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Al-Hawary SIS, Saleh RO, Mansouri S, Noraldeen SAM, Alawadi AH, Kareem AH, Alsalamy A, Shakir MN, Alasheqi MQ, Mustafa YF. Isothermal amplification methods in cancer-related miRNA detection; a new paradigm in study of cancer pathology. Pathol Res Pract 2024; 254:155072. [PMID: 38228039 DOI: 10.1016/j.prp.2023.155072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 12/22/2023] [Accepted: 12/28/2023] [Indexed: 01/18/2024]
Abstract
MicroRNAs (miRNAs) are short, non-coding RNA molecules that regulate gene expression. They are involved in a wide range of biological processes, including development, differentiation, cell cycle regulation, and response to stress. Numerous studies have demonstrated that miRNAs are present in different bodily fluids, which could serve as an important biomarker. The advancement of techniques and strategies for the identification of cancer-associated miRNAs in human specimens offers a novel opportunity to diagnose cancer in early stages, predict patient prognosis and evaluate response to treatment. Isothermal techniques including loop-mediated isothermal amplification (LAMP), rolling circle amplification (RCA), or recombinase polymerase amplification (RPA) offer simplicity, efficiency, and rapidity in miRNA detection processes. In contrast to traditional PCR (polymerase chain reaction), these techniques analysis and quantify miRNA molecules in specimens using a single constant temperature. In this comprehensive review, we summarized the recent advances in cancer-related miRNA detection via highly sensitive isothermal amplification methods by more focusing on the involved mechanism.
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Affiliation(s)
| | - Raed Obaid Saleh
- Department of Medical Laboratory Techniques, Al-Maarif University College, Al-Anbar, Iraq
| | - Sofiene Mansouri
- Department of Biomedical Technology, College of Applied Medical Sciences in Al-Kharj, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia; University of Tunis El Manar, Higher Institute of Medical Technologies of Tunis, Laboratory of Biophysics and Medical Technologies, Tunis, Tunisia.
| | | | - Ahmed Hussien Alawadi
- College of Technical Engineering, University of Najaf, Najaf, Iraq; College of Technical Engineering, the Islamic University of Al Diwaniyah, Iraq; College of Technical Engineering, the Islamic University of Babylon, Iraq
| | | | - Ali Alsalamy
- College of Technical Engineering, Imam Ja'afar Al-Sadiq University, Al-Muthanna 66002, Iraq
| | - Maha Noori Shakir
- Department of Medical Laboratories Technology, AL-Nisour University College, Baghdad, Iraq
| | | | - Yasser Fakri Mustafa
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Mosul, Mosul 41001, Iraq
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2
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CRISPR-Cas12a-assisted elimination of the non-specific signal from non-specific amplification in the Exponential Amplification Reaction. Anal Chim Acta 2023; 1251:340998. [PMID: 36925288 DOI: 10.1016/j.aca.2023.340998] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/13/2023] [Accepted: 02/21/2023] [Indexed: 02/24/2023]
Abstract
Non-specific amplification is a major problem in nucleic acid amplification resulting in false-positive results, especially for exponential amplification reactions (EXPAR). Although efforts were made to suppress the influence of non-specific amplification, such as chemical blocking of the template's 3'-ends and sequence-independent weakening of template-template interactions, it is still a common problem in many conventional EXPAR reactions. In this study, we propose a novel strategy to eliminate the non-specific signal from non-specific amplification by integrating the CRISPR-Cas12a system into two-templates EXPAR. An EXPAR-Cas12a strategy named EXPCas was developed, where the Cas12a system acted as a filter to filter out non-specific amplificons in EXPAR, suppressing and eliminating the influence of non-specific amplification. As a result, the signal-to-background ratio was improved from 1.3 to 15.4 using this method. With microRNA-21 (miRNA-21) as a target, the detection can be finished in 40 min with a LOD of 103 fM and no non-specific amplification was observed.
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3
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Huang L, Zhang L, Chen X. Updated review of advances in microRNAs and complex diseases: experimental results, databases, webservers and data fusion. Brief Bioinform 2022; 23:6696143. [PMID: 36094095 DOI: 10.1093/bib/bbac397] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/19/2022] [Accepted: 08/15/2022] [Indexed: 12/14/2022] Open
Abstract
MicroRNAs (miRNAs) are gene regulators involved in the pathogenesis of complex diseases such as cancers, and thus serve as potential diagnostic markers and therapeutic targets. The prerequisite for designing effective miRNA therapies is accurate discovery of miRNA-disease associations (MDAs), which has attracted substantial research interests during the last 15 years, as reflected by more than 55 000 related entries available on PubMed. Abundant experimental data gathered from the wealth of literature could effectively support the development of computational models for predicting novel associations. In 2017, Chen et al. published the first-ever comprehensive review on MDA prediction, presenting various relevant databases, 20 representative computational models, and suggestions for building more powerful ones. In the current review, as the continuation of the previous study, we revisit miRNA biogenesis, detection techniques and functions; summarize recent experimental findings related to common miRNA-associated diseases; introduce recent updates of miRNA-relevant databases and novel database releases since 2017, present mainstream webservers and new webserver releases since 2017 and finally elaborate on how fusion of diverse data sources has contributed to accurate MDA prediction.
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Affiliation(s)
- Li Huang
- Academy of Arts and Design, Tsinghua University, Beijing, 10084, China.,The Future Laboratory, Tsinghua University, Beijing, 10084, China
| | - Li Zhang
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, 221116, China
| | - Xing Chen
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, 221116, China.,Artificial Intelligence Research Institute, China University of Mining and Technology, Xuzhou, 221116, China
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4
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Song J, Ju Y, Kim S, Kim H, Park HG. Palindromic hyperbranched rolling circle amplification enabling ultrasensitive microRNA detection. Chem Commun (Camb) 2022; 58:6518-6521. [PMID: 35575999 DOI: 10.1039/d2cc01370c] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We herein describe a palindromic hyperbranched rolling circle amplification (PH-RCA) reaction and its application for ultrasensitive detection of microRNAs (miRNAs). In this strategy, target miRNAs bind to a dumb-bell probe (DP) and initiate the RCA reactions, concomitantly converting the dumb-bell structure to the circular form, which then allows the annealing of the palindromic primers to promote an additional two RCA reactions. As a consequence of the RCA reactions promoted by both target miRNAs and palindromic primers, multiple long concatenated DNA strands would be produced. Importantly, the palindromic primers can also bind to numerous palindromic domains of the long linear single DNA strands, consequently promoting highly branched simultaneous extension reactions at multiple sites. By detecting the fluorescence signals resulting from the amplified DNA products, we successfully identified target miRNA under isothermal conditions with excellent specificity. The PH-RCA technique developed in this work would greatly advance the conventional RCA reaction and HRCA reaction by significantly enhancing the sensitivity and reducing the reaction time within 30 min.
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Affiliation(s)
- Jayeon Song
- Department of Chemical and Biomolecular Engineering (BK 21+ program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon 305-701, Republic of Korea.
| | - Yong Ju
- Department of Chemical and Biomolecular Engineering (BK 21+ program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon 305-701, Republic of Korea.
| | - Soohyun Kim
- Department of Chemical and Biomolecular Engineering (BK 21+ program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon 305-701, Republic of Korea.
| | - Hansol Kim
- Department of Chemical and Biomolecular Engineering (BK 21+ program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon 305-701, Republic of Korea.
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK 21+ program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon 305-701, Republic of Korea.
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5
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Wijesinghe KM, Kanak MA, Harrell JC, Dhakal S. Single-Molecule Sensor for High-Confidence Detection of miRNA. ACS Sens 2022; 7:1086-1094. [PMID: 35312280 PMCID: PMC9112324 DOI: 10.1021/acssensors.1c02748] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
MicroRNAs (miRNAs) play a crucial role in regulating gene expression and have been linked to many diseases. Therefore, sensitive and accurate detection of disease-linked miRNAs is vital to the emerging revolution in early diagnosis of diseases. While the detection of miRNAs is a challenge due to their intrinsic properties such as small size, high sequence similarity among miRNAs and low abundance in biological fluids, the majority of miRNA-detection strategies involve either target/signal amplification or involve complex sensing designs. In this study, we have developed and tested a DNA-based fluorescence resonance energy transfer (FRET) sensor that enables ultrasensitive detection of a miRNA biomarker (miRNA-342-3p) expressed by triple-negative breast cancer (TNBC) cells. The sensor shows a relatively low FRET state in the absence of a target but it undergoes continuous FRET transitions between low- and high-FRET states in the presence of the target. The sensor is highly specific, has a detection limit down to low femtomolar (fM) without having to amplify the target, and has a large dynamic range (3 orders of magnitude) extending to 300 000 fM. Using this strategy, we demonstrated that the sensor allows detection of miRNA-342-3p in the miRNA-extracts from cancer cell lines and TNBC patient-derived xenografts. Given the simple-to-design hybridization-based detection, the sensing platform developed here can be used to detect a wide range of miRNAs enabling early diagnosis and screening of other genetic disorders.
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Affiliation(s)
- Kalani M. Wijesinghe
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Mazhar A. Kanak
- Division of Transplant Surgery, Department of Surgery, Virginia Commonwealth University School of Medicine, Richmond, Virginia 23298, United States
| | - J. Chuck Harrell
- Department of Pathology, School of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Soma Dhakal
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
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6
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Wei Z, Wang X, Feng H, Ji F, Bai D, Dong X, Huang W. Isothermal nucleic acid amplification technology for rapid detection of virus. Crit Rev Biotechnol 2022; 43:415-432. [PMID: 35156471 DOI: 10.1080/07388551.2022.2030295] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
While the research field and industrial market of in vitro diagnosis (IVD) thrived during and post the COVID-19 pandemic, the development of isothermal nucleic acid amplification test (INAAT) based rapid diagnosis was engendered in a global wised large measure as a problem-solving exercise. This review systematically analyzed the recent advances of INAAT strategies with practical case for the real-world scenario virus detection applications. With the qualities that make INAAT systems useful for making diagnosis relevant decisions, the key performance indicators and the cost-effectiveness of enzyme-assisted methods and enzyme-free methods were compared. The modularity of nucleic acid amplification reactions that can lead to thresholding signal amplifications using INAAT reagents and their methodology design were examined, alongside the potential application with rapid test platform/device integration. Given that clinical practitioners are, by and large, unaware of many the isothermal nucleic acid test advances. This review could bridge the arcane research field of different INAAT systems and signal output modalities with end-users in clinic when choosing suitable test kits and/or methods for rapid virus detection.
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Affiliation(s)
- Zhenting Wei
- Frontiers Science Center for Flexible Electronics (FSCFE), Institute of Flexible Electronics (IFE), MIIT Key Laboratory of Flexible Electronics (KLoFE), Xi'an Key Laboratory of Special Medicine and Health Engineering, Northwestern Polytechnical University, Xi'an, China
- North Sichuan Medical College, Nanchong, China
| | - Xiaowen Wang
- Frontiers Science Center for Flexible Electronics (FSCFE), Institute of Flexible Electronics (IFE), MIIT Key Laboratory of Flexible Electronics (KLoFE), Xi'an Key Laboratory of Special Medicine and Health Engineering, Northwestern Polytechnical University, Xi'an, China
- North Sichuan Medical College, Nanchong, China
| | - Huhu Feng
- Frontiers Science Center for Flexible Electronics (FSCFE), Institute of Flexible Electronics (IFE), MIIT Key Laboratory of Flexible Electronics (KLoFE), Xi'an Key Laboratory of Special Medicine and Health Engineering, Northwestern Polytechnical University, Xi'an, China
| | - Fanpu Ji
- Department of Infectious Diseases, The 2nd Hospital of Xi'an Jiaotong University, Nanchong, China
- National and Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The 2nd Hospital of Xi'an Jiaotong University, Nanchong, China
- Division of Gastroenterology and Hepatology, Stanford University Medical Center, Nanchong, China
| | - Dan Bai
- Frontiers Science Center for Flexible Electronics (FSCFE), Institute of Flexible Electronics (IFE), MIIT Key Laboratory of Flexible Electronics (KLoFE), Xi'an Key Laboratory of Special Medicine and Health Engineering, Northwestern Polytechnical University, Xi'an, China
- Research and Development Institute of Northwestern Polytechnical University in Shenzhen, Northwestern Polytechnical University, Nanchong, China
| | - Xiaoping Dong
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Nanchong, China
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Nanchong, China
| | - Wei Huang
- Frontiers Science Center for Flexible Electronics (FSCFE), Institute of Flexible Electronics (IFE), MIIT Key Laboratory of Flexible Electronics (KLoFE), Xi'an Key Laboratory of Special Medicine and Health Engineering, Northwestern Polytechnical University, Xi'an, China
- Research and Development Institute of Northwestern Polytechnical University in Shenzhen, Northwestern Polytechnical University, Nanchong, China
- Institute of Advanced Materials (IAM), Nanjing Tech University, Nanchong, China
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7
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Tiwari N, Mishra RK, Gupta S, Srivastava R, Aggarwal S, Bandyopadhyay P, Munde M. Synthetic Tunability and Biophysical Basis for Fabricating Highly Fluorescent and Stable DNA Copper Nanoclusters. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:9385-9395. [PMID: 34313447 DOI: 10.1021/acs.langmuir.1c00949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The real motivation in the present work is to tune the synthesis variables that can result in a highly fluorescent and stable DNA copper nanocluster (CuNC) and also to understand the intricate mechanism behind this process. Here, carefully optimized concentrations of various reactants enabled the creation of a DNA-encapsulated CuNC for AT-DNA, displaying a size of <1.0 nm as confirmed by transmission electron microscopy and dynamic light scattering. The extremely small size of the AT-DNACuNC supports the discrete electronic transitions, also characterized by an exceptionally strong negative circular dichroism (CD) band around 350 nm, whose intensity is well correlated with the observed strong fluorescence emission intensity. This remarkably strong CD can open new applications in the detection and quantification of a specific DNACuNC. Further, time-dependent fluorescence analysis suggested stronger photostabilization of these DNACuNCs. The simulation study, based on Cu ion distribution, explained how AT-DNA is a better candidate for NC formation than GC-DNA. In conclusion, the better-tuned synthesis procedure has resulted in a highly compact, well-defined three-dimensional conformation that promotes a more favorable microenvironment to sequester a DNA-based CuNC with high brightness and outstanding photostability.
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Affiliation(s)
- Neha Tiwari
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Rakesh Kumar Mishra
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sakshi Gupta
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Rakesh Srivastava
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Soumya Aggarwal
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Pradipta Bandyopadhyay
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Manoj Munde
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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8
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Jung Y, Song J, Park HG. Ultrasensitive nucleic acid detection based on phosphorothioated hairpin-assisted isothermal amplification. Sci Rep 2021; 11:8399. [PMID: 33863981 PMCID: PMC8052315 DOI: 10.1038/s41598-021-87948-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 03/24/2021] [Indexed: 02/02/2023] Open
Abstract
Herein, we describe a phosphorothioated hairpin-assisted isothermal amplification (PHAmp) method for detection of a target nucleic acid. The hairpin probe (HP) is designed to contain a 5' phosphorothioate (PS)-modified overhang, a target recognition site, and a 3' self-priming (SP) region. Upon binding to the target nucleic acid, the HP opens and the SP region is rearranged to serve as a primer. The subsequent process of strand displacement DNA synthesis recycles the bound target to open another HP and produces an extended HP (EP) with a PS-DNA/DNA duplex at the end, which would be readily denatured due to its reduced thermal stability. The trigger then binds to the denatured 3' end of the EP and is extended, producing an intermediate double-stranded (ds) DNA product (IP). The trigger also binds to the denatured 3' end of the IP, and its extension produces the final dsDNA product along with concomitant displacement and recycling of EP. By monitoring the dsDNA products, the target nucleic acid can be identified down to 0.29 fM with a wide dynamic range from 1 nM to 1 fM yielding an excellent specificity to discriminate even a single base-mismatched target. The unique design principle could provide new insights into the development of novel isothermal amplification methods for nucleic acid detection.
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Affiliation(s)
- Yujin Jung
- Department of Chemical and Biomolecular Engineering (BK 21+ Program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Jayeon Song
- 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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9
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Song J, Kim HY, Kim S, Jung Y, Park HG. Self-priming phosphorothioated hairpin-mediated isothermal amplification. Biosens Bioelectron 2021; 178:113051. [PMID: 33548651 DOI: 10.1016/j.bios.2021.113051] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 01/21/2021] [Accepted: 01/27/2021] [Indexed: 01/06/2023]
Abstract
We herein describe a novel technology, termed self-priming phosphorothioated hairpin-mediated isothermal amplification (SP-HAMP), enabling target nucleic acid detection. Isothermal amplification strategies are a simple process that efficiently raises the amount of nucleic acid at a constant temperature, but still has lots of problems such as the requirement of multiple exogenous primers and enzymes, which trigger non-specific background signal and increase the complexity of procedures. The key component for overcoming the above-mentioned limitations is the designed hairpin probe (HP) consisting of self-priming region along the 3' stem and the 3' overhang and phosphorothioate modifications at the 5' overhang and the specific loop part. The HP was designed to open through binding to target nucleic acid. Upon opening of HP, its self-priming (SP) region is rearranged to form a smaller hairpin whose 3' end could serve as a primer. The following extension produces the extended HP and displaces the bound target nucleic acid, which is then recycled to open another HP. Due to the reduced stability caused by the specific two phosphorothioate (PS) modifications, the 3' end of EP1 is readily rearranged to form the foldback hairpin structure, which would promote the foldback extension to produce once more extended HP. Since the two PS modifications are always located at the same positions along the 5' stem within the further extended HPs, the foldback reaction followed by the extension would be continuously repeated, consequently producing a large number of the long hairpin concatamers. Based on this unique design principle, we successfully detected even a single copy of target DNA with outstanding discrimination capability under an isothermal condition by employing only a single HP without the requirement for the complicated multiple primers. In conclusion, the sophisticated design principle employed in this work would provide great insight for the development of self-operative isothermal amplifying system enabling short target nucleic acid detection such as microRNAs or any target which is less than 200 mer.
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Affiliation(s)
- Jayeon Song
- Department of Chemical and Biomolecular Engineering (BK 21+ Program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Hyo Yong Kim
- Department of Chemical and Biomolecular Engineering (BK 21+ Program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Soohyun Kim
- Department of Chemical and Biomolecular Engineering (BK 21+ Program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Yujin Jung
- 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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Kim HY, Song J, Park HG. Ultrasensitive isothermal method to detect microRNA based on target-induced chain amplification reaction. Biosens Bioelectron 2021; 178:113048. [PMID: 33550160 DOI: 10.1016/j.bios.2021.113048] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 01/21/2021] [Accepted: 01/27/2021] [Indexed: 02/06/2023]
Abstract
We herein describe an ultrasensitive isothermal method to detect microRNA (miRNA) by utilizing target-induced chain amplification reaction (CAR). The hairpin probe (HP) employed in this strategy is designed to be opened upon binding to target miRNA. The exponential amplification reaction (EXPAR) template (ET) then binds to the exposed stem of HP and DNA polymerase (DP) promotes the extension reactions for both HP and ET, consequently producing intermediate double-stranded DNA product (IP) and concomitantly recycling target miRNA to open another intact HP. The IPs would produce a large number of target-mimicking probes (TMPs) and trigger probes (TPs) through the continuously repeated nicking and extension reactions at the two separated nicking sites within the IP. TMP triggers another CAR cycle by binding to intact HP as target miRNA did while TP promotes conventional EXPAR by independently binding to free ET. As a consequence of these interconnected reaction systems, a large number of final double-stranded DNA products (FPs) are produced, which can be monitored by measuring the fluorescent signal produced from duplex-specific fluorescent dye. Based on this unique design principle, the target miRNA was successfully determined down to even a single copy with high selectivity against non-specific miRNAs. The practical applicability of this method was also verified by reliably detecting target miRNA included in the total RNA extracted from the human cancer cell.
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Affiliation(s)
- Hyo Yong Kim
- Department of Chemical and Biomolecular Engineering (BK21+ Program), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Jayeon Song
- Department of Chemical and Biomolecular Engineering (BK21+ Program), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK21+ Program), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
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11
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Guo J, Yu H, Cui T. Applications of fluorescent materials in the detection of alkaline phosphatase activity. J Biomed Mater Res B Appl Biomater 2020; 109:214-226. [PMID: 32790135 DOI: 10.1002/jbm.b.34693] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 06/26/2020] [Accepted: 07/09/2020] [Indexed: 12/15/2022]
Abstract
Alkaline phosphatase (ALP) is important in the diagnosis of many diseases. Because ALP is used to detect biomarkers for many diseases, many researchers conduct investigations to develop ALP detection strategies. The use of fluorescent material has attracted attention because of the technique's high sensitivity and the low sample volume required. Herein, we review and discuss the working mechanisms and advantages of four main categories:DNA fluorescent probes, molecular fluorescent probes, chemical coordination-based probes, and nanoparticle probes. Development prospects and trends are also discussed.
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Affiliation(s)
- Jiantao Guo
- Department of Cardiac Surgery, The First Hospital of Jilin University, Changchun, China
| | - Hongbo Yu
- Department of Cardiac Surgery, The First Hospital of Jilin University, Changchun, China
| | - Tingting Cui
- Department of Ultrasound, China-Japan Union Hospital of Jilin University, Changchun, China
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12
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Song JY, Jung Y, Lee S, Park HG. Self-Priming Hairpin-Utilized Isothermal Amplification Enabling Ultrasensitive Nucleic Acid Detection. Anal Chem 2020; 92:10350-10356. [PMID: 32551503 DOI: 10.1021/acs.analchem.0c00511] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We presented a novel method, referred to as self-priming hairpin-utilized isothermal amplification (SPHIA), to enable nucleic acid detection. The hairpin probe (HP1) employed in this strategy was designed to be opened through binding to the target nucleic acid. Upon opening of HP1, the self-priming domain within the HP1 stem region was exposed and rearranged to serve as a primer. The following extension displaced the bound target nucleic acid, which was then recycled to open another HP1. The extended HP1 was subjected to continuously repeated extension and nicking reaction, and abundant triggers were produced as a result. The triggers entered and initiated phase 2 reaction through binding to HP2, and this produced numerous target mimic strands (Target'). The target' entered and activated the phase 1 reaction, mimicking the target nucleic acid. As a consequence of these interconnected two amplification reactions initiated by a positive feedback mechanism, a considerable number of final double-stranded DNA products (FPs) were ultimately produced, which could be monitored in real-time through duplex-specific fluorescent signaling. Exploiting this novel design principle, we detected target DNA down to 28.9 aM with outstanding discrimination capability. The practical diagnostic ability of this strategy was also successfully demonstrated for target RNA detection by rationally redesigning the hairpin probes.
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Affiliation(s)
- Ja Yeon Song
- Department of Chemical and Biomolecular Engineering (BK 21+ program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Yujin Jung
- Department of Chemical and Biomolecular Engineering (BK 21+ program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Seoyoung Lee
- 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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13
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A Label-Free Fluorescent Sensor Based on the Formation of Poly(thymine)-Templated Copper Nanoparticles for the Sensitive and Selective Detection of MicroRNA from Cancer Cells. CHEMOSENSORS 2020. [DOI: 10.3390/chemosensors8030052] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In this work, a simple and label-free fluorescence “off” to “on” platform was designed for the sensitive and selective detection of microRNA (miRNA) in cancer cells. This method utilized a padlock DNA-based rolling circle amplification (P-RCA) to synthesize fluorescent poly(thymine) (PolyT) which acted as a template for the synthesis of copper nanoparticles (CuNPs) within 10 minutes under mild conditions. While the repeated PolyT sequence was used as the template for CuNP synthesis, other non-PolyT parts (single strand-DNAs without the capacity to act as the template for CuNP formation) served as “smart glues” or rigid linkers to build complex nanostructures. Under the excitation wavelength of 340 nm, the synthesized CuNPs emitted strong red fluorescence effectively at 620 nm. To demonstrate the use of this method as a universal biosensor platform, lethal-7a (let-7a) miRNA was chosen as the standard target. This sensor could achieve highly sensitive and selective detection of miRNA in the presence of other homologous analogues for the combination of P-RCA with the fluorescent copper nanoparticle. Overall, this novel label-free method holds great potential in the sensitive detection of miRNA with high specificity in real samples.
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Beyond native deoxyribonucleic acid, templating fluorescent nanomaterials for bioanalytical applications: A review. Anal Chim Acta 2020; 1105:11-27. [DOI: 10.1016/j.aca.2020.01.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 01/10/2020] [Accepted: 01/10/2020] [Indexed: 12/16/2022]
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Jamali Z, Taheri-Anganeh M, Shabaninejad Z, Keshavarzi A, Taghizadeh H, Razavi ZS, Mottaghi R, Abolhassan M, Movahedpour A, Mirzaei H. Autophagy regulation by microRNAs: Novel insights into osteosarcoma therapy. IUBMB Life 2020; 72:1306-1321. [PMID: 32233112 DOI: 10.1002/iub.2277] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 03/04/2020] [Accepted: 03/14/2020] [Indexed: 12/16/2022]
Abstract
Osteosarcoma (OS) is a kind of primary bone cancer that is considered as the leading cause of children death. Surgery and chemotherapy are considered as common treatment approaches for OS; the rate of survival for patients is almost 60-70%. Besides the used therapeutic approaches, it seems that there is a crucial need to launch new treatments for OS. In this regard, more understanding about cellular and molecular pathways involved in OS can contribute to recovery and develop new therapeutic platforms. Autophagy is a cellular machinery that digests and degrades dysfunctional proteins and organelles, so it can regulate the cell proliferation and survival. Most of the time, OS cells use autophagy to increase their survival and proliferation and to gain the ability to resist chemotherapy. Although, there are several controversial evidences on how OS cells use autophagy. A variety of cellular and molecular pathways, that is, microRNAs (miRNAs) can modulate autophagy. MiRNAs are some endogenous, approximately 22 nucleotide RNAs that have an important role in posttranscriptional regulation of mRNAs by targeting them. There are many evidences that the various miRNA expressions in OS cells are dysregulated, so it can propel a normal cell to cancerous one by influencing the cell survival, apoptosis, and autophagy, and eventually increased chemoresitance. Hence, miRNAs can be considered as new biomarkers for OS diagnosis, and according to the role of autophagy in OS progression, miRNAs can use inhibiting or promoting autophagy agents. The present review summarizes the effects of aberrant expression of miRNAs in OS diagnosis and treatment with focus on their roles in autophagy.
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Affiliation(s)
- Zeinab Jamali
- Cardiovascular Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mortaza Taheri-Anganeh
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Shabaninejad
- Department of Biological Sciences, Faculty of Nanotechnology, Tarbiat Modares University, Tehran, Iran.,Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Abdolkhalegh Keshavarzi
- Burn and Wound Healing Research Center, Surgical Department, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hajar Taghizadeh
- School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Reza Mottaghi
- Department of Oral and Maxillofacial Surgery, Kashan University of Medical Sciences, Kashan, Iran
| | - Mohammadreza Abolhassan
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
| | - Ahmad Movahedpour
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran.,Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
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Lee S, Jang H, Kim HY, Park HG. Three-way junction-induced isothermal amplification for nucleic acid detection. Biosens Bioelectron 2019; 147:111762. [PMID: 31654822 DOI: 10.1016/j.bios.2019.111762] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 09/27/2019] [Accepted: 10/03/2019] [Indexed: 02/04/2023]
Abstract
We, herein, describe a three-way junction (3WJ)-induced isothermal amplification (ThIsAmp) reaction for target nucleic acid detection. In this strategy, target nucleic acid induces the formation of 3WJ structure by associating a specially designed ThIsAmp template and ThIsAmp primer. Upon the formation of 3WJ structure, ThIsAmp primer is subjected to continuously repeated extension and nicking reaction by the combined activities of DNA polymerase and nicking endonuclease, consequently producing a large number of trigger strands. The trigger strands then initiate two separate but interconnected pathways by binding to either 3' overhang of ThIsAmp template within the 3WJ structure or free ThIsAmp template. As a consequence, a large number of final double-stranded DNA products are produced under an isothermal condition, which can be monitored in real-time by detecting the fluorescence intensity resulting from SYBR Green I staining. Based on this principle, we successfully detected target DNA down to 78.1 aM with excellent specificity. The sophisticated design principle employed in this work would provide great insight for the development of self-operative isothermal amplifying system enabling target nucleic acid detection.
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Affiliation(s)
- Seoyoung Lee
- Department of Chemical and Biomolecular Engineering (BK 21+ Program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 305-338, Republic of Korea
| | - Hyowon Jang
- Department of Chemical and Biomolecular Engineering (BK 21+ Program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 305-338, Republic of Korea
| | - Hyo Yong Kim
- Department of Chemical and Biomolecular Engineering (BK 21+ Program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 305-338, Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK 21+ Program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 305-338, Republic of Korea.
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Chan HN, Ho SL, He D, Li HW. Direct and sensitive detection of circulating miRNA in human serum by ligase-mediated amplification. Talanta 2019; 206:120217. [PMID: 31514897 DOI: 10.1016/j.talanta.2019.120217] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 07/13/2019] [Accepted: 07/31/2019] [Indexed: 12/18/2022]
Abstract
MicroRNAs (miRNA) involve in regulating different physiological processes whose dysregulation is associated with a wide range of diseases including cancers, diabetes and cardiovascular problems. Herein, we report a direct, sensitive and highly selective detection assay for circulating microRNA (miRNA). This detection strategy employs magnetic nanoparticles as the reaction platform which can not only allow online pre-concentration and selective separation but also integrates ligation reaction with amplification to enhance the sensitivity of the detection assay. With the presence of the target miRNA, the locked nucleic acid (LNA)-modified molecular beacon (MB) opens up, exposing the binding sites at two ends. The 3'- and 5'-end of the MB responsible for the attachment onto the magnetic nanoparticles, and reporting probe for the attachment of the pair of amplification probes respectively. The ligase ligate RNA to DNA enhance the amplification efficiency. Upon labelled with intercalating fluorophores (YOYO-1) on the hybrids, the quantification of the target miRNA was determined by measuring the fluorescence intensity. A detection limit of 314 fM was achieved with trace amount of sample consumption (~20 μL). As a proof of concept, miRNA-149 was chosen as the target miRNA. This assay is capable of discriminating single-base and reliably quantifying circulating miRNA-149 in both healthy and cancer patient's serums. The result obtained was comparable with that of quantitative reverse transcription polymerase chain reaction (qRT-PCR), suggesting that this direct and sensitive assay can be served as a promising, non-invasive tool for early diagnosis of breast cancer and colorectal cancer.
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Affiliation(s)
- Hei-Nga Chan
- Department of Chemistry, Hong Kong Baptist University, Hong Kong, China
| | - See-Lok Ho
- Department of Chemistry, Hong Kong Baptist University, Hong Kong, China
| | - Dinggeng He
- Department of Chemistry, Hong Kong Baptist University, Hong Kong, China
| | - Hung-Wing Li
- Department of Chemistry, Hong Kong Baptist University, Hong Kong, China.
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18
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Synthesis of DNA-templated copper nanoparticles with enhanced fluorescence stability for cellular imaging. Mikrochim Acta 2019; 186:479. [PMID: 31250120 DOI: 10.1007/s00604-019-3620-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 06/15/2019] [Indexed: 12/14/2022]
Abstract
Fluorescence of DNA-templated copper nanoparticles (DNA-CuNPs) is not stable over time which limits applications in cellular imaging. This is due to the presence of oxygen during synthesis which oxidizes Cu(0) to Cu(II) and also produces the free hydroxyl radical. The authors have prepared DNA-CuNPs with enhanced temporal stability of fluorescence by optimizing the reaction conditions so as to minimize the deleterious effects of oxygen. The operational lifetime of DNA-CuNPs was increased from 25 min to 200 min. Fluorescence spectra of DNA-CuNPs in optimized condition show an emission peak at 650 nm when excited at 340 nm. DNA-CuNPs synthesized in this manner were used for cell imaging. As a proof of concept, the nucleus of a human colon cell line (HCT116) was stained. The method does not involve any chemicals other that copper sulfate and ascorbate. This new approach for generating DNA-CuNPs improves imaging of biological processes and provides a basis for developing other types of DNA-templated nanomaterials. Graphical abstract Schematic presentation of the formation of fluorescent DNA-templated copper nanoparticles (DNA-CuNPs). A large amount of ascorbate provides long operational lifetime for cellular imaging under the condition exposed to oxygen. *Asc- and **DHA stand for ascorbate and dehydroascorbic acid.
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Ye J, Xu M, Tian X, Cai S, Zeng S. Research advances in the detection of miRNA. J Pharm Anal 2019; 9:217-226. [PMID: 31452959 PMCID: PMC6702429 DOI: 10.1016/j.jpha.2019.05.004] [Citation(s) in RCA: 184] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 05/10/2019] [Accepted: 05/22/2019] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) are a family of endogenous, small (approximately 22 nucleotides in length), noncoding, functional RNAs. With the development of molecular biology, the research of miRNA biological function has attracted significant interest, as abnormal miRNA expression is identified to contribute to serious human diseases such as cancers. Traditional methods for miRNA detection do not meet current demands. In particular, nanomaterial-based methods, nucleic acid amplification-based methods such as rolling circle amplification (RCA), loop-mediated isothermal amplification (LAMP), strand-displacement amplification (SDA) and some enzyme-free amplifications have been employed widely for the highly sensitive detection of miRNA. MiRNA functional research and clinical diagnostics have been accelerated by these new techniques. Herein, we summarize and discuss the recent progress in the development of miRNA detection methods and new applications. This review will provide guidelines for the development of follow-up miRNA detection methods with high sensitivity and specificity, and applicability to disease diagnosis and therapy.
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Affiliation(s)
- Jiawei Ye
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Mingcheng Xu
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xueke Tian
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Sheng Cai
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Zhejiang University, Hangzhou, Zhejiang 310058, China
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Sensitive detection of DNA from Chlamydia trachomatis by using flap endonuclease-assisted amplification and graphene oxide-based fluorescence signaling. Mikrochim Acta 2019; 186:330. [DOI: 10.1007/s00604-019-3453-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 04/15/2019] [Indexed: 10/26/2022]
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21
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Qian C, Wang R, Wu H, Ji F, Wu J. Nicking enzyme-assisted amplification (NEAA) technology and its applications: A review. Anal Chim Acta 2019; 1050:1-15. [DOI: 10.1016/j.aca.2018.10.054] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 10/22/2018] [Accepted: 10/23/2018] [Indexed: 01/13/2023]
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22
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Jang H, Lee CY, Lee S, Park KS, Park HG. Flap endonuclease-initiated enzymatic repairing amplification for ultrasensitive detection of target nucleic acids. NANOSCALE 2019; 11:3633-3638. [PMID: 30741288 DOI: 10.1039/c8nr06699j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A new isothermal nucleic acid amplification method termed FERA (Flap endonuclease-initiated Enzymatic Repairing Amplification) is developed for the ultrasensitive detection of target nucleic acids. In the FERA method, flap endonuclease (FEN) catalyzes the hydrolytic cleavage at the junction of single- and double-stranded DNAs which is formed only in the presence of target nucleic acids, and releases short oligonucleotides to promote the cyclic enzymatic repairing amplification (ERA) combined with FEN-based amplification. As a result, a large amount of single- and double-stranded DNAs are generated under the isothermal conditions, leading to the high fluorescence intensity from the SYBR I green dye. Relying on the powerful amplification method, we successfully determined the target nucleic acids with a limit of detection as low as 15.16 aM, which corresponds to approximately 180 molecules in 20 μL reaction volume, and verified the practical applicability by detecting long target nucleic acids derived from Chlamydia trachomatis.
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Affiliation(s)
- Hyowon Jang
- Department of Chemical and Biomolecular Engineering (BK 21+ program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon 305-701, Republic of Korea.
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Wang J, Zhang L, Lu L, Kang T. Molecular beacon immobilized on graphene oxide for enzyme-free signal amplification in electrochemiluminescent determination of microRNA. Mikrochim Acta 2019; 186:142. [PMID: 30707306 DOI: 10.1007/s00604-019-3252-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 01/13/2019] [Indexed: 01/01/2023]
Abstract
An electrochemiluminescence (ECL) based biosensor is described for determination of microRNAs in the A549 cell line. Firstly, graphene oxide (GO) is dripped onto a glassy carbon electrode surface to form an interface to which one end of the capture probe (with a stem-loop structure) can be anchored through π-interaction via dangling unpaired bases. The other end of the capture probe is directed away from the GO surface to make it stand upright. Target microRNAs can open the hairpin structure to form a double-stranded DNA-RNA structure. Two auxiliary probes, generating a hybridization chain reaction, are used to elongate the DNA duplex. Finally, doxorubicin-modified cadmium telluride quantum dot nanoparticles (Dox-CdTe QD) are intercalated into the base pairs of the hybrid duplexes to act as signalling molecules. The ECL signal of the Dox-CdTe QD increases proportionally with the concentration of microRNAs, specifically for microRNA-21. The assay covers a wide linear range (1 fM to 0.1 nM), has a low detection limit for microRNA-21 (1 fM), and is selective, reproducible, and stable. Graphical abstract An enzyme-free amplification electrochemiluminescent assay is described to quantitative detection of microRNA in the A549 cell line. Graphene oxide was used to immobilize capture probes obviating the special modification. Doxorubicin-modified cadmium telluride quantum dot nanoparticles are intercalated into the base pairs of the hybrid duplexes to act as signalling molecules.
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Affiliation(s)
- Jiaxing Wang
- Key Laboratory of Beijing on Regional Air Pollution Control, Beijing University of Technology, Beijing, 100124, China
| | - Linlin Zhang
- Key Laboratory of Beijing on Regional Air Pollution Control, Beijing University of Technology, Beijing, 100124, China
| | - Liping Lu
- Key Laboratory of Beijing on Regional Air Pollution Control, Beijing University of Technology, Beijing, 100124, China.
| | - Tianfang Kang
- Key Laboratory of Beijing on Regional Air Pollution Control, Beijing University of Technology, Beijing, 100124, China
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Cao Q, Li J, Wang E. Recent advances in the synthesis and application of copper nanomaterials based on various DNA scaffolds. Biosens Bioelectron 2019; 132:333-342. [PMID: 30897540 DOI: 10.1016/j.bios.2019.01.046] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 01/12/2019] [Accepted: 01/15/2019] [Indexed: 12/29/2022]
Abstract
Fluorescent copper nanomaterials (CuNMs), including copper nanoparticles (CuNPs) and copper nanoclusters (CuNCs), become more and more popular with the abundant raw materials and low cost. A wide range of applications has been explored due to their fascinating properties such as low toxicity, remarkable water solubility, facile synthesis, large Stokes shifts, and good biocompatibility. As a kind of genetic material, DNA exhibits its molecular recognition function and diversity. The marriage between CuNMs and DNA endows DNA-templated CuNMs (DNA-CuNMs) with unique properties such as fluorescence, electrochemiluminescence and catalytic features. In this review, we summarize the synthesis and recent applications of DNA-CuNMs. Fluorescent CuNMs can be grown on various DNA scaffolds with special sequence design. T base plays an important role in the formation of CuNMs on DNA templates. These fluorescent DNA-CuNMs hold great prospect in logic gate construction, staining and biosensing of DNAs and RNAs, ions, proteins and enzymes, small molecules and so on.
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Affiliation(s)
- Qiao Cao
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, PR China; University of the Chinese Academy of Sciences, Beijing 100049, PR China
| | - Jing Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, PR China; University of the Chinese Academy of Sciences, Beijing 100049, PR China.
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, PR China; University of the Chinese Academy of Sciences, Beijing 100049, PR China.
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Xu F, Luo L, Shi H, He X, Lei Y, Tang J, He D, Qiao Z, Wang K. Label-free and sensitive microRNA detection based on a target recycling amplification-integrated superlong poly(thymine)-hosted copper nanoparticle strategy. Anal Chim Acta 2018; 1010:54-61. [PMID: 29447671 DOI: 10.1016/j.aca.2018.01.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 01/07/2018] [Accepted: 01/15/2018] [Indexed: 11/17/2022]
Abstract
Poly(thymine)-hosted copper nanoparticles (poly T-CuNPs) have emerged as a promising label-free fluorophore for bioanalysis, but its application in RNA-related studies is still rarely explored. Herein, by utilizing duplex-specific nuclease (DSN) as a convertor to integrate target recycling mechanism into terminal deoxynucleotidyl transferase (TdT)-mediated superlong poly T-CuNPs platform, a specific and sensitive method for microRNA detection has been developed. In this strategy, a 3'-phosphorylated DNA probe can hybridize with target RNA and then be cut by DSN to produce 3'-hydroxylated fragments, which can be further tailed by TdT with superlong poly T for fluorescent CuNPs synthesis. As proof of concept, an analysis of let-7d was achieved with a good linear correlation between 20 and 1000 pM (R2 = 0.9965) and a detection limit of 20 pM. Moreover, both homologous and heterologous microRNAs were also effectively discriminated. This strategy might pave a brand-new way for designing label-free and sensitive microRNA assays.
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Affiliation(s)
- Fengzhou Xu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082, China
| | - Lan Luo
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082, China
| | - Hui Shi
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082, China.
| | - Xiaoxiao He
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082, China
| | - Yanli Lei
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082, China
| | - Jinlu Tang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082, China
| | - Dinggeng He
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082, China
| | - Zhenzhen Qiao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082, China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082, China.
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Lee JY, Ahn JK, Park KS, Park HG. An impedimetric determination of alkaline phosphatase activity based on the oxidation reaction mediated by Cu2+ bound to poly-thymine DNA. RSC Adv 2018; 8:11241-11246. [PMID: 35541507 PMCID: PMC9078965 DOI: 10.1039/c7ra13642k] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Accepted: 03/10/2018] [Indexed: 11/21/2022] Open
Abstract
A novel impedimetric assay for the accurate determination of alkaline phosphatase (ALP) activity is developed based on the Cu2+-mediated oxidation of ascorbic acid on a poly-thymine DNA-modified electrode.
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Affiliation(s)
- Joon Young Lee
- Department of Chemical and Biomolecular Engineering (BK 21+ Program)
- KAIST
- Daejeon 305-338
- Republic of Korea
| | - Jun Ki Ahn
- Department of Chemical and Biomolecular Engineering (BK 21+ Program)
- KAIST
- Daejeon 305-338
- Republic of Korea
| | - Ki Soo Park
- Department of Biological Engineering
- College of Engineering
- Konkuk University
- Seoul 05029
- Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK 21+ Program)
- KAIST
- Daejeon 305-338
- Republic of Korea
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27
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Park KW, Lee CY, Batule BS, Park KS, Park HG. Ultrasensitive DNA detection based on target-triggered rolling circle amplification and fluorescent poly(thymine)-templated copper nanoparticles. RSC Adv 2018; 8:1958-1962. [PMID: 35542615 PMCID: PMC9077274 DOI: 10.1039/c7ra11071e] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 12/26/2017] [Indexed: 11/21/2022] Open
Abstract
An ultrasensitive DNA detection method is developed based on target-triggered rolling circle amplification coupled with fluorescent poly(thymine)-templated copper nanoparticles.
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Affiliation(s)
- Kwan Woo Park
- Department of Chemical and Biomolecular Engineering (BK 21+ Program)
- KAIST
- Daejeon 34141
- Republic of Korea
| | - Chang Yeol Lee
- Department of Chemical and Biomolecular Engineering (BK 21+ Program)
- KAIST
- Daejeon 34141
- Republic of Korea
| | - Bhagwan S. Batule
- Department of Chemical and Biomolecular Engineering (BK 21+ Program)
- KAIST
- Daejeon 34141
- Republic of Korea
| | - Ki Soo Park
- Department of Biological Engineering
- College of Engineering
- Konkuk University
- Seoul 05029
- Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK 21+ Program)
- KAIST
- Daejeon 34141
- Republic of Korea
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28
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Zhang X, Jin Y, Li B. Copper nanocluster as a fluorescent indicator for label-free and sensitive detection of DNA hybridization assisted with a cascade isothermal exponential amplification reaction. NEW J CHEM 2018. [DOI: 10.1039/c7nj05130a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A copper nanocluster (CuNCs)-based fluorescence biosensing platform was developed for label-free DNA detection through a cascade isothermal exponential amplification reaction (EXPAR).
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Affiliation(s)
- Xingxing Zhang
- Key laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry & Chemical Engineering
- Shaanxi Normal University
- Xi’an 710062
- China
| | - Yan Jin
- Key laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry & Chemical Engineering
- Shaanxi Normal University
- Xi’an 710062
- China
| | - Baoxin Li
- Key laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry & Chemical Engineering
- Shaanxi Normal University
- Xi’an 710062
- China
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A rapid method for the detection of humic acid based on the poly(thymine)-templated copper nanoparticles. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2017.09.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Chen M, Xiang X, Wu K, He H, Chen H, Ma C. A Novel Detection Method of Human Serum Albumin Based on the Poly(Thymine)-Templated Copper Nanoparticles. SENSORS 2017; 17:s17112684. [PMID: 29160831 PMCID: PMC5712895 DOI: 10.3390/s17112684] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 11/13/2017] [Accepted: 11/14/2017] [Indexed: 12/19/2022]
Abstract
In this work, we developed a facile fluorescence method for quantitative detection of human serum albumin (HSA) based on the inhibition of poly(thymine) (poly T)-templated copper nanoparticles (CuNPs) in the presence of HSA. Under normal circumstances, poly T-templated CuNPs can display strong fluorescence with excitation/emission peaks at 340/610 nm. However, in the presence of HSA, it will absorb cupric ion, which will prevent the formation of CuNPs. As a result, the fluorescence intensity will become obviously lower in the presence of HSA. The analyte HSA concentration had a proportional linear relationship with the fluorescence intensity of CuNPs. The detection limit for HSA was 8.2 × 10−8 mol·L−1. Furthermore, it was also successfully employed to determine HSA in biological samples. Thus, this method has potential applications in point-of-care medical diagnosis and biomedical research.
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Affiliation(s)
- Mingjian Chen
- School of Life Sciences, Central South University, Changsha 410013, China.
| | - Xinying Xiang
- School of Life Sciences, Central South University, Changsha 410013, China.
| | - Kefeng Wu
- School of Life Sciences, Central South University, Changsha 410013, China.
| | - Hailun He
- School of Life Sciences, Central South University, Changsha 410013, China.
| | - Hanchun Chen
- School of Life Sciences, Central South University, Changsha 410013, China.
| | - Changbei Ma
- School of Life Sciences, Central South University, Changsha 410013, China.
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He Y, Yang X, Yuan R, Chai Y. Switchable Target-Responsive 3D DNA Hydrogels As a Signal Amplification Strategy Combining with SERS Technique for Ultrasensitive Detection of miRNA 155. Anal Chem 2017; 89:8538-8544. [DOI: 10.1021/acs.analchem.7b02321] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Yi He
- Key Laboratory
of Luminescent and Real-Time Analytical Chemistry, Ministry of Education,
College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Xia Yang
- Key Laboratory
of Luminescent and Real-Time Analytical Chemistry, Ministry of Education,
College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ruo Yuan
- Key Laboratory
of Luminescent and Real-Time Analytical Chemistry, Ministry of Education,
College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Yaqin Chai
- Key Laboratory
of Luminescent and Real-Time Analytical Chemistry, Ministry of Education,
College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
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A turn-on fluorescent method for determination of the activity of alkaline phosphatase based on dsDNA-templated copper nanoparticles and exonuclease based amplification. Mikrochim Acta 2017. [DOI: 10.1007/s00604-017-2256-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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