1
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Chu LT, Kwong HK, Cui C, Chen TH. Theranostic DNA nanostructure based on phenotype-specific activation of antisense oligonucleotides. Talanta 2024; 269:125399. [PMID: 37979506 DOI: 10.1016/j.talanta.2023.125399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 09/29/2023] [Accepted: 11/05/2023] [Indexed: 11/20/2023]
Abstract
Antisense oligonucleotide (ASO) is a powerful agent for gene therapy, designed to form complementary pairs with specific mRNA to inhibit gene expression. However, low specificity limits its potential. To overcome this challenge, we developed a Y-shape DNA nanostructure that enhances the specificity in ASO-based treatment by introducing a detection trigger. The design incorporates the phenotype-specific miR21 activation and the sequential release of Bcl2 ASO. As a result, our Y-shape DNA nanostructure downregulates >50 % Bcl2 mRNA expression and induces >60 % cell death in breast cancer cells. Meanwhile, this approach shows no obvious damage to the non-cancerous cells, indicating the therapeutic potential as a theranostics agent in precision medicine with the combination of biomarker sensing and treatment. Overall, our Y-shape DNA nanostructure serves as a promising strategy providing potential in customized conformation design with specific target sequences in gene therapy.
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Affiliation(s)
- Lok Ting Chu
- Department of Biomedical Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Hong Kong Special Administrative Region, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Guang Dong Medical University, 524023, Zhanjiang, China
| | - Hoi Kwan Kwong
- Department of Biomedical Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Hong Kong Special Administrative Region, China
| | - Chenyu Cui
- Department of Biomedical Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Hong Kong Special Administrative Region, China
| | - Ting-Hsuan Chen
- Department of Biomedical Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Hong Kong Special Administrative Region, China; City University of Hong Kong Shenzhen Research Institute, Shenzhen, China.
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2
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Chowdhury M, Hudson RHE. Exploring Nucleobase Modifications in Oligonucleotide Analogues for Use as Environmentally Responsive Fluorophores and Beyond. CHEM REC 2023; 23:e202200218. [PMID: 36344432 DOI: 10.1002/tcr.202200218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/07/2022] [Indexed: 11/09/2022]
Abstract
Over the past two decades, it has become abundantly clear that nucleic acid biochemistry, especially with respect to RNA, is more convoluted and complex than previously appreciated. Indeed, the application and exploitation of nucleic acids beyond their predestined role as the medium for storage and transmission of genetic information to the treatment and study of diseases has been achieved. In other areas of endeavor, utilization of nucleic acids as a probe molecule requires that they possess a reporter group. The reporter group of choice is often a luminophore because fluorescence spectroscopy has emerged as an indispensable tool to probe the structural and functional properties of modified nucleic acids. The scope of this review spans research done in the Hudson lab at The University of Western Ontario and is focused on modified pyrimidine nucleobases and their applications as environmentally sensitive fluorophores, base discriminating fluorophores, and in service of antisense applications as well as tantalizing new results as G-quadruplex destabilizing agents. While this review is a focused personal account, particularly influential work of colleagues in the chemistry community will be highlighted. The intention is not to make a comprehensive review, citations to the existing excellent reviews are given, any omission of the wonderful and impactful work being done by others globally is not intentional. Thus, this review will briefly introduce the context of our work, summarize what has been accomplished and finish with the prospects of future developments.
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Affiliation(s)
- Mria Chowdhury
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, N6A 5B7
| | - Robert H E Hudson
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, N6A 5B7
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3
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Wang Q, Xiao F, Su H, Liu H, Xu J, Tang H, Qin S, Fang Z, Lu Z, Wu J, Weng X, Zhou X. Inert Pepper aptamer-mediated endogenous mRNA recognition and imaging in living cells. Nucleic Acids Res 2022; 50:e84. [PMID: 35580055 PMCID: PMC9371900 DOI: 10.1093/nar/gkac368] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 04/01/2022] [Accepted: 05/12/2022] [Indexed: 02/06/2023] Open
Abstract
The development of RNA aptamers/fluorophores system is highly desirable for understanding the dynamic molecular biology of RNAs in vivo. Peppers-based imaging systems have been reported and applied for mRNA imaging in living cells. However, the need to insert corresponding RNA aptamer sequences into target RNAs and relatively low fluorescence signal limit its application in endogenous mRNA imaging. Herein, we remolded the original Pepper aptamer and developed a tandem array of inert Pepper (iPepper) fluorescence turn-on system. iPepper allows for efficient and selective imaging of diverse endogenous mRNA species in live cells with minimal agitation of the target mRNAs. We believe iPepper would significantly expand the applications of the aptamer/fluorophore system in endogenous mRNA imaging, and it has the potential to become a powerful tool for real-time studies in living cells and biological processing.
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Affiliation(s)
- Qi Wang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Feng Xiao
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Haomiao Su
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China.,Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT 06520, USA
| | - Hui Liu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Jinglei Xu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Heng Tang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Shanshan Qin
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Zhentian Fang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Ziang Lu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Jian Wu
- School of Medicine, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Xiaocheng Weng
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China.,The Institute of Advanced Studies, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
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4
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Dziuba D, Didier P, Ciaco S, Barth A, Seidel CAM, Mély Y. Fundamental photophysics of isomorphic and expanded fluorescent nucleoside analogues. Chem Soc Rev 2021; 50:7062-7107. [PMID: 33956014 DOI: 10.1039/d1cs00194a] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Fluorescent nucleoside analogues (FNAs) are structurally diverse mimics of the natural essentially non-fluorescent nucleosides which have found numerous applications in probing the structure and dynamics of nucleic acids as well as their interactions with various biomolecules. In order to minimize disturbance in the labelled nucleic acid sequences, the FNA chromophoric groups should resemble the natural nucleobases in size and hydrogen-bonding patterns. Isomorphic and expanded FNAs are the two groups that best meet the criteria of non-perturbing fluorescent labels for DNA and RNA. Significant progress has been made over the past decades in understanding the fundamental photophysics that governs the spectroscopic and environmentally sensitive properties of these FNAs. Herein, we review recent advances in the spectroscopic and computational studies of selected isomorphic and expanded FNAs. We also show how this information can be used as a rational basis to design new FNAs, select appropriate sequences for optimal spectroscopic response and interpret fluorescence data in FNA applications.
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Affiliation(s)
- Dmytro Dziuba
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| | - Pascal Didier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| | - Stefano Ciaco
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France. and Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Anders Barth
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Claus A M Seidel
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Yves Mély
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
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5
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Podder A, Lee HJ, Kim BH. Fluorescent Nucleic Acid Systems for Biosensors. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20200351] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Arup Podder
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Ha Jung Lee
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Byeang Hyean Kim
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
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6
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Zhao Y, Zuo X, Li Q, Chen F, Chen YR, Deng J, Han D, Hao C, Huang F, Huang Y, Ke G, Kuang H, Li F, Li J, Li M, Li N, Lin Z, Liu D, Liu J, Liu L, Liu X, Lu C, Luo F, Mao X, Sun J, Tang B, Wang F, Wang J, Wang L, Wang S, Wu L, Wu ZS, Xia F, Xu C, Yang Y, Yuan BF, Yuan Q, Zhang C, Zhu Z, Yang C, Zhang XB, Yang H, Tan W, Fan C. Nucleic Acids Analysis. Sci China Chem 2020; 64:171-203. [PMID: 33293939 PMCID: PMC7716629 DOI: 10.1007/s11426-020-9864-7] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 09/04/2020] [Indexed: 12/11/2022]
Abstract
Nucleic acids are natural biopolymers of nucleotides that store, encode, transmit and express genetic information, which play central roles in diverse cellular events and diseases in living things. The analysis of nucleic acids and nucleic acids-based analysis have been widely applied in biological studies, clinical diagnosis, environmental analysis, food safety and forensic analysis. During the past decades, the field of nucleic acids analysis has been rapidly advancing with many technological breakthroughs. In this review, we focus on the methods developed for analyzing nucleic acids, nucleic acids-based analysis, device for nucleic acids analysis, and applications of nucleic acids analysis. The representative strategies for the development of new nucleic acids analysis in this field are summarized, and key advantages and possible limitations are discussed. Finally, a brief perspective on existing challenges and further research development is provided.
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Affiliation(s)
- Yongxi Zhao
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, 710049 China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Feng Chen
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, 710049 China
| | - Yan-Ru Chen
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108 China
| | - Jinqi Deng
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190 China
| | - Da Han
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Changlong Hao
- State Key Lab of Food Science and Technology, International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, 214122 China
| | - Fujian Huang
- Faculty of Materials Science and Chemistry, Engineering Research Center of Nano-Geomaterials of Ministry of Education, China University of Geosciences, Wuhan, 430074 China
| | - Yanyi Huang
- College of Chemistry and Molecular Engineering, Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 China
| | - Guoliang Ke
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 China
| | - Hua Kuang
- State Key Lab of Food Science and Technology, International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, 214122 China
| | - Fan Li
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Jiang Li
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800 China
- Bioimaging Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210 China
| | - Min Li
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Na Li
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan, 250014 China
| | - Zhenyu Lin
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, 350116 China
| | - Dingbin Liu
- College of Chemistry, Research Center for Analytical Sciences, State Key Laboratory of Medicinal Chemical Biology, and Tianjin Key Laboratory of Molecular Recognition and Biosensing, Nankai University, Tianjin, 300071 China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1 Canada
| | - Libing Liu
- Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190 China
- College of Chemistry, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Xiaoguo Liu
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Chunhua Lu
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, 350116 China
| | - Fang Luo
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, 350116 China
| | - Xiuhai Mao
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Jiashu Sun
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190 China
| | - Bo Tang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan, 250014 China
| | - Fei Wang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Jianbin Wang
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology (ICSB), Chinese Institute for Brain Research (CIBR), Tsinghua University, Beijing, 100084 China
| | - Lihua Wang
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800 China
- Bioimaging Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210 China
| | - Shu Wang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1 Canada
| | - Lingling Wu
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Zai-Sheng Wu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108 China
| | - Fan Xia
- Faculty of Materials Science and Chemistry, Engineering Research Center of Nano-Geomaterials of Ministry of Education, China University of Geosciences, Wuhan, 430074 China
| | - Chuanlai Xu
- State Key Lab of Food Science and Technology, International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, 214122 China
| | - Yang Yang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Bi-Feng Yuan
- Department of Chemistry, Wuhan University, Wuhan, 430072 China
| | - Quan Yuan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 China
| | - Chao Zhang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Zhi Zhu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005 China
| | - Chaoyong Yang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005 China
| | - Xiao-Bing Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 China
| | - Huanghao Yang
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, 350116 China
| | - Weihong Tan
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 China
| | - Chunhai Fan
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240 China
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7
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Gouda AS, Przypis Ł, Walczak K, Jørgensen PT, Wengel J. Carbazole modified oligonucleotides: synthesis, hybridization studies and fluorescence properties. Org Biomol Chem 2020; 18:6935-6948. [PMID: 32936176 DOI: 10.1039/d0ob01553a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Synthesis of the novel thiophenyl carbazole phosphoramidite DNA building block 5 was accomplished in four steps using a Suzuki-Miyaura cross-coupling reaction from the core carbazole and it was seamlessly accommodated into a 9-mer DNA-based oligonucleotide by incorporation at the flanking 5'-end in combination with a central insertion of an LNA-T nucleotide. The carbazole-containing oligonucleotide was combined in different duplex hybrids, which were characterized by thermal denaturation, circular dichroism and fluorescence studies. The carbazole monomer modulates the duplex stability in various ways. Thus, monomer Z increased the thermal stability of the 9-mer towards the complementary 9-mer/15-mer DNA duplex by 4.2 °C. Furthermore, indications of its intercalation into the duplex were obtained by modeling studies and robust decreases in fluorescence emission intensities upon duplex formation. In contrast, no clear intercalating tendency was corroborated for monomer Z within the DNA/RNA hybrid duplex as indicated by moderate quenching of the fluorescence and similar duplex thermal stabilities relative to the corresponding control duplex. The recognition efficiencies of the carbazole modified oligonucleotide toward single nucleotide mismatches were studied with two 15-mer model targets (DNA and RNA). For both systems, mismatches positioned at the juxtaposition of the carbazole monomer showed pronounced deceases in thermal denaturation temperature. Steady-state fluorescence emission studies of all mismatched duplexes with incorporation of Z monomer typically displayed efficient fluorescence quenching.
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Affiliation(s)
- Alaa S Gouda
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
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8
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Charoenpakdee C, Vilaivan T. Quenching of fluorescently labeled pyrrolidinyl peptide nucleic acid by oligodeoxyguanosine and its application in DNA sensing. Org Biomol Chem 2020; 18:5951-5962. [PMID: 32696797 DOI: 10.1039/d0ob01299h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
Quenching by nucleobases can significantly affect the fluorescence properties of many fluorophores. The quenching efficiency depends on the electronic properties of the fluorophore and adjacent nucleobases. In this study, we present a hitherto unreported high-efficiency quenching (up to 90%) of various fluorescently labeled pyrrolidinyl peptide nucleic acid (acpcPNA) probes by oligodeoxyguanosine (dGX). The quenching principle relies on the electrostatic interaction between the positively charged lysine-modified acpcPNA probe and the negatively charged oligodeoxyguanosine. The addition of stoichiometric quantities of a DNA target with the sequence complementary to the PNA probe restored the fluorescence to the original level. This was explained by the binding of the DNA to the PNA via a specific base pairing, which resulted in the separation of the oligodeoxyguanosine quencher from the fluorophore. Much less fluorescence restoration was observed in the DNA containing one or more mismatched bases. Applications of the oligodeoxyguanosine-quenched PNA probes for DNA sequence determination, including in multiplex formats, are demonstrated. The performance in terms of sensitivity and mismatch discrimination is comparable to classical PNA-based molecular beacons but without the need for double-labeling, which is expensive and presents solubility issues, or a dedicated quencher probe. This exemplifies a novel use of the unique electrostatic properties of PNA to develop a DNA sensing platform for DNA sequence determination.
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Affiliation(s)
- Chayan Charoenpakdee
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand.
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand.
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9
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Yang Z, Hu Q, Qin L, Zhu S, Qiu L, Su Y, Jin J. RNase H amplified RNA probe and graphene oxide system for highly sensitive detection of (CAG)n DNA repeat sequences. NANOTECHNOLOGY 2019; 30:465502. [PMID: 31426052 DOI: 10.1088/1361-6528/ab3c8b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Huntington's disease is a chronic progressive neurodegeneration which is caused by CAG repeat sequences expanding in the huntingtin gene. There is currently no disease-modifying treatment for the disease, and its progression can only be slowed down before the onset of symptoms. A novel fluorescent platform which contains an RNA probe and graphene oxide for detection of the biomarker of Huntington's disease, CAG repeat sequences, was constructed in this investigation. In addition, RNase H was employed in the fluorescent system to enhance the sensitivity of the detection capability. The fluorescent signal was increased through the cyclic amplified reaction, which results from RNase H, specifically digestion of the RNA strand in the complement of the RNA-DNA duplex. The designed measurement method can detect CAG repeat sequences with a detection limit of 108 pM (R2 = 0.968) under which we optimized assay conditions. Furthermore, the detection limit is approximately 18 times lower than the traditional DNA and graphene oxide detection method without assistance of RNase H. Additionally, the probing platform also shows stronger ability to discriminate between the fluorescence of the target sequence and that of other non-target sequences. The results of our studies demonstrate that the RNase H amplified RNA probe and graphene oxide system exhibited excellent sensitivity and selectivity to the target of CAG repeats sequences.
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10
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Soni R, Sharma D, Krishna AM, Sathiri J, Sharma A. A highly efficient Baby Spinach-based minimal modified sensor (BSMS) for nucleic acid analysis. Org Biomol Chem 2019; 17:7222-7227. [PMID: 31329202 DOI: 10.1039/c9ob01414d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Molecular recognition between nucleic acids has proven to be a powerful tool for designing hybridization probes for the detection of DNA and RNA sequences. Most detection probes rely on the conjugation of small molecule dyes to nucleic acids for fluorescence output, which is not cost-effective and also limits their applications in vivo, as they are not genetically encodable. More affordable sensors devoid of any chemical labeling are needed that show high fluorescence output and are genetically encodable. Here, we have designed a label-free Baby Spinach-based minimal modified sensor (BSMS) for the analysis of nucleic acids. The minimal modification in the sensor design reduces the complexity of the design, and provides additional stabilization after binding the target nucleic acids, leading to a high fluorescence output. BSMS is able to detect both DNA and RNA of potentially any lengths and is based on a Baby Spinach aptamer that binds and enhances the fluorescence of a small molecule dye. BSMS shows specificity towards its analyte in the presence of other sequences and selectively differentiates between closely related sequences. BSMS comprises genetically encodable unmodified RNA and has been shown to function at ambient temperature, and thus is anticipated to provide nucleic acid monitoring in vivo.
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Affiliation(s)
- Rashi Soni
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Tirupati 517507, India.
| | - Deepti Sharma
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Tirupati 517507, India.
| | - A Murali Krishna
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Tirupati 517507, India.
| | - Jagadeesh Sathiri
- Department of Biology, Indian Institute of Science Education and Research (IISER), Tirupati 517507, India
| | - Ashwani Sharma
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Tirupati 517507, India. and Department of Biology, Indian Institute of Science Education and Research (IISER), Tirupati 517507, India
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11
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Liu WJ, Xu Q, Ma F, Li CC, Zhang CY. Exonuclease III-assisted multiple cycle amplification for the sensitive detection of DNA with zero background signal. Analyst 2019; 143:5461-5466. [PMID: 30280732 DOI: 10.1039/c8an01365a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Detection of low-abundant DNA is essential for disease diagnosis and treatment. DNA polymerase-based amplification is frequently used due to its excellent sensitivity, but it suffers from time-consuming and labour-intensive procedures, complex template/primer design, and inherent nonspecific amplification. Alternatively, Exonuclease III (Exo III)-assisted target recycling provides a new approach for DNA assay because of its simplicity and general applicability, but it suffers from high background signal due to the nonspecific Exo III digestion and poor sensitivity due to single cycle signal amplification. Herein, we demonstrate the development of Exo III-assisted multiple cycle amplification (exonuclease chain reaction) for the sensitive detection of DNA with zero background signal. The binding of single-stranded DNA binding protein (SSB) to the hairpin probes can protect them from nonspecific digestion by Exo III, resulting in near zero background signal. The presence of the target DNA initiates the Exo III-triggered multiple cycle amplification, enabling the achievement of high sensitivity with a detection limit of 3 fM and excellent selectivity with single base mismatch discrimination capability, holding great potential in disease diagnosis and biomedical research.
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Affiliation(s)
- Wen-Jing Liu
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China.
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12
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Fang X, Zheng Y, Duan Y, Liu Y, Zhong W. Recent Advances in Design of Fluorescence-Based Assays for High-Throughput Screening. Anal Chem 2019; 91:482-504. [PMID: 30481456 PMCID: PMC7262998 DOI: 10.1021/acs.analchem.8b05303] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Xiaoni Fang
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Yongzan Zheng
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Yaokai Duan
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Yang Liu
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521, United States
| | - Wenwan Zhong
- Department of Chemistry, University of California, Riverside, California 92521, United States
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521, United States
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13
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Tsuchiya A, Hashim SN, Ise S, Furuhata T, Kawai K, Wakabayashi R, Goto M, Kamiya N, Sando S. BODIPY-labeled Fluorescent Aptamer Sensors for Turn-on Sensing of Interferon-gamma and Adenine Compounds on Cells. ANAL SCI 2018; 32:543-7. [PMID: 27169654 DOI: 10.2116/analsci.32.543] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
An on-cell aptamer sensor has the potential to reveal cell-cell communications by signalling molecules. We attempted to design new fluorescent aptamer sensors for the sensing of IFN-γ and adenine compounds on cells. BODIPY-labeled external quencher-free aptamer sensors have allowed a turn-on detection of the target molecule with improved off/on efficiency.
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Affiliation(s)
- Akira Tsuchiya
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo
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14
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Zhou J, Opoku-Temeng C, Sintim HO. Fluorescent 2-Aminopurine c-di-GMP and GpG Analogs as PDE Probes. Methods Mol Biol 2018; 1657:245-261. [PMID: 28889299 DOI: 10.1007/978-1-4939-7240-1_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
c-di-GMP is widely recognized as an important ubiquitous signaling molecule in bacteria. c-di-GMP phosphodiesterases (PDEs) regulate the intracellular concentration of c-di-GMP and some could be potential drug targets. Here, we describe a class of dinucleotide probes suitable for monitoring the enzymatic activities of c-di-GMP PDEs in real time. Such probes contain fluorescent nucleobases and can be readily cleaved by PDEs, resulting in a change in fluorescence. Fluorescent cyclic and linear dinucleotide probes could be used in diverse applications, such as confirming the activity of an expressed PDE or oligoribonuclease (Orns) or identifying inhibitors of PDEs or Orns using high-throughput screening formats.
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Affiliation(s)
- Jie Zhou
- Purdue Institute for Drug Discovery, Purdue University, 500 Oval Drive, West Lafayette, IN, 47907, USA.,Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Clement Opoku-Temeng
- Purdue Institute for Drug Discovery, Purdue University, 500 Oval Drive, West Lafayette, IN, 47907, USA.,Biochemistry Graduate Program, University of Maryland, College Park, MD, 20742, USA.,Department of Chemistry, Center for Drug Discovery, Purdue University, West Lafayette, IN, 47907, USA
| | - Herman O Sintim
- Purdue Institute for Drug Discovery, Purdue University, 500 Oval Drive, West Lafayette, IN, 47907, USA. .,Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA. .,Purdue Institute of Inflammation, Immunology and Infectious Disease, West Lafayette, IN, 47907, USA.
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15
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Kanamori T, Takamura A, Tago N, Masaki Y, Ohkubo A, Sekine M, Seio K. Fluorescence enhancement of oligodeoxynucleotides modified with green fluorescent protein chromophore mimics upon triplex formation. Org Biomol Chem 2018; 15:1190-1197. [PMID: 28084483 DOI: 10.1039/c6ob01278g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Green fluorescent protein (GFP)-based molecular-rotor chromophores were attached to the 5-positions of deoxyuridines, and subsequently, incorporated into the middle positions of oligodeoxynucleotides. These oligonucleotides were designed to form triplex DNA in order to encapsulate the GFP chromophores, mimicking GFP structures. Upon triplex formation, the embedded GFP chromophores exhibited fluorescence enhancement, suggesting the potential application of these fluorescent probes for the detection of nucleic acids.
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Affiliation(s)
- Takashi Kanamori
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta-Cho, Midori-ku, Yokohama 226-8501, Japan.
| | - Akihiro Takamura
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta-Cho, Midori-ku, Yokohama 226-8501, Japan.
| | - Nobuhiro Tago
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta-Cho, Midori-ku, Yokohama 226-8501, Japan.
| | - Yoshiaki Masaki
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta-Cho, Midori-ku, Yokohama 226-8501, Japan.
| | - Akihiro Ohkubo
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta-Cho, Midori-ku, Yokohama 226-8501, Japan.
| | - Mitsuo Sekine
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta-Cho, Midori-ku, Yokohama 226-8501, Japan.
| | - Kohji Seio
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta-Cho, Midori-ku, Yokohama 226-8501, Japan.
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16
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Hwang GT. Single-Labeled Oligonucleotides Showing Fluorescence Changes Upon Hybridization with Target Nucleic Acids. Molecules 2018; 23:E124. [PMID: 29316733 PMCID: PMC6017082 DOI: 10.3390/molecules23010124] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 01/05/2018] [Accepted: 01/08/2018] [Indexed: 12/12/2022] Open
Abstract
Sequence-specific detection of nucleic acids has been intensively studied in the field of molecular diagnostics. In particular, the detection and analysis of single-nucleotide polymorphisms (SNPs) is crucial for the identification of disease-causing genes and diagnosis of diseases. Sequence-specific hybridization probes, such as molecular beacons bearing the fluorophore and quencher at both ends of the stem, have been developed to enable DNA mutation detection. Interestingly, DNA mutations can be detected using fluorescently labeled oligonucleotide probes with only one fluorophore. This review summarizes recent research on single-labeled oligonucleotide probes that exhibit fluorescence changes after encountering target nucleic acids, such as guanine-quenching probes, cyanine-containing probes, probes containing a fluorophore-labeled base, and microenvironment-sensitive probes.
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Affiliation(s)
- Gil Tae Hwang
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, Daegu 41566, Korea.
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17
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Lee HJ, Go GH, Ro JJ, Kim BH. Detection of cofilin mRNA by hybridization-sensitive double-stranded fluorescent probes. RSC Adv 2018; 8:7514-7517. [PMID: 35539109 PMCID: PMC9078427 DOI: 10.1039/c7ra13349a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 02/10/2018] [Indexed: 12/13/2022] Open
Abstract
We have developed hybridization-sensitive fluorescent oligonucleotide probes that, in the presence of quencher strands, undergo efficient fluorescence quenching through the formation of partial DNA/DNA duplexes.
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Affiliation(s)
- Ha Jung Lee
- Department of Chemistry
- Division of Advanced Materials Science
- Pohang University of Science and Technology (POSTECH)
- Pohang 37673
- Republic of Korea
| | - Gui Han Go
- Department of Chemistry
- Division of Advanced Materials Science
- Pohang University of Science and Technology (POSTECH)
- Pohang 37673
- Republic of Korea
| | - Jong Jin Ro
- Department of Chemistry
- Division of Advanced Materials Science
- Pohang University of Science and Technology (POSTECH)
- Pohang 37673
- Republic of Korea
| | - Byeang Hyean Kim
- Department of Chemistry
- Division of Advanced Materials Science
- Pohang University of Science and Technology (POSTECH)
- Pohang 37673
- Republic of Korea
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18
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Duprey JLHA, Bassani DM, Hyde EI, Jonusauskas G, Ludwig C, Rodger A, Spencer N, Vyle JS, Wilkie J, Zhao ZY, Tucker JHR. Rationalisation of a mechanism for sensing single point variants in target DNA using anthracene-tagged base discriminating probes. Org Biomol Chem 2018; 16:6576-6585. [DOI: 10.1039/c8ob01710g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The fluorescence sensing mechanism for identifying single base changes in target DNA strands has been established through detailed biophysical measurements.
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Affiliation(s)
| | - Dario M. Bassani
- Institut des Sciences Moléculaires, CNRS UMR 5255
- Université Bordeaux
- Talence 33405
- France
| | - Eva I. Hyde
- School of Biosciences
- The University of Birmingham
- Edgbaston
- UK
| | - Gediminas Jonusauskas
- Laboratoire Ondes et Matière d'Aquitaine
- UMR CNRS 5798
- Université Bordeaux
- Talence 33405
- France
| | - Christian Ludwig
- Henry Wellcome Building for Biomolecular NMR Spectroscopy
- Institute of Cancer & Genomic Sciences
- College of Medical & Dental Sciences
- University of Birmingham
- Edgbaston
| | - Alison Rodger
- Department of Molecular Sciences
- Faculty of Science and Engineering
- Macquarie University
- North Ryde
- Australia
| | - Neil Spencer
- School of Chemistry
- University of Birmingham
- Edgbaston
- UK
| | - Joseph S. Vyle
- School of Chemistry and Chemical Engineering
- Queen's University Belfast
- Belfast
- UK
| | - John Wilkie
- School of Chemistry
- University of Birmingham
- Edgbaston
- UK
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19
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Park Y, Nim-Anussornkul D, Vilaivan T, Morii T, Kim BH. Facile conversion of ATP-binding RNA aptamer to quencher-free molecular aptamer beacon. Bioorg Med Chem Lett 2017; 28:77-80. [PMID: 29248297 DOI: 10.1016/j.bmcl.2017.12.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 11/23/2017] [Accepted: 12/05/2017] [Indexed: 01/02/2023]
Abstract
We have developed RNA-based quencher-free molecular aptamer beacons (RNA-based QF-MABs) for the detection of ATP, taking advantage of the conformational changes associated with ATP binding to the ATP-binding RNA aptamer. The RNA aptamer, with its well-defined structure, was readily converted to the fluorescence sensors by incorporating a fluorophore into the loop region of the hairpin structure. These RNA-based QF-MABs exhibited fluorescence signals in the presence of ATP relative to their low background signals in the absence of ATP. The fluorescence emission intensity increased upon formation of a RNA-based QF-MAB·ATP complex.
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Affiliation(s)
- Yoojin Park
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | | | - Tirayut Vilaivan
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Byeang Hyean Kim
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea.
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20
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Maity D, Matković M, Li S, Ehlers M, Wu J, Piantanida I, Schmuck C. Peptide-Based Probes with an Artificial Anion-Binding Motif for Direct Fluorescence "Switch-On" Detection of Nucleic Acid in Cells. Chemistry 2017; 23:17356-17362. [PMID: 28967979 DOI: 10.1002/chem.201703813] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Indexed: 01/08/2023]
Abstract
This work reports two new peptide-based fluorescence probes (1 and 2) for the detection of ds-DNA at physiological pH. Probes 1 and 2 contain a fluorophore, either amino-naphthalimide or diethyl-aminocoumarin, respectively, and two identical peptide arms each equipped with a guanidiniocarbonylpyrrole (GCP) anion-binding motif. These probes show "switch-on" fluorescence response upon binding to ds-DNA, whereby they can differentiate between various types of polynucleotides. For instance, they exhibit more pronounced fluorescence response for AT-rich polynucleotides than GC-rich polynucleotides, and both give only negligible response to ds-RNA. The fluorimetric response of 1 is proportional to the AT-basepair content in DNA, whereas the fluorescence of 2 is sensitive to the secondary structure of the polynucleotide. Fluorescence experiments, thermal melting experiments and circular dichroism studies suggest that 1 interacts with ds-DNA in a combined intercalation and minor groove binding, whereas 2 interacts mainly with the outer surface of DNA/RNA. As 1 and 2 have a very low cytotoxicity, 1 can be applied for the imaging of nuclear DNA in cells.
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Affiliation(s)
- Debabrata Maity
- Institute of Organic Chemistry, University of Duisburg-Essen, 45117, Essen, Germany
| | | | - Shang Li
- Key Lab for Advanced Materials and Institute of Fine Chemicals, East China University of Science and Technology, 200237, Shanghai, P. R. China
| | - Martin Ehlers
- Institute of Organic Chemistry, University of Duisburg-Essen, 45117, Essen, Germany
| | - Junchen Wu
- Key Lab for Advanced Materials and Institute of Fine Chemicals, East China University of Science and Technology, 200237, Shanghai, P. R. China
| | | | - Carsten Schmuck
- Institute of Organic Chemistry, University of Duisburg-Essen, 45117, Essen, Germany
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21
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Hu Y, Cecconello A, Idili A, Ricci F, Willner I. Triplex DNA Nanostructures: From Basic Properties to Applications. Angew Chem Int Ed Engl 2017; 56:15210-15233. [PMID: 28444822 DOI: 10.1002/anie.201701868] [Citation(s) in RCA: 227] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Indexed: 12/16/2022]
Abstract
Triplex nucleic acids have recently attracted interest as part of the rich "toolbox" of structures used to develop DNA-based nanostructures and materials. This Review addresses the use of DNA triplexes to assemble sensing platforms and molecular switches. Furthermore, the pH-induced, switchable assembly and dissociation of triplex-DNA-bridged nanostructures are presented. Specifically, the aggregation/deaggregation of nanoparticles, the reversible oligomerization of origami tiles and DNA circles, and the use of triplex DNA structures as functional units for the assembly of pH-responsive systems and materials are described. Examples include semiconductor-loaded DNA-stabilized microcapsules, DNA-functionalized dye-loaded metal-organic frameworks (MOFs), and the pH-induced release of the loads. Furthermore, the design of stimuli-responsive DNA-based hydrogels undergoing reversible pH-induced hydrogel-to-solution transitions using triplex nucleic acids is introduced, and the use of triplex DNA to assemble shape-memory hydrogels is discussed. An outlook for possible future applications of triplex nucleic acids is also provided.
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Affiliation(s)
- Yuwei Hu
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Alessandro Cecconello
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Andrea Idili
- Department of Chemistry, University of Rome, Tor Vergata, via della Ricerca Scientifica, 00133, Rome, Italy
| | - Francesco Ricci
- Department of Chemistry, University of Rome, Tor Vergata, via della Ricerca Scientifica, 00133, Rome, Italy
| | - Itamar Willner
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
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22
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Hu Y, Cecconello A, Idili A, Ricci F, Willner I. Triplex-DNA-Nanostrukturen: von grundlegenden Eigenschaften zu Anwendungen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701868] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Yuwei Hu
- Institute of Chemistry; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
| | | | - Andrea Idili
- Department of Chemistry; Universität Rom; Tor Vergata, via della Ricerca Scientifica 00133 Rom Italien
| | - Francesco Ricci
- Department of Chemistry; Universität Rom; Tor Vergata, via della Ricerca Scientifica 00133 Rom Italien
| | - Itamar Willner
- Institute of Chemistry; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
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23
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Ma H, Li W, Zhou W, Liu J. Site-Selective Labeling of Chromium(III) as a Quencher on DNA for Molecular Beacons. Chempluschem 2017; 82:1224-1230. [DOI: 10.1002/cplu.201700361] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Huan Ma
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
| | - Wang Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
- Department of Chemistry; Water Institute and Waterloo Institute for Nanotechnology; University of Waterloo; Waterloo ON N2L 3G1 Canada
| | - Wenhu Zhou
- Department of Chemistry; Water Institute and Waterloo Institute for Nanotechnology; University of Waterloo; Waterloo ON N2L 3G1 Canada
- Xiangya School of Pharmaceutical Sciences; Central South University; Changsha Hunan 410013 P. R. China
| | - Juewen Liu
- Department of Chemistry; Water Institute and Waterloo Institute for Nanotechnology; University of Waterloo; Waterloo ON N2L 3G1 Canada
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24
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A novel quantitative PCR mediated by high-fidelity DNA polymerase. Sci Rep 2017; 7:10365. [PMID: 28871131 PMCID: PMC5583327 DOI: 10.1038/s41598-017-10782-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 08/14/2017] [Indexed: 01/19/2023] Open
Abstract
The biggest challenge for accurate diagnosis of viral infectious disease is the high genetic variability of involved viruses, which affects amplification efficiency and results in low sensitivity and narrow spectrum. Here, we developed a new simple qPCR mediated by high-fidelity (HF) DNA polymerase. The new method utilizes an HFman probe and one primer. Fluorescent signal was generated from the 3'-5' hydrolysis of HFman probe by HF DNA polymerase before elongation initiation. Mismatches between probe/primer and template have less influence on the amplification efficiency of the new method. The new qPCR exhibited higher sensitivity and better adaptability to sequence variable templates than the conventional TaqMan probe based-qPCR in quantification of HIV-1 viral load. Further comparison with COBAS TaqMan HIV-1 Test (v2.0) showed a good correlation coefficient (R2 = 0.79) between both methods in quantification of HIV-1 viral load among 21 clinical samples. The characteristics of tolerance to variable templates and one probe-one primer system imply that the probe/primer design for the new method will be easier and more flexible than the conventional method for highly heterogeneous viruses. Therefore, the HF DNA polymerase-mediated qPCR method is a simple, sensitive and promising approach for the development of diagnostics for viral infectious diseases.
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25
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Lin F, Zhou Y, Li Q, Zhou X, Shao Y, Habermeyer B, Wang H, Shi X, Xu Z. Prototropically Allosteric Probe for Superbly Selective DNA Analysis. Anal Chem 2017; 89:9299-9306. [DOI: 10.1021/acs.analchem.7b02077] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Fan Lin
- Institute
of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Yufeng Zhou
- Institute
of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Qiusha Li
- Institute
of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Xiaoshun Zhou
- Institute
of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Yong Shao
- Institute
of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | | | - Hui Wang
- Chinese
Academy of Sciences (CAS) Key Laboratory of Nanosystem and Hierarchy
Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Xinghua Shi
- Chinese
Academy of Sciences (CAS) Key Laboratory of Nanosystem and Hierarchy
Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Zhiai Xu
- School
of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
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26
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Nguyen TVT, Le BH, Seo YJ. Highly fluorescence quenching graphene oxide-based oligodeoxynucleotide hairpin systems for probing CNG DNA repeat sequences. Tetrahedron Lett 2017. [DOI: 10.1016/j.tetlet.2017.07.035] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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27
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Astakhova K, Golovin AV, Prokhorenko IA, Ustinov AV, Stepanova IA, Zatsepin TS, Korshun VA. Design of 2′-phenylethynylpyrene excimer forming DNA/RNA probes for homogeneous SNP detection: The attachment manner matters. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.04.045] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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28
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Ma F, Liu WJ, Zhang Q, Zhang CY. Sensitive detection of microRNAs by duplex specific nuclease-assisted target recycling and pyrene excimer switching. Chem Commun (Camb) 2017; 53:10596-10599. [DOI: 10.1039/c7cc06290g] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Herein, we develop a sensitive fluorescence method for microRNA assay based on duplex specific nuclease-assisted target recycling and pyrene excimer switching.
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Affiliation(s)
- 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
| | - Wen-jing Liu
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | | | - 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
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29
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Zhou J, Zheng Y, Roembke BT, Robinson S, Opoku-Temeng C, Sayre DA, Sintim HO. Fluorescent analogs of cyclic and linear dinucleotides as phosphodiesterase and oligoribonuclease activity probes. RSC Adv 2017. [DOI: 10.1039/c6ra25394f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
2-Aminopurine or etheno adenosine cyclic dinucleotide probes can report the activity of cyclic dinucleotide PDEs or oligoribonucleases.
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Affiliation(s)
- Jie Zhou
- Purdue Institute for Drug Discovery
- Purdue University
- West Lafayette
- USA
- Department of Chemistry
| | - Yue Zheng
- Purdue Institute for Drug Discovery
- Purdue University
- West Lafayette
- USA
- Department of Chemistry and Biochemistry
| | - Benjamin T. Roembke
- Department of Chemistry and Biochemistry
- University of Maryland
- College Park
- USA
| | - Sarah M. Robinson
- Department of Chemistry and Biochemistry
- University of Maryland
- College Park
- USA
| | - Clement Opoku-Temeng
- Purdue Institute for Drug Discovery
- Purdue University
- West Lafayette
- USA
- Department of Chemistry and Biochemistry
| | - David A. Sayre
- Department of Chemistry and Biochemistry
- University of Maryland
- College Park
- USA
| | - Herman O. Sintim
- Purdue Institute for Drug Discovery
- Purdue University
- West Lafayette
- USA
- Department of Chemistry
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30
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Wang H, Ma K, Xu B, Tian W. Tunable Supramolecular Interactions of Aggregation-Induced Emission Probe and Graphene Oxide with Biomolecules: An Approach toward Ultrasensitive Label-Free and "Turn-On" DNA Sensing. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:6613-6622. [PMID: 27717201 DOI: 10.1002/smll.201601544] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Revised: 08/28/2016] [Indexed: 06/06/2023]
Abstract
Aggregation-induced emission (AIE) probes have shown great potential applications in fluorescent sensing of biomolecules, and the integration of AIE probe and graphene oxide (GO) attracts intense interest in developing new tools for label-free and "turn-on" fluorescent biomolecular analysis. Herein, an ultrasensitive label-free and "turn-on" DNA sensing is realized by tuning the supramolecular interactions of AIE probe and GO with DNA. The investigation of supramolecular interactions of AIE probes and GO with DNA demonstrate that AIE probe with short alkyl chains substitute shows highest binding affinity with DNA strand, and GO with low oxidation degree possesses strong binding interactions to ssDNA and the highest fluorescence quenching efficiency. As a result, the optimized AIE probes and GO-based fluorescent sensor can selectively detect the target DNA sequence and exhibits the detection limitation as low as 0.17 × 10-9 m. It is believed that the research efforts will provide an efficient approach to improve the performance of DNA sensing assay and an indepth understanding of the supramolecular interactions of AIE probes and GO with DNA, and thus facilitate their extended applications in biosensors and biomedicine.
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Affiliation(s)
- Hui Wang
- State Key Laboratory of Supramolecular, Structure and Materials, Jilin University, Changchun, 130012, P. R. China
| | - Ke Ma
- State Key Laboratory of Supramolecular, Structure and Materials, Jilin University, Changchun, 130012, P. R. China
| | - Bin Xu
- State Key Laboratory of Supramolecular, Structure and Materials, Jilin University, Changchun, 130012, P. R. China
| | - Wenjing Tian
- State Key Laboratory of Supramolecular, Structure and Materials, Jilin University, Changchun, 130012, P. R. China
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31
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Pyrrolidinyl peptide nucleic acid terminally labeled with fluorophore and end-stacking quencher as a probe for highly specific DNA sequence discrimination. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.10.040] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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32
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Fluorescent Oligonucleotides Containing a 2-Ethynylfluorene- or 2-Ethynylfluorenone-labeled 2′-Deoxyguanosine Unit: Fluorescence Changes upon Duplex Formation. B KOREAN CHEM SOC 2016. [DOI: 10.1002/bkcs.10856] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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33
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Kikuchi N, Kolpashchikov DM. Split Spinach Aptamer for Highly Selective Recognition of DNA and RNA at Ambient Temperatures. Chembiochem 2016; 17:1589-92. [PMID: 27305425 DOI: 10.1002/cbic.201600323] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Indexed: 12/25/2022]
Abstract
Split spinach aptamer (SSA) probes for fluorescent analysis of nucleic acids were designed and tested. In SSA design, two RNA or RNA/DNA strands hybridized to a specific nucleic acid analyte and formed a binding site for low-fluorescent 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI) dye, which resulted in up to a 270-fold increase in fluorescence. The major advantage of the SSA over state-of-the art fluorescent probes is high selectivity: it produces only background fluorescence in the presence of a single-base-mismatched analyte, even at room temperature. SSA is therefore a promising tool for label-free analysis of nucleic acids at ambient temperatures.
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Affiliation(s)
- Nanami Kikuchi
- Chemistry Department, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL, 32816-2366, USA
| | - Dmitry M Kolpashchikov
- Chemistry Department, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL, 32816-2366, USA.
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34
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Kumar Verma R, Takei F, Nakatani K. Synthesis and Photophysical Properties of Fluorescence Molecular Probe for Turn-ON-Type Detection of Cytosine Bulge DNA. Org Lett 2016; 18:3170-3. [DOI: 10.1021/acs.orglett.6b01378] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Rajiv Kumar Verma
- Department
of Regulatory Bioorganic Chemistry, The Institute of Scientific and
Industrial Research, Osaka University, Mihogaoka, 8-1,
Ibaraki, Osaka 567-0047, Japan
| | - Fumie Takei
- National Defense Medical College, Namiki, 3-2, Tokorozawa, Saitama 359-8513, Japan
| | - Kazuhiko Nakatani
- Department
of Regulatory Bioorganic Chemistry, The Institute of Scientific and
Industrial Research, Osaka University, Mihogaoka, 8-1,
Ibaraki, Osaka 567-0047, Japan
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35
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Chakraborty K, Khatua P, Bandyopadhyay S. Exploring ion induced folding of a single-stranded DNA oligomer from molecular simulation studies. Phys Chem Chem Phys 2016; 18:15899-910. [PMID: 27241311 DOI: 10.1039/c6cp00663a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
One crucial issue in DNA hydration is the effect of salts on its conformational features. This has relevance in biology as cations present in the cellular environment shield the negative charges on the DNA backbone, thereby reducing the repulsive force between them. By screening the negative charges along the backbone, cations stabilize the folded structure of DNA. To study the effect of the added salt on single-stranded DNA (ss-DNA) conformations, we have performed room temperature molecular dynamics simulations of an aqueous solution containing the ss-DNA dodecamer with the 5'-CGCGAATTCGCG-3' sequence in the presence of 0.2, 0.5, and 0.8 M NaCl. Our calculations reveal that in the presence of the salt, the DNA molecule forms more collapsed coil-like conformations due to the screening of negative charges along the backbone. Additionally, we demonstrated that the formation of an octahedral inner-sphere complex by the strongly bound ion plays an important role in the stabilization of such folded conformation of DNA. Importantly, it is found that ion-DNA interactions can also explain the formation of non-sequential base stackings with longer lifetimes. Such non-sequential base stackings further stabilize the collapsed coil-like folded form of the DNA oligomer.
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Affiliation(s)
- Kaushik Chakraborty
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur - 721302, India.
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36
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Maity D, Jiang J, Ehlers M, Wu J, Schmuck C. A FRET-enabled molecular peptide beacon with a significant red shift for the ratiometric detection of nucleic acids. Chem Commun (Camb) 2016; 52:6134-7. [PMID: 27071707 DOI: 10.1039/c6cc02138g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A cationic molecular peptide beacon NAP1 functionalized with a fluorescence resonance energy transfer-pair at its ends allows the ratiometric detection of ds-DNA with a preference for AT rich sequences. NAP1 most likely binds in a folded form into the minor groove of ds-DNA, which results in a remarkable change in its fluorescence properties. As NAP1 exhibits quite low cytotoxicity, it can also be used for imaging of nuclear DNA in cells.
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Affiliation(s)
- Debabrata Maity
- Institute for Organic Chemistry, University of Duisburg-Essen, 45117, Essen, Germany.
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37
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Imincan G, Pei F, Yu L, Jin H, Zhang L, Yang X, Zhang L, Tang X. Microenvironmental Effect of 2'-O-(1-Pyrenylmethyl)uridine Modified Fluorescent Oligonucleotide Probes on Sensitive and Selective Detection of Target RNA. Anal Chem 2016; 88:4448-55. [PMID: 27021236 DOI: 10.1021/acs.analchem.6b00227] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
2'-O-(1-Pyrenylmethyl)uridine modified oligoribonucleotides provide highly sensitive pyrene fluorescent probes for detecting specific nucleotide mutation of RNA targets. To develop more stable and cost-effective oligonucleotide probes, we investigated the local microenvironmental effects of nearby nucleobases on pyrene fluorescence in duplexes of RNAs and 2'-O-(1-pyrenylmethyl)uridine modified oligonucleotides. By incorporation of deoxyribonucleotides, ribonucleotides, 2'-MeO-nucleotides and 2'-F-nucleotides at both sides of 2'-O-(1-pyrenylmethyl)uridine (U(p)) in oligodeoxynucleotide probes, we synthesized a series of pyrene modified oligonucleotide probes. Their pyrene fluorescence emission spectra indicated that only two proximal nucleotides have a substantial effect on the pyrene fluorescence properties of these oligonucleotide probes hybridized with target RNA with an order of fluorescence sensitivity of 2'-F-nucleotides > 2'-MeO-nucleotides > ribonucleotides ≫ deoxyribonucleotides. While based on circular dichroism spectra, overall helix conformations (either A- or B-form) of the duplexes have marginal effects on the sensitivity of the probes. Instead, the local substitution reflected the propensity of the nucleotide sugar ring to adopt North type conformation and, accordingly, shifted their helix geometry toward a more A-type like conformation in local microenvironments. Thus, higher enhancement of pyrene fluorescence emission favored local A-type helix structures and more polar and hydrophobic environments (F > MeO > OH at 2' substitution) of duplex minor grooves of probes with the target RNA. Further dynamic simulation revealed that local microenvironmental effect of 2'-F-nucleotides or ribonucleotides was enough for pyrene moiety to move out of nucleobases to the minor groove of duplexes; in addition, 2'-F-nucleotide had less effect on π-stack of pyrene-modified uridine with upstream and downstream nucleobases. The present oligonucleotide probes successfully distinguished target RNA from single-mutated RNA analyte during an in vitro assay of RNA synthesis.
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Affiliation(s)
- Gülnur Imincan
- State Key Laboratory of Natural and Biomimetic Drugs, the School of Pharmaceutical Sciences, Peking University , Beijing, 100191, China
| | - Fen Pei
- State Key Laboratory of Natural and Biomimetic Drugs, the School of Pharmaceutical Sciences, Peking University , Beijing, 100191, China
| | - Lijia Yu
- State Key Laboratory of Natural and Biomimetic Drugs, the School of Pharmaceutical Sciences, Peking University , Beijing, 100191, China
| | - Hongwei Jin
- State Key Laboratory of Natural and Biomimetic Drugs, the School of Pharmaceutical Sciences, Peking University , Beijing, 100191, China
| | - Liangren Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, the School of Pharmaceutical Sciences, Peking University , Beijing, 100191, China
| | - Xiaoda Yang
- State Key Laboratory of Natural and Biomimetic Drugs, the School of Pharmaceutical Sciences, Peking University , Beijing, 100191, China
| | - Lihe Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, the School of Pharmaceutical Sciences, Peking University , Beijing, 100191, China
| | - XinJing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, the School of Pharmaceutical Sciences, Peking University , Beijing, 100191, China
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38
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Selective amyloid β oligomer assay based on abasic site-containing molecular beacon and enzyme-free amplification. Biosens Bioelectron 2016; 78:206-212. [DOI: 10.1016/j.bios.2015.11.048] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 10/31/2015] [Accepted: 11/15/2015] [Indexed: 12/21/2022]
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39
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Li P, He H, Wang Z, Feng M, Jin H, Wu Y, Zhang L, Zhang L, Tang X. Sensitive Detection of Single-Nucleotide Mutation in the BRAF Mutation Site (V600E) of Human Melanoma Using Phosphate-Pyrene-Labeled DNA Probes. Anal Chem 2015; 88:883-9. [PMID: 26652624 DOI: 10.1021/acs.analchem.5b03523] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A series of novel nucleotide phosphoramidites were rationally designed and synthesized and were then site-specifically incorporated in DNA oligonucleotide probes with pyrene-modified phosphate. These oligodeoxynucleotide (ODN) probes almost have no inherent fluorescence emission with pyrene modification at 3' phosphate of corresponding nucleotides as a result of the photoinduced electron-transfer quenching effect of nucleobases (thymidine ∼ cytidine > guanosine ≫ adenosine). However, strong fluorescence emission was observed only with the perfectly matched duplex for the probes with pyrene modified at 3' phosphate of thymidine and cytidine. These rationally designed ODN probes successfully worked as "turn on" fluorescence oligonucleotide sensors for single-nucleotide polymorphism (SNP) and were used for detecting a single BRAF mutation site (V600E) of human melanoma.
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Affiliation(s)
- Pengfei Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, People's Republic of China
| | - Hongyan He
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, People's Republic of China
| | - Zhixuan Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, People's Republic of China
| | - Mengke Feng
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, People's Republic of China
| | - Hongwei Jin
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, People's Republic of China
| | - Yun Wu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, People's Republic of China
| | - Liangren Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, People's Republic of China
| | - Lihe Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, People's Republic of China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, People's Republic of China.,State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University , Nanjing, Jiangsu 210093, People's Republic of China.,Center for Noncoding RNA Medicine, Peking University Health Center , Beijing 100191, People's Republic of China
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40
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Hashim SN, Tsuchiya A, Kamiya N, Sando S. A Single Fluorophore-labeled Aptamer Sensor for the Detection of Interferon Gamma. CHEM LETT 2015. [DOI: 10.1246/cl.150794] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
| | - Akira Tsuchiya
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo
| | - Noriho Kamiya
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University
- Center for Future Chemistry, Kyushu University
| | - Shinsuke Sando
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo
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41
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Dong H, Wu ZS, Xu J, Ma J, Zhang H, Wang J, Shen W, Xie J, Jia L. Novel multifunction-integrated molecular beacon for the amplification detection of DNA hybridization based on primer/template-free isothermal polymerization. Biosens Bioelectron 2015; 72:182-90. [DOI: 10.1016/j.bios.2015.04.090] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 04/20/2015] [Accepted: 04/27/2015] [Indexed: 01/10/2023]
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42
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Ghosh S, Dixit MK, Chakrabarti R. Thermodynamics of site-specific small molecular ion interactions with DNA duplex: a molecular dynamics study. MOLECULAR SIMULATION 2015. [DOI: 10.1080/08927022.2015.1085123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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43
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Aso T, Saito K, Suzuki A, Saito Y. Synthesis and photophysical properties of pyrene-labeled 3-deaza-2'-deoxyadenosines comprising a non-π-conjugated linker: fluorescence quenching-based oligodeoxynucleotide probes for thymine identification. Org Biomol Chem 2015; 13:10540-7. [PMID: 26338764 DOI: 10.1039/c5ob01605c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Pyrene-labeled 3-deaza-2'-deoxyadenosine comprising a non-π-conjugated linker (py3z)A (1) was synthesized and its photophysical properties were investigated. Oligodeoxynucleotide (ODN) probes containing (py3z)A (1) exhibited remarkable fluorescence quenching only when the opposite base of the complementary strand was the perfectly matched thymine. Such fluorescence quenching-based ODN probes exhibited excellent on-off switching properties, making them useful tools for single nucleotide polymorphism (SNP) genotyping and for the identification of target genes and structural studies of nucleic acids.
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Affiliation(s)
- Tatsuya Aso
- Department of Chemical Biology and Applied Chemistry, College of Engineering, Nihon University, Koriyama, Fukushima 963-8642, Japan.
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44
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Wang X, Hudson RHE. PNA Molecular Beacons Assembled by Post-Synthetic Click Chemistry Functionalization. Chembiochem 2015; 16:2156-61. [PMID: 26227668 DOI: 10.1002/cbic.201500248] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Indexed: 12/12/2022]
Abstract
To avoid the tedious synthesis of functionalized peptide nucleic acid (PNA) monomers for probe development, we proposed a simple approach to modify PNA oligomers by post-synthetic on-resin click chemistry. PNA molecular beacons (MBs) were prepared by incorporation of azide-containing monomers into the oligomer by automatic solid-phase peptide synthesis and subsequent derivatization with pyrene moieties by copper-catalyzed azide-alkyne cycloaddition. Two pyrene-based quencher-free PNA molecular beacons, a stemless MB and one possessing a stem-loop structure, targeting a portion of the cystic fibrosis gene, were successfully synthesized by using this method. Fluorescence studies showed that the stem-loop MB exhibited better discrimination of changes in excimer/monomer ratios as compared to the stemless MB construct.
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Affiliation(s)
- Xiaoxiao Wang
- Department of Chemistry, The University of Western Ontario, 1151 Richmond Street, London, ON, N6A 2K5, Canada
| | - Robert H E Hudson
- Department of Chemistry, The University of Western Ontario, 1151 Richmond Street, London, ON, N6A 2K5, Canada.
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45
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Park JW, Park Y, Kim BH. Quencher-free molecular aptamer beacons (QF-MABs) for detection of ATP. Bioorg Med Chem Lett 2015; 25:4597-600. [PMID: 26320623 DOI: 10.1016/j.bmcl.2015.08.052] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 08/18/2015] [Accepted: 08/20/2015] [Indexed: 12/11/2022]
Abstract
We have constructed a simple and efficient system-based on quencher-free molecular aptamer beacons (QF-MABs)-for probing ATP. In the absence of ATP, the fluorescence of a pyrene fluorophore on the loop position (15 nucleotides from the 5' end) of the optimal QF-MAB was quenched by the neighboring nucleobases; in its presence, fluorescence was recovered, due to a conformational change in the secondary structure of the QF-MAB.
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Affiliation(s)
- Jung Woo Park
- Department of Chemistry, BK School of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, South Korea.
| | - Yoojin Park
- Department of Chemistry, BK School of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, South Korea
| | - Byeang Hyean Kim
- Department of Chemistry, BK School of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, South Korea.
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46
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Takahashi K, Ito S, Nakamoto K, Ito Y, Ueno Y. Photoinduced Electron-Transfer-Based Hybridization Probes for Detection of DNA and RNA. J Org Chem 2015; 80:8561-70. [PMID: 26258850 DOI: 10.1021/acs.joc.5b01132] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Here, we report the synthesis of a hybridization probe for detection of RNA and DNA based on photoinduced electron transfer (PeT). We designed and synthesized an oligonucleotide containing an adenosine analogue with a 9-(N,N-dimethylaminomethyl)anthracenyl moiety at its 6-position via an ethynylene linker as the hybridization probe. When the probe was hybridized with a complementary RNA or DNA, the fluorescence intensity increased 3-fold or 4.5-fold, respectively, compared to the single-stranded state.
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Affiliation(s)
| | | | | | - Yasutomo Ito
- Division for Medical Research Engineering, Nagoya University Graduate School of Medicine , Nagoya 466-8550, Japan
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47
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Takei F, Chen X, Yu G, Shibata T, Dohno C, Nakatani K. Cytosine-bulge-dependent fluorescence quenching for the real-time hairpin primer PCR. Chem Commun (Camb) 2015; 50:15195-8. [PMID: 25338232 DOI: 10.1039/c4cc06780k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The progress of a polymerase chain reaction (PCR) was sensitively monitored based on the increase in fluorescence of N,N'-bis(3-aminopropyl)-2,7-diamino-1,8-naphthyridine, which was covalently anchored on the cytosine bulge directly neighbouring the 5'-T_G-3'/5'-CCA-3' sequence in the hairpin tag at the 5' end of the PCR primer.
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Affiliation(s)
- F Takei
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, 567-0047 Japan.
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48
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Shen W, Tian Y, Ran T, Gao Z. Genotyping and quantification techniques for single-nucleotide polymorphisms. Trends Analyt Chem 2015. [DOI: 10.1016/j.trac.2015.03.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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49
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Saito Y, Suzuki A, Yamauchi T, Saito I. Design and synthesis of 7-naphthyl-8-aza-7-deaza-2′-deoxyadenosines as environmentally sensitive fluorescent nucleosides. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2014.10.116] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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50
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Leung KH, He HZ, He B, Zhong HJ, Lin S, Wang YT, Ma DL, Leung CH. Label-free luminescence switch-on detection of hepatitis C virus NS3 helicase activity using a G-quadruplex-selective probe. Chem Sci 2015; 6:2166-2171. [PMID: 28808523 PMCID: PMC5539802 DOI: 10.1039/c4sc03319a] [Citation(s) in RCA: 134] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 11/16/2014] [Indexed: 12/16/2022] Open
Abstract
A series of luminescent Ir(iii) complexes were synthesised and evaluated for their ability to act as luminescent G-quadruplex-selective probes. The Ir(iii) complex 9, [Ir(phq)2(phen)]PF6 (where phq = 2-phenylquinoline; phen = 1,10-phenanthroline), exhibited high luminescence in the presence of G-quadruplex DNA compared to dsDNA and ssDNA, and was employed to construct a label-free G-quadruplex-based assay for hepatitis C virus NS3 helicase activity in aqueous solution. Moreover, the application of the assay for screening potential helicase inhibitors was demonstrated. To our knowledge, this is the first G-quadruplex-based assay for helicase activity.
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Affiliation(s)
- Ka-Ho Leung
- Department of Chemistry , Hong Kong Baptist University , Kowloon Tong , Hong Kong , China .
| | - Hong-Zhang He
- Department of Chemistry , Hong Kong Baptist University , Kowloon Tong , Hong Kong , China .
| | - Bingyong He
- Department of Chemistry , Hong Kong Baptist University , Kowloon Tong , Hong Kong , China .
| | - Hai-Jing Zhong
- State Key Laboratory of Quality Research in Chinese Medicine , Institute of Chinese Medical Sciences , University of Macau , Macao , China .
| | - Sheng Lin
- Department of Chemistry , Hong Kong Baptist University , Kowloon Tong , Hong Kong , China .
| | - Yi-Tao Wang
- 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 .
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine , Institute of Chinese Medical Sciences , University of Macau , Macao , China .
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