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Gao YP, Huang KJ, Wang FT, Hou YY, Xu J, Li G. Recent advances in biological detection with rolling circle amplification: design strategy, biosensing mechanism, and practical applications. Analyst 2022; 147:3396-3414. [DOI: 10.1039/d2an00556e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Rolling circle amplification (RCA) is a simple and isothermal DNA amplification technique that is used to generate thousands of repeating DNA sequences using circular templates under the catalysis of DNA polymerase.
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Affiliation(s)
- Yong-ping Gao
- International Joint Research Laboratory of New Energy Materials and Devices of Henan Province, School of Physics and Electronics, Henan University, Kaifeng, 475004, PR China
- Analysis and Testing Center, Xinyang College, Xinyang 464000, PR China
| | - Ke-Jing Huang
- Key Laboratory of Guangxi Colleges and Universities for Food Safety and Pharmaceutical Analytical Chemistry, School of Chemistry and Chemical and Engineering, Guangxi Minzu University, Nanning 530008, PR China
| | - Fu-Ting Wang
- College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang 464000, PR China
| | - Yang-Yang Hou
- College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang 464000, PR China
| | - Jing Xu
- College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang 464000, PR China
| | - Guoqiang Li
- International Joint Research Laboratory of New Energy Materials and Devices of Henan Province, School of Physics and Electronics, Henan University, Kaifeng, 475004, PR China
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Zhang P, Guo X, Gao J, Liu H, Wan C, Li J, Zhang Q, Song Y, Ding C. A Dual-Control Strategy by Phosphate Ions and Local Microviscosity for Tracking Adenosine Triphosphate Metabolism in Mitochondria and Cellular Activity Dynamically. ACS Sens 2021; 6:4225-4233. [PMID: 34709795 DOI: 10.1021/acssensors.1c01850] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Adenosine triphosphate (ATP) acts as the main energy source for growth and development in organisms, and the disorder reflects the mitochondrial damage to a large extent. Therefore, an efficient tool for the evaluation of the ATP metabolic level is important to track mitochondrial health, providing an additional perspective for an in-depth long-term study on living activities. Herein, a twisted intramolecular charge transfer (TICT) framework is utilized to build up a sensitive receptor, Mito-VP, with a negligible background to target mitochondrial ATP metabolism by monitoring the phosphate ion (Pi) level upon ATP hydrolysis under the overall consideration of the structural and functional features of mitochondria. The responsive fluorescence could be lighted on under the dual control of Pi and local microviscosity, and the two steps of ATP hydrolysis could be captured through fluorescence. In addition to the well-behaved mitochondrial targeting, the energy metabolism at cellular and organism levels has been clarified via mitosis and zebrafish development, respectively.
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Affiliation(s)
- Peng Zhang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Xinjie Guo
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Jian Gao
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Haihong Liu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Chenyang Wan
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Jiajia Li
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Qian Zhang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Yuqing Song
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Caifeng Ding
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
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3
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Meng YR, Zhang D, Zou X, Ma F, Kang Q, Zhang CY. A trifunctional split dumbbell probe coupled with ligation-triggered isothermal rolling circle amplification for label-free and sensitive detection of nicotinamide adenine dinucleotide. Talanta 2020; 224:121962. [PMID: 33379129 DOI: 10.1016/j.talanta.2020.121962] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/17/2020] [Accepted: 11/30/2020] [Indexed: 11/15/2022]
Abstract
The nicotinamide adenine dinucleotide (NAD+) is an important small biomolecule that participates in a variety of physiological functions, and it has been regarded as a potential biomarker for disease diagnosis and a promising target for disease treatment. The conventional methods for NAD+ assay often suffer from complicated procedures, expensive labeling, poor selectivity, and unsatisfactory sensitivity. Herein, we develop a label-free and sensitive method for NAD+ assay based on the integration of a trifunctional split dumbbell probe with ligation-triggered isothermal rolling circle amplification (RCA). We design a trifunctional split dumbbell probe that can act as a probe for NAD+ recognition, a template for RCA reaction, and a substrate for SYBR Green I binding. In the presence of target NAD+, it can serve as a cofactor to active E. coli DNA ligase which subsequently catalyzes the ligation of split dumbbell probe to form a circular template for RCA reaction, generating numerous dumbbell probe amplicons which can be easily and label-free monitored by using SYBR Green I as the fluorescent indicator. Due to the high fidelity of NAD+-dependent ligation and high amplification efficiency of RCA amplification, this method exhibits high sensitivity with a detection limit of 85.6 fM and good selectivity with the capability of discriminating target NAD+ from its analogs. Moreover, this method can be applied for accurate and sensitive detection of NAD+ in complex biological samples and cancer cells, holding great potential in NAD+-related biological researches and clinical diagnosis.
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Affiliation(s)
- Ya-Ru Meng
- 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
| | - Dandan 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
| | - Xiaoran Zou
- 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
| | - Fei Ma
- 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.
| | - Qi Kang
- 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.
| | - 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.
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Li J, Mohammed-Elsabagh M, Paczkowski F, Li Y. Circular Nucleic Acids: Discovery, Functions and Applications. Chembiochem 2020; 21:1547-1566. [PMID: 32176816 DOI: 10.1002/cbic.202000003] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 02/13/2020] [Indexed: 12/14/2022]
Abstract
Circular nucleic acids (CNAs) are nucleic acid molecules with a closed-loop structure. This feature comes with a number of advantages including complete resistance to exonuclease degradation, much better thermodynamic stability, and the capability of being replicated by a DNA polymerase in a rolling circle manner. Circular functional nucleic acids, CNAs containing at least a ribozyme/DNAzyme or a DNA/RNA aptamer, not only inherit the advantages of CNAs but also offer some unique application opportunities, such as the design of topology-controlled or enabled molecular devices. This article will begin by summarizing the discovery, biogenesis, and applications of naturally occurring CNAs, followed by discussing the methods for constructing artificial CNAs. The exploitation of circular functional nucleic acids for applications in nanodevice engineering, biosensing, and drug delivery will be reviewed next. Finally, the efforts to couple functional nucleic acids with rolling circle amplification for ultra-sensitive biosensing and for synthesizing multivalent molecular scaffolds for unique applications in biosensing and drug delivery will be recapitulated.
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Affiliation(s)
- Jiuxing Li
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Mostafa Mohammed-Elsabagh
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Freeman Paczkowski
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Yingfu Li
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
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An electric potential modulated cascade of catalyzed hairpin assembly and rolling chain amplification for microRNA detection. Biosens Bioelectron 2018; 126:565-571. [PMID: 30500771 DOI: 10.1016/j.bios.2018.09.088] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 09/20/2018] [Accepted: 09/27/2018] [Indexed: 11/24/2022]
Abstract
MicroRNAs serve as a new type of biomarker for multifarious diseases due to its critical roles in post transcriptional gene regulation. Herein, we firstly integrate the catalyzed hairpin assembly (CHA) and rolling circle amplification (RCA) into an electrochemical biosensor for sensitive and specific detection of miR-21. Meanwhile, an electric potential was employed to modulate the efficiency of CHA occurred on the electrode, which offer a simple but effective method to surmount the accessibility problem of probes. The biosensor achieved an ultrasensitive determination of miR-21 with a low limit of detection of 13.5 fM and a linear range from 15 fM to 250 pM. This research encourages us to challenge the hyphenated multiple amplification strategies and provides a stable and effective method for the detection of diseases-related miRNAs in peripheral biofluids, as well as paves a road for the future clinical diagnostics and treatment of disease.
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Chen Z, Duan X, Wei H, Tang S, Xu C, Li Y, Guan Y, Zhao G. Screening oligonucleotide sequences for silver staining and d-galactose visual detection using RCA silver staining in a tube. Acta Biochim Biophys Sin (Shanghai) 2018; 50:507-515. [PMID: 29635339 DOI: 10.1093/abbs/gmy034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 03/07/2018] [Indexed: 02/04/2023] Open
Abstract
Oligonucleotides were screened for strongly silver-stained repetitive sequences. An 'AG'-clustered purine sequence showed strong staining, and the staining density can be compromised by disrupting the continuity of the 'AG'-clustered sequence. The staining-favored sequence was then employed in rolling circle amplification (RCA) for its product detection. A tube-staining method was developed for convenient and visual RCA assay. Moreover, by introducing GalR into RCA, d-galactose was detected by RCA tube-staining with naked eyes without any equipment. About 10 mM d-galactose can be easily identified, and the detection of d-galactose was specific in comparison with that of several other monosaccharides.
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Affiliation(s)
- Ziwei Chen
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110122, China
| | - Xuying Duan
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110122, China
| | - Hua Wei
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110122, China
| | - Suming Tang
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110122, China
| | - Chidong Xu
- Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
| | - Yanlei Li
- Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
| | - Yifu Guan
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110122, China
| | - Guojie Zhao
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110122, China
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Wang S, Sun J, Zhao J, Lu S, Yang X. Photo-Induced Electron Transfer-Based Versatile Platform with G-Quadruplex/Hemin Complex as Quencher for Construction of DNA Logic Circuits. Anal Chem 2018; 90:3437-3442. [PMID: 29425022 DOI: 10.1021/acs.analchem.7b05145] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
G-quadruplex has been developed as an innovator for analytical chemistry and biomedicine due to its vibrant binding activity, structural polymorphism, and critical roles in biological regulation. Herein, a simple but versatile platform was obtained by integrating split G-quadruplex and fluorophore into a molecular beacon, where the photoinduced electron transfer could occur when the fluorophore approached the preformed G-quadruplex/hemin complexes. Such design subtly combined the G4 disruption-induced fluorescent turn-on strategy and the photoinduced electron transfer property into one platform for constructing the logic circuits. On the basis of such a universal platform, a series of binary logic gates (OR, INHIBIT, AND, and XOR), a combinatorial gate (INHIBIT-OR), and even a complex logic operation for discrimination of multiples of three from natural numbers less than ten have been successfully achieved only by employing such platform as work unit and single-strand DNAs as inputs. The set-reset function of this platform could be realized by alternatively introducing blocking and releasing strands. In addition, this platform could operate in a biological matrix stably and precisely. Therefore, such a universal platform lays the foundation for complicating the logic systems, realizing the biocomputing and also points out a new direction for target detection.
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Affiliation(s)
- Shuang Wang
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Changchun , Jilin 130022 , China.,University of Science and Technology of China , Hefei , Anhui 230026 , China
| | - Jian Sun
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Changchun , Jilin 130022 , China
| | - Jiahui Zhao
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Changchun , Jilin 130022 , China.,University of Chinese Academy of Sciences , Beijing 100039 , China
| | - Shasha Lu
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Changchun , Jilin 130022 , China.,University of Science and Technology of China , Hefei , Anhui 230026 , China
| | - Xiurong Yang
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Changchun , Jilin 130022 , China
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Song Q, Yang L, Chen H, Zhang R, Na N, Ouyang J. A label-free fluorometric assay for actin detection based on enzyme-responsive DNA-templated copper nanoparticles. Talanta 2017; 174:444-447. [DOI: 10.1016/j.talanta.2017.06.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 06/08/2017] [Accepted: 06/12/2017] [Indexed: 11/26/2022]
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Sergelen K, Fossati S, Turupcu A, Oostenbrink C, Liedberg B, Knoll W, Dostálek J. Plasmon Field-Enhanced Fluorescence Energy Transfer for Hairpin Aptamer Assay Readout. ACS Sens 2017; 2:916-923. [PMID: 28750521 PMCID: PMC5537696 DOI: 10.1021/acssensors.7b00131] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
Surface plasmon field-enhanced fluorescence
energy transfer is
employed for sensitive optical readout of a reversible hairpin aptamer
assay that is suitable for continuous monitoring of low-molecular-weight
chemical analytes. A hairpin aptamer specific to adenosine and adenosine
triphosphate with Alexa Fluor 647 fluorophore attached to its 5′
end was anchored via 3′ end thiol to a gold thin film. Molecular
spacers were used to control the distance of the fluorophore from
the surface in the aptamer “off” and “on”
states. The specific binding of the target analyte changes the aptamer
conformation, which alters the distance of the fluorophore from the
gold surface and translates to variations in the detected fluorescence
intensity. The plasmonically mediated fluorescence signal increases
the measured signal-to-noise ratio and allows for real-time observation
of the analyte binding. Theoretical as well as experimental study
of the optical signal dependence on fluorophore orientation, design
of spacers, and angular distribution of collected light is presented
for rational design of the assay. The detected sensor signal increased
by a factor as large as 23 upon switching the aptamer from the “off”
to “on” state due to the hairpin opening associated
with the specific capture of target analyte.
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Affiliation(s)
- Khulan Sergelen
- BioSensor
Technologies, AIT-Austrian Institute of Technology, Muthgasse
11, 1190 Vienna, Austria
- Nanyang Technological University, Centre for Biomimetic
Sensor Science, School of Materials Science and Engineering, 50 Nanyang Drive, Singapore 637553
- International
Graduate School on Bionanotechnology, University of Natural Resources and Life Sciences, Austrian Institute of Technology, and Nanyang Technological University, 1190 Vienna, Austria
| | - Stefan Fossati
- BioSensor
Technologies, AIT-Austrian Institute of Technology, Muthgasse
11, 1190 Vienna, Austria
| | - Aysegül Turupcu
- University of Natural Resources and Life Sciences, Institute of Molecular Modeling and Simulation, Muthgasse 18, 1190 Vienna, Austria
| | - Chris Oostenbrink
- University of Natural Resources and Life Sciences, Institute of Molecular Modeling and Simulation, Muthgasse 18, 1190 Vienna, Austria
| | - Bo Liedberg
- Nanyang Technological University, Centre for Biomimetic
Sensor Science, School of Materials Science and Engineering, 50 Nanyang Drive, Singapore 637553
| | - Wolfgang Knoll
- BioSensor
Technologies, AIT-Austrian Institute of Technology, Muthgasse
11, 1190 Vienna, Austria
| | - Jakub Dostálek
- BioSensor
Technologies, AIT-Austrian Institute of Technology, Muthgasse
11, 1190 Vienna, Austria
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Hu B, Guo J, Xu Y, Wei H, Zhao G, Guan Y. A sensitive colorimetric assay system for nucleic acid detection based on isothermal signal amplification technology. Anal Bioanal Chem 2017; 409:4819-4825. [PMID: 28689323 DOI: 10.1007/s00216-017-0425-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 04/05/2017] [Accepted: 05/22/2017] [Indexed: 12/12/2022]
Abstract
Rapid and accurate detection of microRNAs in biological systems is of great importance. Here, we report the development of a visual colorimetric assay which possesses the high amplification capabilities and high selectivity of the rolling circle amplification (RCA) method and the simplicity and convenience of gold nanoparticles used as a signal indicator. The designed padlock probe recognizes the target miRNA and is circularized, and then acts as the template to extend the target miRNA into a long single-stranded nucleotide chain of many tandem repeats of nucleotide sequences. Next, the RCA product is hybridized with oligonucleotides tagged onto gold nanoparticles. This interaction leads to the aggregation of gold nanoparticles, and the color of the system changes from wine red to dark blue according to the abundance of miRNA. A linear correlation between fluorescence and target oligonucleotide content was obtained in the range 0.3-300 pM, along with a detection limit of 0.13 pM (n = 7) and a RSD of 3.9% (30 pM, n = 9). The present approach provides a simple, rapid, and accurate visual colorimetric assay that allows sensitive biodetection and bioanalysis of DNA and RNA nucleotides of interest in biologically important samples. Graphical abstract The colorimetric assay system for analyzing target oligonucleotides.
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Affiliation(s)
- Bo Hu
- Department of Biochemistry and Molecular Biology, College of Basic Medicine, China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, China
| | - Jing Guo
- Department of Biochemistry and Molecular Biology, College of Basic Medicine, China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, China
| | - Ying Xu
- Department of Biochemistry and Molecular Biology, College of Basic Medicine, China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, China
| | - Hua Wei
- Department of Biochemistry and Molecular Biology, College of Basic Medicine, China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, China
| | - Guojie Zhao
- Department of Biochemistry and Molecular Biology, College of Basic Medicine, China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, China
| | - Yifu Guan
- Department of Biochemistry and Molecular Biology, College of Basic Medicine, China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, China.
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Production of dumbbell probe through hairpin cleavage-ligation and increasing RCA sensitivity and specificity by circle to circle amplification. Sci Rep 2016; 6:29229. [PMID: 27385060 PMCID: PMC4935871 DOI: 10.1038/srep29229] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 06/16/2016] [Indexed: 11/23/2022] Open
Abstract
Dumbbell probe (DP) attracts increasing interests in rolling circle amplification (RCA). A universal DP production method through cleavage-ligation of hairpin was proposed and optimized. The production is characterized by restriction endonuclease (RE)-induced cleavage ends ligation. It has the advantage of phosphorylation-free, splint-free and purification-free. To optimize designing, we found that the position of RE cleavage sequence in the stem and the primer position in the loop affected the formation and amplification of DP obviously. Both sticky and blunt ends cleaved by RE produce DP efficiently. Moreover, we introduced this DP into circle to circle (C2C) RCA based on the same cleavage-ligation principle, and acquired high sensitivity. By combining a two-ligation design and the C2C strategy, specificity for detecting let-7 family members was increased extremely. Furthermore, coreaction of different steps facilitated convenient formation and amplification process of DP.
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Hong L, Zhou F, Wang G, Zhang X. Synthesis and sensing integration: A novel enzymatic reaction modulated Nanoclusters Beacon (NCB) "Illumination" strategy for label-free biosensing and logic gate operation. Biosens Bioelectron 2016; 86:588-594. [PMID: 27453987 DOI: 10.1016/j.bios.2016.07.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 06/27/2016] [Accepted: 07/06/2016] [Indexed: 01/13/2023]
Abstract
A novel fluorescent label-free "turn-on" NAD(+) and adenosine triphosphate (ATP) biosensing strategy is proposed by fully exploiting ligation triggered Nanocluster Beacon (NCB). In the presence of the target, the split NCB was brought to intact, which brought the C-rich sequence and enhancer sequence in close proximity resulting in the lightening of dark DNA/AgNCs ("On" mode). Further application was presented for logic gate operation and aptasensor construction. The feasibility was investigated by Ultraviolet-visible spectroscopy (UV-vis), Fluorescence, lifetime and High Resolution Transmission Electron Microscopy (HRTEM) etc. The strategy displayed good performance in the detection of NAD(+) and ATP, with the detection limit of 0.002nM and 0.001mM, the linear range of 10-1000nM and 0.003-0.01mM, respectively. Due to the DNA/AgNCs as fluorescence reporter, the completely label-free fluorescent strategy boasts the features of simplicity and low cost, and showing little reliance on the sensing environment. Meanwhile, the regulation by overhang G-rich sequence not relying on Förster energy transfer quenching manifests the high signal-to-background ratios (S/B ratios). This method not only provided a simple, economical and reliable fluorescent NAD(+) assay but also explored a flexible G-rich sequence regulated NCB probe for the fluorescent biosensors. Furthermore, this sensing mode was expanded to the application of a logic gate design, which exhibited a high performance for not only versatile biosensors construction but also for molecular computing application.
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Affiliation(s)
- Lu Hong
- Key Laboratory of Functional Molecular Solids, Wuhu, Anhui Province, 241000 PR China; College of Chemistry and Materials Science, Center for Nano Science and Technology, Anhui Normal University, Wuhu, 241000 PR China; Key Laboratory of Chem-Biosensing, Wuhu, Anhui Province, 241000 PR China
| | - Fu Zhou
- Key Laboratory of Functional Molecular Solids, Wuhu, Anhui Province, 241000 PR China; College of Chemistry and Materials Science, Center for Nano Science and Technology, Anhui Normal University, Wuhu, 241000 PR China; Key Laboratory of Chem-Biosensing, Wuhu, Anhui Province, 241000 PR China
| | - Guangfeng Wang
- Key Laboratory of Functional Molecular Solids, Wuhu, Anhui Province, 241000 PR China; College of Chemistry and Materials Science, Center for Nano Science and Technology, Anhui Normal University, Wuhu, 241000 PR China; Key Laboratory of Chem-Biosensing, Wuhu, Anhui Province, 241000 PR China; State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082 PR China.
| | - Xiaojun Zhang
- Key Laboratory of Functional Molecular Solids, Wuhu, Anhui Province, 241000 PR China; College of Chemistry and Materials Science, Center for Nano Science and Technology, Anhui Normal University, Wuhu, 241000 PR China; Key Laboratory of Chem-Biosensing, Wuhu, Anhui Province, 241000 PR China
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Miao X, Yang C, Leung CH, Ma DL. Application of iridium(III) complex in label-free and non-enzymatic electrochemical detection of hydrogen peroxide based on a novel "on-off-on" switch platform. Sci Rep 2016; 6:25774. [PMID: 27170211 PMCID: PMC4864421 DOI: 10.1038/srep25774] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 04/22/2016] [Indexed: 12/15/2022] Open
Abstract
We herein report a label-free and non-enzymatic electrochemical sensor for the highly sensitive detection of hydrogen peroxide (H2O2) based on a novel "on-off-on" switch system. In our design, MB was used as an electron mediator to accelerate the electron transfer while AuNPs was used to amplify the electrochemical signal due to its excellent biocompatibility and good conductivity. The "switch-off" state was achieved by introducing the guanine-rich capture probe (CP) and an iridium complex onto the electrode surface to form a hydrophobic layer, which then hinders electron transfer. Upon addition of H2O2, fenton reaction occurs and produces OH• in the presence of Fe(2+). The OH• cleaves the CP into DNA fragments, thus resulting in the release of CP and iridium complex from the sensing interface, recovering the electrochemical signal to generate a "switch-on" state. Based on this novel switch system, a detection limit as low as 3.2 pM can be achieved for H2O2 detection. Moreover, satisfactory results were obtained by using this method for the detection of H2O2 in sterilized milk. To the best of our knowledge, this is the first G-quadruplex-based electrochemical sensor using an iridium(III) complex.
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Affiliation(s)
- Xiangmin Miao
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Chao Yang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
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14
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15
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Abstract
Isothermal amplification of nucleic acids is a simple process that rapidly and efficiently accumulates nucleic acid sequences at constant temperature. Since the early 1990s, various isothermal amplification techniques have been developed as alternatives to polymerase chain reaction (PCR). These isothermal amplification methods have been used for biosensing targets such as DNA, RNA, cells, proteins, small molecules, and ions. The applications of these techniques for in situ or intracellular bioimaging and sequencing have been amply demonstrated. Amplicons produced by isothermal amplification methods have also been utilized to construct versatile nucleic acid nanomaterials for promising applications in biomedicine, bioimaging, and biosensing. The integration of isothermal amplification into microsystems or portable devices improves nucleic acid-based on-site assays and confers high sensitivity. Single-cell and single-molecule analyses have also been implemented based on integrated microfluidic systems. In this review, we provide a comprehensive overview of the isothermal amplification of nucleic acids encompassing work published in the past two decades. First, different isothermal amplification techniques are classified into three types based on reaction kinetics. Then, we summarize the applications of isothermal amplification in bioanalysis, diagnostics, nanotechnology, materials science, and device integration. Finally, several challenges and perspectives in the field are discussed.
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Affiliation(s)
- 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, 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, China
| | - Qian Li
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Lihua Wang
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Chunhai Fan
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China.,School of Life Science & Technology, ShanghaiTech University , Shanghai 200031, China
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16
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Chen X, Lin C, Chen Y, Wang Y, Chen X. A label-free fluorescence strategy for selective detection of nicotinamide adenine dinucleotide based on a dumbbell-like probe with low background noise. Biosens Bioelectron 2015; 77:486-90. [PMID: 26454831 DOI: 10.1016/j.bios.2015.10.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 09/15/2015] [Accepted: 10/02/2015] [Indexed: 01/04/2023]
Abstract
In this work we developed a novel label-free fluorescence sensing approach for the detection of nicotinamide adenine dinucleotide (NAD(+)) based on a dumbbell-like DNA probe designed for both ligation reaction and digestion reaction with low background noise. SYBR Green I (SG I), a double-helix dye, was chosen as the readout fluorescence signal. In the absence of NAD(+), the ligation reaction did not occur, but the probe was digested to mononucleotides after the addition of exonuclease I (Exo I) and exonuclease I (Exo III), resulting in a weak fluorescence intensity due to the weak interaction between SG I and mononucleotides. In the presence of NAD(+), the DNA probe was ligated by Escherichia coli DNA ligase, blocking the digestion by Exo I and Exo III. As a result, SG I was intercalated into the stem part of the DNA dumbbell probe and fluorescence enhancement was achieved. This method was simple in design, fast to operate, with good sensitivity and selectivity which could discriminate NAD(+) from its analogs.
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Affiliation(s)
- Xuexu Chen
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Chunshui Lin
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China; School of Physics and Centre for Climate and Air Pollution Studies, Ryan Institute, National University of Ireland Galway, University Road, Galway, Ireland
| | - Yiying Chen
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yiru Wang
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
| | - Xi Chen
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China; State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China.
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17
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Guo Y, Yao W, Xie Y, Zhou X, Hu J, Pei R. Logic gates based on G-quadruplexes: principles and sensor applications. Mikrochim Acta 2015. [DOI: 10.1007/s00604-015-1633-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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18
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Song Q, Peng M, Wang L, He D, Ouyang J. A fluorescent aptasensor for amplified label-free detection of adenosine triphosphate based on core-shell Ag@SiO2 nanoparticles. Biosens Bioelectron 2015; 77:237-41. [PMID: 26409024 DOI: 10.1016/j.bios.2015.09.008] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 08/25/2015] [Accepted: 09/04/2015] [Indexed: 12/21/2022]
Abstract
The novel, facile and universal aptamer-based methods for the highly sensitive and selective fluorescence detection of important biomolecules have attracted considerable interest. Here, we present a label-free aptasensor for adenosine triphosphate (ATP) detection in aqueous solutions by using an ultra-sensitive nucleic acid stain PicoGreen (PG) as a fluorescent indicator and core-shell Ag@SiO2 nanoparticles (NPs) as a metal-enhanced fluorescence (MEF) platform. In the presence of ATP, the complementary DNA (cDNA)/aptamer duplexes confined onto the Ag@SiO2 NPs surface can release their aptamers into the buffered solution, causing a significant reduction in fluorescence intensity. By virtue of the amplified fluorescence signal, this aptasensor toward ATP can achieve a detection limit of 14.2 nM with a wide linear range and exhibit a good assay performance in complex biological samples. This sensing approach is cost-effective and efficient because it avoids the fluorescence labeling process and the use of any enzymes. Hence, this method may offer an alternative tool for determining the concentrations of ATP in biochemical and biomedical research.
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Affiliation(s)
- Quanwei Song
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Manshu Peng
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Le Wang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Dacheng He
- Key laboratory for Cell Proliferation and Regulation Biology, Ministry of Education, Beijing Normal University, Beijing 100875, China
| | - Jin Ouyang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.
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19
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Wang P, Zhang T, Yang T, Jin N, Zhao Y, Fan A. A cascade amplification strategy based on rolling circle amplification and hydroxylamine amplified gold nanoparticles enables chemiluminescence detection of adenosine triphosphate. Analyst 2015; 139:3796-803. [PMID: 24899364 DOI: 10.1039/c4an00458b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A highly sensitive and selective chemiluminescent (CL) biosensor for adenosine triphosphate (ATP) was developed by taking advantage of the ATP-dependent enzymatic reaction (ATP-DER), the powerful signal amplification capability of rolling circle amplification (RCA), and hydroxylamine-amplified gold nanoparticles (Au NPs). The strategy relies on the ability of ATP, a cofactor of T4 DNA ligase, to trigger the ligation-RCA reaction. In the presence of ATP, the T4 DNA ligase catalyzes the ligation reaction between the two ends of the padlock probe, producing a closed circular DNA template that initiates the RCA reaction with phi29 DNA polymerase and dNTP. Therein, many complementary copies of the circular template can be generated. The ATP-DER is eventually converted into a detectable CL signal after a series of processes, including gold probe hybridization, hydroxylamine amplification, and oxidative gold metal dissolution coupled with a simple and sensitive luminol CL reaction. The CL signal is directly proportional to the ATP level. The results showed that the detection limit of the assay is 100 pM of ATP, which compares favorably with those of other ATP detection techniques. In addition, by taking advantage of ATP-DER, the proposed CL sensing system exhibits extraordinary specificity towards ATP and could distinguish the target molecule ATP from its analogues. The proposed method provides a new and versatile platform for the design of novel DNA ligation reaction-based CL sensing systems for other cofactors. This novel ATP-DER based CL sensing system may find wide applications in clinical diagnosis as well as in environmental and biomedical fields.
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Affiliation(s)
- Ping Wang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, People's Republic of China.
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20
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Zhao G, Hu T, Li J, Wei H, Shang H, Guan Y. A RCA-based assay for analyzing individual strand break in DNA heteroduplex cleavage by restriction endonucleases. Chem Commun (Camb) 2015; 50:11930-3. [PMID: 25157639 DOI: 10.1039/c4cc05314a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We have developed a rapid and high-throughput assay based on rolling circle amplification, to distinguish individual strand cleavage of DNA duplexes by restriction endonucleases. As an illustration, we analyzed nicking activity of Nb.BbvCI and uneven cleavage of LNA modified DNA by EcoRI. This assay has potential for analyzing protein-DNA interactions.
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Affiliation(s)
- Guojie Zhao
- Key Laboratory of Medical Cell Biology (Ministry of Education), Department of Biochemistry and Molecular Biology, China Medical University, Shenyang, Liaoning 110001, China.
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21
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Zhao G, Hu T, Li J, Wei H, Shang H, Guan Y. A novel strategy to analyze L-tryptophan through allosteric Trp repressor based on rolling circle amplification. Biosens Bioelectron 2015; 71:103-107. [PMID: 25889351 DOI: 10.1016/j.bios.2015.04.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 03/25/2015] [Accepted: 04/05/2015] [Indexed: 10/23/2022]
Abstract
Rolling circle amplification (RCA) has been considered as a powerful tool for nucleic acids detection. Here, a novel repressor-RCA-based method for L-tryptophan (L-Trp) detection was developed. This method utilizes the specific interaction between the RCA circular template and the Trp repressor protein (TrpR) involved in trp operon of Escherichia coli (E. coli). In the absence of L-Trp, the TrpR protein could not bind to the RCA template, and the RCA process can be continued. When L-Trp is present, the activated TrpR will bind to the operon sequence on the RCA template and inhibit the RCA reaction. Thus, the concentration of L-Trp is correlated directly with the fluorescent RCA signals. We succeeded in detecting L-Trp in a single step in simple homogeneous reaction system. The detection limit was estimated to be 0.77 μM (S/N=3) with good linearity. The method can unambiguously distinguish L-Trp from other 19 standard amino acids and L-Trp analogs. This strategy is also promising for detecting many small molecules such as other amino acids and carbohydrates.
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Affiliation(s)
- Guojie Zhao
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang, Liaoning 110001, China
| | - Tianyu Hu
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang, Liaoning 110001, China
| | - Jun Li
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang, Liaoning 110001, China
| | - Hua Wei
- Animal Science and Veterinary Medicine College, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Hong Shang
- Department of Clinical Diagnosis, the First Affiliated Hospital, China Medical University, Shenyang, Liaoning 110001, China
| | - Yifu Guan
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang, Liaoning 110001, China.
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22
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Zhao H, Wang L, Liu X, Gao Z, Jiang W. Label-free detection of nicotinamide adenine dinucleotide based on ligation-triggered exonuclease III-assisted signal amplification. RSC Adv 2015. [DOI: 10.1039/c5ra13722e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Schematic illustration of the Exo III-assisted amplification strategy for NAD+ detection.
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Affiliation(s)
- Haiyan Zhao
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry
- School of Chemistry and Chemical Engineering
- Shandong University
- 250100 Jinan
- P. R. China
| | - Lei Wang
- School of Pharmaceutical Sciences
- Shandong University
- 250012 Jinan
- P. R. China
| | - Xingti Liu
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry
- School of Chemistry and Chemical Engineering
- Shandong University
- 250100 Jinan
- P. R. China
| | - Zhiyue Gao
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry
- School of Chemistry and Chemical Engineering
- Shandong University
- 250100 Jinan
- P. R. China
| | - Wei Jiang
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry
- School of Chemistry and Chemical Engineering
- Shandong University
- 250100 Jinan
- P. R. China
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23
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Guo LE, Zhang JF, Liu XY, Zhang LM, Zhang HL, Chen JH, Xie XG, Zhou Y, Luo K, Yoon J. Phosphate ion targeted colorimetric and fluorescent probe and its use to monitor endogeneous phosphate ion in a hemichannel-closed cell. Anal Chem 2014; 87:1196-201. [PMID: 25511872 DOI: 10.1021/ac503818p] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Fluorescent probe 1, the first inorganic phosphate (Pi) targeted colorimetric and fluorescent probe to detect endogenous Pi in hemichannel-closed cells, has been developed. Probe 1 undergoes a unique Pi induced hydrolytic reaction in DMSO-HEPES (V/V = 9:1) buffered (0.02 M, pH 7.4) solutions that produces a colorimetric change associated with a 62 nm red-shift in the UV-vis absorption maximum and up to a 780-fold enhancement in the fluorescence intensity. The mechanistic proposal that these spectroscopic changes are associated with reaction Pi with 1 to form coumarin gains support from the results of theoretical calculations and mass spectrometry studies. Observations made in fluorescence imaging studies with HeLa cells and C. elegans show that 1 can be employed to monitor Pi production in vivo caused by apyrase-catalyzed ATP hydrolysis. Moreover, probe 1 was utilized to show that apoptosis of hemichannel-closed Sf9 cells is caused by Inx3 promoted dephosphorylation of Akt (RAC serine/threonine-protein kinase), leading to an elevation of the concentration of Pi. Overall, the study has produced the first fluorescent sensor 1 for endogenous inorganic phosphate. Moreover, the utility of 1 for measuring Pi release in vitro has been demonstrated and utilized to elucidate the mechanism of Inx3 action in hemichannel-closed Sf9 cells.
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Affiliation(s)
- Lin E Guo
- College of Chemical Science and Technology, Yunnan University , Kunming 650091, China
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24
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Yu J, Zhang L, Xu X, Liu S. Quantitative detection of potassium ions and adenosine triphosphate via a nanochannel-based electrochemical platform coupled with G-quadruplex aptamers. Anal Chem 2014; 86:10741-8. [PMID: 25333881 DOI: 10.1021/ac502752g] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The development of synthetic nanopores and nanochannels that mimick ion channels in living organisms for biosensing applications has been, and still remains, a great challenge. Although the biological applications of nanopores and nanochannels have achieved considerable development as a result of nanotechnology advancements, there are few reports of a facile way to realize those applications. Herein, a nanochannel-based electrochemical platform was developed for the quantitative detection of biorelated small molecules such as potassium ions (K(+)) and adenosine triphosphate (ATP) in a facile way. For this purpose, K(+) or ATP G-quadruplex aptamers were covalently assembled onto the inner wall of porous anodic alumina (PAA) nanochannels through a Schiff reaction between -CHO groups in the aptamer and amino groups on the inner wall of the PAA nanochannels under mild reaction conditions. Conformational switching of the aptamers confined in the nanochannels occurs in the presence of the target molecules, resulting in increased steric hindrance in the nanochannels. Changes in steric hindrance in the nanochannels were monitored by the anodic current of indicator molecules transported through the nanochannels. As a result, quantitative detection of K(+) and ATP was realized with a concentration ranging from 0.005 to 1.0 mM for K(+) and 0.05 to 10.0 mM for ATP. The proposed platform displayed significant selectivity, good reproducibility, and universality. Moreover, this platform showed its potential for use in the detection of other aptamer-based analytes, which could promote its development for use in biological detection and clinical diagnosis.
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Affiliation(s)
- Jiachao Yu
- Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, Suzhou Research Institute of Southeast University, School of Chemistry and Chemical Engineering, Southeast University , Nanjing 210096, P. R. China
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25
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Liu Y, Lei J, Huang Y, Ju H. "Off-on" electrochemiluminescence system for sensitive detection of ATP via target-induced structure switching. Anal Chem 2014; 86:8735-41. [PMID: 25118587 DOI: 10.1021/ac501913c] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
An "off-on" electrochemiluminescence (ECL) strategy was constructed for highly sensitive and selective detection of adenosine 5'-triphosphate (ATP) with a quantum dots (QDs) modified electrode and a DNAzyme signal probe. The immobilized QDs were functionalized with a DNA sequence (DNA1) and then aptamer for recognition of target analyte. The signal probe was prepared by assembling another DNA sequence (DNA2) and G-quadruplex on gold nanoparticle via Au-S chemistry, which was used to bind the probe to electrode surface through a hybridization reaction with aptamer and hemin for forming G-quadruplex/hemin DNAzyme, respectively. Upon the sandwich hybridization of DNA1-aptamer-DNA2, the signal probe could be captured on the aptasensor to catalyze the reduction of dissolved oxygen, the coreactant for cathodic ECL emission of QDs, leading to a decrease of ECL intensity and thus the "off" state. In the presence of target, its recognition by aptamer led to the release of aptamer from electrode surface and decreased the amount of captured signal probe, thus the ECL emission was in its "on" state. The "off-on" strategy resulted from the target-induced structure switching could be used for specific detection of ATP with a linear range of 8-2000 nM and a detection limit of 7.6 nM. The proposed aptasensor could be successfully applied in the ECL detection of ATP in human serum. This method could resist environmental interfering agents and be extended for sensitive and reliable detection of a wide range of analytes in complex sample.
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Affiliation(s)
- Yueting Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210093, P.R. China
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26
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Jiang HX, Kong DM, Shen HX. Amplified detection of DNA ligase and polynucleotide kinase/phosphatase on the basis of enrichment of catalytic G-quadruplex DNAzyme by rolling circle amplification. Biosens Bioelectron 2014; 55:133-8. [DOI: 10.1016/j.bios.2013.12.001] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Revised: 11/24/2013] [Accepted: 12/01/2013] [Indexed: 12/01/2022]
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27
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Liu S, Wang X, Pang S, Na W, Yan X, Su X. Fluorescence detection of adenosine-5'-triphosphate and alkaline phosphatase based on the generation of CdS quantum dots. Anal Chim Acta 2014; 827:103-10. [PMID: 24833001 DOI: 10.1016/j.aca.2014.04.027] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 04/15/2014] [Accepted: 04/17/2014] [Indexed: 12/24/2022]
Abstract
We have developed an analytical method to detect adenosine-5'-triphosphate (ATP) and alkaline phosphatase (ALP) based on the generation of CdS quantum dots (QDs). We demonstrated that Cd(2+) cation reacts with S(2-) anion to generate fluorescent CdS QDs in the presence of some certain amount of ATP. With increase in the ATP concentration, the fluorescence intensity of CdS QDs was also enhanced. ATP can be converted into adenosine by the dephosphorylation of ALP, so that the generation of CdS QDs would be inhibited in the presence of ALP. Therefore, this novel analysis system could be applied to assay ATP and ALP based on the growth of fluorescent CdS QDs.
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Affiliation(s)
- Siyu Liu
- Department of Analytical Chemistry, College of Chemistry, Jilin University, Changchun 130012, China
| | - Xinyan Wang
- Department of Analytical Chemistry, College of Chemistry, Jilin University, Changchun 130012, China
| | - Shu Pang
- Department of Analytical Chemistry, College of Chemistry, Jilin University, Changchun 130012, China
| | - Weidan Na
- Department of Analytical Chemistry, College of Chemistry, Jilin University, Changchun 130012, China
| | - Xu Yan
- Department of Analytical Chemistry, College of Chemistry, Jilin University, Changchun 130012, China
| | - Xingguang Su
- Department of Analytical Chemistry, College of Chemistry, Jilin University, Changchun 130012, China.
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28
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Ippolito JE, Piwnica-Worms D. A fluorescence-coupled assay for gamma aminobutyric acid (GABA) reveals metabolic stress-induced modulation of GABA content in neuroendocrine cancer. PLoS One 2014; 9:e88667. [PMID: 24551133 PMCID: PMC3923810 DOI: 10.1371/journal.pone.0088667] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 01/15/2014] [Indexed: 11/18/2022] Open
Abstract
Pathways involved in the synthesis of the neurotransmitter gamma-aminobutyric acid (GABA) have been implicated in the pathogenesis of high grade neuroendocrine (NE) neoplasms as well as neoplasms from a non-NE lineage. Using The Cancer Genome Atlas, overexpression of the GABA synthetic enzyme, glutamate decarboxylase 1 (GAD1), was found to be associated with decreased disease free-survival in prostate adenocarcinoma and decreased overall survival in clear cell renal cell carcinomas. Furthermore, GAD1 was found to be expressed in castrate-resistant prostate cancer cell lines, but not androgen-responsive cell lines. Using a novel fluorescence-coupled enzymatic microplate assay for GABA mediated through reduction of resazurin in a prostate neuroendocrine carcinoma (PNEC) cell line, acid microenvironment-induced stress increased GABA levels while alkaline microenvironment-induced stress decreased GABA through modulation of GAD1 and glutamine synthetase (GLUL) activities. Moreover, glutamine but not glucose deprivation decreased GABA through modulation of GLUL. Consistent with evidence in prokaryotic and eukaryotic organisms that GABA synthesis mediated through GAD1 may play a crucial role in surviving stress, GABA may be an important mediator of stress survival in neoplasms. These findings identify GABA synthesis and metabolism as a potentially important pathway for regulating cancer cell stress response as well as a potential target for therapeutic strategies.
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Affiliation(s)
- Joseph E. Ippolito
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail: (JEI); (DP-W)
| | - David Piwnica-Worms
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- BRIGHT Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Cancer Systems Imaging, University of Texas M.D. Anderson Cancer Center, Houston, Texas, United States of America
- * E-mail: (JEI); (DP-W)
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29
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Liu B, Zhang B, Chen G, Tang D. An omega-like DNA nanostructure utilized for small molecule introduction to stimulate formation of DNAzyme-aptamer conjugates. Chem Commun (Camb) 2014; 50:1900-2. [PMID: 24407587 DOI: 10.1039/c3cc49005j] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An omega (Ω)-like DNA nanostructure was for the first time utilized for homogenous electrochemical monitoring of small molecules (ATP used in this case) based on target-induced formation of DNAzyme-aptamer conjugates without the need for sample separation and washing.
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Affiliation(s)
- Bingqian Liu
- Ministry of Education Key Laboratory of Analysis and Detection of Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection of Food Safety, Department of Chemistry and Chemical Engineering, Fuzhou University, Fuzhou 350108, P.R. China.
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30
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Zou B, Song Q, Wang J, Liu Y, Zhou G. Invasive reaction assisted strand-displacement signal amplification for sensitive DNA detection. Chem Commun (Camb) 2014; 50:13722-4. [PMID: 25249213 DOI: 10.1039/c4cc06079b] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An extension-block base in a molecular beacon enables beacon-assisted strand-displacement amplification to couple with invasive reaction efficiently by flap extension.
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Affiliation(s)
- Bingjie Zou
- Department of Pharmacology
- Jinling Hospital, Medical School of Nanjing University
- Nanjing, China
| | - Qinxin Song
- Department of Pharmacology
- Jinling Hospital, Medical School of Nanjing University
- Nanjing, China
- School of Life Science and Technology
- China Pharmaceutical University
| | - Jianping Wang
- Department of Pharmacology
- Jinling Hospital, Medical School of Nanjing University
- Nanjing, China
- School of Life Science and Technology
- China Pharmaceutical University
| | - Yunlong Liu
- Department of Pharmacology
- Jinling Hospital, Medical School of Nanjing University
- Nanjing, China
| | - Guohua Zhou
- Department of Pharmacology
- Jinling Hospital, Medical School of Nanjing University
- Nanjing, China
- State Key Laboratory of Analytical Chemistry for Life Science
- Nanjing University
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31
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Xue Q, Lv Y, Zhang Y, Xu S, Yue Q, Li R, Wang L, Li H, Gu X, Zhang S, Liu J. Target-responsive dumbbell probe-mediated rolling circle amplification strategy for highly sensitive Hg2+ detection. RSC Adv 2014. [DOI: 10.1039/c4ra02266a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
A novel label-free amplified fluorescent sensing scheme based on target-responsive dumbbell probe-mediated rolling circle amplification (D-RCA) has been developed for sensitive and selective detection of mercuric ions.
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Affiliation(s)
- Qingwang Xue
- Department of Chemistry
- Liaocheng University
- Liaocheng, China
| | - Yanqin Lv
- Department of Chemistry
- Liaocheng University
- Liaocheng, China
| | - Yuanfu Zhang
- Department of Chemistry
- Liaocheng University
- Liaocheng, China
| | - Shuling Xu
- Department of Chemistry
- Liaocheng University
- Liaocheng, China
| | - Qiaoli Yue
- Department of Chemistry
- Liaocheng University
- Liaocheng, China
| | - Rui Li
- Department of Chemistry
- Liaocheng University
- Liaocheng, China
| | - Lei Wang
- Department of Chemistry
- Liaocheng University
- Liaocheng, China
| | - Haibo Li
- Department of Chemistry
- Liaocheng University
- Liaocheng, China
| | - Xiaohong Gu
- Shandong Provincial Key Lab of Test Technology on Food Quality and Safety
- Shandong Academy of Agricultural Sciences
- Jinan, China
| | - Shuqiu Zhang
- Shandong Provincial Key Lab of Test Technology on Food Quality and Safety
- Shandong Academy of Agricultural Sciences
- Jinan, China
| | - Jifeng Liu
- Department of Chemistry
- Liaocheng University
- Liaocheng, China
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32
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Liu B, Zhang B, Chen G, Yang H, Tang D. Metal sulfide-functionalized DNA concatamer for ultrasensitive electronic monitoring of ATP using a programmable capillary-based aptasensor. Biosens Bioelectron 2013; 53:390-8. [PMID: 24201002 DOI: 10.1016/j.bios.2013.10.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 10/08/2013] [Accepted: 10/12/2013] [Indexed: 12/16/2022]
Abstract
A new flow-through electrochemical aptasensor was designed for ultrasensitive monitoring of adenosine triphosphate (ATP) by coupling microvalve-programmable capillary column with CdS-functionalized DNA concatamer for signal amplification. Initially, a layer of primary DNA-conjugated polyacrylamide hydrogel was covalently linked onto the internal surface of capillary column, and then an automated sequenctial injection format with a syringe pump was employed for development of the programmable capillary-based aptasensor. In the presence of target DNA aptamer, the immobilized primary DNA hybridized with partial bases of the aptamer. The excess aptamer fregment could trigger the formation of DNA concatamer between auxiliary DNA1 and CdS-labeled auxiliary DNA2. Upon target ATP introduction, a specific ATP-aptamer reaction was excuated, thereby resulting in the release of CdS-functionalized DNA concatamer from the capillary. Subsenquent anodic stripping voltammetric detection of cadmium released under acidic conditions from the released CdS nanoparticles could be conducted in a homemade detection cell. Under optimal conditions, the dynamic concentration range spanned from 0.1 pM to 10nM ATP with a detection limit of 0.06 pM ATP. The electrochemical aptasensor showed good reproducibility, selectivity, and stability. In addition, the methodology was evaluated for the analysis of ATP spiked serum samples, and the recoveries was 81-140%.
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Affiliation(s)
- Bingqian Liu
- Key Laboratory of Analysis and Detection for Food Safety, Ministry of Education & Fujian Province, Department of Chemistry, Fuzhou University, Fuzhou 350108, People's Republic of China
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