51
|
Xu J, Zheng T, Le J, Jia L. Stepwise nanoassembly of a single hairpin probe and its biosensing. Talanta 2018; 187:272-278. [PMID: 29853047 DOI: 10.1016/j.talanta.2018.05.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 04/20/2018] [Accepted: 05/08/2018] [Indexed: 01/06/2023]
Abstract
Herein, we describe a novel trigger-induced DNA nanoassembly method using only one loop-stem shaped hairpin probe (HP) that consists of three different functional regions as a single building unit. The Region I is designed complementary to the trigger, while the Region II and Region III are projected to complementary with each other. When hybridized with the trigger, a toehold mediated strand displacement (TMSD) occurred on the strand of Region I, leading to the release of Region III for further hybridization with the Region II on another HP molecule and in turn inducing a stepwise growth of HP with the aid of polymerase. Unlike the conventional assembly approaches that rely on the sophisticated sequence design and complex operation, the single-HP nanoassembly is easy and fast. Moreover, because many HPs are opened during the assembly process, we exemplified the nanoassembly strategy by re-designing a new labeled hairpin probe to analyze the Kras oncogene with a high sensitivity and specificity. The present study demonstrated a novel promising DNA nanoassembly strategy for biological applications.
Collapse
Affiliation(s)
- Jianguo Xu
- Cancer Metastasis Alert and Prevention Center, and Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry; Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Fuzhou University, Fuzhou 350116 China; School of Food Science and Engineering, Hefei University of Technology, Hefei 230009, China
| | - Tingting Zheng
- Cancer Metastasis Alert and Prevention Center, and Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry; Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Fuzhou University, Fuzhou 350116 China
| | - Jingqing Le
- Cancer Metastasis Alert and Prevention Center, and Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry; Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Fuzhou University, Fuzhou 350116 China
| | - Lee Jia
- Cancer Metastasis Alert and Prevention Center, and Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry; Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Fuzhou University, Fuzhou 350116 China.
| |
Collapse
|
52
|
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
| |
Collapse
|
53
|
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
| |
Collapse
|
54
|
Ou M, Huang J, Yang X, He X, Quan K, Yang Y, Xie N, Li J, Wang K. Live-Cell MicroRNA Imaging through MnO2
Nanosheet-Mediated DD-A Hybridization Chain Reaction. Chembiochem 2017; 19:147-152. [DOI: 10.1002/cbic.201700573] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Min Ou
- State Key Laboratory of Chemo/Biosensing and Chemometrics; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province; College of Chemistry and Chemical Engineering; College of Biology; Hunan University; Changsha 410082 China
| | - Jin Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province; College of Chemistry and Chemical Engineering; College of Biology; Hunan University; Changsha 410082 China
| | - Xiaohai Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province; College of Chemistry and Chemical Engineering; College of Biology; Hunan University; Changsha 410082 China
| | - Xiaoxiao He
- State Key Laboratory of Chemo/Biosensing and Chemometrics; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province; College of Chemistry and Chemical Engineering; College of Biology; Hunan University; Changsha 410082 China
| | - Ke Quan
- State Key Laboratory of Chemo/Biosensing and Chemometrics; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province; College of Chemistry and Chemical Engineering; College of Biology; Hunan University; Changsha 410082 China
| | - Yanjing Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province; College of Chemistry and Chemical Engineering; College of Biology; Hunan University; Changsha 410082 China
| | - Nuli Xie
- State Key Laboratory of Chemo/Biosensing and Chemometrics; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province; College of Chemistry and Chemical Engineering; College of Biology; Hunan University; Changsha 410082 China
| | - Jing Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province; College of Chemistry and Chemical Engineering; College of Biology; Hunan University; Changsha 410082 China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province; College of Chemistry and Chemical Engineering; College of Biology; Hunan University; Changsha 410082 China
| |
Collapse
|
55
|
Luby BM, Zheng G. Specific and Direct Amplified Detection of MicroRNA with MicroRNA:Argonaute-2 Cleavage (miRACle) Beacons. Angew Chem Int Ed Engl 2017; 56:13704-13708. [DOI: 10.1002/anie.201707366] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Benjamin M. Luby
- Princess Margaret Cancer Centre and Techna Institute; University Health Network; 101 College St. Toronto ON Canada
- Institute of Biomaterials and Biomedical Engineering; University of Toronto; Toronto Ontario Canada
| | - Gang Zheng
- Princess Margaret Cancer Centre and Techna Institute; University Health Network; 101 College St. Toronto ON Canada
- Institute of Biomaterials and Biomedical Engineering; University of Toronto; Toronto Ontario Canada
- Department of Medical Biophysics; University of Toronto; Toronto Ontario Canada
| |
Collapse
|
56
|
Luby BM, Zheng G. Specific and Direct Amplified Detection of MicroRNA with MicroRNA:Argonaute-2 Cleavage (miRACle) Beacons. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201707366] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Benjamin M. Luby
- Princess Margaret Cancer Centre and Techna Institute; University Health Network; 101 College St. Toronto ON Canada
- Institute of Biomaterials and Biomedical Engineering; University of Toronto; Toronto Ontario Canada
| | - Gang Zheng
- Princess Margaret Cancer Centre and Techna Institute; University Health Network; 101 College St. Toronto ON Canada
- Institute of Biomaterials and Biomedical Engineering; University of Toronto; Toronto Ontario Canada
- Department of Medical Biophysics; University of Toronto; Toronto Ontario Canada
| |
Collapse
|
57
|
Wang X, Yan N, Song T, Wang B, Wei B, Lin L, Chen X, Tian H, Liang H. Robust Fuel Catalyzed DNA Molecular Machine for in Vivo MicroRNA Detection. ACTA ACUST UNITED AC 2017. [DOI: 10.1002/adbi.201700060] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Xiaojing Wang
- CAS Key Laboratory of Soft Matter Chemistry; Collaborative Innovation Center of Chemistry for Energy Materials (iChEM); Department of Polymer Science and Engineering; University of Science and Technology of China; Hefei Anhui 230026 P. R. China
| | - Nan Yan
- Key Laboratory of Polymer Ecomaterials; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun 130022 P. R. China
| | - Tingjie Song
- CAS Key Laboratory of Soft Matter Chemistry; Collaborative Innovation Center of Chemistry for Energy Materials (iChEM); Department of Polymer Science and Engineering; University of Science and Technology of China; Hefei Anhui 230026 P. R. China
| | - Bei Wang
- CAS Key Laboratory of Soft Matter Chemistry; Collaborative Innovation Center of Chemistry for Energy Materials (iChEM); Department of Polymer Science and Engineering; University of Science and Technology of China; Hefei Anhui 230026 P. R. China
| | - Bing Wei
- Hefei National Laboratory for Physical Sciences at Microscale; University of Science and Technology of China; Hefei Anhui 230026 P. R. China
| | - Lin Lin
- Key Laboratory of Polymer Ecomaterials; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun 130022 P. R. China
| | - Xuesi Chen
- Key Laboratory of Polymer Ecomaterials; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun 130022 P. R. China
| | - Huayu Tian
- Key Laboratory of Polymer Ecomaterials; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun 130022 P. R. China
| | - Haojun Liang
- CAS Key Laboratory of Soft Matter Chemistry; Collaborative Innovation Center of Chemistry for Energy Materials (iChEM); Department of Polymer Science and Engineering; University of Science and Technology of China; Hefei Anhui 230026 P. R. China
- Hefei National Laboratory for Physical Sciences at Microscale; University of Science and Technology of China; Hefei Anhui 230026 P. R. China
| |
Collapse
|
58
|
Fang GM, Seitz O. Bivalent Display of Dicysteine on Peptide Nucleic Acids for Homogenous DNA/RNA Detection through in Situ Fluorescence Labelling. Chembiochem 2016; 18:189-194. [PMID: 27883258 DOI: 10.1002/cbic.201600623] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Indexed: 01/06/2023]
Abstract
Fluorogenic probes that signal the presence of specific DNA or RNA sequences are key enabling tools for molecular disease diagnosis and imaging studies. Usually, at least one fluorophore is attached through covalent bonding to an oligonucleotide probe. However, the additional conjugation step increases costs. Here we introduce a method that avoids the requirement for the preparation of fluorescence-labelled oligonucleotides and provides the opportunity to alter the fluorogenic reporter dye without resynthesis. The method is based on adjacent hybridization of two dicysteine-containing peptide nucleic acid (PNA) probes to form a bipartite tetracysteine motif that binds profluorescent bisarsenical dyes such as FIAsH, ReAsH or CrAsH. Binding is accompanied by strong increases in fluorescence emission (with response factors of up to 80-fold and high brightness up to 50 mL mol-1 cm-1 ). The detection system provides sub-nanomolar limits of detection and allows discrimination of single nucleotide variations through more than 20-fold changes in fluorescence intensity. To demonstrate its usefulness, the FIAsH-based readout of the bivalent CysCys-PNA display was interfaced with a rolling-circle amplification (RCA) assay used to detect disease-associated microRNA let-7a.
Collapse
Affiliation(s)
- Ge-Min Fang
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489, Berlin, Germany
| | - Oliver Seitz
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489, Berlin, Germany
| |
Collapse
|
59
|
Ji D, Mohsen MG, Harcourt EM, Kool ET. ATP‐Releasing Nucleotides: Linking DNA Synthesis to Luciferase Signaling. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201509131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Debin Ji
- Department of Chemistry Stanford University Stanford CA 94305 USA
| | | | | | - Eric T. Kool
- Department of Chemistry Stanford University Stanford CA 94305 USA
| |
Collapse
|
60
|
Ji D, Mohsen MG, Harcourt EM, Kool ET. ATP-Releasing Nucleotides: Linking DNA Synthesis to Luciferase Signaling. Angew Chem Int Ed Engl 2016; 55:2087-91. [PMID: 26836342 DOI: 10.1002/anie.201509131] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 11/20/2015] [Indexed: 12/13/2022]
Abstract
A new strategy is reported for the production of luminescence signals from DNA synthesis through the use of chimeric nucleoside tetraphosphate dimers in which ATP, rather than pyrophosphate, is the leaving group. ATP-releasing nucleotides (ARNs) were synthesized as derivatives of the four canonical nucleotides. All four derivatives are good substrates for DNA polymerase, with Km values averaging 13-fold higher than those of natural dNTPs, and kcat values within 1.5-fold of those of native nucleotides. Importantly, ARNs were found to yield very little background signal with luciferase. DNA synthesis experiments show that the ATP byproduct can be harnessed to elicit a chemiluminescence signal in the presence of luciferase. When using a polymerase together with the chimeric nucleotides, target DNAs/RNAs trigger the release of stoichiometrically large quantities of ATP, thereby allowing sensitive isothermal luminescence detection of nucleic acids as diverse as phage DNAs and short miRNAs.
Collapse
Affiliation(s)
- Debin Ji
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Michael G Mohsen
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Emily M Harcourt
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA.
| |
Collapse
|
61
|
He X, Zeng T, Li Z, Wang G, Ma N. Catalytic Molecular Imaging of MicroRNA in Living Cells by DNA-Programmed Nanoparticle Disassembly. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201509726] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Xuewen He
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials; The Key Lab of Health Chemistry and Molecular Diagnosis of Suzhou, College of Chemistry; Chemical Engineering and Materials Science; Soochow University; Suzhou 215123 P.R. China
| | - Tao Zeng
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials; The Key Lab of Health Chemistry and Molecular Diagnosis of Suzhou, College of Chemistry; Chemical Engineering and Materials Science; Soochow University; Suzhou 215123 P.R. China
| | - Zhi Li
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials; The Key Lab of Health Chemistry and Molecular Diagnosis of Suzhou, College of Chemistry; Chemical Engineering and Materials Science; Soochow University; Suzhou 215123 P.R. China
| | - Ganglin Wang
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials; The Key Lab of Health Chemistry and Molecular Diagnosis of Suzhou, College of Chemistry; Chemical Engineering and Materials Science; Soochow University; Suzhou 215123 P.R. China
| | - Nan Ma
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials; The Key Lab of Health Chemistry and Molecular Diagnosis of Suzhou, College of Chemistry; Chemical Engineering and Materials Science; Soochow University; Suzhou 215123 P.R. China
| |
Collapse
|
62
|
He X, Zeng T, Li Z, Wang G, Ma N. Catalytic Molecular Imaging of MicroRNA in Living Cells by DNA-Programmed Nanoparticle Disassembly. Angew Chem Int Ed Engl 2015; 55:3073-6. [PMID: 26694689 DOI: 10.1002/anie.201509726] [Citation(s) in RCA: 206] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Revised: 11/26/2015] [Indexed: 12/19/2022]
Abstract
Molecular imaging is an essential tool for disease diagnostics and treatment. Direct imaging of low-abundance nucleic acids in living cells remains challenging because of the relatively low sensitivity and insufficient signal-to-background ratio of conventional molecular imaging probes. Herein, we report a class of DNA-templated gold nanoparticle (GNP)-quantum dot (QD) assembly-based probes for catalytic imaging of cancer-related microRNAs (miRNA) in living cells with signal amplification capacity. We show that a single miRNA molecule could catalyze the disassembly of multiple QDs with the GNP through a DNA-programmed thermodynamically driven entropy gain process, yielding significantly amplified QD photoluminescence (PL) for miRNA imaging. By combining the robust PL of QDs with the catalytic amplification strategy, three orders of magnitude improvement in detection sensitivity is achieved in comparison with non-catalytic imaging probe, which enables facile and accurate differentiation between cancer cells and normal cells by miRNA imaging in living cells.
Collapse
Affiliation(s)
- Xuewen He
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, The Key Lab of Health Chemistry and Molecular Diagnosis of Suzhou, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, 215123, P.R. China
| | - Tao Zeng
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, The Key Lab of Health Chemistry and Molecular Diagnosis of Suzhou, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, 215123, P.R. China
| | - Zhi Li
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, The Key Lab of Health Chemistry and Molecular Diagnosis of Suzhou, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, 215123, P.R. China
| | - Ganglin Wang
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, The Key Lab of Health Chemistry and Molecular Diagnosis of Suzhou, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, 215123, P.R. China
| | - Nan Ma
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, The Key Lab of Health Chemistry and Molecular Diagnosis of Suzhou, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, 215123, P.R. China.
| |
Collapse
|
63
|
Liu M, Zhang W, Zhang Q, Brennan JD, Li Y. Biosensing by Tandem Reactions of Structure Switching, Nucleolytic Digestion, and DNA Amplification of a DNA Assembly. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503182] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
64
|
Liu M, Zhang W, Zhang Q, Brennan JD, Li Y. Biosensing by Tandem Reactions of Structure Switching, Nucleolytic Digestion, and DNA Amplification of a DNA Assembly. Angew Chem Int Ed Engl 2015; 54:9637-41. [PMID: 26119600 DOI: 10.1002/anie.201503182] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 05/28/2015] [Indexed: 12/20/2022]
Abstract
ϕ29 DNA polymerase (ϕ29DP) is able to carry out repetitive rounds of DNA synthesis using a circular DNA template by rolling circle amplification (RCA). It also has the ability to execute 3'-5' digestion of single-stranded but not double-stranded DNA. A biosensor engineering strategy is presented that takes advantage of these two properties of ϕ29DP coupled with structure-switching DNA aptamers. The design employs a DNA assembly made of a circular DNA template, a DNA aptamer, and a pre-primer. The DNA assembly is unable to undergo RCA in the absence of cognate target owing to the formation of duplex structures. The presence of the target, however, triggers a structure-switching event that causes nucleolytic conversion of the pre-primer by ϕ29DP into a mature primer to facilitate RCA. This method relays target detection by the aptamer to the production of massive DNA amplicons, giving rise to dramatically enhanced detection sensitivity.
Collapse
Affiliation(s)
- Meng Liu
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada)
| | - Wenqing Zhang
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada)
| | - Qiang Zhang
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada)
| | - John D Brennan
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada).
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada). .,Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada).
| |
Collapse
|
65
|
Mao Y, Liu M, Tram K, Gu J, Salena BJ, Jiang Y, Li Y. Optimal DNA templates for rolling circle amplification revealed by in vitro selection. Chemistry 2015; 21:8069-74. [PMID: 25877998 DOI: 10.1002/chem.201500994] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Indexed: 01/21/2023]
Abstract
Rolling circle amplification (RCA) has been widely used as an isothermal DNA amplification technique for diagnostic and bioanalytical applications. Because RCA involves repeated copying of the same circular DNA template by a DNA polymerase thousands of times, we hypothesized there exist DNA sequences that can function as optimal templates and produce more DNA amplicons within an allocated time. Herein we describe an in vitro selection effort conducted to search from a random sequence DNA pool for such templates for phi29 DNA polymerase, a frequently used polymerase for RCA. Diverse DNA molecules were isolated and they were characterized by richness in adenosine (A) and cytidine (C) nucleotides. The top ranked sequences exhibit superior RCA efficiency and the use of these templates for RCA results in significantly improved detection sensitivity. AC-rich sequences are expected to find useful applications for setting up effective RCA assays for biological sensing.
Collapse
Affiliation(s)
- Yu Mao
- Departments of Biochemistry and Biomedical Sciences and Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada).,The Ministry-Province Jointly Constructed Base for State Key Laboratory, Shenzhen Key Laboratory of Chemical Biology, The Graduate School at Shenzhen, Tsinghua University, Shenzhen, Guangdong 518055 (P. R. China).,School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055 (P. R. China)
| | - Meng Liu
- Departments of Biochemistry and Biomedical Sciences and Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada)
| | - Kha Tram
- Departments of Biochemistry and Biomedical Sciences and Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada)
| | - Jimmy Gu
- Departments of Biochemistry and Biomedical Sciences and Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada)
| | - Bruno J Salena
- Department of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada)
| | - Yuyang Jiang
- The Ministry-Province Jointly Constructed Base for State Key Laboratory, Shenzhen Key Laboratory of Chemical Biology, The Graduate School at Shenzhen, Tsinghua University, Shenzhen, Guangdong 518055 (P. R. China).
| | - Yingfu Li
- Departments of Biochemistry and Biomedical Sciences and Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada).
| |
Collapse
|
66
|
Li X, Wang L, Li C. Rolling-Circle Amplification Detection of Thrombin Using Surface-Enhanced Raman Spectroscopy with Core-Shell Nanoparticle Probe. Chemistry 2015; 21:6817-22. [DOI: 10.1002/chem.201405884] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 02/09/2015] [Indexed: 12/26/2022]
|
67
|
Tian Q, Wang Y, Deng R, Lin L, Liu Y, Li J. Carbon nanotube enhanced label-free detection of microRNAs based on hairpin probe triggered solid-phase rolling-circle amplification. NANOSCALE 2015; 7:987-93. [PMID: 25470558 DOI: 10.1039/c4nr05243a] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The detection of microRNAs (miRNAs) is imperative for gaining a better understanding of the functions of these biomarkers and has great potential for the early diagnosis of human disease. High sensitivity and selectivity for miRNA detection brings new challenges. Herein, an ultrasensitive protocol for electrochemical detection of miRNA is designed through carbon nanotube (CNT) enhanced label-free detection based on hairpin probe triggered solid-phase rolling-circle amplification (RCA). Traditionally, RCA, widely applied for signal enhancement in the construction of a variety of biosensors, has an intrinsic limitation of ultrasensitive detection, as it is difficult to separate the enzymes, templates, and padlock DNAs from the RCA products in the homogeneous solution. We purposely designed a solid-phase RCA strategy, using CNTs as the solid substrate, integrated with a hairpin structured probe to recognize target miRNA. In the presence of miRNA the stem-loop structure will be unfolded, triggering the CNT based RCA process. Due to the efficient blocking effect originating from the polymeric RCA products, the label-free assay of miRNA exhibits an ultrasensitive detection limit of 1.2 fM. Furthermore, the protocol possesses excellent specificity for resolving lung cancer-related let-7 family members which have only one-nucleotide variations. The high sensitivity and selectivity give the method great potential for applications in online diagnostics and in situ detection in long-term development.
Collapse
Affiliation(s)
- Qianqian Tian
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China.
| | | | | | | | | | | |
Collapse
|
68
|
Zhou DM, Du WF, Xi Q, Ge J, Jiang JH. Isothermal nucleic acid amplification strategy by cyclic enzymatic repairing for highly sensitive microRNA detection. Anal Chem 2014; 86:6763-7. [PMID: 24949808 DOI: 10.1021/ac501857m] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Technologies enabling highly sensitive and selective detection of microRNAs (miRNAs) are critical for miRNA discovery and clinical theranostics. Here we develop a novel isothermal nucleic acid amplification technology based on cyclic enzymatic repairing and strand-displacement polymerase extension for highly sensitive miRNA detection. The enzymatic repairing amplification (ERA) reaction is performed via replicating DNA template using lesion bases by DNA polymerase and cleaving the DNA replicate at the lesions by repairing enzymes, uracil-DNA glycosylase, and endonuclease IV, to prime a next-round replication. By utilizing the miRNA target as the primer, the ERA reaction is capable of producing a large number of reporter sequences from the DNA template, which can then be coupled to a cyclic signal output reaction mediated by endonuclease IV. The ERA reaction can be configured as a single-step, close-tube, and real-time format, which enables highly sensitive and selective detection of miRNA with excellent resistance to contaminants. The developed technology is demonstrated to give a detection limit of 0.1 fM and show superb specificity in discriminating single-base mismatch. The results reveal that the ERA reaction may provide a new paradigm for efficient nucleic acid amplification and may hold the potential for miRNA expression profiling and related theranostic applications.
Collapse
Affiliation(s)
- Dian-Ming Zhou
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University , Changsha 410082, P. R. China
| | | | | | | | | |
Collapse
|
69
|
Wang Z, Sun N, He Y, Liu Y, Li J. DNA assembled gold nanoparticles polymeric network blocks modular highly sensitive electrochemical biosensors for protein kinase activity analysis and inhibition. Anal Chem 2014; 86:6153-9. [PMID: 24814403 DOI: 10.1021/ac501375s] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A highly sensitive electrochemical biosensor was built for the detection of kinase activity based on the DNA induced gold nanoparticles (AuNPs) polymeric network block signal amplification. In this strategy, the DNA1 conjugated AuNPs were integrated with the phosphorylated peptide by Zr(4+) and assembled into DNA-AuNPs polymeric network block by the hybridization of cDNA with each side sequences of DNA1 and joint DNA2. The kinase activity was determined by the amperometric responses of [Ru(NH3)6](3+) absorbed on the network block by electrostatic interaction. Due to its excellent electroactivity and high accommodation of the DNA-AuNPs polymeric network block for [Ru(NH3)6](3+), the current signal was significantly amplified, affording a highly sensitive electrochemical analysis of kinase activity. The as-proposed biosensor presents a low detection limit of 0.03 U mL(-1) for protein kinase A (PKA) activity, wide linear range (from 0.03 to 40 U mL(-1)), and excellent stability even in cell lysates and serum samples. This biosensor can also be applied for quantitative kinase inhibitor screening. Finally, the PKA activities from BE4S-2B, A549, and MCF-7 cell lysates were further analyzed, which provided a valuable strategy in developing a high-throughput assay of in vitro kinase activity and inhibitor screening for clinic diagnostics and therapeutics.
Collapse
Affiliation(s)
- Zonghua Wang
- Laboratory of Fiber Materials and Modern Textiles, the Growing Base for State Key Laboratory, Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials, Qingdao University , Qingdao, Shandong 266071, China
| | | | | | | | | |
Collapse
|