020.121982] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 12/02/2020] [Accepted: 12/05/2020] [Indexed: 01/02/2023]
Abstract
A sensitive and selective, aptamer and spectroscopic ellipsometry based sensor is reported here for the early diagnosis of breast cancer, which is a common type of cancer following lung cancer. It was aimed to develop a single-step and label-free assay for the sensitive and selective detection of VEGF165. To this end, two different aptamers and spectroscopic ellipsometry were used. In the presented study, by determining the appropriate aptamer immobilization conditions, the spectroscopic ellipsometry technique was successfully applied for the detection of VEGF165 at the range of 1 pM-1000 pM in the buffer. Aptasensors have a detection limit of 5.81 pM and 4.29 pM, respectively.
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Affiliation(s)
| | - Zafer Üstündağ
- Dumlupinar University, Chemistry Department, 43100, Kütahya, Turkey
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18
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Zhang P, Wang W, Fu H, Rich J, Su X, Bachman H, Xia J, Zhang J, Zhao S, Zhou J, Huang TJ. Deterministic droplet coding via acoustofluidics. LAB ON A CHIP 2020; 20:4466-4473. [PMID: 33103674 PMCID: PMC7688411 DOI: 10.1039/d0lc00538j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Droplet microfluidics has become an indispensable tool for biomedical research and lab-on-a-chip applications owing to its unprecedented throughput, precision, and cost-effectiveness. Although droplets can be generated and screened in a high-throughput manner, the inability to label the inordinate amounts of droplets hinders identifying the individual droplets after generation. Herein, we demonstrate an acoustofluidic platform that enables on-demand, real-time dispensing, and deterministic coding of droplets based on their volumes. By dynamically splitting the aqueous flow using an oil jet triggered by focused traveling surface acoustic waves, a sequence of droplets with deterministic volumes can be continuously dispensed at a throughput of 100 Hz. These sequences encode barcoding information through the combination of various droplet lengths. As a proof-of-concept, we encoded droplet sequences into end-to-end packages (e.g., a series of 50 droplets), which consisted of an address barcode with binary volumetric combinations and a sample package with consistent volumes for hosting analytes. This acoustofluidics-based, deterministic droplet coding technique enables the tagging of droplets with high capacity and high error-tolerance, and can potentially benefit various applications involving single cell phenotyping and multiplexed screening.
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Affiliation(s)
- Peiran Zhang
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC 27708, USA
| | - Wei Wang
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC 27708, USA
- ASIC and System State Key Laboratory, School of Microelectronics, Fudan University, Shanghai 200433, P. R. China
| | - Hai Fu
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC 27708, USA
- Department of Fluid Control and Automation, School of Mechanics Engineering, Harbin Institute of Technology, Harbin, Heilongjiang 150000, P. R. China
| | - Joseph Rich
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Xingyu Su
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC 27708, USA
| | - Hunter Bachman
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC 27708, USA
| | - Jianping Xia
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC 27708, USA
| | - Jinxin Zhang
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC 27708, USA
| | - Shuaiguo Zhao
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC 27708, USA
| | - Jia Zhou
- ASIC and System State Key Laboratory, School of Microelectronics, Fudan University, Shanghai 200433, P. R. China
| | - Tony Jun Huang
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC 27708, USA
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
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19
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Wei J, Wang H, Gong X, Wang Q, Wang H, Zhou Y, Wang F. A proteinase-free DNA replication machinery for in vitro and in vivo amplified MicroRNA imaging. Nucleic Acids Res 2020; 48:e60. [PMID: 32347938 PMCID: PMC7261173 DOI: 10.1093/nar/gkaa250] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 03/05/2020] [Accepted: 04/01/2020] [Indexed: 12/13/2022] Open
Abstract
The construction of robust, modular and compact DNA machinery facilitates us to build more intelligent and ingenious sensing strategies in complex biological systems. However, the performance of conventional DNA amplifiers is always impeded by their limited in-depth amplifications and miscellaneously enzymatic requirements. Here, a proteinase-free reciprocal DNA replication machinery is developed by exploiting the synergistic cross-activation between hybridization chain reaction (HCR) and DNAzyme. The DNAzyme provides an efficient way to simplify the sophisticated design of HCR machinery and simultaneously to promote the amplification capacity. And the HCR-assembled tandem DNAzyme nanowires produce numerous new triggers for reversely stimulating HCR amplifier as systematically explored by experiments and computer-aided simulations. The reciprocal amplifier can be executed as a versatile and powerful sensing platform for analyzing miRNA in living cells and even in mice, originating from the inherent reaction accelerations and multiple-guaranteed recognitions. The reciprocal catalytic DNA machine holds great potential in clinical diagnosis and assessment.
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Affiliation(s)
- Jie Wei
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430000, P. R. China
| | - Huimin Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430000, P. R. China
| | - Xue Gong
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430000, P. R. China
| | - Qing Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430000, P. R. China
| | - Hong Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430000, P. R. China
| | - Yangjie Zhou
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430000, P. R. China
| | - Fuan Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430000, P. R. China
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20
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Kong J, Wang Y, Qi W, Su R, He Z. Enzyme-free visualization of nucleic acids during HIV infection by octopus-like DNA. Int J Biol Macromol 2020; 150:122-128. [PMID: 32045606 DOI: 10.1016/j.ijbiomac.2020.02.063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 02/06/2020] [Accepted: 02/07/2020] [Indexed: 11/27/2022]
Abstract
It is highly desirable to develop a facile approach for the detection of the human immunodeficiency virus (HIV). To address this need, an octopus-like DNA (OLD) is designed in a one-pot method by direct folding of nine short single strands of DNA (ssDNA), which can be used to capture all the conserved HIV-1 gene efficiently though the sticky arms. The branched OLD was applied for the enzyme-free detection of HIV-1 nucleic acid and the visualization of the virus during HIV infection. The total detection procedure can be finished within 2 h with high specificity, making the OLD system a valuable tool for the rapid detection of HIV virus and further biomedical application.
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Affiliation(s)
- Jia Kong
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
| | - Yuefei Wang
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China; Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin 300072, PR China.
| | - Wei Qi
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, PR China; Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin 300072, PR China
| | - Rongxin Su
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, PR China; Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin 300072, PR China
| | - Zhimin He
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
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21
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Polymethacrylate Sphere-Based Assay for Ultrasensitive miRNA Detection. ADVANCES IN POLYMER TECHNOLOGY 2020. [DOI: 10.1155/2020/7310657] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Although microRNAs (miRNAs) have emerged as increasingly important target analytes, their biorecognition remains challenging due to their small size, high sequence homology, and low abundance in clinical samples. Nanospheres and microspheres have also gained increasing attention in biosensor applications due to their high specific surface area and the wide variety of compositions available. In this study, chemically designed and synthesized microspheres with active functional groups were used to promote effective miRNA immobilization resulting in better biorecognition. Upon conjugation with fluorescence-labeled complimentary probes, acylate-based spheres have indirectly detected MiR159, offering significantly enhanced analytical sensitivity, specificity, and accuracy while yielding a considerably low limit of detection (LOD) of 40 picomolar. Furthermore, MiR159 presence, which is known to be inversely correlated to breast cancer incidence and progression, was successfully detected in a competitive assay, which is promising for upgrading the current assay to clinical use.
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22
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Lee T, Mohammadniaei M, Zhang H, Yoon J, Choi HK, Guo S, Guo P, Choi J. Single Functionalized pRNA/Gold Nanoparticle for Ultrasensitive MicroRNA Detection Using Electrochemical Surface-Enhanced Raman Spectroscopy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:1902477. [PMID: 32042566 PMCID: PMC7001639 DOI: 10.1002/advs.201902477] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/14/2019] [Indexed: 05/07/2023]
Abstract
Controlling the selective one-to-one conjugation of RNA with nanoparticles is vital for future applications of RNA nanotechnology. Here, the monofunctionalization of a gold nanoparticle (AuNP) with a single copy of RNA is developed for ultrasensitive microRNA-155 quantification using electrochemical surface-enhanced Raman spectroscopy (EC-SERS). A single AuNP is conjugated with one copy of the packaging RNA (pRNA) three-way junction (RNA 3WJ). pRNA 3WJ containing one strand of the 3WJ is connected to a Sephadex G100 aptamer and a biotin group at each arm (SEPapt/3WJ/Bio) which is then immobilized to the Sephadex G100 resin. The resulting complex is connected to streptavidin-coated AuNP (STV/AuNP). Next, the STV/AuNP-Bio/3WJa is purified and reassembled with another 3WJ to form a single-labeled 3WJ/AuNP. Later, the monoconjugate is immobilized onto the AuNP-electrodeposited indium tin oxide coated substrate for detecting microRNA-155 based on EC-SERS. Application of an optimum potential of +0.2 V results in extraordinary amplification (≈7 times) of methylene blue (reporter) SERS signal compared to the normal SERS signal. As a result, a highly sensitive detection of 60 × 10-18 m microRNA-155 in 1 h in serum based on monoconjugated AuNP/RNA is achieved. Thus, the monofunctionalization of RNA onto nanoparticle can provide a new methodology for biosensor construction and diverse RNA nanotechnology development.
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Affiliation(s)
- Taek Lee
- College of PharmacyCollege of Medicine/Department of Physiology and Cell Biology/Dorothy M. Davis Heart and Lung Research InstituteOhio State UniversityColumbusOH43210USA
- Department of Chemical and Biomolecular EngineeringSogang University35 Baekbeom‐ro, Mapo‐guSeoul121‐742Republic of Korea
- Department of Chemical EngineeringKwangwoon University20 Kwangwoon‐Ro, Nowon‐GuSeoul01897Republic of Korea
| | - Mohsen Mohammadniaei
- Department of Chemical and Biomolecular EngineeringSogang University35 Baekbeom‐ro, Mapo‐guSeoul121‐742Republic of Korea
| | - Hui Zhang
- College of PharmacyCollege of Medicine/Department of Physiology and Cell Biology/Dorothy M. Davis Heart and Lung Research InstituteOhio State UniversityColumbusOH43210USA
| | - Jinho Yoon
- Department of Chemical and Biomolecular EngineeringSogang University35 Baekbeom‐ro, Mapo‐guSeoul121‐742Republic of Korea
| | - Hye Kyu Choi
- Department of Chemical and Biomolecular EngineeringSogang University35 Baekbeom‐ro, Mapo‐guSeoul121‐742Republic of Korea
| | - Sijin Guo
- College of PharmacyCollege of Medicine/Department of Physiology and Cell Biology/Dorothy M. Davis Heart and Lung Research InstituteOhio State UniversityColumbusOH43210USA
| | - Peixuan Guo
- College of PharmacyCollege of Medicine/Department of Physiology and Cell Biology/Dorothy M. Davis Heart and Lung Research InstituteOhio State UniversityColumbusOH43210USA
| | - Jeong‐Woo Choi
- Department of Chemical and Biomolecular EngineeringSogang University35 Baekbeom‐ro, Mapo‐guSeoul121‐742Republic of Korea
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23
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Xu S, Jiang L, Wang J, Gao Y, Luo X. Ratiometric Multicolor Analysis of Intracellular MicroRNA Using a Chain Hybrid Substitution-Triggered Self-Assembly of Silver Nanocluster-Based Label-Free Sensing Platform. ACS APPLIED MATERIALS & INTERFACES 2020; 12:373-379. [PMID: 31840494 DOI: 10.1021/acsami.9b19709] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
A simple and label-free sensing platform with low background based on the chain-displacement triggered self-assembly of Ag NCs was developed for ratiometric visual analysis of intracellular miRNA-21. Based on this sensitively ratiometric sensing approach, a picomole limit detection for miRNA-21 can be obtained. Most importantly, compared with the traditional single base mismatch detection method, our proposed method can realize single base mismatch detection according to the remarkable fluorescence color conversion, rather than simple fluorescence intensity change, which can obviously improve the accuracy and reliability. In addition, successful multicolor real-time monitoring of intracellular miRNA-21 makes the probe a potential candidate for miRNA-21 inhibiting drug screening. Furthermore, MCF-7, HeLa, and normal L02 cells can also be visually differentiated according to the fluorescence color by using the label-free sensing platform, showing its potential prospect in target visual analysis.
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Affiliation(s)
- Shenghao Xu
- 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 , P. R. China
| | - Liping 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 , P. R. China
| | - Jun 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 , P. R. China
| | - Yuhuan Gao
- 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 , P. R. China
| | - Xiliang Luo
- 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 , P. R. China
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24
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Chen WY, Wang CH, Wang KH, Chen YL, Chau LK, Wang SC. Development of microfluidic concentrator using ion concentration polarization mechanism to assist trapping magnetic nanoparticle-bound miRNA to detect with Raman tags. BIOMICROFLUIDICS 2020; 14:014102. [PMID: 31933712 PMCID: PMC6941943 DOI: 10.1063/1.5126293] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 12/18/2019] [Indexed: 06/10/2023]
Abstract
MicroRNAs (miRNAs) are small noncoding single-stranded ribonucleic acid molecules. This type of endogenous oligonucleotide could be secreted into the circulation and exist stably. The detection of specific miRNAs released by cancer cells potentially provides a noninvasive means to achieve early diagnosis and prognosis of cancers. However, the typical concentration of miRNAs in blood is below the ultratrace level. This study uses a simple thermoplastic microfluidic concentration device based on an ion concentration polarization mechanism to perform enrichment and cleanup and Raman sensing beads to determine miRNA quantitatively. One sample solution containing target miRNA molecules having been hybridized with two nucleotide probes, where one probe is on a Raman tag of a nanoaggregate embedded bead (NAEB) and the other probe is on a magnetic nanoparticle (MNP), is first filled into the device. When an external field is applied across a cation exchange membrane stationed in the middle conduit of the device, the MNP-miRNA-NAEB complexed particles are enriched near the membrane edge of the cathode side. The concentrated complexed particles are further trapped using an external magnet to perform washing steps to remove excess noncomplexed NAEBs. When cleanup steps are accomplished, the remaining complexed particles are loaded into one detection capillary to acquire Raman signals from the sensing beads. Compared with that using a conventional magnetic trapping device, the cleanup time is shortened from nearly an hour to less than 10 min. Sample loss during the washing steps becomes more controllable, resulting in adequate standard curve linearity (R > 0.99) ranging from 1 to 100 pM.
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Affiliation(s)
- Wen-Yu Chen
- Department of Chemistry and Biochemistry and the Center for Nano Bio-Detection, National Chung Cheng University, Chia-Yi 62102, Taiwan
| | - Chih-Hsien Wang
- Department of Chemistry and Biochemistry and the Center for Nano Bio-Detection, National Chung Cheng University, Chia-Yi 62102, Taiwan
| | - Kai-Hao Wang
- Department of Chemistry and Biochemistry and the Center for Nano Bio-Detection, National Chung Cheng University, Chia-Yi 62102, Taiwan
| | - Yuh-Ling Chen
- Institute of Oral Medicine, National Cheng Kung University, Tainan 70101, Taiwan
| | - Lai-Kwan Chau
- Department of Chemistry and Biochemistry and the Center for Nano Bio-Detection, National Chung Cheng University, Chia-Yi 62102, Taiwan
| | - Shau-Chun Wang
- Department of Chemistry and Biochemistry and the Center for Nano Bio-Detection, National Chung Cheng University, Chia-Yi 62102, Taiwan
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25
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Lee H, Lee SH. Single to three nucleotide polymorphisms assay of miRNA-21 using DNA capped gold nanoparticle-electrostatic force microscopy system. MICRO AND NANO SYSTEMS LETTERS 2019. [DOI: 10.1186/s40486-019-0100-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Abstract
Aberrant expression of microRNA (miRNA) in biological cells is crucial evidence for early diagnosis of cancer. Improvements in molecular detection techniques enabled miRNA to be detected in human blood obtained from liquid biopsies (e.g., Polymerase chain reaction, microcantilever sensor, and surface-enhanced Raman spectroscopy). Despite the advances in molecular detection technology, a simultaneous detection of single or multiple mutations of miRNAs is still a challenge. Here, we show electrostatic force microscopy (EFM) imaging of DNA-capped gold nanoparticles (DCNP) that enables discrimination between single and three-nucleotide polymorphism (SNP, TNP): 1 and 3-point mismatched nucleotides in miRNA-21 (M1_RNA, M3_RNA). Detection of the miRNA-21 and their mutant sequence is owing to sterically well-adjusted DNA–RNA interactions that take place within the confined spaces of DCNP. The average absolute EFM amplitudes of DCNP interacting with M1_RNA, and M3_RNA (− 81.0 ± 11.5, and − 65.7 ± 8.2 mV) were found to be lower than the DCNP reacting with normal (non-mutant) miRNA-21 (− 100.2 ± 13.6 mV).
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Lin S, Tan L, Luo D, Peng X, Zhu Y, Li H. Linc01278 inhibits the development of papillary thyroid carcinoma by regulating miR-376c-3p/DNM3 axis. Cancer Manag Res 2019; 11:8557-8569. [PMID: 31572010 PMCID: PMC6756842 DOI: 10.2147/cmar.s217886] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/22/2019] [Indexed: 12/11/2022] Open
Abstract
Purpose Papillary thyroid carcinoma (PTC) is the most common endocrine malignancy, and its incidence has continuously increased in recent years. Therefore, it is essential to develop more useful therapeutic strategies. Methods We collected 56 pairs of PTC tissues and adjacent normal tissues and determined the expression patterns of linc01278, miR-376c-3p and DNM3. In addition, we analyzed the relationship between linc01278 expression and pathological information of PTC patients. Furthermore, the effects of linc01278, miR-376c-3p and DNM3 overexpression on proliferation, clonality, apoptosis, migration and invasion of PTC cell lines TPC1 and BCPAP were evaluated. The dual luciferase reporter assay was used to confirm the direct interaction between miR-376c-3p and linc01278. Results Linc01278 and DNM3 were remarkably down-regulated in PTC tissues and cell lines, whereas miR-376c-3p was significantly up-regulated. In addition, lower linc01278 expression was associated with increased tumor size, lymph node metastasis and higher clinical stage. Linc01278 inhibited cell proliferation of PTC cells by inducing apoptosis, and demonstrated attenuating effects on migration and invasion abilities of PTC cells by regulating the EMT process. More importantly, dual luciferase reporter experiments demonstrated the direct interaction between miR-376c-3p and linc01278, which revealed that DNM3 was a novel target of miR-376c-3p. The miR-376c-3p mimic significantly promoted the proliferation, migration and invasion of PTC cells, and inhibited cell apoptosis. Overexpression of DNM3 abolished the effects of the miR-376c-3p mimic on PTC cells. DNM3 expression was negatively correlated with miR-376c-3p expression, but was positively correlated with linc01278 expression. Conclusion Overall, we found that linc01278 can act as a competing endogenous RNA (ceRNA) to sponge miR-376c-3p, thereby positively regulating DNM3 expression and ultimately acting as a tumor suppressor gene in PTC progression.
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Affiliation(s)
- Shaojian Lin
- Department of Thyroid Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, Guangdong, People's Republic of China
| | - Langping Tan
- Department of Thyroid Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, Guangdong, People's Republic of China
| | - Dingyuan Luo
- Department of Thyroid Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, Guangdong, People's Republic of China
| | - Xinzhi Peng
- Department of Thyroid Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, Guangdong, People's Republic of China
| | - Yue Zhu
- Department of Thyroid Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, Guangdong, People's Republic of China
| | - Honghao Li
- Department of Thyroid Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, Guangdong, People's Republic of China
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27
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Ma F, Zhang Q, Zhang CY. Catalytic Self-Assembly of Quantum-Dot-Based MicroRNA Nanosensor Directed by Toehold-Mediated Strand Displacement Cascade. NANO LETTERS 2019; 19:6370-6376. [PMID: 31460766 DOI: 10.1021/acs.nanolett.9b02544] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Semiconductor quantum dots (QDs) are highly attractive nanomaterials with wide biomedical applications owing to their unique photophysical properties. However, the adaptation of the nonenzymatic QD nanosensor assembly to sense low-abundance targets remains a great challenge. Herein, taking advantage of the dynamic DNA nanotechnology and single-molecule fluorescence detection, we demonstrate the catalytic self-assembly of a QD-based microRNA nanosensor directed by toehold-mediated strand displacement cascade for the simple and sensitive detection of microRNA at femtomolar concentration without the requirement of any enzymes. Moreover, this QD nanosensor is capable of detecting circulating microRNA in clinical serum samples and even imaging microRNA in living cells. This work may extend the use of an enzyme-free QD nanosensor assembly for low-abundance biomarker detection and offer a novel platform for fundamental biomedical research and clinical applications.
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Affiliation(s)
- Fei Ma
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan 250014 , China
| | - Qian Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan 250014 , China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan 250014 , China
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Mohammadniaei M, Park C, Min J, Sohn H, Lee T. Fabrication of Electrochemical-Based Bioelectronic Device and Biosensor Composed of Biomaterial-Nanomaterial Hybrid. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1064:263-296. [PMID: 30471039 PMCID: PMC7120487 DOI: 10.1007/978-981-13-0445-3_17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The field of bioelectronics has paved the way for the development of biochips, biomedical devices, biosensors and biocomputation devices. Various biosensors and biomedical devices have been developed to commercialize laboratory products and transform them into industry products in the clinical, pharmaceutical, environmental fields. Recently, the electrochemical bioelectronic devices that mimicked the functionality of living organisms in nature were applied to the use of bioelectronics device and biosensors. In particular, the electrochemical-based bioelectronic devices and biosensors composed of biomolecule-nanoparticle hybrids have been proposed to generate new functionality as alternatives to silicon-based electronic computation devices, such as information storage, process, computations and detection. In this chapter, we described the recent progress of bioelectronic devices and biosensors based on biomaterial-nanomaterial hybrid.
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Affiliation(s)
- Mohsen Mohammadniaei
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, South Korea
| | - Chulhwan Park
- Department of Chemical Engineering, Kwangwoon University, Seoul, South Korea
| | - Junhong Min
- School of Integrative Engineering Chung-Ang University, Seoul, South Korea
| | - Hiesang Sohn
- Department of Chemical Engineering, Kwangwoon University, Seoul, South Korea.
| | - Taek Lee
- Department of Chemical Engineering, Kwangwoon University, Seoul, South Korea.
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29
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Tollefson EJ, Allen CR, Chong G, Zhang X, Rozanov ND, Bautista A, Cerda JJ, Pedersen JA, Murphy CJ, Carlson EE, Hernandez R. Preferential Binding of Cytochrome c to Anionic Ligand-Coated Gold Nanoparticles: A Complementary Computational and Experimental Approach. ACS NANO 2019; 13:6856-6866. [PMID: 31082259 DOI: 10.1021/acsnano.9b01622] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Membrane-bound proteins can play a role in the binding of anionic gold nanoparticles (AuNPs) to model bilayers; however, the mechanism for this binding remains unresolved. In this work, we determine the relative orientation of the peripheral membrane protein cytochrome c in binding to a mercaptopropionic acid-functionalized AuNP (MPA-AuNP). As this is nonrigid binding, traditional methods involving crystallographic or rigid molecular docking techniques are ineffective at resolving the question. Instead, we have implemented a computational assay technique using a cross-correlation of a small ensemble of 200 ns long molecular dynamics trajectories to identify a preferred nonrigid binding orientation or pose of cytochrome c on MPA-AuNPs. We have also employed a mass spectrometry-based footprinting method that enables the characterization of the stable protein corona that forms at long time-scales in solution but remains in a dynamic state. Through the combination of these computational and experimental primary results, we have established a consensus result establishing the identity of the exposed regions of cytochrome c in proximity to MPA-AuNPs and its complementary pose(s) with amino-acid specificity. Moreover, the tandem use of the two methods can be applied broadly to determine the accessibility of membrane-binding sites for peripheral membrane proteins upon adsorption to AuNPs or to determine the exposed amino-acid residues of the hard corona that drive the acquisition of dynamic soft coronas. We anticipate that the combined use of simulation and experimental methods to characterize biomolecule-nanoparticle interactions, as demonstrated here, will become increasingly necessary as the complexity of such target systems grows.
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Affiliation(s)
- Emily J Tollefson
- Department of Chemistry , University of Minnesota-Twin Cities , Minneapolis , Minnesota 55455 , United States
| | - Caley R Allen
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Gene Chong
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Xi Zhang
- Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Nikita D Rozanov
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Anthony Bautista
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Jennifer J Cerda
- Department of Chemistry , University of Minnesota-Twin Cities , Minneapolis , Minnesota 55455 , United States
| | - Joel A Pedersen
- Environmental Chemistry and Technology Program , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Catherine J Murphy
- Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Erin E Carlson
- Department of Chemistry , University of Minnesota-Twin Cities , Minneapolis , Minnesota 55455 , United States
| | - Rigoberto Hernandez
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
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30
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Wang G, Yu M, Wang G. A versatile dynamic light scattering strategy for the sensitive detection of microRNAs based on plasmonic core-satellites nanoassembly coupled with strand displacement reaction. Biosens Bioelectron 2019; 138:111319. [PMID: 31108381 DOI: 10.1016/j.bios.2019.111319] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 05/08/2019] [Accepted: 05/10/2019] [Indexed: 01/28/2023]
Abstract
A low-cost, effective and enzyme-free sensing strategy for ultrasensitive microRNA (miRNA) detection was developed based on dynamic light scattering (DLS) coupled with strand displacement reaction (SDR). The combination of DLS and SDR was used to assess the size changes of core-satellites nanoassembly. This strategy realized the limit of detection (LOD) as low as 0.24 pM (S/N = 3) and the detection range of 5 pM-150 pM, which might urge this strategy as an ideal candidate for the sensitive detection of miRNA in the future. In addition, the proposed strategy could be successfully used to analyze target miRNA in various cancer cells, indicating that the developed SDR-DLS strategy has promising clinical implications for rapid and early diagnosis of cancer-related diseases.
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Affiliation(s)
- Ganglin Wang
- Hubei Bioinformatics & Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, PR China
| | - Mingxia Yu
- Department of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, 430071, PR China
| | - Guoping Wang
- Hubei Bioinformatics & Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, PR China.
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31
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Borghei YS, Hosseini M. A New Eye Dual-readout Method for MiRNA Detection based on Dissolution of Gold nanoparticles via LSPR by CdTe QDs Photoinduction. Sci Rep 2019; 9:5453. [PMID: 30931995 PMCID: PMC6443804 DOI: 10.1038/s41598-019-41898-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 03/20/2019] [Indexed: 01/27/2023] Open
Abstract
Breast cancer (BC) is the most frequent cancer that affects one in eight women worldwide. Recent advances in early cancer diagnosis anticipates more efficient treatment and prolong patient survival. MicroRNAs expression profiling plays a key role in diagnosis of cancer such as BC in early stages. For the first time we describe direct injection of hot electrons from plasmonic gold nanoparticles (AuNPs) to adsorbed water molecules with photoinduction of CdTe quantum dots (QDs) with emission wavelength at ~560 nm. As a result of hot electrons exiting from AuNPs with red color, gold cations (holes) are gradually discharged (AuNPs dissolution) leading to a colorless solution. Our group applied this phenomenon to propose a spectral method for miRNA recognition based on different responsive disaggregation and aggregation of CdTe QDs interacted with single strand DNA probes and DNA/RNA heteroduplex respectively resulting in a detection limit of 4.4 pM. This method has been applied also for the determination of miR-155 in the human breast carcinoma MCF-7 cells and normal human embryonic kidney cell line (HEK 293).
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Affiliation(s)
- Yasaman-Sadat Borghei
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran
| | - Morteza Hosseini
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran.
- Department of Pharmaceutical Biomaterials and Medicinal Biomaterials Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran.
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32
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Wen Q, Zhao L, Wang T, Lv N, Cheng X, Zhang G, Bai L. LncRNA SNHG16 drives proliferation and invasion of papillary thyroid cancer through modulation of miR-497. Onco Targets Ther 2019; 12:699-708. [PMID: 30705598 PMCID: PMC6343509 DOI: 10.2147/ott.s186923] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Background Long noncoding small nucleolar RNA host gene 16 (SNHG16) has been shown to play an oncogenic role in multiple cancers. However, the biological roles and mechanism of SNHG16 action in the regulation of papillary thyroid cancer (PTC) remains unknown. The aims of this study were to investigate the roles and the possible mechanism of SNHG16 in PTC progression. Materials and methods The expression of SNHG16 PTC tissues and cell lines was detected by reverse-transcription quantitative PCR (qRT-PCR). The effect of SNHG16 on cell proliferation, apoptosis, migration, and invasion was detected by Cell Counting Kit-8, flow cytometry, wound-healing assay, and Matrigel invasion assay, respectively. In addition, the regulatory relationships between SNHG16 and miR-497 were explored by luciferase reporter assay and qRT-PCR. Results The SNHG16 expression was upregulated in PTC tissues and cell lines, whose expression was positively associated with advanced TNM stage and lymph node metastasis. Function analysis demonstrated that depletion of SNHG16 in PTC cells significantly inhibited cell proliferation, induced cell apoptosis, and suppressed cell migration and invasion abilities. Mechanistic studies indicated that SNHG16 functioned as an endogenous sponge for miR-497 to regulate its target genes brain-derived neurotrophic factor and yes-associated protein 1 expression. Furthermore, the inhibition of miR-497 antagonized the suppressive effect of SNHG16-depleted cells on cell proliferation, migration, and invasion. Conclusion These findings revealed that SNHG16 drived the PTC progression possibly via regulating miR-497, suggesting that SNHG16 might be a novel therapeutic agent for PTC.
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Affiliation(s)
- Qiang Wen
- Department of Nuclear Medicine, China-Japan Union Hospital of Jilin University, ErDao District, Changchun 13033, China,
| | - Lina Zhao
- Department of Thyroid Surgery, China-Japan Union Hospital of Jilin University, ErDao District, Changchun 13033, China,
| | - Tongtong Wang
- Department of Nuclear Medicine, China-Japan Union Hospital of Jilin University, ErDao District, Changchun 13033, China,
| | - Ningning Lv
- Department of Nuclear Medicine, China-Japan Union Hospital of Jilin University, ErDao District, Changchun 13033, China,
| | - Xuejiao Cheng
- Department of Nuclear Medicine, China-Japan Union Hospital of Jilin University, ErDao District, Changchun 13033, China,
| | - Guang Zhang
- Department of Thyroid Surgery, China-Japan Union Hospital of Jilin University, ErDao District, Changchun 13033, China,
| | - Lin Bai
- Department of Nuclear Medicine, China-Japan Union Hospital of Jilin University, ErDao District, Changchun 13033, China,
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33
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Oh YJ, Koehler M, Lee Y, Mishra S, Park JW, Hinterdorfer P. Ultra-Sensitive and Label-Free Probing of Binding Affinity Using Recognition Imaging. NANO LETTERS 2019; 19:612-617. [PMID: 30560669 DOI: 10.1021/acs.nanolett.8b04883] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Reliable quantification of binding affinity is important in biotechnology and pharmacology and increasingly coupled with a demand for ultrasensitivity, nanoscale resolution, and minute sample amounts. Standard techniques are not able to meet these criteria. This study provides a new platform based on atomic force microscopy (AFM)-derived recognition imaging to determine affinity by visualizing single molecular bindings on nanosize dendrons. Using DNA hybridization as a demonstrator, an AFM sensor adorned with a cognate binding strand senses and localizes target DNAs at nanometer resolution. To overcome the limitations of speed and resolution, the AFM cantilever is sinusoidally oscillated close to resonance conditions at small amplitudes. The equilibrium dissociation constant of capturing DNA duplexes was obtained, yielding 2.4 × 10-10 M. Our label-free single-molecular biochemical analysis approach evidences the utility of recognition imaging and analysis in quantifying biomolecular interactions of just a few hundred molecules.
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Affiliation(s)
- Yoo Jin Oh
- Institute of Biophysics , Johannes Kepler University Linz , Gruberstrasse 40 , A-4020 Linz , Austria
| | - Melanie Koehler
- Institute of Biophysics , Johannes Kepler University Linz , Gruberstrasse 40 , A-4020 Linz , Austria
| | - Yoonhee Lee
- Department of Chemistry , Pohang University of Science and Technology , 77 Cheongam-Ro , Nam-Gu, Pohang 37673 , Republic of Korea
| | - Sourav Mishra
- Department of Chemistry , Pohang University of Science and Technology , 77 Cheongam-Ro , Nam-Gu, Pohang 37673 , Republic of Korea
| | - Joon Won Park
- Department of Chemistry , Pohang University of Science and Technology , 77 Cheongam-Ro , Nam-Gu, Pohang 37673 , Republic of Korea
| | - Peter Hinterdorfer
- Institute of Biophysics , Johannes Kepler University Linz , Gruberstrasse 40 , A-4020 Linz , Austria
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34
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Abstract
Barcoded bioassays are ready to promote bioanalysis and biomedicine toward the point of care.
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Affiliation(s)
- Mingzhu Yang
- Beijing Engineering Research Center for BioNanotechnology
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety
- CAS Center for Excellence in Nanoscience
- National Center for NanoScience and Technology
- Beijing
| | - Yong Liu
- Beijing Engineering Research Center for BioNanotechnology
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety
- CAS Center for Excellence in Nanoscience
- National Center for NanoScience and Technology
- Beijing
| | - Xingyu Jiang
- Beijing Engineering Research Center for BioNanotechnology
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety
- CAS Center for Excellence in Nanoscience
- National Center for NanoScience and Technology
- Beijing
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35
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Khoothiam K, Treerattrakoon K, Iempridee T, Luksirikul P, Dharakul T, Japrung D. Ultrasensitive detection of lung cancer-associated miRNAs by multiple primer-mediated rolling circle amplification coupled with a graphene oxide fluorescence-based (MPRCA-GO) sensor. Analyst 2019; 144:4180-4187. [DOI: 10.1039/c9an00517j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
MPRCA-GO sensor can detect low amount of miRNAs, which are biomarkers in cancer diagnosis.
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Affiliation(s)
- Krissana Khoothiam
- Graduate Program in Immunology
- Department of Immunology
- Faculty of Medicine Siriraj Hospital
- Mahidol University
- Bangkok
| | - Kiatnida Treerattrakoon
- National Nanotechnology Center (NANOTEC)
- National Science and Technology Development Agency (NSTDA)
- Pathumthani
- Thailand
| | - Tawin Iempridee
- National Nanotechnology Center (NANOTEC)
- National Science and Technology Development Agency (NSTDA)
- Pathumthani
- Thailand
| | | | - Tararaj Dharakul
- Department of Immunology
- Faculty of Medicine Siriraj Hospital
- Mahidol University
- Bangkok
- Thailand
| | - Deanpen Japrung
- National Nanotechnology Center (NANOTEC)
- National Science and Technology Development Agency (NSTDA)
- Pathumthani
- Thailand
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36
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Li Z, Lu Q, Zhu D, Han Y, Zhou X, Ren T. Lnc-SNHG1 may promote the progression of non-small cell lung cancer by acting as a sponge of miR-497. Biochem Biophys Res Commun 2018; 506:632-640. [DOI: 10.1016/j.bbrc.2018.10.086] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 10/14/2018] [Indexed: 12/28/2022]
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37
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Spectroelectrochemical detection of microRNA-155 based on functional RNA immobilization onto ITO/GNP nanopattern. J Biotechnol 2018; 274:40-46. [DOI: 10.1016/j.jbiotec.2018.03.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 03/02/2018] [Accepted: 03/23/2018] [Indexed: 01/29/2023]
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38
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Fan W, Qi Y, Qiu L, He P, Liu C, Li Z. Click Chemical Ligation-Initiated On-Bead DNA Polymerization for the Sensitive Flow Cytometric Detection of 3'-Terminal 2'-O-Methylated Plant MicroRNA. Anal Chem 2018; 90:5390-5397. [PMID: 29600844 DOI: 10.1021/acs.analchem.8b00589] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A versatile flow cytometric strategy is developed for the sensitive detection of plant microRNA (miRNA) by coupling the target-templated click nucleic acid ligation (CNAL) with on-bead terminal enzymatic DNA polymerization (TEP). Unlike ligase-catalyzed ligation reaction, the plant miRNA-templated enzyme-free CNAL between two single-stranded DNA (ssDNA) probes, respectively modified with Aza-dibenzocyclooctyne (Aza-DBCO) and N3, can not only simplify the operation, but also achieve a much higher ligation efficiency. More importantly, the undesirable nonspecific ligation between the Aza-DBCO- and N3-modified ssDNA, can be effectively eliminated by adding Tween-20, which allows the use of cycling CNAL (CCNAL) in a background-free manner. So each plant miRNA can template many rounds of CNAL reaction to produce numerous ligation products, forming efficient signal amplification. The ligated ssDNA can be anchored on the magnetic beads (MBs) with the 3'-OH termini exposed outside. Then terminal deoxynucleotidyl transferase (TdT), a sequence-independent and template-free polymerase, would specifically catalyze the DNA polymerization along these 3'-OH termini on the MBs, forming poly(T) tails up to thousands of nucleotides long. Each poly(T) tail allows specific binding of numerous 6-carboxyfluorescein (FAM)-labeled poly(A)25 oligonucleotides to accumulate a lot of fluorophores on the MBs, leading to the second step of signal amplification. By integrating the advantages of CCNAL-TEP for highly efficient signal amplification and robust MBs signal readout with powerful flow cytometer, high sensitivity is achieved and the detection limit of plant miRNA has been pushed down to a low level of 5 fM with high specificity to well discriminate even single-base difference between miRNA targets.
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Affiliation(s)
- Wenjiao Fan
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710119 , Shaanxi Province , People's Republic of China
| | - Yan Qi
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710119 , Shaanxi Province , People's Republic of China
| | - Liying Qiu
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710119 , Shaanxi Province , People's Republic of China
| | - Pan He
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710119 , Shaanxi Province , People's Republic of China
| | - Chenghui Liu
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710119 , Shaanxi Province , People's Republic of China
| | - Zhengping Li
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710119 , Shaanxi Province , People's Republic of China
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39
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Dai W, Zhang J, Meng X, He J, Zhang K, Cao Y, Wang D, Dong H, Zhang X. Catalytic hairpin assembly gel assay for multiple and sensitive microRNA detection. Theranostics 2018; 8:2646-2656. [PMID: 29774065 PMCID: PMC5956999 DOI: 10.7150/thno.24480] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 02/21/2018] [Indexed: 01/28/2023] Open
Abstract
As important modulators of gene expression, microRNAs (miRNAs) have been identified as promising biomarkers with powerful predictive value in diagnosis and prognosis for several diseases, especially for cancers. Here we report a facile, multiple and sensitive miRNA detection method that uses conventional gel electrophoresis and catalytic hairpin assembly (CHA) system without any complex nanomaterials or enzymatic amplification. Methods: In this study, three pairs of hairpin probes are rationally designed with thermodynamically and kinetically preferable feasibility for the CHA process. In the present of target miRNA, the stem of the corresponding hairpin detection probe (HDP) will be unfolded and expose the concealed domain. The corresponding hairpin assistant probe (HAP) then replaces the hybridized target miRNA to form specific HDP/HAP complexes and releases miRNA based on thermodynamically driven entropy gain process, and the released miRNA triggers the next recycle to produce tremendous corresponding HDP/HAP complexes. Results: The results showed that the CHA gel assay can detect miRNA at fM levels and shows good capability of discriminating miRNA family members and base-mismatched miRNAs. It is able to analyze miRNAs extracted from cell lysates, which are consistent with the results of conventional polymerase chain reaction (PCR) method. Depending on the length of the designed hairpin probes, the CHA gel assay consisting of different hairpin probes effectively discriminated and simultaneously detected multiple miRNAs in homogenous solution and miRNAs extracted from cell lysates. Conclusion: The work highlights the practical use of a conventional gel electrophoresis for sensitive interesting nucleic acid sequences detection.
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Affiliation(s)
- Wenhao Dai
- Research Center for Bioengineering and Sensing Technology, Beijing Key Lab for Bioengineering and Sensing Technology, School of Chemistry and bioengineering, University of Science & Technology Beijing, Beijing 100083, P.R. China
| | - Jing Zhang
- School of Petrochemical Engineering, School of Food Science and Technology, Changzhou University, Changzhou 213164, P.R. China
| | - Xiangdan Meng
- Research Center for Bioengineering and Sensing Technology, Beijing Key Lab for Bioengineering and Sensing Technology, School of Chemistry and bioengineering, University of Science & Technology Beijing, Beijing 100083, P.R. China
| | - Jie He
- School of Computer and Communication Engineering, University of Science & Technology Beijing, Beijing 100083, P.R. China
| | - Kai Zhang
- Research Center for Bioengineering and Sensing Technology, Beijing Key Lab for Bioengineering and Sensing Technology, School of Chemistry and bioengineering, University of Science & Technology Beijing, Beijing 100083, P.R. China
| | - Yu Cao
- Research Center for Bioengineering and Sensing Technology, Beijing Key Lab for Bioengineering and Sensing Technology, School of Chemistry and bioengineering, University of Science & Technology Beijing, Beijing 100083, P.R. China
| | - Dongdong Wang
- Research Center for Bioengineering and Sensing Technology, Beijing Key Lab for Bioengineering and Sensing Technology, School of Chemistry and bioengineering, University of Science & Technology Beijing, Beijing 100083, P.R. China
| | - Haifeng Dong
- Research Center for Bioengineering and Sensing Technology, Beijing Key Lab for Bioengineering and Sensing Technology, School of Chemistry and bioengineering, University of Science & Technology Beijing, Beijing 100083, P.R. China
| | - Xueji Zhang
- Research Center for Bioengineering and Sensing Technology, Beijing Key Lab for Bioengineering and Sensing Technology, School of Chemistry and bioengineering, University of Science & Technology Beijing, Beijing 100083, P.R. China
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40
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Highly-sensitive microRNA detection based on bio-bar-code assay and catalytic hairpin assembly two-stage amplification. Anal Chim Acta 2018; 1004:1-9. [DOI: 10.1016/j.aca.2017.12.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 11/27/2017] [Accepted: 12/01/2017] [Indexed: 12/17/2022]
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41
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Pei X, Yin H, Lai T, Zhang J, Liu F, Xu X, Li N. Multiplexed Detection of Attomoles of Nucleic Acids Using Fluorescent Nanoparticle Counting Platform. Anal Chem 2018; 90:1376-1383. [DOI: 10.1021/acs.analchem.7b04551] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
| | | | | | | | | | - Xiao Xu
- Division
of Nano Metrology and Materials Measurement, National Institute of Metrology, Beijing 100029, P. R. China
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42
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Liu J, Cui M, Zhou H, Yang W. DNAzyme Based Nanomachine for in Situ Detection of MicroRNA in Living Cells. ACS Sens 2017; 2:1847-1853. [PMID: 29181969 DOI: 10.1021/acssensors.7b00710] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The capability of in situ detection of microRNA in living cells with signal amplification strategy is of fundamental importance, and it will open up a new opportunity in development of diagnosis and prognosis of many diseases. Herein we report a swing DNA nanomachine for intracellular microRNA detection. The surfaces of Au nanoparticles (NPs) are modified by two hairpin DNA. We observe that one DNA (MB2) will open its hairpin structure upon partial hybridization with target miR-21 after entering into cells, and the other part of its hairpin structure could further react with the other hairpin DNA (MB1) to form a Zn2+-specific DNAzyme. This results in the disruption of MB1 through shearing action and the release of fluorescein Cy5. To provide an intelligent DNA nanomachine, MB2 is available again with the shearing action to bind with MB1, which provides effective signal amplification. This target-responsive, DNA nanomachine-based method showed a detection limit of 0.1 nM in vitro, and this approach could be an important step toward intracellular amplified detection and imaging of various analytes in living cells.
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Affiliation(s)
- Jing Liu
- Shandong
Provincial Key Laboratory of Detection Technology for Tumor Markers,
College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
- Centre
for Chemistry and Biotechnology, School of Life and Environmental
Sciences, Deakin University, Geelong, Victoria 3217, Australia
| | - Meirong Cui
- Shandong
Provincial Key Laboratory of Detection Technology for Tumor Markers,
College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
- Collaborative
Innovation Center of Functionalized Probes for Chemical Imaging in
Universities of Shandong, Shandong Normal University, Jinan 250014, P. R. China
| | - Hong Zhou
- Shandong
Provincial Key Laboratory of Detection Technology for Tumor Markers,
College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
- Centre
for Chemistry and Biotechnology, School of Life and Environmental
Sciences, Deakin University, Geelong, Victoria 3217, Australia
| | - Wenrong Yang
- Shandong
Provincial Key Laboratory of Detection Technology for Tumor Markers,
College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
- Centre
for Chemistry and Biotechnology, School of Life and Environmental
Sciences, Deakin University, Geelong, Victoria 3217, Australia
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Mohammadniaei M, Lee T, Yoon J, Lee D, Choi JW. Electrochemical nucleic acid detection based on parallel structural dsDNA/recombinant azurin hybrid. Biosens Bioelectron 2017; 98:292-298. [PMID: 28697440 PMCID: PMC7125781 DOI: 10.1016/j.bios.2017.07.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Revised: 06/22/2017] [Accepted: 07/04/2017] [Indexed: 02/07/2023]
Abstract
Several challenges remained to fabricate a molecular-level nucleic acid biosensor such as surface immobilization control, single mismatch detection and low current response. To overcome those issues, for the first time, authors presented a novel parallel structural dsDNA/recombinant azurin (PSD/rAzu) hybrid structure for the general nucleic acid detection. The PSD was designed and introduced by the optimized 8 Ag+ ions to have greater conductivity than the canonical dsDNA, and conjugated with rAzu to develop a general platform for electrochemical detection of miRNAs and viral DNAs with high reproducibility and ultra-sensitivity towards single base pair mutation. Thanks to the bifunctional rAzu as the selective spacer and electrochemical signal mediator, in the presence of the target strand, the imperfect PSD switched rapidly to the upright position where the Ag+ ions intercalated between C-C mismatches of dsDNAs at the top of each structure brought further from the electrode surface resulting in a significant electrochemical signal drop of the Ag+ ions. The charge transfer (CT) mechanism across the hybrid structure was simply clarified on the basis of the redox potential location of the species. The electrical conductivity of DNAs were measured using scanning tunneling spectroscopy (STS) at the molecular scale and cyclic voltammetry (CV) technique based on the reduction of Ag+ ion. The proposed PSD/rAzu hybrid structure with a great capability of single mutation recognition and miRNA expression level profiling in cancer cells holds a very promising platform to be studied for further development of various kinds of nanoscale biosensors, bioelectronic devices.
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Affiliation(s)
- Mohsen Mohammadniaei
- Department of Chemical and Biomolecular Engineering, Sogang University, 35 Baekbeom-ro (Sinsu-dong), Mapo-gu, Seoul 121-742, Republic of Korea
| | - Taek Lee
- Department of Chemical and Biomolecular Engineering, Sogang University, 35 Baekbeom-ro (Sinsu-dong), Mapo-gu, Seoul 121-742, Republic of Korea; Department of Chemical Engineering, Kwangwoon University, 20 Kwangwoon-Ro, Nowon-Gu, Seoul 01897, Republic of Korea
| | - Jinho Yoon
- Department of Chemical and Biomolecular Engineering, Sogang University, 35 Baekbeom-ro (Sinsu-dong), Mapo-gu, Seoul 121-742, Republic of Korea
| | - Donghyun Lee
- School of Integrative Engineering Chung-Ang University, Heukseok-dong, Dongjak-gu, Seoul 156-756, Republic of Korea.
| | - Jeong-Woo Choi
- Department of Chemical and Biomolecular Engineering, Sogang University, 35 Baekbeom-ro (Sinsu-dong), Mapo-gu, Seoul 121-742, Republic of Korea.
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Ahmad R, Destgeer G, Afzal M, Park J, Ahmed H, Jung JH, Park K, Yoon TS, Sung HJ. Acoustic Wave-Driven Functionalized Particles for Aptamer-Based Target Biomolecule Separation. Anal Chem 2017; 89:13313-13319. [PMID: 29148722 DOI: 10.1021/acs.analchem.7b03474] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We developed a hybrid microfluidic device that utilized acoustic waves to drive functionalized microparticles inside a continuous flow microchannel and to separate particle-conjugated target proteins from a complex fluid. The acoustofluidic device is composed of an interdigitated transducer that produces high-frequency surface acoustic waves (SAW) and a polydimethylsiloxane (PDMS) microfluidic channel. The SAW interacted with the sample fluid inside the microchannel and deflected particles from their original streamlines to achieve separation. Streptavidin-functionalized polystyrene (PS) microparticles were used to capture aptamer (single-stranded DNA) labeled at one end with a biotin molecule. The free end of the customized aptamer15 (apt15), which was attached to the microparticles via streptavidin-biotin linkage to form the PS-apt15 conjugate, was used to capture the model target protein, thrombin (th), by binding at exosite I to form the PS-apt15-th complex. We demonstrated that the PS-apt15 conjugate selectively captured thrombin molecules in a complex fluid. After the PS-apt15-th complex was formed, the sample fluid was pumped through a PDMS microchannel along with two buffer sheath flows that hydrodynamically focused the sample flow prior to SAW exposure for PS-apt15-th separation from the non-target proteins. We successfully separated thrombin from mCardinal2 and human serum using the proposed acoustofluidic device.
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Affiliation(s)
- Raheel Ahmad
- Department of Mechanical Engineering, KAIST , 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea
| | - Ghulam Destgeer
- Department of Mechanical Engineering, KAIST , 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea
| | - Muhammad Afzal
- Department of Proteome Structural Biology, KRIBB School of Bioscience, Korea University of Science and Technology , 125 Gwahak-ro Yuseong-gu, Daejeon 34141, Korea
| | - Jinsoo Park
- Department of Mechanical Engineering, KAIST , 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea
| | - Husnain Ahmed
- Department of Mechanical Engineering, KAIST , 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea
| | - Jin Ho Jung
- Department of Mechanical Engineering, KAIST , 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea
| | - Kwangseok Park
- Department of Mechanical Engineering, KAIST , 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea
| | - Tae-Sung Yoon
- Department of Proteome Structural Biology, KRIBB School of Bioscience, Korea University of Science and Technology , 125 Gwahak-ro Yuseong-gu, Daejeon 34141, Korea
| | - Hyung Jin Sung
- Department of Mechanical Engineering, KAIST , 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea
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Czarnek M, Bereta J. SmartFlares fail to reflect their target transcripts levels. Sci Rep 2017; 7:11682. [PMID: 28916792 PMCID: PMC5600982 DOI: 10.1038/s41598-017-11067-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 08/18/2017] [Indexed: 12/28/2022] Open
Abstract
SmartFlare probes have recently emerged as a promising tool for visualisation and quantification of specific RNAs in living cells. They are supposed to overcome the common drawbacks of current methods for RNA analysis: the need of cell fixation or lysis, or the requirements for genetic manipulations. In contrast to the traditional methods, SmartFlare probes are also presumed to provide information on RNA levels in single cells. Disappointingly, the results of our comprehensive study involving probes specific to five different transcripts, HMOX1, IL6, PTGS2, Nrg1, and ERBB4, deny the usefulness of SmartFlare probes for RNA analysis. We report a total lack of correlation between fluorescence intensities of SmartFlare probes and the levels of corresponding RNAs assessed by RT-qPCR. To ensure strong differences in the levels of analysed RNAs, their expression was modified via: (i) HMOX1-knockdown generated by CRISPR-Cas9 genome editing, (ii) hemin-mediated stimulation of HMOX1- and IL1β-mediated stimulation of IL6- and PTGS2 transcription, (iii) lentiviral vector-mediated Nrg1 overexpression. Additionally, ERBB4-specific SmartFlare probe failed to distinguish between ERBB4-expressing and non-expressing cell lines. Finally, we demonstrated that fluorescence intensity of HMOX1-specific SmartFlare probe corresponds to the efficacy of its uptake and/or accumulation.
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Affiliation(s)
- Maria Czarnek
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Gronostajowa 7, 30-387, Kraków, Poland
| | - Joanna Bereta
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Gronostajowa 7, 30-387, Kraków, Poland.
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Broto M, Galve R, Marco MP. Sandwich NP-based biobarcode assay for quantification C-reactive protein in plasma samples. Anal Chim Acta 2017; 992:112-118. [PMID: 29054144 DOI: 10.1016/j.aca.2017.09.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/29/2017] [Accepted: 09/01/2017] [Indexed: 12/20/2022]
Abstract
A NP-based biobarcode for C-reactive protein (CRP) quantification in plasma samples is reported for the first time. The assay uses capture antibody functionalized magnetic beads (pAbCRP2-MP), multifunctional oligonucleotide encoded probes modified with a detection antibody (pAbCRP1-ePSP), and a fluorescent DNA microarray. Thus, magnetic beads are added to the sample to form immunocomplexes that will be isolated, to then add the codified particles to form a sandwich complex with both particles and the target protein, subsequently the complexes are treated to release the oligonucleotide codes, which are finally hybridized in a fluorescent DNA microarray. The assay has been implemented to the analysis of plasma samples being able to quantify this biomarker within 900 ng mL-1 to 12500 ng mL-1 with an excellent accuracy (mean of recovery of 99.5 ± 4.2%, N = 3). The CRP biobarcode has been used on a small pilot clinical study in which plasma samples from patients suffering different pathologies, most of them related to cardiovascular diseases (CVDs). The samples have been analyzed and the results compared to a reference method demonstrating that the assay can be useful for monitoring this biomarker on patients being suspicious to be under risk of suffering CVDs or other diseases involving inflammatory processes.
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Affiliation(s)
- Marta Broto
- Nanobiotechnology for Diagnostics (Nb4D), Department of Chemical and Biomolecular Nanotechnology, Institute for Advanced Chemistry of Catalonia (IQAC) of the Spanish Council for Scientific Research (CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Roger Galve
- Nanobiotechnology for Diagnostics (Nb4D), Department of Chemical and Biomolecular Nanotechnology, Institute for Advanced Chemistry of Catalonia (IQAC) of the Spanish Council for Scientific Research (CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Jordi Girona 18-26, 08034 Barcelona, Spain.
| | - M-Pilar Marco
- Nanobiotechnology for Diagnostics (Nb4D), Department of Chemical and Biomolecular Nanotechnology, Institute for Advanced Chemistry of Catalonia (IQAC) of the Spanish Council for Scientific Research (CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Jordi Girona 18-26, 08034 Barcelona, Spain
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Broto M, Salvador JP, Galve R, Marco MP. Biobarcode assay for the oral anticoagulant acenocoumarol. Talanta 2017; 178:308-314. [PMID: 29136827 DOI: 10.1016/j.talanta.2017.09.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 08/29/2017] [Accepted: 09/02/2017] [Indexed: 12/28/2022]
Abstract
A novel approach for therapeutic drug monitoring of oral anticoagulants (OA) in clinical samples is reported, based on a NP-based biobarcode assay. The proposed strategy uses specific antibodies for acenocumarol (ACL) covalently bound to magnetic particles (pAb236-MP) and a bioconjugate competitor (hACL-BSA) linked to encoded polystyrene probes (hACL-BSA-ePSP) on a classical competitive immunochemical format. By using this scheme ACL can be detected in low nM range (LOD, 0.96 ± 0.26, N = 3, in buffer) even in complex samples such as serum or plasma (LOD 4 ± 1). The assay shows a high reproducibility (%CV 1.1 day-to-day) and is robust, as it is demonstrated by the fact that ACL can be quantified in complex biological samples with a very good accuracy (slope = 0.97 and R2 = 0.91, of the linear regression obtained when analyzing spiked vs measured values). Moreover, we have demonstrated that the biobarcode approach has the potential to overcome one of the main challenges of the multiplexed diagnostic, which is the possibility to measure in a single run biomarker targets present at different concentration ranges. Thus, it has been proven that the signal and the detectability can be modulated by just modifying the oligonucleotide load of the encoded probes. This fact opens the door for combining in the same assay encoded probes with the necessary oligonucleotide load to achieve the detectability required for each biomarker target.
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Affiliation(s)
- Marta Broto
- Nanobiotechnology for Diagnostics (Nb4D), Institute for Advanced Chemistry of Catalonia of the Spanish Council for Scientific Research (IQAC-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Jordi Girona 18-26, 08034 Barcelona, Spain
| | - J Pablo Salvador
- Nanobiotechnology for Diagnostics (Nb4D), Institute for Advanced Chemistry of Catalonia of the Spanish Council for Scientific Research (IQAC-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Roger Galve
- Nanobiotechnology for Diagnostics (Nb4D), Institute for Advanced Chemistry of Catalonia of the Spanish Council for Scientific Research (IQAC-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Jordi Girona 18-26, 08034 Barcelona, Spain.
| | - M Pilar Marco
- Nanobiotechnology for Diagnostics (Nb4D), Institute for Advanced Chemistry of Catalonia of the Spanish Council for Scientific Research (IQAC-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Jordi Girona 18-26, 08034 Barcelona, Spain
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Ahmad R, Jang H, Batule BS, Park HG. Barcode DNA-Mediated Signal Amplifying Strategy for Ultrasensitive Biomolecular Detection on Matrix-Assisted Laser Desorption Ionization Time of Flight (MALDI-TOF) Mass Spectrometry. Anal Chem 2017; 89:8966-8973. [DOI: 10.1021/acs.analchem.7b01535] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Raheel Ahmad
- Department of Chemical and
Biomolecular Engineering (BK 21+ program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Hyowon Jang
- Department of Chemical and
Biomolecular Engineering (BK 21+ program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Bhagwan S. Batule
- Department of Chemical and
Biomolecular Engineering (BK 21+ program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and
Biomolecular Engineering (BK 21+ program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon 34141, Republic of Korea
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Xia Y, Zhang R, Wang Z, Tian J, Chen X. Recent advances in high-performance fluorescent and bioluminescent RNA imaging probes. Chem Soc Rev 2017; 46:2824-2843. [PMID: 28345687 PMCID: PMC5472208 DOI: 10.1039/c6cs00675b] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
RNA plays an important role in life processes. Imaging of messenger RNAs (mRNAs) and micro-RNAs (miRNAs) not only allows us to learn the formation and transcription of mRNAs and the biogenesis of miRNAs involved in various life processes, but also helps in detecting cancer. High-performance RNA imaging probes greatly expand our view of life processes and enhance the cancer detection accuracy. In this review, we summarize the state-of-the-art high-performance RNA imaging probes, including exogenous probes that can image RNA sequences with special modification and endogeneous probes that can directly image endogenous RNAs without special treatment. For each probe, we review its structure and imaging principle in detail. Finally, we summarize the application of mRNA and miRNA imaging probes in studying life processes as well as in detecting cancer. By correlating the structures and principles of various probes with their practical uses, we compare different RNA imaging probes and offer guidance for better utilization of the current imaging probes and the future design of higher-performance RNA imaging probes.
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Affiliation(s)
- Yuqiong Xia
- Engineering Research Center of Molecular-imaging and Neuro-imaging of Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, Shaanxi 710126, China.
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Ravan H, Amandadi M, Esmaeili-Mahani S. DNA Domino-Based Nanoscale Logic Circuit: A Versatile Strategy for Ultrasensitive Multiplexed Analysis of Nucleic Acids. Anal Chem 2017; 89:6021-6028. [PMID: 28459545 DOI: 10.1021/acs.analchem.7b00607] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
In recent years, the analytical application of logical nanodevices has attracted much attention for making accurate decisions on molecular diagnosis. Herein, a DNA domino-based nanoscale logic circuit has been constructed by integrating three logic gates (AND-AND-YES) for simultaneous analysis of multiple nucleic acid biomarkers. In the first AND gate, a chimeric target DNA comprising of four biomarkers was hybridized to three biomarker-specific oligonucleotides (TRs) via their 5'-end regions and to a capture probe-magnetic microparticle. After harvesting the complex, 3' overhang regions of the TRs were labeled with three distinct monolayer double-stranded (ds) DNA-gold nanoparticles (DNA-AuNPs). Upon gleaning the complex and addition of initiator oligonucleotide, a series of toehold-mediated strand displacement reactions, which are reminiscent of a domino chain, spontaneously occurred between the confined dsDNAs on the nanoparticles' surface in the second AND gate. The output of the second gate entered into the last gate and triggered an exponential hairpin assembly to form four-way junction nanostructures. The resulting nanostructures bear split parts of DNAzyme at each end of the four arms which, in the presence of hemin, form catalytic hemin/G-quadruplex DNAzymes with peroxidase activity. The smart biosensor has exhibited a turn-on signal when all biomarkers are present in the sample. In fact, should any of the biomarkers be nonexistent, the signal remains turned-off. The biosensor can detect the biomarkers with a LOD value of 100 aM and a noticeable capability to discriminate single-nucleotide substitutions.
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Affiliation(s)
- Hadi Ravan
- Department of Biology, Faculty of Science, Shahid Bahonar University of Kerman , Kerman, Iran 7616914111
| | - Mojdeh Amandadi
- Department of Biology, Faculty of Science, Shahid Bahonar University of Kerman , Kerman, Iran 7616914111
| | - Saeed Esmaeili-Mahani
- Department of Biology, Faculty of Science, Shahid Bahonar University of Kerman , Kerman, Iran 7616914111
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