101
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Xu J, Shi M, Huang H, Hu K, Chen W, Huang Y, Zhao S. A fluorescent aptasensor based on single oligonucleotide-mediated isothermal quadratic amplification and graphene oxide fluorescence quenching for ultrasensitive protein detection. Analyst 2019; 143:3918-3925. [PMID: 30043777 DOI: 10.1039/c8an01032c] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In this work, we have developed a novel fluorescent aptasensor based on single oligonucleotide-mediated isothermal quadratic amplification (SOIQA) and graphene oxide (GO)-mediated fluorescence quenching for the ultrasensitive detection of proteins in a homogeneous solution. The SOIQA consists of a fluorophore-labeled aptamer hairpin probe containing T7 exonuclease (T7 Exo)-resistant 5'-protruding termini and a mismatch base at its 3'-end, DNA polymerase, T7 Exo and GO. The target analyte binds with the aptamer sequences and unfolds the fluorophore-labeled aptamer hairpin probe to form a new DNA hairpin, inducing the catalytic recycling of the target analyte (assisted by DNA polymerase) and DNA sequences (aided by T7 Exo) to achieve SOIQA, which results in the digestion of numerous fluorophore-labeled aptamer hairpin probes and the generation of a large amount of mononucleotides carrying the fluorophore. These mononucleotide products cannot be adsorbed onto the GO, leading to a dramatic increase in the fluorescence intensity for the amplified detection of the target molecules. In the absence of the target analyte, however, the SOIQA reaction is inhibited and the fluorophore-labeled aptamer hairpin probe is adsorbed onto the GO, leading to an extremely low fluorescence background signal. To test the feasibility of the SOIQA systems, a protein cancer marker, carcinoembryonic antigen (CEA) was used as the model analyte. The developed aptasensor could detect CEA with a detection limit of 28.5 fg mL-1 (∼142 aM), high specificity and a broad detection range of 6 orders of magnitude. And this one-step incubation can be completed in 60 min. In addition, the approach uses only one oligonucleotide strand, and is simple. Moreover, this SOIQA sensing method is suitable for rapid and direct quantification of proteins in complex biological samples such as clinical serum. Considering the simplicity and superior sensitivity/specificity, the developed sensing method provides a promising platform for the analysis of a variety of low-abundance biomolecules.
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Affiliation(s)
- Jiayao Xu
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, College of Chemistry and Pharmacy, Guangxi Normal University, Yucai Road 15, Guilin, 541004, P. R. China
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102
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Guk K, Hwang SG, Lim J, Son HY, Choi Y, Huh YM, Kang T, Jung J, Lim EK. Fluorescence amplified sensing platforms enabling miRNA detection by self-circulation of a molecular beacon circuit. Chem Commun (Camb) 2019; 55:3457-3460. [PMID: 30735212 DOI: 10.1039/c9cc00351g] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We have proposed a novel strategy for miRNA detection through enzyme-free signal amplification by self-circulation of the hybridization between the miRNAs and molecular beacon (MB) circuits. Unlike general MB-based miRNA detection based on the one-to-one (1 : 1) hybridization between MBs and miRNA, our system consists of four species of MBs (MBs A, B, C and D) (MB circuits) and is activated by a hybridization chain reaction. MBs stably coexist as hairpin structures that hardly show fluorescence signals in the absence of target miRNA. After miRNA detection, this MB circuit is able to generate fluorescence signals and amplify the fluorescence signal, contributing to improvement in detection sensitivity under iso-thermal conditions without an enzyme. Furthermore, in vitro and in vivo studies have proven that MB circuits can detect low levels of miRNA with high sensitivity, compared to when only one MB alone is used. Therefore, the MB circuits can provide a useful platform for target miRNA detection.
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Affiliation(s)
- Kyeonghye Guk
- BioNano Technology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
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103
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Li H, Tang Y, Zhao W, Wu Z, Wang S, Yu R. Palindromic molecular beacon-based intramolecular strand-displacement amplification strategy for ultrasensitive detection of K-ras gene. Anal Chim Acta 2019; 1065:98-106. [PMID: 31005156 DOI: 10.1016/j.aca.2019.02.059] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 01/11/2019] [Accepted: 02/27/2019] [Indexed: 10/27/2022]
Abstract
The sensitive detection of tumor proto-oncogenes is indispensable because the early diagnosis and accurate treatment of genetic diseases is the key guarantee of patients' health. In this study, we proposed a novel palindromic molecular beacon (PMB) that it bases on the signal amplification strategy for ultrasensitive detection of Kras gene codon 12. PMB is designed to have two palindromic fragments at its two ends, one of which is locked via folding into a hairpin structure and the other promotes the formation of PMB duplex via intermolecular self-hybridization. Target DNA can hybridize to the loop portion of PMB and release the palindromic fragment at the 3' end. Within the PMB duplex, the two palindromic fragments released hybridize with each other and serve as polymerization primer responsible for the strand-displacement amplification (SDA). Namely, hybridized target DNA can be displaced and initiates the next round of reactions, making the polymerization/displacement/hybridization process go forward circularly. As a result, a large number of polymerization products are produced, dramatically enhancing optical signal. Because primer hybridization and polymerization-based displacement occur within PMB duplex, the reaction process is called intramolecular strand-displacement amplification (ISDA). Via utilizing the newly-proposed PMB-based ISDA strategy, the target K-ras gene could be detected down to 10 pM with a wide response range of 1 × 10-11-1.5 × 10-7 M, and point mutations are easily distinguished, realizing the ultrasensitive, highly selective detection of K-ras gene. This impressive sensing paradigm demonstrates a new concept of signal amplification for the detection of disease-related genes only via using a simple way to efficiently amplify optical signal.
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Affiliation(s)
- Hongbo Li
- Key Laboratory of Functional Small Organic Molecule, Ministry of Education, College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, PR China.
| | - Yongqiong Tang
- Key Laboratory of Functional Small Organic Molecule, Ministry of Education, College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, PR China; Cancer Metastasis Alert and Prevention Center, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, College of Chemistry, Fuzhou University, Fuzhou, 350002, PR China
| | - Weihua Zhao
- Key Laboratory of Functional Small Organic Molecule, Ministry of Education, College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, PR China
| | - Zaisheng Wu
- Cancer Metastasis Alert and Prevention Center, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, College of Chemistry, Fuzhou University, Fuzhou, 350002, PR China.
| | - Suqin Wang
- Key Laboratory of Functional Small Organic Molecule, Ministry of Education, College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, PR China.
| | - Ruqin Yu
- State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering Hunan University, Changsha, 410082, PR China
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104
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Oladepo SA, Yusuf BO. Simple protocol for sequence-specific detection of mixed-base nucleic acids using a smart probe with NABs. Anal Biochem 2019; 568:53-56. [PMID: 30610841 DOI: 10.1016/j.ab.2018.12.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 12/17/2018] [Accepted: 12/30/2018] [Indexed: 10/27/2022]
Abstract
A fluorescent smart probe (SP) was used to detect a mixed-base ribonucleic acids sequence. While the SP presents excellent sensitivity for the target, it gives subtle discrimination between the perfect target sequence and several mismatch sequences. Its sequence-specificity for the target was greatly enhanced by using nucleic acid blockers (NABs), which are unlabeled, non-fluorescent hairpin oligonucleotides that are perfectly complementary to those mismatch sequences. This approach is simple, feasible at room temperature, requires no amplification enzymes, and it is suitable for applications requiring routine nucleic acids sequence detection and quantification methods such as genetic testing and biomedical diagnostics.
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Affiliation(s)
- Sulayman A Oladepo
- Department of Chemistry, King Fahd University of Petroleum and Minerals, Dhahran, 31261, Saudi Arabia.
| | - Basiru O Yusuf
- Department of Chemistry, King Fahd University of Petroleum and Minerals, Dhahran, 31261, Saudi Arabia
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105
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Rolling circle extension-actuated loop-mediated isothermal amplification (RCA-LAMP) for ultrasensitive detection of microRNAs. Biosens Bioelectron 2019; 128:17-22. [DOI: 10.1016/j.bios.2018.12.041] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 12/10/2018] [Accepted: 12/17/2018] [Indexed: 01/01/2023]
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106
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Wang J, Zhang J, Li T, Shen R, Li G, Ling L. Strand displacement amplification-coupled dynamic light scattering method to detect urinary telomerase for non-invasive detection of bladder cancer. Biosens Bioelectron 2019; 131:143-148. [PMID: 30826649 DOI: 10.1016/j.bios.2019.02.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 01/29/2019] [Accepted: 02/01/2019] [Indexed: 11/28/2022]
Abstract
Despite huge successes achieved by strand displacement amplification (SDA) and gold nanoparticles (AuNPs) in biomolecules sensing, the strategy of combination of SDA and AuNPs-based dynamic light scattering (DLS) for a biomolecule sensing is unexplored. Here we developed a non-invasive, SDA-based DLS method for the diagnosis of bladder cancer by detecting telomerase activity in human urine. In the presence of telomerase, the telomerase substrate (TS) primer was elongated with repeating sequences of (TTAGGG)n, and the resulting product triggers SDA between the hairpin deoxyribonucleic acid (DNA) and the Primer. The SDA product can be recognized by the oligonucleotide-modified AuNPs probes, resulting in DLS measurable AuNPs aggregation. The assay displayed a detection limit of 3 MCF-7 cells with a signal-to-noise ratio of 3 in a dynamic range of 5-1000 cells. The method was simple, reliable and has been successfully applied in the detection of telomerase in urine with good accuracy, selectivity and reproducibility. Moreover, only urine samples from bladder cancer patients induced a significant change in the average hydrodynamic diameter, indicating practical applicability of the method for the non-invasive diagnosis of bladder cancer.
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Affiliation(s)
- Jing Wang
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Ji Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou 510060, PR China
| | - Tingting Li
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Ruidi Shen
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Gongke Li
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Liansheng Ling
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, PR China.
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107
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Zhang B, Zhang F, Zhang P, Shen D, Gao X, Zou G. Ultrasensitive Electrochemiluminescent Sensor for MicroRNA with Multinary Zn–Ag–In–S/ZnS Nanocrystals as Tags. Anal Chem 2019; 91:3754-3758. [DOI: 10.1021/acs.analchem.9b00199] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Bin Zhang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, P. R. China
| | - Fang Zhang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, P. R. China
| | - Ping Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, P. R. China
| | - Dazhong Shen
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, P. R. China
| | - Xuwen Gao
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, P. R. China
| | - Guizheng Zou
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, P. R. China
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108
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Chang J, Wang X, Wang J, Li H, Li F. Nucleic Acid-Functionalized Metal–Organic Framework-Based Homogeneous Electrochemical Biosensor for Simultaneous Detection of Multiple Tumor Biomarkers. Anal Chem 2019; 91:3604-3610. [DOI: 10.1021/acs.analchem.8b05599] [Citation(s) in RCA: 259] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Jiafu Chang
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, People’s Republic of China
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, People’s Republic of China
| | - Xin Wang
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, People’s Republic of China
| | - Jiao Wang
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, People’s Republic of China
| | - Haiyin Li
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, People’s Republic of China
| | - Feng Li
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, People’s Republic of China
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, People’s Republic of China
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109
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Wu L, Pan M, Chen Y, Huang H, Zhang X, Wang F, Zhou X. The construction of DNAzyme-based logic gates for amplified microRNA detection and cancer recognition. Analyst 2019; 144:7278-7282. [DOI: 10.1039/c9an01977d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A series of duplex-specific nuclease-based DNAzyme logic gates was established for detecting multiple low-abundance microRNAs.
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Affiliation(s)
- Lingyu Wu
- College of Chemistry and Molecular Sciences
- Key Laboratory of Biomedical Polymers of Ministry of Education
- Wuhan University
- Wuhan
- P. R. China
| | - Min Pan
- College of Chemistry and Molecular Sciences
- Key Laboratory of Biomedical Polymers of Ministry of Education
- Wuhan University
- Wuhan
- P. R. China
| | - Yuqi Chen
- College of Chemistry and Molecular Sciences
- Key Laboratory of Biomedical Polymers of Ministry of Education
- Wuhan University
- Wuhan
- P. R. China
| | - Haiyan Huang
- College of Chemistry and Molecular Sciences
- Key Laboratory of Biomedical Polymers of Ministry of Education
- Wuhan University
- Wuhan
- P. R. China
| | - Xiaoe Zhang
- College of Chemistry and Molecular Sciences
- Key Laboratory of Biomedical Polymers of Ministry of Education
- Wuhan University
- Wuhan
- P. R. China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences
- Key Laboratory of Biomedical Polymers of Ministry of Education
- Wuhan University
- Wuhan
- P. R. China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences
- Key Laboratory of Biomedical Polymers of Ministry of Education
- Wuhan University
- Wuhan
- P. R. China
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110
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Zhou D, Lin X, Gao W, Piao J, Li S, He N, Qian Z, Zhao M, Gong X. A novel template repairing-PCR (TR-PCR) reaction platform for microRNA detection using translesional synthesis on DNA templates containing abasic sites. Chem Commun (Camb) 2019; 55:2932-2935. [DOI: 10.1039/c8cc10226k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report template repairing-PCR, a novel reverse transcription-free RNA PCR based on miRNA-primed bypass synthesis at the abasic sites on the PCR template.
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Affiliation(s)
- Dianming Zhou
- Department of Toxicology
- Tianjin Centers for Disease Control and Prevention
- Tianjin 300011
- China
| | - Xiaohui Lin
- Department of Toxicology
- Tianjin Centers for Disease Control and Prevention
- Tianjin 300011
- China
| | - Weichen Gao
- School of Life Sciences
- Tianjin University and Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology
- Tianjin 300072
- China
| | - Jiafang Piao
- School of Life Sciences
- Tianjin University and Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology
- Tianjin 300072
- China
| | - Shufei Li
- Department of Toxicology
- Tianjin Centers for Disease Control and Prevention
- Tianjin 300011
- China
| | - Ning He
- Department of Toxicology
- Tianjin Centers for Disease Control and Prevention
- Tianjin 300011
- China
| | - Zhiyong Qian
- Department of Toxicology
- Tianjin Centers for Disease Control and Prevention
- Tianjin 300011
- China
| | - Miao Zhao
- Department of Toxicology
- Tianjin Centers for Disease Control and Prevention
- Tianjin 300011
- China
| | - Xiaoqun Gong
- School of Life Sciences
- Tianjin University and Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology
- Tianjin 300072
- China
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111
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Li L, Lu M, Fan Y, Shui L, Xie S, Sheng R, Si H, Li Q, Wang Y, Tang B. High-throughput and ultra-sensitive single-cell profiling of multiple microRNAs and identification of human cancer. Chem Commun (Camb) 2019; 55:10404-10407. [DOI: 10.1039/c9cc05553c] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We established an efficient method for single-cell multiple miRNA analysis by droplet microfluidics with high sensitivity and high throughput.
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112
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Liu C, An Y, Zhang Y, Li X, Xue Q, Wang H. Digital quantitative detection of serum circulating miRNAs using dual-enhanced magnetobiosensors based on cascaded nucleic acid circuits. Chem Commun (Camb) 2019; 55:13733-13736. [DOI: 10.1039/c9cc07841j] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Here, we developed a dual-enhanced magnetobiosensor based on cascaded nucleic acid circuits for sensitive, portable and digital quantitative detection of circulating miRNAs in serum by a personal glucose meter (PGM).
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Affiliation(s)
- Chunxue Liu
- Department of Chemistry
- Liaocheng University
- Liaocheng
- China
| | - Yayun An
- Department of Chemistry
- Liaocheng University
- Liaocheng
- China
| | - Yuanfu Zhang
- Department of Chemistry
- Liaocheng University
- Liaocheng
- China
| | - Xia Li
- Department of Chemistry
- Liaocheng University
- Liaocheng
- China
| | - Qingwang Xue
- Department of Chemistry
- Liaocheng University
- Liaocheng
- China
| | - Huaisheng Wang
- Department of Chemistry
- Liaocheng University
- Liaocheng
- China
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113
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Liu Q, Kang PJ, Chen ZP, Shi CX, Chen Y, Yu RQ. Highly specific and sensitive detection of microRNAs by tandem signal amplification based on duplex-specific nuclease and strand displacement. Chem Commun (Camb) 2019; 55:14210-14213. [DOI: 10.1039/c9cc06790f] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A platform for microRNA detection was developed based on understanding the hydrolysis patterns of duplex-specific nuclease against probe DNAs.
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Affiliation(s)
- Qing Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
- China
| | - Peng-Jian Kang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
- China
| | - Zeng-Ping Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
- China
| | - Cai-Xia Shi
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
- China
| | - Yao Chen
- Hunan Key Lab of Biomedical Materials and Devices
- College of Life Sciences and Chemistry
- Hunan University of Technology
- Zhuzhou
- P. R. China
| | - Ru-Qin Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
- China
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114
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Qi Y, Lu X, Feng Q, Fan W, Liu C, Li Z. An Enzyme-Free MicroRNA Assay Based On Fluorescence Counting of Click Chemical Ligation-Illuminated Magnetic Nanoparticles with Total Internal Reflection Fluorescence Microscopy. ACS Sens 2018; 3:2667-2674. [PMID: 30456947 DOI: 10.1021/acssensors.8b01169] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
MicroRNAs (miRNAs) have been considered as promising cancer biomarkers. However, the simple but sensitive detection of low levels of miRNAs in biological samples still remains challenging. Herein, we wish to report an entirely enzyme-free, simple, and highly sensitive miRNA assay based on the counting of cycling click chemical ligation (3CL)-illuminated fluorescent magnetic nanoparticles (MNPs) with a total internal reflection fluorescence microscopy (TIRFM). In this strategy, each miRNA molecule can trigger many cycles of click chemical ligation reactions to produce plentiful ligated oligonucleotides (ODNs) with both 5'-biotin and 3'-fluorophore, resulting in efficient signal amplification. It is worth noting that only the ligated ODNs can bring fluorophores onto streptavidin-functionalized MNPs (STV-MNPs). Notably, merely 10 fluorescent molecules on each 50 nm MNP can make it bright enough to be clearly visualized by the TIRFM, which can significantly improve the detection sensitivity for miRNA. Through fluorescence counting of individual MNPs and integrating their fluorescence intensities, the amount of target miRNA can be quantitatively determined. This miRNA assay can be accomplished in a mix-and-read manner just by simply mixing the enzyme-free 3CL reaction system with the MNPs before TIRFM imaging, which avoids tedious immobilization, washing, and purification steps. Despite the extremely simple operation, this strategy exhibits high sensitivity with a quite low detection limit of 50 fM target miRNA as well as high specificity to well discriminate miRNA sequences with a single-base variation. Furthermore, the applicability of this method in real biological samples is also verified through the accurate detection of the miRNA target in cancer cells.
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Affiliation(s)
- 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, Shaanxi Province 710119, P. R. China
| | - Xiaohui Lu
- 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, Shaanxi Province 710119, P. R. China
| | - Qinya Feng
- 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, Shaanxi Province 710119, P. R. China
| | - 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, Shaanxi Province 710119, P. R. 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, Shaanxi Province 710119, P. R. 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, Shaanxi Province 710119, P. R. China
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115
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A novel photosensitive dual-sensor for simultaneous detection of nucleic acids and small chemical molecules. Biosens Bioelectron 2018; 127:108-117. [PMID: 30594890 DOI: 10.1016/j.bios.2018.12.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 12/03/2018] [Accepted: 12/07/2018] [Indexed: 02/05/2023]
Abstract
Sensors that can rapidly and specifically detect nucleic acids and chemical molecules can revolutionize the diagnosis and treatment of diseases by allowing molecular-level informations to be used during the routine medicines. In this study, we demonstrated a novel dual-sensor that can be used to simultaneously detect any nucleic acids and chemical molecules whose binding aptamers can be found or synthesized. In the developed dual-sensor, the specifically designed PTG (a photosensitive azobenzene derivative carrying one photoisomerizable azobenzene moiety, one threoninol terminal and one guanidinium terminal) molecules are introduced into the unwinding region of two T7 promoters, and two DNA bubbles are introduced upstream of the two T7 promoters. Without the target, the indicating gene in the dual-tensor would not be expressed since the binding with RNAPs (RNA polymerases) cannot melt the T7 promoter for the indicating gene due to the integration of the DNA double strands via the PTG molecules, manifesting the absence of the target nucleic acid and chemical molecule. While with the presence of the target nucleic acid and/or chemical molecule, the indicating gene would be expressed as the T7 promoter contained in the enlarged DNA bubble can be melted and transcribed by the bound RNAPs as the enlarged DNA bubble can help the separation of the two DNA strands, demonstrating the existence of target nucleic acid and/or chemical molecule.
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116
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Lu W, Wang Y, Song S, Chen C, Yao B, Wang M. A fishhook probe-based rolling circle amplification (FP-RCA) assay for efficient isolation and detection of microRNA without total RNA extraction. Analyst 2018; 143:5046-5053. [PMID: 30238116 DOI: 10.1039/c8an01544a] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
MicroRNA (miRNA) analysis has vital significance as a potential biomarker in clinical diagnosis and cancer research. In this study, a simple and practical technique was proposed for the detection of microRNAs from cell lysates based on fishhook probe-mediated rolling circle amplification (RCA) and fluorescence imaging with a smartphone. Compared with reported methods related to miRNA detection, this method mainly focused on simplicity, low cost and portability. Fishhook probes were designed and immobilized on the surface of streptavidin-coated magnetic beads for effectively recognizing and capturing target miRNAs, thus achieving simple and selective separation from the sample matrix. Moreover, the captured miRNAs initiated and transferred RCA reaction into solution, thus making the heterogeneous separation and homogeneous amplification reactions compatible. Excess circular probes as well as other nucleic acids were removed by two-step magnetic separation, minimizing nonspecific amplification and background signal. Using magnetic separation, high specificity was obtained even for one base mismatch strand. Moreover, the detection of miR-21 in cell lysates was performed without total RNA extraction. The fishhook probe-based rolling circle amplification (FP-RCA) assay integrated isolation and detection of miRNAs into a compact process, which was simple and effective without the need for bulky and expensive equipment such as centrifuge, thermal cycler and fluorescent microscope except for a blue light source device and a smartphone camera. Our study may provide a low-cost and reliable platform for miRNA detection and related research.
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Affiliation(s)
- Wei Lu
- Department of Chemistry, Zhejiang University, Hangzhou 310058, China.
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Yang J, Wang YQ, Li MY, Ying YL, Long YT. Direct Sensing of Single Native RNA with a Single-Biomolecule Interface of Aerolysin Nanopore. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14940-14945. [PMID: 30462509 DOI: 10.1021/acs.langmuir.8b03264] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
RNA sensing is of vital significance to advance our comprehension of gene expression and to further benefit medical diagnostics. Taking advantage of the excellent sensing capability of the aerolysin nanopore as a single-biomolecule interface, we for the first time achieved the direct characterization of single native RNA of Poly(A)4 and Poly(U)4. Poly(A)4 induces ∼10% larger blockade current amplitude than Poly(U)4. The statistical duration of Poly(A)4 is 18.83 ± 1.08 ms, which is 100 times longer than that of Poly(U)4. Our results demonstrated that the capture of RNA homopolymers is restricted by the biased diffusion. The translocation of RNA needs to overcome a lower free-energy barrier than that of DNA. Moreover, the strong RNA-aerolysin interaction is attributed to the hydroxyl in pentose, which prolongs the translocation time. This study opens an avenue for aerolysin nanopores to directly achieve RNA sensing, including discrimination of RNA epigenetic modification and selective detection of miRNA.
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Affiliation(s)
- Jie Yang
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai 200237 , P. R. China
| | - Ya-Qian Wang
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai 200237 , P. R. China
| | - Meng-Yin Li
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai 200237 , P. R. China
| | - Yi-Lun Ying
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai 200237 , P. R. China
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai 200237 , P. R. China
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118
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Fan TW, Hsing IM. Kinetically modulated specificity against single-base mutants in nucleic acid recycling circuitry using the destabilization motif. Analyst 2018; 142:2786-2795. [PMID: 28671226 DOI: 10.1039/c6an02731h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Signal amplification in nucleic acid sensing improves detection sensitivity, but difficulties remain in sustaining specificity over time, particularly under excess amounts of single-base mutants. Here, we report simple, self-refining target recycling circuitry, which cumulates differentiation between on and off targets by 2-step cyclic interaction with the sensing probe. In the reaction, the analyte recycles only if the protective strand of the sensing probe is removed. The dissociation kinetics of such interaction was modulated by reacting it with different lengths of assistant strands. When shorter assistant strands are used, the destabilization motif of the sensing probe has to spontaneously dissociate before another assistant strand approaches and fully displaces it. This sets up a high kinetic barrier sensitive to the subtle reaction energy differences imposed by the single-base mutants, and substantially improved specificity. As a proof of concept, a microRNA 21 DNA analogue was chosen as our target analyte together with its 14 point mutants (substitution, insertion, or deletion) for specificity measurements. The experimental results corroborate that our system amplifies signals in a comparable manner to the traditional one-layer recycling approach but with negligible system leakage. With the use of shortened assistant strands, up to 100 fold increase in the discrimination factor against the single-base mutants is observed. Specificity is sustainable or even increased over long period measurements (i.e. 4 days). More importantly, target differentiation is successfully demonstrated even in excess amounts of spurious analogs (100×) and low target frequency mixtures (i.e. 0.1%), which mimic the lean conditions practically encountered. Explicit mechanisms of the system specificity are elucidated through analytical calculations and free energy level diagrams. The modularity of the destabilization motif herein promises detection of different nucleic acid based targets and integration into other signal amplification approaches for specificity enhancement.
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Affiliation(s)
- Tsz Wing Fan
- Department of Chemical and Biomolecular Engineering, Clear Water Bay, Kowloon, Hong Kong.
| | - I-Ming Hsing
- Department of Chemical and Biomolecular Engineering, Clear Water Bay, Kowloon, Hong Kong. and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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119
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Qin Y, Liao S, Huang Y, Zhao J, Zhao S. Ultrasensitive fluorescent detection of nucleic acids based on label-free enzymatic-assisted cascade signal amplification. Anal Chim Acta 2018; 1039:91-97. [DOI: 10.1016/j.aca.2018.07.038] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 07/01/2018] [Accepted: 07/17/2018] [Indexed: 01/21/2023]
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120
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Mintz RL, Gao MA, Lo K, Lao YH, Li M, Leong KW. CRISPR Technology for Breast Cancer: Diagnostics, Modeling, and Therapy. ADVANCED BIOSYSTEMS 2018; 2:1800132. [PMID: 32832592 PMCID: PMC7437870 DOI: 10.1002/adbi.201800132] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Indexed: 12/17/2022]
Abstract
Molecularly, breast cancer represents a highly heterogenous family of neoplastic disorders, with substantial interpatient variations regarding genetic mutations, cell composition, transcriptional profiles, and treatment response. Consequently, there is an increasing demand for alternative diagnostic approaches aimed at the molecular annotation of the disease on a patient-by-patient basis and the design of more personalized treatments. The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) technology enables the development of such novel approaches. For instance, in diagnostics, the use of the RNA-specific C2c2 system allows ultrasensitive nucleic acid detection and could be used to characterize the mutational repertoire and transcriptional breast cancer signatures. In disease modeling, CRISPR/Cas9 technology can be applied to selectively engineer oncogenes and tumor-suppressor genes involved in disease pathogenesis. In treatment, CRISPR/Cas9 can be used to develop gene-therapy, while its catalytically-dead variant (dCas9) can be applied to reprogram the epigenetic landscape of malignant cells. As immunotherapy becomes increasingly prominent in cancer treatment, CRISPR/Cas9 can engineer the immune cells to redirect them against cancer cells and potentiate antitumor immune responses. In this review, CRISPR strategies for the advancement of breast cancer diagnostics, modeling, and treatment are highlighted, culminating in a perspective on developing a precision medicine-based approach against breast cancer.
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Affiliation(s)
- Rachel L. Mintz
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Madeleine A. Gao
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Kahmun Lo
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Yeh-Hsing Lao
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Mingqiang Li
- Guangdong Provincial Key Laboratory of Liver Disease The Third Affiliated Hospital of Sun Yat-Sen University Guangzhou, Guangdong 510630, China
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Kam W. Leong
- Department of Systems Biology, Columbia University Medical Center, New York, NY 10032, USA
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
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121
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Xiao M, Chandrasekaran AR, Ji W, Li F, Man T, Zhu C, Shen X, Pei H, Li Q, Li L. Affinity-Modulated Molecular Beacons on MoS 2 Nanosheets for MicroRNA Detection. ACS APPLIED MATERIALS & INTERFACES 2018; 10:35794-35800. [PMID: 30277380 DOI: 10.1021/acsami.8b14035] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
DNA-functionalized layered two-dimensional transition-metal dichalcogenides have attracted tremendous interest for constructing biosensors in recent years. In this work, we report diblock molecular beacons with poly-cytosine (polyC) tails anchored on molybdenum disulfide (MoS2) nanosheets as probes for microRNA detection. The polyC block is adsorbed on MoS2 and the molecular beacon block is available for hybridization to the target; duplex-specific nuclease provides signal amplification by target recycling. By changing the length of polyC, we regulate the density of probes on MoS2 and inhibit the adsorption of enzyme-cleaved oligonucleotides, thereby leading to higher quenching efficiency. PolyC-mediated molecular beacons on MoS2 have very low background signal, ultrahigh sensitivity (limit of detection ∼3.4 fM), specificity to detect a single nucleotide mismatch, and selectivity to detect target microRNA from serum samples. This detection platform holds great potential for quantitative analysis of miRNAs in clinical diagnosis and biomedical research.
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Affiliation(s)
- Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering , East China Normal University , 500 Dongchuan Road , Shanghai 200241 , P. R. China
| | - Arun Richard Chandrasekaran
- The RNA Institute, University at Albany , State University of New York , Albany , New York 12222 , United States
| | - Wei Ji
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering , East China Normal University , 500 Dongchuan Road , Shanghai 200241 , P. R. China
| | - Fan Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering , East China Normal University , 500 Dongchuan Road , Shanghai 200241 , P. R. China
| | - Tiantian Man
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering , East China Normal University , 500 Dongchuan Road , Shanghai 200241 , P. R. China
| | - Changfeng Zhu
- Department of Gastroenterology, Zhongshan Hospital , Fudan University , Shanghai 200032 , P. R. China
| | - Xizhong Shen
- Department of Gastroenterology, Zhongshan Hospital , Fudan University , Shanghai 200032 , P. R. China
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering , East China Normal University , 500 Dongchuan Road , Shanghai 200241 , P. R. China
| | - Qian Li
- School of Chemistry and Chemical Engineering , Shanghai Jiao Tong University , Shanghai 200240 , P. R. China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering , East China Normal University , 500 Dongchuan Road , Shanghai 200241 , P. R. China
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122
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Cheng L, Zhang Z, Zuo D, Zhu W, Zhang J, Zeng Q, Yang D, Li M, Zhao Y. Ultrasensitive Detection of Serum MicroRNA Using Branched DNA-Based SERS Platform Combining Simultaneous Detection of α-Fetoprotein for Early Diagnosis of Liver Cancer. ACS APPLIED MATERIALS & INTERFACES 2018; 10:34869-34877. [PMID: 30238748 DOI: 10.1021/acsami.8b10252] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We provided an ultrasensitive sensing strategy for microRNA detection by first employing branched DNA. With the aid of microcontact printing, we realized the multiplex sensing of different kinds of liver cancer biomarkers: microRNA and protein simultaneously. Delicately designed branched DNA included multiple complementary sticky ends as probe to microRNA capture and the double-stranded rigid branched core to increase the active sticky-ends distance and expose more DNA probes for sensitivity. The branched DNA enables 2 orders of magnitude increase in sensitivity for microRNA detection over single-stranded DNA. The limit of detection reaches as low as 10 attomolar (S/N = 3) for miR-223 and 10-12 M for α-fetoprotein. In addition, this system shows high selectivity and appropriate reproducibility (the relative standard deviation is less than 20%) in physiological media. Serum samples are tested and the results of α-fetoprotein are in good agreement with the current gold-standard method, electrochemiluminescence immunoassay analyzer. The results suggest the reliability of this approach in physiological media and show high potential in the sensing of low abundant microRNA in serum, especially for early diagnosis of primary liver cancers.
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Affiliation(s)
- Linxiu Cheng
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Institute of High Energy Physics , Chinese Academy of Sciences , 19B, Yuquan Road , Shijingshan District, Beijing 100049 , China
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology (NCNST) , Beijing 100190 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Zhikun Zhang
- School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering (Ministry of Education), Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) , Tianjin University , Tianjin 300072 , China
| | - Duo Zuo
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy , Tianjin's Clinical Research Center for Cancer , Tianjin 300060 , China
| | - Wenfeng Zhu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Institute of High Energy Physics , Chinese Academy of Sciences , 19B, Yuquan Road , Shijingshan District, Beijing 100049 , China
| | - Jie Zhang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Institute of High Energy Physics , Chinese Academy of Sciences , 19B, Yuquan Road , Shijingshan District, Beijing 100049 , China
- School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering (Ministry of Education), Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) , Tianjin University , Tianjin 300072 , China
| | - Qingdao Zeng
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology (NCNST) , Beijing 100190 , China
| | - Dayong Yang
- School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering (Ministry of Education), Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) , Tianjin University , Tianjin 300072 , China
| | - Min Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Institute of High Energy Physics , Chinese Academy of Sciences , 19B, Yuquan Road , Shijingshan District, Beijing 100049 , China
| | - Yuliang Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Institute of High Energy Physics , Chinese Academy of Sciences , 19B, Yuquan Road , Shijingshan District, Beijing 100049 , China
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology (NCNST) , Beijing 100190 , China
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123
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Ou X, Zhan S, Sun C, Cheng Y, Wang X, Liu B, Zhai T, Lou X, Xia F. Simultaneous detection of telomerase and miRNA with graphene oxide-based fluorescent aptasensor in living cells and tissue samples. Biosens Bioelectron 2018; 124-125:199-204. [PMID: 30388562 DOI: 10.1016/j.bios.2018.10.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 09/18/2018] [Accepted: 10/04/2018] [Indexed: 11/29/2022]
Abstract
Telomerase and microRNAs (miRNAs) as important biomarkers are closely related to cancers. Simultaneous detection of telomerase activity and miRNAs would be beneficial to improve the specificity and reliability. Here, we establish a telomerase and miRNA-21 (miR-21) simultaneous sensing platform with graphene oxide-based fluorescent aptasensors (GOFA) including graphene oxide (GO), template strand (TS) primer and fluorophore-labeled telomerase/miR-21 oligonucleotides. Owing to π-π stacking interaction, TS primer and telomerase/miR-21 probes would be loaded onto GO, resulting in fluorescence quenching. However, in the presence of the telomerase or miR-21, the double-stranded oligonucleotides would be away from the GO surface attribute to the hybridization between the extended TS primers and telomerase probe as well as miR-21 and miR-21 probe, leading to obvious fluorescence recovery. We found that GOFA could simultaneously detect telomerase activity and miR-21 with low background signal, high sensitivity and simplified operation. Moreover, GOFA could be used for accurately detecting telomerase activity and miRNA in living cells and cancer patient tissue sample. This sensing platform shows great potential in improving the accuracy in clinical diagnosis of cancer.
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Affiliation(s)
- Xiaowen Ou
- State Key Laboratory of Material Processing and Die & Mould Technology, School of Materials Science and Engineering, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, National Engineering Research Center for Nanomedicine, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, PR China
| | - Shenshan Zhan
- State Key Laboratory of Material Processing and Die & Mould Technology, School of Materials Science and Engineering, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, National Engineering Research Center for Nanomedicine, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, PR China
| | - Chunli Sun
- State Key Laboratory of Material Processing and Die & Mould Technology, School of Materials Science and Engineering, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, National Engineering Research Center for Nanomedicine, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, PR China
| | - Yong Cheng
- State Key Laboratory of Material Processing and Die & Mould Technology, School of Materials Science and Engineering, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, National Engineering Research Center for Nanomedicine, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, PR China.
| | - Xudong Wang
- State Key Laboratory of Material Processing and Die & Mould Technology, School of Materials Science and Engineering, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, National Engineering Research Center for Nanomedicine, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, PR China
| | - Bifeng Liu
- State Key Laboratory of Material Processing and Die & Mould Technology, School of Materials Science and Engineering, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, National Engineering Research Center for Nanomedicine, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, PR China
| | - Tianyou Zhai
- State Key Laboratory of Material Processing and Die & Mould Technology, School of Materials Science and Engineering, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, National Engineering Research Center for Nanomedicine, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, PR China
| | - Xiaoding Lou
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, PR China
| | - Fan Xia
- State Key Laboratory of Material Processing and Die & Mould Technology, School of Materials Science and Engineering, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, National Engineering Research Center for Nanomedicine, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, PR China; Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, PR China
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124
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Meng X, Zhang K, Dai W, Cao Y, Yang F, Dong H, Zhang X. Multiplex microRNA imaging in living cells using DNA-capped-Au assembled hydrogels. Chem Sci 2018; 9:7419-7425. [PMID: 30542546 PMCID: PMC6237120 DOI: 10.1039/c8sc02858c] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 08/06/2018] [Indexed: 12/14/2022] Open
Abstract
Non-invasively imaging multiplex microRNAs (miRNAs) in living cells is pivotal to understanding their physiological functions and pathological development due to the key regulatory roles of miRNAs in gene expression. However, developing smart delivery systems with large gene loading capacity, biocompatibility and responsiveness remains a significant challenge. Herein, we successfully incorporated DNA-capped Au nanoparticles (NPs) and their complementary fluorescent DNA sequences into a porous 3D hydrogel network (AuDH), in which hairpin-locked DNAzyme strands and active metal ions were loaded (AuDH/M n+/H) for simultaneously imaging multiplex miRNAs in living cells. After transfection into cells, the specific miRNAs trigger the strand-displacement reaction and sequentially activate the DNAzyme-assisted target recycling, leading to a strong increase in the corresponding fluorescence intensity for imaging. This enables simultaneous assessment of the abundance of multiplex cancer-related miRNAs, even if at a very low expression level, in different cells through the different fluorescence intensities due to the dual signal amplification, and the change in abundance of miRNAs induced by siRNA or miRNA mimics in living cells can also be efficiently monitored. The versatile and responsive DNA hydrogel system holds great potential for miRNA biomedical applications.
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Affiliation(s)
- Xiangdan Meng
- Beijing Key Laboratory for Bioengineering and Sensing Technology , Research Center for Bioengineering and Sensing Technology , School of Chemistry and Biological Engineering , University of Science & Technology Beijing , Beijing 100083 , P. R. China . ;
- Beijing Advanced Innovation Center for Materials Genome Engineering , University of Science and Technology Beijing , Beijing 100083 , P. R. China
| | - Kai Zhang
- Beijing Key Laboratory for Bioengineering and Sensing Technology , Research Center for Bioengineering and Sensing Technology , School of Chemistry and Biological Engineering , University of Science & Technology Beijing , Beijing 100083 , P. R. China . ;
- Beijing Advanced Innovation Center for Materials Genome Engineering , University of Science and Technology Beijing , Beijing 100083 , P. R. China
| | - Wenhao Dai
- Beijing Key Laboratory for Bioengineering and Sensing Technology , Research Center for Bioengineering and Sensing Technology , School of Chemistry and Biological Engineering , University of Science & Technology Beijing , Beijing 100083 , P. R. China . ;
- Beijing Advanced Innovation Center for Materials Genome Engineering , University of Science and Technology Beijing , Beijing 100083 , P. R. China
| | - Yu Cao
- Beijing Key Laboratory for Bioengineering and Sensing Technology , Research Center for Bioengineering and Sensing Technology , School of Chemistry and Biological Engineering , University of Science & Technology Beijing , Beijing 100083 , P. R. China . ;
- Beijing Advanced Innovation Center for Materials Genome Engineering , University of Science and Technology Beijing , Beijing 100083 , P. R. China
| | - Fan Yang
- Beijing Key Laboratory for Bioengineering and Sensing Technology , Research Center for Bioengineering and Sensing Technology , School of Chemistry and Biological Engineering , University of Science & Technology Beijing , Beijing 100083 , P. R. China . ;
- Beijing Advanced Innovation Center for Materials Genome Engineering , University of Science and Technology Beijing , Beijing 100083 , P. R. China
| | - Haifeng Dong
- Beijing Key Laboratory for Bioengineering and Sensing Technology , Research Center for Bioengineering and Sensing Technology , School of Chemistry and Biological Engineering , University of Science & Technology Beijing , Beijing 100083 , P. R. China . ;
- Beijing Advanced Innovation Center for Materials Genome Engineering , University of Science and Technology Beijing , Beijing 100083 , P. R. China
| | - Xueji Zhang
- Beijing Key Laboratory for Bioengineering and Sensing Technology , Research Center for Bioengineering and Sensing Technology , School of Chemistry and Biological Engineering , University of Science & Technology Beijing , Beijing 100083 , P. R. China . ;
- Beijing Advanced Innovation Center for Materials Genome Engineering , University of Science and Technology Beijing , Beijing 100083 , P. R. China
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125
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Mao D, Chen H, Tang Y, Li J, Cao Y, Zhao J. Application of Isothermal Nucleic Acid Signal Amplification in the Detection of Hepatocellular Carcinoma-Associated MicroRNA. Chempluschem 2018; 84:8-17. [DOI: 10.1002/cplu.201800382] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Dongsheng Mao
- Center for Molecular Recognition and Biosensing; School of Life Sciences; Shanghai University; Shanghai 200444 P. R. China
| | - Hong Chen
- Center for Molecular Recognition and Biosensing; School of Life Sciences; Shanghai University; Shanghai 200444 P. R. China
| | - Yingying Tang
- Center for Molecular Recognition and Biosensing; School of Life Sciences; Shanghai University; Shanghai 200444 P. R. China
| | - Jingwen Li
- Center for Molecular Recognition and Biosensing; School of Life Sciences; Shanghai University; Shanghai 200444 P. R. China
- CAS Key Lab of Bio-Medical Diagnostics Institution; Suzhou Institute of Biomedical Engineering and Technology; Chinese Academy of Sciences; Suzhou 215163 P. R. China
| | - Ya Cao
- Center for Molecular Recognition and Biosensing; School of Life Sciences; Shanghai University; Shanghai 200444 P. R. China
| | - Jing Zhao
- Center for Molecular Recognition and Biosensing; School of Life Sciences; Shanghai University; Shanghai 200444 P. R. China
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126
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Oh SW, Pereira A, Zhang T, Li T, Lane A, Fu J. DNA‐Mediated Proximity‐Based Assembly Circuit for Actuation of Biochemical Reactions. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Sung Won Oh
- Center for Computational and Integrative Biology Rutgers University—Camden 315 Penn Street, Science Building Camden NJ 08102 USA
| | - Adriana Pereira
- Department of Chemistry Rutgers University—Camden 315 Penn Street Camden NJ 08102 USA
| | - Ting Zhang
- Center for Computational and Integrative Biology Rutgers University—Camden 315 Penn Street, Science Building Camden NJ 08102 USA
- Department of Chemistry Rutgers University—Camden 315 Penn Street Camden NJ 08102 USA
| | - Tianran Li
- Center for Computational and Integrative Biology Rutgers University—Camden 315 Penn Street, Science Building Camden NJ 08102 USA
| | - Ariel Lane
- Department of Chemistry Rutgers University—Camden 315 Penn Street Camden NJ 08102 USA
| | - Jinglin Fu
- Center for Computational and Integrative Biology Rutgers University—Camden 315 Penn Street, Science Building Camden NJ 08102 USA
- Department of Chemistry Rutgers University—Camden 315 Penn Street Camden NJ 08102 USA
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127
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Li D, Wu Y, Gan C, Yuan R, Xiang Y. Bio-cleavable nanoprobes for target-triggered catalytic hairpin assembly amplification detection of microRNAs in live cancer cells. NANOSCALE 2018; 10:17623-17628. [PMID: 30204195 DOI: 10.1039/c8nr05229h] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The monitoring and imaging of intracellular microRNAs (miRNAs) with specific sequences plays a vital role in cell biology as it can potentially elucidate many cellular processes and diseases related to miRNAs in living cells with accurate information. However, the detection of trace amounts of under-expressed intracellular miRNAs in living cells represents one of the current major challenges. In an effort to address this issue, we describe the establishment of an in cell catalytic hairpin assembly (CHA) signal amplification strategy for imaging under-expressed intracellular miRNAs in this work. Gold nanoparticles functionalized with FAM- and TAMRA-labeled hairpins with disulfide bonds in the stems are readily delivered into cells via endocytosis. Glutathione with evaluated concentrations in cancer cells cleaves the disulfide bonds in the hairpins by reduction to release the hairpins, and the target miRNAs further trigger CHA between the two hairpins to form many DNA duplexes, which bring the FAM and TAMRA labels into close proximity to generate apparently enhanced fluorescence resonance energy transfer (FRET) for the sensitive monitoring of low amounts of under-expressed miRNAs in live cancer cells. Using CHA to amplify the signal output and FRET to reduce the background noise, a significantly enhanced signal-to-noise ratio, thereby high sensitivity, over conventional fluorescence imaging can be realized, making our method particularly suitable for monitoring low levels of intracellular species.
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Affiliation(s)
- Daxiu Li
- Key Laboratory on Luminescence and Real-Time Analysis, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China.
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128
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Liu S, Cao H, Wang X, Tu W, Dai Z. Green light excited ultrasensitive photoelectrochemical biosensing for microRNA at a low applied potential based on the dual role of Au NPs in TiO 2 nanorods/Au NPs composites. NANOSCALE 2018; 10:16474-16478. [PMID: 30155535 DOI: 10.1039/c8nr05513k] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
An ultrasensitive photoelectrochemical biosensing strategy for microRNA at a low applied potential was designed based on the robust photocurrent generated by TiO2 nanorods/Au nanoparticles (Au NPs) composites under green light excitation. The dual role of Au NPs dramatically improved the photocurrent, which guaranteed enough sensitivity, leading to the excellent performance in microRNA detection.
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Affiliation(s)
- Shanshan Liu
- Jiangsu Key Laboratory of Biofunctional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China.
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129
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Oh SW, Pereira A, Zhang T, Li T, Lane A, Fu J. DNA-Mediated Proximity-Based Assembly Circuit for Actuation of Biochemical Reactions. Angew Chem Int Ed Engl 2018; 57:13086-13090. [PMID: 30129087 DOI: 10.1002/anie.201806749] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 07/25/2018] [Indexed: 01/09/2023]
Abstract
Smart nanodevices that integrate molecular recognition and signal production hold great promise for the point-of-care (POC) diagnostic applications. Herein, the development of a DNA-mediated proximity assembly of biochemical reactions, which was capable of sensing various bio-targets and reporting easy-to-read signals is reported. The circuit was composed of a DNA hairpin-locked catalytic cofactor with inhibited activity. Specific molecular inputs can trigger a conformational switch of the DNA locks through the mechanisms of toehold displacement and aptamer switching, exposing an active cofactor. The subsequent assembly of an enzyme/cofactor pair actuated a reaction to produce colorimetric or fluorescence signals for detecting target molecules. The developed system could be potentially applied to smart biosensing in molecular diagnostics and POC tests.
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Affiliation(s)
- Sung Won Oh
- Center for Computational and Integrative Biology, Rutgers University-Camden, 315 Penn Street, Science Building, Camden, NJ, 08102, USA
| | - Adriana Pereira
- Department of Chemistry, Rutgers University-Camden, 315 Penn Street, Camden, NJ, 08102, USA
| | - Ting Zhang
- Center for Computational and Integrative Biology, Rutgers University-Camden, 315 Penn Street, Science Building, Camden, NJ, 08102, USA
- Department of Chemistry, Rutgers University-Camden, 315 Penn Street, Camden, NJ, 08102, USA
| | - Tianran Li
- Center for Computational and Integrative Biology, Rutgers University-Camden, 315 Penn Street, Science Building, Camden, NJ, 08102, USA
| | - Ariel Lane
- Department of Chemistry, Rutgers University-Camden, 315 Penn Street, Camden, NJ, 08102, USA
| | - Jinglin Fu
- Center for Computational and Integrative Biology, Rutgers University-Camden, 315 Penn Street, Science Building, Camden, NJ, 08102, USA
- Department of Chemistry, Rutgers University-Camden, 315 Penn Street, Camden, NJ, 08102, USA
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130
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Xue C, Zhang SX, Ouyang CH, Chang D, Salena BJ, Li Y, Wu ZS. Target-Induced Catalytic Assembly of Y-Shaped DNA and Its Application for In Situ Imaging of MicroRNAs. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804741] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Chang Xue
- Cancer Metastasis Alert and Prevention Center; Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy; Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment; College of Chemistry; Fuzhou University; Fuzhou 350002 China
| | - Shu-Xin Zhang
- Cancer Metastasis Alert and Prevention Center; Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy; Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment; College of Chemistry; Fuzhou University; Fuzhou 350002 China
| | - Chang-He Ouyang
- Cancer Metastasis Alert and Prevention Center; Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy; Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment; College of Chemistry; Fuzhou University; Fuzhou 350002 China
| | - Dingran Chang
- Department of Biochemistry & Biomedical Sciences; McMaster University; 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - Bruno J. Salena
- Department of Medicine; McMaster University; 1280 Main St. W. Hamilton ON L8S 4K1 Canada
| | - Yingfu Li
- Department of Biochemistry & Biomedical Sciences; McMaster University; 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - Zai-Sheng Wu
- Cancer Metastasis Alert and Prevention Center; Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy; Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment; College of Chemistry; Fuzhou University; Fuzhou 350002 China
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131
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Xue C, Zhang SX, Ouyang CH, Chang D, Salena BJ, Li Y, Wu ZS. Target-Induced Catalytic Assembly of Y-Shaped DNA and Its Application for In Situ Imaging of MicroRNAs. Angew Chem Int Ed Engl 2018; 57:9739-9743. [PMID: 29901854 DOI: 10.1002/anie.201804741] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 06/04/2018] [Indexed: 12/22/2022]
Affiliation(s)
- Chang Xue
- Cancer Metastasis Alert and Prevention Center; Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy; Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment; College of Chemistry; Fuzhou University; Fuzhou 350002 China
| | - Shu-Xin Zhang
- Cancer Metastasis Alert and Prevention Center; Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy; Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment; College of Chemistry; Fuzhou University; Fuzhou 350002 China
| | - Chang-He Ouyang
- Cancer Metastasis Alert and Prevention Center; Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy; Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment; College of Chemistry; Fuzhou University; Fuzhou 350002 China
| | - Dingran Chang
- Department of Biochemistry & Biomedical Sciences; McMaster University; 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - Bruno J. Salena
- Department of Medicine; McMaster University; 1280 Main St. W. Hamilton ON L8S 4K1 Canada
| | - Yingfu Li
- Department of Biochemistry & Biomedical Sciences; McMaster University; 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - Zai-Sheng Wu
- Cancer Metastasis Alert and Prevention Center; Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy; Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment; College of Chemistry; Fuzhou University; Fuzhou 350002 China
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132
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Huang C, Wang J, Lv X, Liu L, Liang L, Hu W, Luo C, Wang F, Yuan Q. Redefining Molecular Amphipathicity in Reversing the "Coffee-Ring Effect": Implications for Single Base Mutation Detection. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:6777-6783. [PMID: 29779375 DOI: 10.1021/acs.langmuir.8b01248] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The "coffee ring effect" is a natural phenomenon wherein sessile drops leave ring-shaped structures on the solid surfaces upon drying. It drives a nonuniform deposition of suspended compounds on the substrates, which adversely affects many processes, including surface-assisted biosensing and molecular self-assembly. In this study, we describe how the coffee ring effect can be eliminated by controlling the amphipathicity of the suspended compounds, for example, DNA modified with hydrophobic dye. Specifically, nuclease digestion of the hydrophilic DNA end converts the dye-labeled molecule into an amphipathic molecule (one with comparably weighted hydrophobic and hydrophilic ends) and reverses the coffee ring effect and results in a uniform disk-shaped feature deposition of the dye. The amphipathic product decreases the surface tension of the sessile drops and induces the Marangoni flow, which drives the uniform distribution of the amphipathic dye-labeled product in the drops. As a proof of concept, this strategy was used in a novel enzymatic amplification method for biosensing to eliminate the coffee ring effect on a nitrocellulose membrane and increase assay reliability and sensitivity. Importantly, the reported strategy for eliminating the coffee ring effect can be extended to other sessile drop systems for potentially improving assay reliability and sensitivity.
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Affiliation(s)
- Chi Huang
- Institute of Chemical Biology and Nanomedicine, Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering , Hunan University , Changsha 410082 , China
| | | | | | | | - Ling Liang
- Institute of Chemical Biology and Nanomedicine, Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering , Hunan University , Changsha 410082 , China
| | | | | | | | - Quan Yuan
- Institute of Chemical Biology and Nanomedicine, Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering , Hunan University , Changsha 410082 , China
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133
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Dong J, Chen G, Wang W, Huang X, Peng H, Pu Q, Du F, Cui X, Deng Y, Tang Z. Colorimetric PCR-Based microRNA Detection Method Based on Small Organic Dye and Single Enzyme. Anal Chem 2018; 90:7107-7111. [PMID: 29847923 DOI: 10.1021/acs.analchem.8b01111] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
microRNAs (miRNAs) have been a class of promising disease diagnostic biomarkers and therapeutic targets for their important biological functions. However, because of the high homology, interference from precursors (pri-miRNA, pre-miRNA), as well as limitations in the current assay technologies, it poses high demand and challenge for a specific, efficient, and economic miRNA assay method. Here, we propose a new miRNA detection method based on a label-free probe and a small organic dye with sequence dependence, realizing the sequence-specific and colorimetric detection of target miRNA. What is pleasantly surprising, only one enzyme is enough to propel the whole miRNA assay process, greatly simplifying the reaction component and detection process. Together with PCR amplification for the high enough sensitivity and three checks for specificity control, a detection limit of 5 fM was obtained and even one mutation could be discriminated visually. Overall, the new method makes much progress in convenience and economy of PCR-based miRNA assay method so that miRNA assay is going to be more friendly and affordable.
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Affiliation(s)
- Juan Dong
- Natural Products Research Center, Chengdu Institute of Biology , Chinese Academy of Science , Sichuan , Chengdu 610041 , PR China
| | - Gangyi Chen
- Natural Products Research Center, Chengdu Institute of Biology , Chinese Academy of Science , Sichuan , Chengdu 610041 , PR China
| | - Wei Wang
- Natural Products Research Center, Chengdu Institute of Biology , Chinese Academy of Science , Sichuan , Chengdu 610041 , PR China
| | - Xin Huang
- Natural Products Research Center, Chengdu Institute of Biology , Chinese Academy of Science , Sichuan , Chengdu 610041 , PR China
| | - Huipan Peng
- Natural Products Research Center, Chengdu Institute of Biology , Chinese Academy of Science , Sichuan , Chengdu 610041 , PR China
| | - Qinlin Pu
- Natural Products Research Center, Chengdu Institute of Biology , Chinese Academy of Science , Sichuan , Chengdu 610041 , PR China
| | - Feng Du
- Natural Products Research Center, Chengdu Institute of Biology , Chinese Academy of Science , Sichuan , Chengdu 610041 , PR China
| | - Xin Cui
- Natural Products Research Center, Chengdu Institute of Biology , Chinese Academy of Science , Sichuan , Chengdu 610041 , PR China
| | - Yun Deng
- State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resource , Chengdu University of TCM , Chengdu 611137 , PR China
| | - Zhuo Tang
- Natural Products Research Center, Chengdu Institute of Biology , Chinese Academy of Science , Sichuan , Chengdu 610041 , PR China
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134
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Li P, Kumar A, Ma J, Kuang Y, Luo L, Sun X. Density gradient ultracentrifugation for colloidal nanostructures separation and investigation. Sci Bull (Beijing) 2018; 63:645-662. [PMID: 36658885 DOI: 10.1016/j.scib.2018.04.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 03/27/2018] [Accepted: 03/28/2018] [Indexed: 01/21/2023]
Abstract
In this article, we review the advancement in nanoseparation and concomitant purification of nanoparticles (NPs) by using density gradient ultracentrifugation technique (DGUC) and demonstrated by taking several typical examples. Study emphasizes the conceptual advances in classification, mechanism of DGUC and synthesis-structure-property relationships of NPs to provide the significant clue for the further synthesis optimization. Separation, concentration, and purification of NPs by DGUC can be achieved at the same time by introducing the water/oil interfaces into the separation chamber. We can develop an efficient method "lab in a tube" by introducing a reaction zone or an assembly zone in the gradient to find the surface reaction and assembly mechanism of NPs since the reaction time can be precisely controlled and the chemical environment change can be extremely fast. Finally, to achieve the best separation parameters for the colloidal systems, we gave the mathematical descriptions and computational optimized models as a new direction for making practicable and predictable DGUC separation method. Thus, it can be helpful for an efficient separation as well as for the synthesis optimization, assembly and surface reactions as a potential cornerstone for the future development in the nanotechnology and this review can be served as a plethora of advanced notes on the DGUC separation method.
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Affiliation(s)
- Pengsong Li
- State Key Laboratory of Chemical Resource Engineering, College of Energy, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Anuj Kumar
- State Key Laboratory of Chemical Resource Engineering, College of Energy, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jun Ma
- State Key Laboratory of Chemical Resource Engineering, College of Energy, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yun Kuang
- State Key Laboratory of Chemical Resource Engineering, College of Energy, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Liang Luo
- State Key Laboratory of Chemical Resource Engineering, College of Energy, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Xiaoming Sun
- State Key Laboratory of Chemical Resource Engineering, College of Energy, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
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135
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Fang H, Xie N, Ou M, Huang J, Li W, Wang Q, Liu J, Yang X, Wang K. Detection of Nucleic Acids in Complex Samples via Magnetic Microbead-Assisted Catalyzed Hairpin Assembly and “DD–A” FRET. Anal Chem 2018; 90:7164-7170. [DOI: 10.1021/acs.analchem.8b01330] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Hongmei Fang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, China
| | - Nuli Xie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, China
| | - Min Ou
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, China
| | - Jin Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, China
| | - Wenshan Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, China
| | - Qing Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, China
| | - Jianbo Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, China
| | - Xiaohai Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, China
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136
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Ma Y, Chen J, Chen D, Xu Y, Zhang L, Dai Z, Zou X. Short-probe-based duplex-specific nuclease signal amplification strategy enables imaging of endogenous microRNAs in living cells with ultrahigh specificity. Talanta 2018; 186:256-264. [PMID: 29784358 DOI: 10.1016/j.talanta.2018.04.071] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 04/17/2018] [Accepted: 04/20/2018] [Indexed: 11/30/2022]
Abstract
Specific nucleic acids amplification at a constant and mild temperature is important for imaging assay of endogenous microRNAs (miRNAs) in living cells. Duplex-specific nuclease (DSN) is attractive in one-step isothermal assay of miRNA; however, its intrinsic limitations of low amplification specificity and high reaction temperature greatly restrict the application scope. Herein, we present a short-probe-based DSN signal amplification (spDSNSA) strategy enabling analysis of miRNAs at body temperature with significantly high specificity. From systematic investigation of amplification reaction on different types of DNA probes, we revealed that the annealing rate between probe and target miRNA greatly affects the dynamics of amplification process. By simply shortening the length of DNA probe, the spDSNSA remarkably improved specificity without loss of amplification efficiency at 37 °C. As a proof-of-concept, let-7a was sensitively detected by spDSNSA with a limit of detection down to 30 p.M., and a specificity 102 ‒ 104 folds higher than those of traditional DSNSA methods. The analysis of the let-7a in the lysates of A549 human lung cancer cells and BEAS-2B human lung normal bronchial epithelial cells exhibited well agreement with rt-qPCR method. Furthermore, the endogenous let-7a in A549 and BEAS-2B living cells was clearly imaged without damaging the original morphology of cells. The method provide a facile idea for extension of DNS related signal amplification strategies in the application in living cells and POCTs, and would pose a great impact on the development of simple and rapid molecular diagnostic applications for short oligonucleotides.
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Affiliation(s)
- Yingjun Ma
- School of Chemistry, Sun Yat-Sen University, 135 Xingang West Road, Guangzhou 510275, PR China
| | - Jun Chen
- School of Chemistry, Sun Yat-Sen University, 135 Xingang West Road, Guangzhou 510275, PR China
| | - Danping Chen
- School of Chemistry, Sun Yat-Sen University, 135 Xingang West Road, Guangzhou 510275, PR China
| | - Yuzhi Xu
- School of Chemistry, Sun Yat-Sen University, 135 Xingang West Road, Guangzhou 510275, PR China
| | - Li Zhang
- School of Chemistry, Sun Yat-Sen University, 135 Xingang West Road, Guangzhou 510275, PR China
| | - Zong Dai
- School of Chemistry, Sun Yat-Sen University, 135 Xingang West Road, Guangzhou 510275, PR China.
| | - Xiaoyong Zou
- School of Chemistry, Sun Yat-Sen University, 135 Xingang West Road, Guangzhou 510275, PR China
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137
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Yang X, Wang S, Wang Y, He Y, Chai Y, Yuan R. Stimuli-Responsive DNA Microcapsules for SERS Sensing of Trace MicroRNA. ACS APPLIED MATERIALS & INTERFACES 2018; 10:12491-12496. [PMID: 29595245 DOI: 10.1021/acsami.8b01974] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In this work, one stimuli-responsive DNA microcapsule was designed to combine duplex-specific nuclease (DSN) amplification strategy and surface-enhanced Raman spectroscopy (SERS) technology for sensitive detection of microRNA 155 (miRNA 155). First, toluidine blue (TB) as Raman dye and CaCO3 as core templates co-precipitated to form TB@CaCO3 composite. Then, DNA networks were layer by layer constructed with oligonucleotide layers cross-linked by linker ssDNA L to lock TB@CaCO3 inside. In the presence of ethylenediaminetetraacetic acid, the core CaCO3 would be dissolved to form TB-loading DNA microcapsule. With target miRNA 155-induced DSN signal amplification, a large amount of simulative target ssDNA D was obtained, which can completely complement with the linker L on the DNA networks, destroying the microcapsule to release TB and obtain a strong Raman signal. So by this smart design, a SERS platform was fabricated on the basis of the stimuli-responsive DNA microcapsule to detect miRNA 155 from 1 fM to 10 nM with a detection limit of 0.67 fM. In the present study, the programmable property and rapid response speed of DNA microcapsule, which helped in fabrication of a new potential biosensing technology for miRNA detection that is anticipated to be applied for clinical diagnosis.
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Affiliation(s)
- Xia Yang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, College of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , P. R. China
| | - Shufan Wang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, College of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , P. R. China
| | - Yue Wang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, College of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , P. R. China
- No. 1 High School of DaLian Development Area , Dalian , Liaoning 116000 , P. R. China
| | - Yi He
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, College of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , P. R. 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 , P. R. 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 , P. R. China
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138
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Özay B, Robertus CM, Negri JL, McCalla SE. First characterization of a biphasic, switch-like DNA amplification. Analyst 2018; 143:1820-1828. [PMID: 29577124 PMCID: PMC5969907 DOI: 10.1039/c8an00130h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We report the first DNA amplification chemistry with switch-like characteristics: the chemistry is biphasic, with an expected initial phase followed by an unprecedented high gain burst of product oligonucleotide in a second phase. The first and second phases are separated by a temporary plateau, with the second phase producing 10 to 100 times more product than the first. The reaction is initiated when an oligonucleotide binds and opens a palindromic looped DNA template with two binding domains. Upon loop opening, the oligonucleotide trigger is rapidly amplified through cyclic extension and nicking of the bound trigger. Loop opening and DNA association drive the amplification reaction, such that reaction acceleration in the second phase is correlated with DNA association thermodynamics. Without a palindromic sequence, the chemistry resembles the exponential amplification reaction (EXPAR). EXPAR terminates at the initial plateau, revealing a previously unknown phenomenon that causes early reaction cessation in this popular oligonucleotide amplification reaction. Here we present two distinct types of this biphasic reaction chemistry and propose dominant reaction pathways for each type based on thermodynamic arguments. These reactions create an endogenous switch-like output that reacts to approximately 1 pM oligonucleotide trigger. The chemistry is isothermal and can be adapted to respond to a broad range of input target molecules such as proteins, genomic bacterial DNA, viral DNA, and microRNA. This rapid DNA amplification reaction could potentially impact a variety of disciplines such as synthetic biology, biosensors, DNA computing, and clinical diagnostics.
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Affiliation(s)
- Burcu Özay
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT 59717, USA.
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139
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Hu J, Liu MH, Zhang CY. Integration of isothermal amplification with quantum dot-based fluorescence resonance energy transfer for simultaneous detection of multiple microRNAs. Chem Sci 2018; 9:4258-4267. [PMID: 29780556 PMCID: PMC5944210 DOI: 10.1039/c8sc00832a] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 04/10/2018] [Indexed: 12/14/2022] Open
Abstract
The integration of quantum dot-based fluorescence resonance energy transfer with rolling circle amplification enables simultaneous sensitive detection of multiple microRNAs.
MicroRNAs (miRNAs) are small non-coding RNAs that regulate important physiological processes, and their dysregulation is associated with various human diseases. Simultaneous sensitive detection of multiple miRNAs may facilitate early clinical diagnosis. In this research, we demonstrate for the first time the integration of hyperbranched rolling circle amplification (HRCA) with quantum dot (QD)-based fluorescence resonance energy transfer (FRET) for the simultaneous detection of multiple microRNAs with a single-color QD as the donor and two fluorescent dyes as the acceptors. We used miR-21 and miR-221 as target miRNAs. We designed two circular templates which may specifically hybridize with miR-21 and miR-221, respectively, for the initiation of the HRCA reaction. The products of the HRCA reaction may hybridize with both capture probes and reporter probes to form the biotinylated acceptor-labeled sandwich hybrids. The resultant sandwich hybrids can assemble on the surface of the QD, enabling efficient FRET between the QD and the acceptors, with the Cy3 signal indicating the presence of miR-21 and the Texas Red signal indicating the presence of miR-221. This assay has significant advantages of simplicity and low cost. The HRCA reaction can be performed under isothermal conditions with the same reverse primer for different target miRNAs, and the products of the HRCA reaction for both miR-21 and miR-221 can specifically hybridize with the same capture probes. This assay exhibits excellent specificity and high sensitivity with a detection limit of 7.2 × 10–16 M for miR-21 and 1.6 × 10–17 M for miR-221, and it can be used for simultaneous detection of multiple miRNAs in human cancer cells, holding great potential in biomedical research and clinical diagnosis.
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Affiliation(s)
- Juan Hu
- College of Chemistry, Chemical Engineering and Materials Science , Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong , Key Laboratory of Molecular and Nano Probes , Ministry of Education , Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan 250014 , China . ; ; Tel: +86 531 86186033
| | - Ming-Hao Liu
- College of Chemistry, Chemical Engineering and Materials Science , Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong , Key Laboratory of Molecular and Nano Probes , Ministry of Education , Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan 250014 , China . ; ; Tel: +86 531 86186033
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science , Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong , Key Laboratory of Molecular and Nano Probes , Ministry of Education , Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan 250014 , China . ; ; Tel: +86 531 86186033
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140
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Wu J, Xianyu Y, Wang X, Hu D, Zhao Z, Lu N, Xie M, Lei H, Chen Y. Enzyme-Free Amplification Strategy for Biosensing Using Fe3+–Poly(glutamic acid) Coordination Chemistry. Anal Chem 2018; 90:4725-4732. [DOI: 10.1021/acs.analchem.7b05344] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Jing Wu
- Analytical and Testing Center of Beijing Normal University, Beijing 100875, China
| | - Yunlei Xianyu
- CAS Key Laboratory
for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Xiangfeng Wang
- Analytical and Testing Center of Beijing Normal University, Beijing 100875, China
| | - Dehua Hu
- Analytical and Testing Center of Beijing Normal University, Beijing 100875, China
| | - Zhitao Zhao
- Analytical and Testing Center of Beijing Normal University, Beijing 100875, China
| | - Ning Lu
- Guangdong Provincial
Key Laboratory of Food Quality and Safety/College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Mengxia Xie
- Analytical and Testing Center of Beijing Normal University, Beijing 100875, China
| | - Hongtao Lei
- Guangdong Provincial
Key Laboratory of Food Quality and Safety/College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Yiping Chen
- CAS Key Laboratory
for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, China
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141
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Zhou H, Liu J, Xu JJ, Zhang SS, Chen HY. Optical nano-biosensing interface via nucleic acid amplification strategy: construction and application. Chem Soc Rev 2018; 47:1996-2019. [PMID: 29446429 DOI: 10.1039/c7cs00573c] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Modern optical detection technology plays a critical role in current clinical detection due to its high sensitivity and accuracy. However, higher requirements such as extremely high detection sensitivity have been put forward due to the clinical needs for the early finding and diagnosing of malignant tumors which are significant for tumor therapy. The technology of isothermal amplification with nucleic acids opens up avenues for meeting this requirement. Recent reports have shown that a nucleic acid amplification-assisted modern optical sensing interface has achieved satisfactory sensitivity and accuracy, high speed and specificity. Compared with isothermal amplification technology designed to work completely in a solution system, solid biosensing interfaces demonstrated better performances in stability and sensitivity due to their ease of separation from the reaction mixture and the better signal transduction on these optical nano-biosensing interfaces. Also the flexibility and designability during the construction of these nano-biosensing interfaces provided a promising research topic for the ultrasensitive detection of cancer diseases. In this review, we describe the construction of the burgeoning number of optical nano-biosensing interfaces assisted by a nucleic acid amplification strategy, and provide insightful views on: (1) approaches to the smart fabrication of an optical nano-biosensing interface, (2) biosensing mechanisms via the nucleic acid amplification method, (3) the newest strategies and future perspectives.
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Affiliation(s)
- Hong Zhou
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, China.
| | - Jing Liu
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, China.
| | - Jing-Juan Xu
- Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.
| | - Shu-Sheng Zhang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, China.
| | - Hong-Yuan Chen
- Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.
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142
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Qu X, Jin H, Liu Y, Sun Q. Strand Displacement Amplification Reaction on Quantum Dot-Encoded Silica Bead for Visual Detection of Multiplex MicroRNAs. Anal Chem 2018; 90:3482-3489. [DOI: 10.1021/acs.analchem.7b05235] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Xiaojun Qu
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Haojun Jin
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Yuqian Liu
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Qingjiang Sun
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
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143
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Meng X, Dai W, Zhang K, Dong H, Zhang X. Imaging multiple microRNAs in living cells using ATP self-powered strand-displacement cascade amplification. Chem Sci 2018; 9:1184-1190. [PMID: 29675163 PMCID: PMC5885591 DOI: 10.1039/c7sc04725h] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 11/30/2017] [Indexed: 12/14/2022] Open
Abstract
Herein, we design a smart autonomous ATP self-powered strand-displacement cascade amplification (SDCA) system for highly sensitive multiple intracellular miRNA detection. Rationally engineered Y-motif DNA structures are functionalized on mesoporous silica-coated copper sulfide nanoparticles loaded with numerous ATPs (CuS@mSiO2-Y/ATP) through pH stimulus-responsive disulfide bonds. The SDCA system is implemented by endogenous specific miRNA as a trigger and ATP as fuel released from the nanocarrier at acidic pH and photothermal stimuli-responsive CuS. The ATP self-powered SDCA process presents higher sensitivity compared to that without amplification for intracellular miRNA imaging. Two-color simultaneous and sensitive imaging of multiple cancer-related miRNAs in living cells is also confirmed. This enables facile and accurate differentiation between normal cells and different types of cancer cell using intracellular miRNA imaging, which improves the veracity and timeliness for early cancer diagnosis.
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Affiliation(s)
- Xiangdan Meng
- Research Center for Bioengineering and Sensing Technology , School of Chemistry and Bioengineering , University of Science & Technology Beijing , Beijing 100083 , P. R. China . ;
- National Institute of Precision Medicine & Health , Beijing , 100083 , P. R. China
| | - Wenhao Dai
- Research Center for Bioengineering and Sensing Technology , School of Chemistry and Bioengineering , University of Science & Technology Beijing , Beijing 100083 , P. R. China . ;
- National Institute of Precision Medicine & Health , Beijing , 100083 , P. R. China
| | - Kai Zhang
- Research Center for Bioengineering and Sensing Technology , School of Chemistry and Bioengineering , University of Science & Technology Beijing , Beijing 100083 , P. R. China . ;
- National Institute of Precision Medicine & Health , Beijing , 100083 , P. R. China
| | - Haifeng Dong
- Research Center for Bioengineering and Sensing Technology , School of Chemistry and Bioengineering , University of Science & Technology Beijing , Beijing 100083 , P. R. China . ;
- National Institute of Precision Medicine & Health , Beijing , 100083 , P. R. China
| | - Xueji Zhang
- Research Center for Bioengineering and Sensing Technology , School of Chemistry and Bioengineering , University of Science & Technology Beijing , Beijing 100083 , P. R. China . ;
- National Institute of Precision Medicine & Health , Beijing , 100083 , P. R. China
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144
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Zhao Y, Chen F, Qin J, Wei J, Wu W, Zhao Y. Engineered Janus probes modulate nucleic acid amplification to expand the dynamic range for direct detection of viral genomes in one microliter crude serum samples. Chem Sci 2018; 9:392-397. [PMID: 29629109 PMCID: PMC5868314 DOI: 10.1039/c7sc03994h] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 10/27/2017] [Indexed: 11/21/2022] Open
Abstract
The viral genome load in diverse clinical samples varies over several orders of magnitude (e.g. 1-104 copies per μL), thus a dynamic range-extended and sensitive analysis method is highly desired. However, existing well-developed nucleic acid amplification systems always suffer from either a limited dynamic range or modest sensitivity for analysis of these samples. Herein, we propose a general engineered Janus probe to modulate the thermodynamics and kinetic properties of the amplification reaction. Through rational regulation, the Janus system improves the performance by both reducing the background and enhancing the signal, expanding the operative dynamic range by 2 orders of magnitude. This proposed approach achieves a detection limit for hepatitis B virus (HBV) DNA of down to 3 copies and can be successfully applied for direct quantification of the HBV genome in one microliter crude serum samples without any pretreatment. The results are consistent with clinical diagnosis and hold considerable potential to discriminate healthy volunteers and patients at different disease stages. Whereas, following the same operation, the representative well-developed system provided serious false-negative results using such trace amounts of samples from clinically confirmed positive patients.
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Affiliation(s)
- Yue Zhao
- Key Laboratory of Biomedical Information Engineering of Education Ministry , School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China .
| | - Feng Chen
- Key Laboratory of Biomedical Information Engineering of Education Ministry , School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China .
| | - Jing Qin
- Key Laboratory of Biomedical Information Engineering of Education Ministry , School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China .
| | - Jing Wei
- Key Laboratory of Biomedical Information Engineering of Education Ministry , School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China .
| | - Wenhua Wu
- Department of Infectious Disease , The Second Affiliated Hospital of Medical College , Xi'an Jiaotong University , Xiwu Road , Xi'an , Shaanxi 710049 , P. R. China
| | - Yongxi Zhao
- Key Laboratory of Biomedical Information Engineering of Education Ministry , School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China .
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145
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Oladepo SA. Design and Characterization of a Singly Labeled Fluorescent Smart Probe for In Vitro Detection of miR-21. APPLIED SPECTROSCOPY 2018; 72:79-88. [PMID: 28946749 DOI: 10.1177/0003702817736527] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A sensitive hairpin smart probe (SP) has been developed and tested for its sequence-specificity and sensitivity for detecting microRNAs (miRNAs). The loop sequence of this SP is perfectly complementary to microRNA-21 (miR-21) sequence. This miRNA regulates certain biological processes and has been implicated in certain forms of cancer. The stem of the new SP consists of a fluorophore on one end and multiple guanine bases on the opposing end are used as quenchers. The fluorescence of the SP is significantly quenched by the guanine bases at room temperature and in the absence of the miR-21 target. The presence of miR-21 switches on the fluorescence due to spontaneous hybridization of the SP with this target, which also forces the stem hybrid of the SP apart. This new SP successfully discriminated between the perfect miR-21 target and two closely similar single-base mismatch sequences. When the SP was incubated with the miR-21 at 37 ℃, the hybridization kinetics increased seven times, compared to room temperature hybridization. Overall, this new SP shows good detection sensitivity and gives a limit of detection and limit of quantitation of 14.0 nM and 46.7 nM, respectively. This detection platform represents a simple, fast, mix-and-read homogeneous assay for sequence-specific detection of miR-21, and it can be adapted for other related diagnostic applications.
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Affiliation(s)
- Sulayman A Oladepo
- 108765 Department of Chemistry, King Fahd University of Petroleum and Minerals, Dhahran 31261, Kingdom of Saudi Arabia
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146
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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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147
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Nie Y, Zhang P, Wang H, Zhuo Y, Chai Y, Yuan R. Ultrasensitive Electrochemiluminescence Biosensing Platform for Detection of Multiple Types of Biomarkers toward Identical Cancer on a Single Interface. Anal Chem 2017; 89:12821-12827. [DOI: 10.1021/acs.analchem.7b03240] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Yamin Nie
- Key Laboratory of Luminescent and Real-Time
Analytical Chemistry (Southwest University), Ministry of Education,
College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People’s Republic of China
| | - Pu Zhang
- Key Laboratory of Luminescent and Real-Time
Analytical Chemistry (Southwest University), Ministry of Education,
College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People’s Republic of China
| | - Haijun Wang
- Key Laboratory of Luminescent and Real-Time
Analytical Chemistry (Southwest University), Ministry of Education,
College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People’s Republic of China
| | - Ying Zhuo
- Key Laboratory of Luminescent and Real-Time
Analytical Chemistry (Southwest University), Ministry of Education,
College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People’s Republic of China
| | - Yaqin Chai
- Key Laboratory of Luminescent and Real-Time
Analytical Chemistry (Southwest University), Ministry of Education,
College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People’s Republic of China
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time
Analytical Chemistry (Southwest University), Ministry of Education,
College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People’s Republic of China
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148
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He MQ, Wang K, Wang WJ, Yu YL, Wang JH. Smart DNA Machine for Carcinoembryonic Antigen Detection by Exonuclease III-Assisted Target Recycling and DNA Walker Cascade Amplification. Anal Chem 2017; 89:9292-9298. [PMID: 28806060 DOI: 10.1021/acs.analchem.7b02073] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A synthetic DNA machine performs quasi-mechanical movements in response to external intervention, suggesting the promise of constructing sensitive and specific biosensors. Herein, a smart DNA walker biosensor for label-free detection of carcinoembryonic antigen (CEA) is developed for the first time by a novel cascade amplification strategy of exonuclease (Exo) III-assisted target recycling amplification (ERA) and DNA walker. ERA as the first stage of amplification generates the walker DNA, while the autonomous traveling of the walker DNA on the substrate-modified silica microspheres as the second stage of amplification produces an ultrasensitive fluorescent signal with the help of N-methylmesoporphyrin IX (NMM). The DNA machine as a biosensor could be applied for transducing and quantifying signals from isothermal molecular amplifications, avoiding the complicated reporter elements and thermal cycling. The present biosensor achieves a detection limit of 1.2 pg·mL-1 within a linear range of 10 pg·mL-1 to 100 ng·mL-1 for CEA, along with a favorable specificity. The practical applicability of the biosensor is demonstrated by the detection of CEA in human serum with satisfactory results; thus, it shows great potential in clinical diagnosis.
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Affiliation(s)
- Meng-Qi He
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University , Box 332, Shenyang 110819, China
| | - Kun Wang
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University , Box 332, Shenyang 110819, China
| | - Wen-Jing Wang
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University , Box 332, Shenyang 110819, China
| | - Yong-Liang Yu
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University , Box 332, Shenyang 110819, China
| | - Jian-Hua Wang
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University , Box 332, Shenyang 110819, China
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149
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Ma W, Fu P, Sun M, Xu L, Kuang H, Xu C. Dual Quantification of MicroRNAs and Telomerase in Living Cells. J Am Chem Soc 2017; 139:11752-11759. [DOI: 10.1021/jacs.7b03617] [Citation(s) in RCA: 225] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Wei Ma
- State
Key Lab of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
- International Joint Research Laboratory for Biointerface
and Biodetection and School of
Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
- Collaborative
Innovationcenter of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Pan Fu
- State
Key Lab of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
- International Joint Research Laboratory for Biointerface
and Biodetection and School of
Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
- Collaborative
Innovationcenter of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Maozhong Sun
- State
Key Lab of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
- International Joint Research Laboratory for Biointerface
and Biodetection and School of
Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
- Collaborative
Innovationcenter of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Liguang Xu
- State
Key Lab of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
- International Joint Research Laboratory for Biointerface
and Biodetection and School of
Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
- Collaborative
Innovationcenter of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Hua Kuang
- State
Key Lab of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
- International Joint Research Laboratory for Biointerface
and Biodetection and School of
Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
- Collaborative
Innovationcenter of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Chuanlai Xu
- State
Key Lab of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
- International Joint Research Laboratory for Biointerface
and Biodetection and School of
Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
- Collaborative
Innovationcenter of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
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150
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