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Gabrusenok PV, Ramazanov RR, Kasyanenko NA, Lantushenko AO, Sokolov PA. pH-dependent binding of ATP aptamer to the target and competition strands: Fluorescent melting curve fitting study. Biochim Biophys Acta Gen Subj 2024; 1868:130689. [PMID: 39134247 DOI: 10.1016/j.bbagen.2024.130689] [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: 05/06/2024] [Revised: 08/02/2024] [Accepted: 08/05/2024] [Indexed: 08/18/2024]
Abstract
The pH varies in different tissues and organelles and also changes during some diseases. In this regard, the application of molecular switches that use a competition-based aptamer switch design in biological systems requires studying the thermodynamics of such systems at different pH values. In this work, we studied the binding of the classical ATP aptamer to ATP and competition strands under different pH and ionic conditions using fluorescent melting curve analysis. We have developed an original approach to processing source data from a PCR thermal cycler. It is based on constructing a thermodynamic model of the melting profile and the subsequent fit of experimental curves within this model. We have shown that this approach enables us to narrow the temperature region under study to the width of the melting region without a significant loss in the quality of the result. This impressively expands the application area of this approach compared to frequently used techniques that require mandatory measurement of the signal outside the melting region. The results obtained by the method showed that the thermodynamic parameters of the ATP aptamer and its duplexes with competition strands change depending on pH. Therefore, molecular switches that use a competition strand to the ATP aptamer may have a pH-dependent sensitivity that has not been previously considered. This should be taken into account for future rational design of similar systems.
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Affiliation(s)
- P V Gabrusenok
- St. Petersburg University, 13B Universitetskaya Emb., St. Petersburg, 199034, Russia
| | - R R Ramazanov
- St. Petersburg University, 13B Universitetskaya Emb., St. Petersburg, 199034, Russia
| | - N A Kasyanenko
- St. Petersburg University, 13B Universitetskaya Emb., St. Petersburg, 199034, Russia
| | - A O Lantushenko
- Sevastopol State University, 33 Universitetskaya Street, Sevastopol, 299053, Russia
| | - P A Sokolov
- St. Petersburg University, 13B Universitetskaya Emb., St. Petersburg, 199034, Russia.
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2
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Du J, He JS, Wang R, Wu J, Yu X. Ultrasensitive reporter DNA sensors built on nucleic acid amplification techniques: Application in the detection of trace amount of protein. Biosens Bioelectron 2024; 243:115761. [PMID: 37864901 DOI: 10.1016/j.bios.2023.115761] [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: 08/26/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 10/23/2023]
Abstract
The detection of protein is of great significance for the study of biological physiological function, early diagnosis of diseases and drug research. However, the sensitivity of traditional protein detection methods for detecting trace amount of proteins was relatively low. By integrating sensitive nucleic acid amplification techniques (NAAT) with protein detection methods, the detection limit of protein detection methods can be substantially improved. The DNA that can specifically bind to protein targets and convert protein signals into DNA signals is collectively referred to reporter DNA. Various NAATs have been used to establish NAAT-based reporter DNA sensors. And according to whether enzymes are involved in the amplification process, the NAAT-based reporter DNA sensors can be divided into two types: enzyme-assisted NAAT-based reporter DNA sensors and enzyme-free NAAT-based reporter DNA sensors. In this review, we will introduce the principles and applications of two types of NAAT-based reporter DNA sensors for detecting protein targets. Finally, the main challenges and application prospects of NAAT-based reporter DNA sensors are discussed.
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Affiliation(s)
- Jungang Du
- College of Biosystems Engineering and Food Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 311215, China
| | - Jin-Song He
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201, China
| | - Rui Wang
- Human Phenome Institute, State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200438, China.
| | - Jian Wu
- College of Biosystems Engineering and Food Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 311215, China.
| | - Xiaoping Yu
- College of Life Sciences, China Jiliang University, Hangzhou, 310018, China.
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3
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Limanskaya OY, Limanskii OP. Intramolecular Interactions in the Fluorophore–Quencher System in Linear and Hairpin Probes for Real-Time PCR. CYTOL GENET+ 2023. [DOI: 10.3103/s009545272302007x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
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4
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Jimenez VO, Hwang KY, Nguyen D, Rahman Y, Albrecht C, Senator B, Thiabgoh O, Devkota J, Bui VDA, Lam DS, Eggers T, Phan MH. Magnetoimpedance Biosensors and Real-Time Healthcare Monitors: Progress, Opportunities, and Challenges. BIOSENSORS 2022; 12:bios12070517. [PMID: 35884320 PMCID: PMC9313129 DOI: 10.3390/bios12070517] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/30/2022] [Accepted: 07/08/2022] [Indexed: 12/17/2022]
Abstract
A small DC magnetic field can induce an enormous response in the impedance of a soft magnetic conductor in various forms of wire, ribbon, and thin film. Also known as the giant magnetoimpedance (GMI) effect, this phenomenon forms the basis for the development of high-performance magnetic biosensors with magnetic field sensitivity down to the picoTesla regime at room temperature. Over the past decade, some state-of-the-art prototypes have become available for trial tests due to continuous efforts to improve the sensitivity of GMI biosensors for the ultrasensitive detection of biological entities and biomagnetic field detection of human activities through the use of magnetic nanoparticles as biomarkers. In this review, we highlight recent advances in the development of GMI biosensors and review medical devices for applications in biomedical diagnostics and healthcare monitoring, including real-time monitoring of respiratory motion in COVID-19 patients at various stages. We also discuss exciting research opportunities and existing challenges that will stimulate further study into ultrasensitive magnetic biosensors and healthcare monitors based on the GMI effect.
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Affiliation(s)
- Valery Ortiz Jimenez
- Laboratory for Advanced Materials and Sensors, Department of Physics, University of South Florida, Tampa, FL 33620, USA; (V.O.J.); (K.Y.H.); (D.N.); (Y.R.); (C.A.); (B.S.); (J.D.); (D.S.L.)
| | - Kee Young Hwang
- Laboratory for Advanced Materials and Sensors, Department of Physics, University of South Florida, Tampa, FL 33620, USA; (V.O.J.); (K.Y.H.); (D.N.); (Y.R.); (C.A.); (B.S.); (J.D.); (D.S.L.)
| | - Dang Nguyen
- Laboratory for Advanced Materials and Sensors, Department of Physics, University of South Florida, Tampa, FL 33620, USA; (V.O.J.); (K.Y.H.); (D.N.); (Y.R.); (C.A.); (B.S.); (J.D.); (D.S.L.)
- Department of Biomedical Engineering, University of South Florida, Tampa, FL 33620, USA
| | - Yasif Rahman
- Laboratory for Advanced Materials and Sensors, Department of Physics, University of South Florida, Tampa, FL 33620, USA; (V.O.J.); (K.Y.H.); (D.N.); (Y.R.); (C.A.); (B.S.); (J.D.); (D.S.L.)
| | - Claire Albrecht
- Laboratory for Advanced Materials and Sensors, Department of Physics, University of South Florida, Tampa, FL 33620, USA; (V.O.J.); (K.Y.H.); (D.N.); (Y.R.); (C.A.); (B.S.); (J.D.); (D.S.L.)
| | - Baylee Senator
- Laboratory for Advanced Materials and Sensors, Department of Physics, University of South Florida, Tampa, FL 33620, USA; (V.O.J.); (K.Y.H.); (D.N.); (Y.R.); (C.A.); (B.S.); (J.D.); (D.S.L.)
| | - Ongard Thiabgoh
- Department of Physics, Faculty of Science, Ubon Ratchathani University, Warinchamrap, Ubon Ratchathani 34190, Thailand
- Correspondence: (O.T.); (T.E.); (M.-H.P.); Tel.: +813-974-4322 (M.-H.P.)
| | - Jagannath Devkota
- Laboratory for Advanced Materials and Sensors, Department of Physics, University of South Florida, Tampa, FL 33620, USA; (V.O.J.); (K.Y.H.); (D.N.); (Y.R.); (C.A.); (B.S.); (J.D.); (D.S.L.)
- National Energy Technology Laboratory, Pittsburgh, PA 15236, USA
| | | | - Dao Son Lam
- Laboratory for Advanced Materials and Sensors, Department of Physics, University of South Florida, Tampa, FL 33620, USA; (V.O.J.); (K.Y.H.); (D.N.); (Y.R.); (C.A.); (B.S.); (J.D.); (D.S.L.)
- Institute of Materials Science, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Ha Noi 10072, Vietnam
| | - Tatiana Eggers
- Laboratory for Advanced Materials and Sensors, Department of Physics, University of South Florida, Tampa, FL 33620, USA; (V.O.J.); (K.Y.H.); (D.N.); (Y.R.); (C.A.); (B.S.); (J.D.); (D.S.L.)
- Correspondence: (O.T.); (T.E.); (M.-H.P.); Tel.: +813-974-4322 (M.-H.P.)
| | - Manh-Huong Phan
- Laboratory for Advanced Materials and Sensors, Department of Physics, University of South Florida, Tampa, FL 33620, USA; (V.O.J.); (K.Y.H.); (D.N.); (Y.R.); (C.A.); (B.S.); (J.D.); (D.S.L.)
- Correspondence: (O.T.); (T.E.); (M.-H.P.); Tel.: +813-974-4322 (M.-H.P.)
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5
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Optimization and performance evaluation of double-stranded probe in real-time PCR. Anal Biochem 2022; 650:114711. [PMID: 35561816 DOI: 10.1016/j.ab.2022.114711] [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: 01/11/2022] [Revised: 04/18/2022] [Accepted: 05/01/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND TaqMan probe-based real-time PCR (qPCR/RT-qPCR) has been widely used in various fields because of its high sensitivity and specificity. However, TaqMan probes are associated with a relatively higher background signal, and hence negatively affect the detection results. METHODS Double-stranded probes (DSPs) were designed for the high sensitive detection of hepatitis B virus (HBV) DNA and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA using qPCR/RT-qPCR. DSPs consist of different lengths of positive and negative strands with complementary oligonucleotides. We systematically optimized DSP length, the free energy of hybridization (ΔG) between complementary oligonucleotides, and the length of sticky ends, and DSP performance was evaluated in comparison with other types of probes. RESULTS By using similar length positive and negative strands, controlling ΔG between complementary oligonucleotides to approximately -30 kcal/mol, and maintaining the sticky end length at 4-6 nt, the analytical performance of DSP was significantly improved. Compared with other types of probes, DSP is advantageous in fluorescence signal intensity and sensitivity. CONCLUSION DSPs can further improve the detection sensitivity and the detection rate of low-concentration samples in molecular diagnosis.
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Highly multiplex PCR assays by coupling the 5'-flap endonuclease activity of Taq DNA polymerase and molecular beacon reporters. Proc Natl Acad Sci U S A 2022; 119:2110672119. [PMID: 35197282 PMCID: PMC8892341 DOI: 10.1073/pnas.2110672119] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2022] [Indexed: 01/23/2023] Open
Abstract
We describe a highly multiplex PCR approach that can identify 10-fold more targets in current real-time PCR assays without additional enzymes or separate reactions. This single-step, single-tube, homogeneous detection approach, termed MeltArray, is achieved by coupling the 5′-flap endonuclease activity of the Taq DNA polymerase and multiple annealing sites of the molecular beacon reporters. The 5′-flap endonuclease cleaves a probe specifically into a “mediator” primer, and one molecular beacon reporter allows for the extension of multiple “mediator” primers to produce a series of fluorescent hybrids with different melting temperatures unique to each target. The overall number of targets detectable per reaction is equal to the number of the reporters multiplied by the number of mediator primers per reporter. Real-time PCR is the most utilized nucleic acid testing tool in clinical settings. However, the number of targets detectable per reaction are restricted by current modes. Here, we describe a single-step, multiplex approach capable of detecting dozens of targets per reaction in a real-time PCR thermal cycler. The approach, termed MeltArray, utilizes the 5′-flap endonuclease activity of Taq DNA polymerase to cleave a mediator probe into a mediator primer that can bind to a molecular beacon reporter, which allows for the extension of multiple mediator primers to produce a series of fluorescent hybrids of different melting temperatures unique to each target. Using multiple molecular beacon reporters labeled with different fluorophores, the overall number of targets is equal to the number of the reporters multiplied by that of mediator primers per reporter. The use of MeltArray was explored in various scenarios, including in a 20-plex assay that detects human Y chromosome microdeletions, a 62-plex assay that determines Escherichia coli serovars, a 24-plex assay that simultaneously identifies and quantitates respiratory pathogens, and a minisequencing assay that identifies KRAS mutations, and all of these different assays were validated with clinical samples. MeltArray approach should find widespread use in clinical settings owing to its combined merits of multiplicity, versatility, simplicity, and accessibility.
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Sukla S, Mondal P, Biswas S, Ghosh S. A Rapid and Easy-to-Perform Method of Nucleic-Acid Based Dengue Virus Diagnosis Using Fluorescence-Based Molecular Beacons. BIOSENSORS 2021; 11:bios11120479. [PMID: 34940236 PMCID: PMC8699591 DOI: 10.3390/bios11120479] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 12/03/2022]
Abstract
Detecting dengue virus (DENV) infection in patients as early as possible makes the disease management convenient. Conventionally, DENV infection is diagnosed by ELISA-based methods, but sensitivity and specificity are major concerns. Reverse-transcription-PCR (RT-PCR)-based detection confirms the presence of DENV RNA; however, it is expensive, time-consuming, and skilled personnel are required. A fluorescence-based detection system that detects DENV RNA in patient’s serum directly, without any nucleic acid amplification step, has been developed. The method uses target-specific complementary sequence in the molecular beacon, which would specifically bind to the DENV RNA. The molecular beacons are approximately 40 bases long hairpin structures, with a fluorophore-quencher system attached at the terminal ends of the stem. These probes are biotinylated in the stem region, so that they can be immobilized on the streptavidin-tagged magnetic beads. These magnetic beads, coupled with biotinylated molecular beacons, are used for the detection of the target RNA in the serum by incubating the mixture. After incubation, beads are separated and re-suspended in a buffer. The measurement of fluorescence is taken in fluorometer after 15 min incubation at 50 °C. The whole work is carried out in a single tube. This rapid method can precisely detect dengue RNA within two hours, confirming ongoing DENV replication in the patient.
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Affiliation(s)
- Soumi Sukla
- CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India; (S.S.); (P.M.)
- National Institute of Pharmaceuticals Education and Research, 168, Maniktala Main Road, Kolkata 700054, West Bengal, India
| | - Prasenjit Mondal
- CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India; (S.S.); (P.M.)
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Subhajit Biswas
- CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India; (S.S.); (P.M.)
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
- Correspondence: (S.B.); (S.G.)
| | - Surajit Ghosh
- CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India; (S.S.); (P.M.)
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
- Department of Bioscience & Bioengineering, Indian Institute of Technology Jodhpur, NH 62, Surpura Bypass Road, Karwar 342037, Rajasthan, India
- Correspondence: (S.B.); (S.G.)
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Richard ET, Morinaga K, Zheng Y, Sundberg O, Hokugo A, Hui K, Zhou Y, Sasaki H, Kashemirov BA, Nishimura I, McKenna CE. Design and Synthesis of Cathepsin-K-Activated Osteoadsorptive Fluorogenic Sentinel (OFS) Probes for Detecting Early Osteoclastic Bone Resorption in a Multiple Myeloma Mouse Model. Bioconjug Chem 2021; 32:916-927. [PMID: 33956423 PMCID: PMC8137654 DOI: 10.1021/acs.bioconjchem.1c00036] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We describe the design and synthesis of OFS-1, an Osteoadsorptive Fluorogenic Sentinel imaging probe that is adsorbed by hydroxyapatite (HAp) and bone mineral surfaces, where it generates an external fluorescent signal in response to osteoclast-secreted cathepsin K (Ctsk). The probe consists of a bone-anchoring bisphosphonate moiety connected to a Förster resonance energy transfer (FRET) internally quenched fluorescent (IQF) dye pair, linked by a Ctsk peptide substrate, GHPGGPQG. Key structural features contributing to the effectiveness of OFS-1 were defined by structure-activity relationship (SAR) and modeling studies comparing OFS-1 with two cognates, OFS-2 and OFS-3. In solution or when preadsorbed on HAp, OFS-1 exhibited strong fluorescence when exposed to Ctsk (2.5-20 nM). Time-lapse photomicrographs obtained after seeding human osteoclasts onto HAp-coated well plates containing preadsorbed OFS-1 revealed bright fluorescence at the periphery of resorbing cells. OFS-1 administered systemically detected early osteolysis colocalized with orthotopic engraftment of RPMI-8226-Luc human multiple myeloma cells at a metastatic skeletal site in a humanized mouse model. OFS-1 is thus a promising new imaging tool for detecting abnormal bone resorption.
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Affiliation(s)
- Eric T. Richard
- Department of Chemistry, University of Southern California, Los Angeles, California, 90089, USA
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, California, 90033, USA
| | - Kenzo Morinaga
- Weintraub Center for Reconstructive Biotechnology, UCLA School of Dentistry, Los Angeles, California, 90095, USA
- Department of Oral Rehabilitation, Section of Oral Implantology, Fukuoka Dental College, Fukuoka, Japan
| | - Yiying Zheng
- Department of Chemistry, University of Southern California, Los Angeles, California, 90089, USA
| | - Oskar Sundberg
- Department of Chemistry, University of Southern California, Los Angeles, California, 90089, USA
| | - Akishige Hokugo
- Weintraub Center for Reconstructive Biotechnology, UCLA School of Dentistry, Los Angeles, California, 90095, USA
- Division of Plastic and Reconstructive Surgery, David Geffen School of Medicine, UCLA, Los Angeles, California, 90095, USA
| | - Kimberly Hui
- Department of Chemistry, University of Southern California, Los Angeles, California, 90089, USA
| | - Yipin Zhou
- Department of Chemistry, University of Southern California, Los Angeles, California, 90089, USA
| | - Hodaka Sasaki
- Weintraub Center for Reconstructive Biotechnology, UCLA School of Dentistry, Los Angeles, California, 90095, USA
- Department of Oral and Maxillofacial Implantology, Tokyo Dental College, Tokyo 101-0061, Japan
| | - Boris A. Kashemirov
- Department of Chemistry, University of Southern California, Los Angeles, California, 90089, USA
| | - Ichiro Nishimura
- Weintraub Center for Reconstructive Biotechnology, UCLA School of Dentistry, Los Angeles, California, 90095, USA
| | - Charles E. McKenna
- Department of Chemistry, University of Southern California, Los Angeles, California, 90089, USA
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Yurdabak Karaca G, Kuralay F, Bingol Ozakpinar O, Uygun E, Koc U, Ulusoy S, Bosgelmez Tinaz G, Oksuz L, Uygun Oksuz A. Catalytic Au/PEDOT/Pt micromotors for cancer biomarker detection and potential breast cancer treatment. APPLIED NANOSCIENCE 2021. [DOI: 10.1007/s13204-021-01735-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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10
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Bidar N, Oroojalian F, Baradaran B, Eyvazi S, Amini M, Jebelli A, Hosseini SS, Pashazadeh-Panahi P, Mokhtarzadeh A, de la Guardia M. Monitoring of microRNA using molecular beacons approaches: Recent advances. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.116021] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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11
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Kong XJ, Ji X, He T, Xie LH, Zhang YZ, Lv H, Ding C, Li JR. A Green-Emission Metal-Organic Framework-Based Nanoprobe for Imaging Dual Tumor Biomarkers in Living Cells. ACS APPLIED MATERIALS & INTERFACES 2020; 12:35375-35384. [PMID: 32657122 DOI: 10.1021/acsami.0c10038] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The modular nature of metal-organic frameworks (MOFs) permits their tunable structure and function for target application, such as in biomedicine. Herein, a green-emission Zr(IV)-MOF (BUT-88) was constructed from a customized luminescent carbazolyl ligand. BUT-88 represents the first bcu-type MOF with both organic linker and metal node in eight connections and shows medium-sized pores, rich accessible linking sites, and good water stability and biocompatibility. In virtue of these merits, BUT-88 was then fabricated into a MOF-based fluorescent nanoprobe, drDNA-BUT-88. Using it, the live-cell imaging of dual tumor biomarkers was achieved for the first time upon a MOF-based probe, offering enhanced detection precision in early cancer diagnosis. Particularly, the probe showed efficient ratiometric fluorescent sensing toward the cytoplasmic biomarker microRNA-21, further improving the detection accuracy at the cellular level. In this work, the elaborate combination of MOF engineering and the fluorescent detection technique has contributed a facile biosensing platform, unlocking more possibilities of MOF chemistry.
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Affiliation(s)
- Xiang-Jing Kong
- Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry and Chemical Engineering, College of Environmental and Energy Engineering, Beijing University of Technology, Beijing 100124, China
| | - Xiaoting Ji
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Tao He
- Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry and Chemical Engineering, College of Environmental and Energy Engineering, Beijing University of Technology, Beijing 100124, China
| | - Lin-Hua Xie
- Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry and Chemical Engineering, College of Environmental and Energy Engineering, Beijing University of Technology, Beijing 100124, China
| | - Yong-Zheng Zhang
- Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry and Chemical Engineering, College of Environmental and Energy Engineering, Beijing University of Technology, Beijing 100124, China
| | - Haoyuan Lv
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Caifeng Ding
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Jian-Rong Li
- Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry and Chemical Engineering, College of Environmental and Energy Engineering, Beijing University of Technology, Beijing 100124, China
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12
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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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Pereira PM, Gustafsson N, Marsh M, Mhlanga MM, Henriques R. Super-beacons: Open-source probes with spontaneous tuneable blinking compatible with live-cell super-resolution microscopy. Traffic 2020; 21:375-385. [PMID: 32170988 PMCID: PMC7643006 DOI: 10.1111/tra.12728] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/10/2020] [Accepted: 03/11/2020] [Indexed: 11/28/2022]
Abstract
Localization-based super-resolution microscopy relies on the detection of individual molecules cycling between fluorescent and non-fluorescent states. These transitions are commonly regulated by high-intensity illumination, imposing constrains to imaging hardware and producing sample photodamage. Here, we propose single-molecule self-quenching as a mechanism to generate spontaneous photoswitching. To demonstrate this principle, we developed a new class of DNA-based open-source super-resolution probes named super-beacons, with photoswitching kinetics that can be tuned structurally, thermally and chemically. The potential of these probes for live-cell compatible super-resolution microscopy without high-illumination or toxic imaging buffers is revealed by imaging interferon inducible transmembrane proteins (IFITMs) at sub-100 nm resolutions.
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Affiliation(s)
- Pedro M. Pereira
- MRC‐Laboratory for Molecular Cell BiologyUniversity College LondonLondonUK
- The Francis Crick InstituteLondonUK
- Bacterial Cell BiologyMOSTMICRO, ITQB‐NOVAOeirasPortugal
| | - Nils Gustafsson
- MRC‐Laboratory for Molecular Cell BiologyUniversity College LondonLondonUK
- Present address:
Department für Physik and CeNSLudwig‐Maximilians‐UniversitätMunichGermany
| | - Mark Marsh
- MRC‐Laboratory for Molecular Cell BiologyUniversity College LondonLondonUK
| | - Musa M. Mhlanga
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health SciencesUniversity of Cape TownCape TownSouth Africa
| | - Ricardo Henriques
- MRC‐Laboratory for Molecular Cell BiologyUniversity College LondonLondonUK
- The Francis Crick InstituteLondonUK
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14
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Guyon L, Pirrotta M, Duskova K, Granzhan A, Teulade-Fichou MP, Monchaud D. TWJ-Screen: an isothermal screening assay to assess ligand/DNA junction interactions in vitro. Nucleic Acids Res 2019; 46:e16. [PMID: 29149299 PMCID: PMC5815093 DOI: 10.1093/nar/gkx1118] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 10/24/2017] [Indexed: 12/17/2022] Open
Abstract
The quest for chemicals able to operate at selected genomic loci in a spatiotemporally controlled manner is desirable to create manageable DNA damages. Mounting evidence now shows that alternative DNA structures, including G-quadruplexes and branched DNA (or DNA junctions), might hamper proper progression of replication fork, thus triggering DNA damages and genomic instability. Therefore, small molecules that stabilize these DNA structures are currently scrutinized as a promising way to create genomic defects that cannot be dealt with properly by cancer cells. While much emphasis has been recently given to G-quadruplexes and related ligands, we report herein on three-way DNA junctions (TWJ) and related ligands. We first highlight the biological implications of TWJ and their strategic relevance as triggers for replicative stress. Then, we describe a new in vitro high-throughput screening assay, TWJ-Screen, which allows for identifying TWJ ligands with both high affinity and selectivity for TWJ over other DNA structures (duplexes and quadruplexes), in a convenient and unbiased manner as demonstrated by the screening of a library of 25 compounds from different chemical families. TWJ-Screen thus represents a reliable mean to uncover molecular tools able to foster replicative stress through an innovative approach, thus providing new strategic opportunities to combat cancers.
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Affiliation(s)
- Ludivine Guyon
- Institut de Chimie Moléculaire, ICMUB CNRS UMR6302, UBFC, 21078 Dijon, France
| | - Marc Pirrotta
- Institut de Chimie Moléculaire, ICMUB CNRS UMR6302, UBFC, 21078 Dijon, France
| | - Katerina Duskova
- Institut de Chimie Moléculaire, ICMUB CNRS UMR6302, UBFC, 21078 Dijon, France
| | - Anton Granzhan
- Institut Curie, PSL Research University, CNRS UMR9187, INSERM U1196, 91405 Orsay, France
| | | | - David Monchaud
- Institut de Chimie Moléculaire, ICMUB CNRS UMR6302, UBFC, 21078 Dijon, France
- To whom correspondence should be addressed. Tel: +33 380 399 043; Fax: 33 380 396 117;
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15
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Minard A, Liano D, Wang X, Di Antonio M. The unexplored potential of quinone methides in chemical biology. Bioorg Med Chem 2019; 27:2298-2305. [PMID: 30955994 DOI: 10.1016/j.bmc.2019.04.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 03/29/2019] [Accepted: 04/01/2019] [Indexed: 11/16/2022]
Abstract
Quinone methides (QMs) are transient reactive species that can be efficiently generated from stable precursors under a variety of biocompatible conditions. Due to their electrophilic nature, QMs have been widely explored as cross-linking agents of DNA and proteins under physiological conditions. However, QMs also have a diene character and can irreversibly react via Diels-Alder reaction with electron-rich dienophiles. This particular reactivity has been recently exploited to label biomolecules with fluorophores in living cells. QMs are characterised by two unique properties that make them ideal candidates for chemical biology applications: i) they can be efficiently generated in situ from very stable precursors by means of bio-orthogonal protocols ii) they are reversible cross-linking agents, making them suitable for "catch and release" target-enrichment experiments. Nevertheless, there are only few examples reported to date that truly take advantage of QMs unique chemistry in the context of chemical-biology assay development. In this review, we will examine the most relevant examples that illustrate the benefit of using QMs for chemical biology purposes and we will anticipate novel approaches to further their applications in biologically relevant contexts.
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Affiliation(s)
- Aisling Minard
- Imperial College London, Department of Chemistry, Molecular Science Research Hub, Wood Lane, W12 0BZ London, UK
| | - Denise Liano
- Imperial College London, Department of Chemistry, Molecular Science Research Hub, Wood Lane, W12 0BZ London, UK
| | - Xiaofan Wang
- Imperial College London, Department of Chemistry, Molecular Science Research Hub, Wood Lane, W12 0BZ London, UK
| | - Marco Di Antonio
- Imperial College London, Department of Chemistry, Molecular Science Research Hub, Wood Lane, W12 0BZ London, UK.
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16
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Demuth J, Kucera R, Kopecky K, Havlínová Z, Libra A, Novakova V, Miletin M, Zimcik P. Efficient Synthesis of a Wide-Range Absorbing Azaphthalocyanine Dark Quencher and Its Application to Dual-Labeled Oligonucleotide Probes for Quantitative Real-Time Polymerase Chain Reactions. Chemistry 2018; 24:9658-9666. [PMID: 29683215 DOI: 10.1002/chem.201801319] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Indexed: 11/06/2022]
Abstract
Unsymmetrical dialkylamino-substituted zinc azaphthalocyanine (AzaPc) exhibits unique spectral and photophysical properties for dark quenchers of fluorescence in DNA hybridization probes. The panchromatic light absorption of AzaPc from 300 nm up to at least 700 nm and its lack of fluorescence make it an ideal candidate for a universal dark quencher. To prove this experimentally, oligodeoxyribonucleotide probes were labeled at the 3'-end by this AzaPc and at the 5'-end by a fluorophore used in the polymerase chain reaction (PCR)-that is, fluorescein, CAL Fluor Red 610, and Cy5. AzaPc showed a significantly higher quenching efficiency compared to the commercially available dark quenchers (BHQ-1, BHQ-2, BBQ-650) in a developed model of TaqMan PCR assay. The AzaPc-labeled probe proved to also be useful in a practical PCR assay for the quantification of the SLCO2B1 transporter gene expression. The constructed calibration curves indicated linearity in the range from 102 to 107 of target copies.
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Affiliation(s)
- Jiri Demuth
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Charles University, Faculty of Pharmacy in Hradec Kralove, Akademika Heyrovskeho 1203, Hradec Kralove, 500 05, Czech Republic
| | - Radim Kucera
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Charles University, Faculty of Pharmacy in Hradec Kralove, Akademika Heyrovskeho 1203, Hradec Kralove, 500 05, Czech Republic
| | - Kamil Kopecky
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Charles University, Faculty of Pharmacy in Hradec Kralove, Akademika Heyrovskeho 1203, Hradec Kralove, 500 05, Czech Republic
| | - Zuzana Havlínová
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Charles University, Faculty of Pharmacy in Hradec Kralove, Akademika Heyrovskeho 1203, Hradec Kralove, 500 05, Czech Republic.,Generi Biotech, Machkova 587, Hradec Kralove, 500 11, Czech Republic
| | - Antonín Libra
- Generi Biotech, Machkova 587, Hradec Kralove, 500 11, Czech Republic
| | - Veronika Novakova
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Charles University, Faculty of Pharmacy in Hradec Kralove, Akademika Heyrovskeho 1203, Hradec Kralove, 500 05, Czech Republic
| | - Miroslav Miletin
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Charles University, Faculty of Pharmacy in Hradec Kralove, Akademika Heyrovskeho 1203, Hradec Kralove, 500 05, Czech Republic
| | - Petr Zimcik
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Charles University, Faculty of Pharmacy in Hradec Kralove, Akademika Heyrovskeho 1203, Hradec Kralove, 500 05, Czech Republic
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17
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Abstract
Fluorogenic oligonucleotide probes that can produce a change in fluorescence signal upon binding to specific biomolecular targets, including nucleic acids as well as non-nucleic acid targets, such as proteins and small molecules, have applications in various important areas. These include diagnostics, drug development and as tools for studying biomolecular interactions in situ and in real time. The probes usually consist of a labeled oligonucleotide strand as a recognition element together with a mechanism for signal transduction that can translate the binding event into a measurable signal. While a number of strategies have been developed for the signal transduction, relatively little attention has been paid to the recognition element. Peptide nucleic acids (PNA) are DNA mimics with several favorable properties making them a potential alternative to natural nucleic acids for the development of fluorogenic probes, including their very strong and specific recognition and excellent chemical and biological stabilities in addition to their ability to bind to structured nucleic acid targets. In addition, the uncharged backbone of PNA allows for other unique designs that cannot be performed with oligonucleotides or analogues with negatively-charged backbones. This review aims to introduce the principle, showcase state-of-the-art technologies and update recent developments in the areas of fluorogenic PNA probes during the past 20 years.
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Affiliation(s)
- Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
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18
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Chen B, Su Q, Kong W, Wang Y, Shi P, Wang F. Energy transfer-based biodetection using optical nanomaterials. J Mater Chem B 2018; 6:2924-2944. [DOI: 10.1039/c8tb00614h] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This review focuses on recent progress in the development of FRET probes and the applications of FRET-based sensing systems.
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Affiliation(s)
- Bing Chen
- Department of Materials Science and Engineering
- City University of Hong Kong
- China
- City Universities of Hong Kong Shenzhen Research Institute
- Shenzhen 518057
| | - Qianqian Su
- Institute of Nanochemistry and Nanobiology
- Shanghai University
- Shanghai 200444
- China
| | - Wei Kong
- Department of Materials Science and Engineering
- City University of Hong Kong
- China
- City Universities of Hong Kong Shenzhen Research Institute
- Shenzhen 518057
| | - Yuan Wang
- Department of Mechanical and Biomedical Engineering
- City University of Hong Kong
- China
| | - Peng Shi
- City Universities of Hong Kong Shenzhen Research Institute
- Shenzhen 518057
- China
- Department of Mechanical and Biomedical Engineering
- City University of Hong Kong
| | - Feng Wang
- Department of Materials Science and Engineering
- City University of Hong Kong
- China
- City Universities of Hong Kong Shenzhen Research Institute
- Shenzhen 518057
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19
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Kozanitas M, Osmundson TW, Linzer R, Garbelotto M. Interspecific interactions between the Sudden Oak Death pathogen Phytophthora ramorum and two sympatric Phytophthora species in varying ecological conditions. FUNGAL ECOL 2017. [DOI: 10.1016/j.funeco.2017.04.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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20
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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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21
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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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22
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Lv Y, Wu J, Wu P, Chen YZ, Tan Y, Tan C, Jiang Y. A sensitive polymeric dark quencher-based sensing platform for fluorescence “turn on” detection of proteins. RSC Adv 2016. [DOI: 10.1039/c6ra07310g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
A sensing platform consisting of polymeric dark quenchers and oppositely charged probes was constructed for detection of proteins.
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Affiliation(s)
- Ying Lv
- Department of Chemistry
- Tsinghua University
- Beijing 100084
- P. R. China
- The Ministry-Province Jointly Constructed Base for State Key Lab-Shenzhen Key Laboratory of Chemical Biology
| | - Jiatao Wu
- Department of Chemistry
- Tsinghua University
- Beijing 100084
- P. R. China
- The Ministry-Province Jointly Constructed Base for State Key Lab-Shenzhen Key Laboratory of Chemical Biology
| | - Pan Wu
- Department of Chemistry
- Tsinghua University
- Beijing 100084
- P. R. China
- The Ministry-Province Jointly Constructed Base for State Key Lab-Shenzhen Key Laboratory of Chemical Biology
| | - Yu Zong Chen
- Shenzhen Technology and Engineering Laboratory for Personalized Cancer Diagnostics and Therapeutics
- Shenzhen Kivita Innovative Drug Discovery Institute
- Shenzhen 518055
- P. R. China
| | - Ying Tan
- The Ministry-Province Jointly Constructed Base for State Key Lab-Shenzhen Key Laboratory of Chemical Biology
- Graduate School at Shenzhen
- Tsinghua University
- Shenzhen 518055
- P. R. China
| | - Chunyan Tan
- Department of Chemistry
- Tsinghua University
- Beijing 100084
- P. R. China
- The Ministry-Province Jointly Constructed Base for State Key Lab-Shenzhen Key Laboratory of Chemical Biology
| | - Yuyang Jiang
- The Ministry-Province Jointly Constructed Base for State Key Lab-Shenzhen Key Laboratory of Chemical Biology
- Graduate School at Shenzhen
- Tsinghua University
- Shenzhen 518055
- P. R. China
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23
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Aliberti A, Cusano AM, Battista E, Causa F, Netti PA. High sensitive and direct fluorescence detection of single viral DNA sequences by integration of double strand probes onto microgels particles. Analyst 2016; 141:1250-6. [DOI: 10.1039/c5an02001h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel class of probes for fluorescence detection was developed and combined to microgel particles for a high sensitive fluorescence detection of nucleic acids.
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Affiliation(s)
- A. Aliberti
- Center for Advanced Biomaterials for Healthcare@CRIB
- Istituto Italiano di Tecnologia (IIT)
- 80125 Naples
- Italy
| | - A. M. Cusano
- Center for Advanced Biomaterials for Healthcare@CRIB
- Istituto Italiano di Tecnologia (IIT)
- 80125 Naples
- Italy
| | - E. Battista
- Center for Advanced Biomaterials for Healthcare@CRIB
- Istituto Italiano di Tecnologia (IIT)
- 80125 Naples
- Italy
| | - F. Causa
- Center for Advanced Biomaterials for Healthcare@CRIB
- Istituto Italiano di Tecnologia (IIT)
- 80125 Naples
- Italy
- Interdisciplinary Research Centre on Biomaterials (CRIB)
| | - P. A. Netti
- Center for Advanced Biomaterials for Healthcare@CRIB
- Istituto Italiano di Tecnologia (IIT)
- 80125 Naples
- Italy
- Interdisciplinary Research Centre on Biomaterials (CRIB)
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24
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Nyan DC, Swinson KL. A novel multiplex isothermal amplification method for rapid detection and identification of viruses. Sci Rep 2015; 5:17925. [PMID: 26643761 PMCID: PMC4672323 DOI: 10.1038/srep17925] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 11/09/2015] [Indexed: 11/09/2022] Open
Abstract
A rapid multiplex isothermal amplification assay has been developed for detection and identification of multiple blood-borne viruses that infect millions of people world-wide. These infections may lead to chronic diseases or death if not diagnosed and treated in a timely manner. Sets of virus-specific oligonucleotides and oligofluorophores were designed and used in a reverse-transcription loop-mediated multiplexed isothermal amplification reaction for detection and gel electrophoretic identification of human Immunodeficiency virus (HIV), hepatitis-B virus (HBV), hepatitis-C virus (HCV), hepatitis-E virus (HEV), dengue virus (DENV), and West Nile (WNV) virus infection in blood plasma. Amplification was catalyzed with two thermostable enzymes for 30-60 minutes under isothermal condition, utilizing a simple digital heat source. Electrophoretic analysis of amplified products demonstrated simultaneous detection of 6 viruses that were distinctly identified by unique ladder-like banding patterns. Naked-eye fluorescent visualization of amplicons revealed intensely fluorescing products that indicated positive detection. The test demonstrated a 97% sensitivity and a 100% specificity, with no cross-reaction with other viruses observed. This portable detection tool may have clinical and field utility in the developing and developed world settings. This may enable rapid diagnosis and identification of viruses for targeted therapeutic intervention and prevention of disease transmission.
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Affiliation(s)
- Dougbeh-Chris Nyan
- Division of Emerging and Transfusion-Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Kevin L. Swinson
- Department of Biology, Morgan State University, Baltimore Maryland, USA
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25
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Dou X, Chu X, Kong W, Luo J, Yang M. A gold-based nanobeacon probe for fluorescence sensing of organophosphorus pesticides. Anal Chim Acta 2015; 891:291-7. [PMID: 26388389 DOI: 10.1016/j.aca.2015.08.012] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 07/31/2015] [Accepted: 08/05/2015] [Indexed: 11/18/2022]
Abstract
A nanomaterials-based novel molecular beacon has attracted growing attentions in fluorescent assays as many nanomaterials possess excellent quenching efficiency. In this work, a gold-based nanobeacon probe was established to detect organophosphorus pesticides for the first time. The constructed gold-based nanobeacon acted as a signal indicator and could display the decreasing of the intensity in the presence of targets, which competitively bound to single strand DNA. To achieve a high sensitive probe, some parameters including solution pH, temperature and reaction time were investigated and optimized. The gold-based nanobeacon probe assay was proved to be rapid and sensitive to achieve a detection limit of 0.035 μM for isocarbophos, 0.134 μM for profenofos, 0.384 μM for phorate and 2.35 μM for omethoate, respectively. The prepared nanobeacon effectively reduced the background and improved the detection sensitivity and selectivity. The probe is stable, easy to operate and does not need sophisticated instruments. These features makes the probe feasible for screening trace organophosphorus pesticides in real samples.
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Affiliation(s)
- Xiaowen Dou
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Xianfeng Chu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Weijun Kong
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Jiaoyang Luo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Meihua Yang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China; Hainan Branch Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Wanning 571533, China.
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26
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Morimoto N, Muramatsu K, Nomura SIM, Suzuki M. Trading polymeric microspheres: Exchanging DNA molecules via microsphere interaction. Colloids Surf B Biointerfaces 2015; 128:94-99. [DOI: 10.1016/j.colsurfb.2015.02.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 12/18/2014] [Accepted: 02/08/2015] [Indexed: 11/30/2022]
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27
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Causa F, Aliberti A, Cusano AM, Battista E, Netti PA. Supramolecular Spectrally Encoded Microgels with Double Strand Probes for Absolute and Direct miRNA Fluorescence Detection at High Sensitivity. J Am Chem Soc 2015; 137:1758-61. [DOI: 10.1021/ja511644b] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Filippo Causa
- Center
for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy
- Interdisciplinary
Research Centre on Biomaterials (CRIB), University “‘Federico II”’, Piazzale Tecchio 80, 80125 Naples, Italy
- Dipartimento
di Ingegneria Chimica, dei Materiali e della Produzione Industriale
(DICMAPI), University “‘Federico II”’, Piazzale
Tecchio 80, 80125 Naples, Italy
| | - Anna Aliberti
- Center
for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy
| | - Angela M. Cusano
- Center
for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy
| | - Edmondo Battista
- Center
for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy
| | - Paolo A. Netti
- Center
for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy
- Interdisciplinary
Research Centre on Biomaterials (CRIB), University “‘Federico II”’, Piazzale Tecchio 80, 80125 Naples, Italy
- Dipartimento
di Ingegneria Chimica, dei Materiali e della Produzione Industriale
(DICMAPI), University “‘Federico II”’, Piazzale
Tecchio 80, 80125 Naples, Italy
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28
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Chiaraviglio L, Kirby JE. Evaluation of impermeant, DNA-binding dye fluorescence as a real-time readout of eukaryotic cell toxicity in a high throughput screening format. Assay Drug Dev Technol 2015; 12:219-28. [PMID: 24831788 DOI: 10.1089/adt.2014.577] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Interpretation of high throughput screening (HTS) data in cell-based assays may be confounded by cytotoxic properties of screening compounds. Therefore, assessing cell toxicity in real time during the HTS process itself would be highly advantageous. Here, we investigate the potential of putatively impermeant, fluorescent, DNA-binding dyes to give cell toxicity readout during HTS. Amongst 19 DNA-binding dyes examined, three classes were identified that were (1) permeant, (2) cytotoxic, or (3) neither permeant nor cytotoxic during 3-day incubation with a macrophage cell line. In the last class, four dyes (SYTOX Green, CellTox Green, GelGreen, and EvaGreen) gave highly robust cytotoxicity data in 384-well screening plates. As proof of principle, successful combination with a luminescence-based assay in HTS format was demonstrated. Here, both intracellular growth of Legionella pneumophila (luminescence) and host cell viability (SYTOX Green exclusion) were assayed in the same screening well. Incorporation of membrane-impermeant, DNA-binding, fluorescent dyes in HTS assays should prove useful by allowing evaluation of cytotoxicity in real time, eliminating reagent addition steps and effort associated with endpoint cell viability analysis, and reducing the need for follow-up cytotoxicity screening.
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Affiliation(s)
- Lucius Chiaraviglio
- Department of Pathology, Beth Israel Deaconess Medical Center , Boston, Massachusetts
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29
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Zhang R, Kwok RTK, Tang BZ, Liu B. Hybridization induced fluorescence turn-on of AIEgen–oligonucleotide conjugates for specific DNA detection. RSC Adv 2015. [DOI: 10.1039/c5ra00322a] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
We report a two-armed AIE probes for specific DNA detection, and the signal output can be further enhanced when two probes hybridize to each.
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Affiliation(s)
- Ruoyu Zhang
- Department of Chemical and Biomolecular Engineering
- National University of Singapore
- Singapore
| | - Ryan T. K. Kwok
- Department of Chemistry
- Division of Biomedical Engineering
- The Hong Kong University of Science and Technology
- Hong Kong
- China
| | - Ben Zhong Tang
- Department of Chemistry
- Division of Biomedical Engineering
- The Hong Kong University of Science and Technology
- Hong Kong
- China
| | - Bin Liu
- Department of Chemical and Biomolecular Engineering
- National University of Singapore
- Singapore
- Institute of Materials Research and Engineering (A*STAR)
- Singapore
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30
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Yotapan N, Charoenpakdee C, Wathanathavorn P, Ditmangklo B, Wagenknecht HA, Vilaivan T. Synthesis and optical properties of pyrrolidinyl peptide nucleic acid carrying a clicked Nile red label. Beilstein J Org Chem 2014; 10:2166-74. [PMID: 25246975 PMCID: PMC4168962 DOI: 10.3762/bjoc.10.224] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 08/19/2014] [Indexed: 12/16/2022] Open
Abstract
DNA or its analogues with an environment-sensitive fluorescent label are potentially useful as a probe for studying the structure and dynamics of nucleic acids. In this work, pyrrolidinyl peptide nucleic acid (acpcPNA) was labeled at its backbone with Nile red, a solvatochromic benzophenoxazine dye, by means of click chemistry. The optical properties of the Nile red-labeled acpcPNA were investigated by UV–vis and fluorescence spectroscopy in the absence and in the presence of DNA. In contrast to the usual quenching observed in Nile red-labeled DNA, the hybridization with DNA resulted in blue shifting and an enhanced fluorescence regardless of the neighboring bases. More pronounced blue shifts and fluorescence enhancements were observed when the DNA target carried a base insertion in close proximity to the Nile red label. The results indicate that the Nile red label is located in a more hydrophobic environment in acpcPNA–DNA duplexes than in the single-stranded acpcPNA. The different fluorescence properties of the acpcPNA hybrids of complementary DNA and DNA carrying a base insertion are suggestive of different interactions between the Nile red label and the duplexes.
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Affiliation(s)
- Nattawut Yotapan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
| | - Chayan Charoenpakdee
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
| | - Pawinee Wathanathavorn
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
| | - Boonsong Ditmangklo
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
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31
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Salgado MM, Gonçalves MG, Fukasawa LO, Higa FT, Paulino JT, Sacchi CT. Evolution of bacterial meningitis diagnosis in São Paulo State-Brazil and future challenges. ARQUIVOS DE NEURO-PSIQUIATRIA 2014; 71:672-6. [PMID: 24141502 DOI: 10.1590/0004-282x20130148] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Bacterial meningitis (BM) is a severe disease and still represents a serious public health problem with high rates of morbidity and mortality. The most common cases of BM around the world, mainly in Brazil, have been caused by Neisseria meningitidis, Streptococcus pneumoniae, and Haemophilus influenzae type b. Bacterial culture is the gold-standard technique for BM confirmation, but approximately 50% of suspected cases are not culture-confirmed, due to problems related to improper transportation and seeding or previous antibiotic treatment. Immunological methods present low sensitivity and have possibility of cross-reactions. Real time PCR (qPCR) is a molecular technique and has been successful used for BM diagnosis at Instituto Adolfo Lutz in São Paulo State, Brazil, since 2007. The incorporation of qPCR in the Public Health surveillance routine in our state resulted in diminishing 50% of undetermined BM cases. Our efforts are focused on qPCR implementation in the BM diagnostic routine throughout Brazil.
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Ruijter JM, Lorenz P, Tuomi JM, Hecker M, van den Hoff MJB. Fluorescent-increase kinetics of different fluorescent reporters used for qPCR depend on monitoring chemistry, targeted sequence, type of DNA input and PCR efficiency. Mikrochim Acta 2014; 181:1689-1696. [PMID: 25253910 PMCID: PMC4167442 DOI: 10.1007/s00604-013-1155-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 12/19/2013] [Indexed: 11/30/2022]
Abstract
The analysis of quantitative PCR data usually does not take into account the fact that the increase in fluorescence depends on the monitoring chemistry, the input of ds-DNA or ss-cDNA, and the directionality of the targeting of probes or primers. The monitoring chemistries currently available can be categorized into six groups: (A) DNA-binding dyes; (B) hybridization probes; (C) hydrolysis probes; (D) LUX primers; (E) hairpin primers; and (F) the QZyme system. We have determined the kinetics of the increase in fluorescence for each of these groups with respect to the input of both ds-DNA and ss-cDNA. For the latter, we also evaluated mRNA and cDNA targeting probes or primers. This analysis revealed three situations. Hydrolysis probes and LUX primers, compared to DNA-binding dyes, do not require a correction of the observed quantification cycle. Hybridization probes and hairpin primers require a correction of −1 cycle (dubbed C-lag), while the QZyme system requires the C-lag correction and an efficiency-dependent C-shift correction. A PCR efficiency value can be derived from the relative increase in fluorescence in the exponential phase of the amplification curve for all monitoring chemistries. In case of hydrolysis probes, LUX primers and hairpin primers, however, this should be performed after cycle 12, and for the QZyme system after cycle 19, to keep the overestimation of the PCR efficiency below 0.5 %. The qPCR monitoring chemistries form six groups with distinct fluorescence kinetics. The displacement of the amplification curve depends on the chemistry, DNA input and probe-targeting. The observed shift in Cq values can be corrected and PCR efficiencies can be derived. ![]()
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Affiliation(s)
- Jan M. Ruijter
- Department of Anatomy, Embryology & Physiology, Academic Medical Center, Meibergdreef 15, 1105AZ Amsterdam, The Netherlands
| | - Peter Lorenz
- Institute of Immunology, University of Rostock, Rostock, Germany
| | - Jari M. Tuomi
- Northern Ontario School of Medicine, Sault Ste. Marie, ON Canada
| | - Michael Hecker
- Steinbeis Transfer Center for Proteome Analysis, Rostock, Germany
| | - Maurice J. B. van den Hoff
- Department of Anatomy, Embryology & Physiology, Academic Medical Center, Meibergdreef 15, 1105AZ Amsterdam, The Netherlands
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33
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Graham D, Faulds K. Surface-enhanced Raman scattering as a detection technique for molecular diagnostics. Expert Rev Mol Diagn 2014; 9:537-9. [DOI: 10.1586/erm.09.37] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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34
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Lin KC, Kuo CY, Nieh CC, Tseng WL. Molecular beacon-based NAND logic gate for sensing triplex DNA binders. RSC Adv 2014. [DOI: 10.1039/c4ra06158f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Molecular beacon-based NAND logic gate was simple, rapid, selective, and sensitive for probing triplex DNA binders.
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Affiliation(s)
- Kai-Cheng Lin
- Department of Emergency Medicine
- Division of Traumatology
- Kaohsiung Veterans General Hospital
- Taiwan
| | - Chia-Yin Kuo
- Department of Chemistry
- National Sun Yat-sen University
- Kaohsiung, Taiwan
| | - Chih-Chun Nieh
- Department of Chemistry
- National Sun Yat-sen University
- Kaohsiung, Taiwan
| | - Wei-Lung Tseng
- Department of Chemistry
- National Sun Yat-sen University
- Kaohsiung, Taiwan
- School of Pharmacy
- College of Pharmacy
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35
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Lin JH, Tseng WL. Design of two and three input molecular logic gates using non-Watson–Crick base pairing-based molecular beacons. Analyst 2014; 139:1436-41. [DOI: 10.1039/c3an02298f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A single, resettable, and sensitive molecular beacon has been developed to operate two-input, three-input, and set–reset logic gates.
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Affiliation(s)
- Jia-Hui Lin
- Department of Chemistry
- National Sun Yat-sen University
- Kaohsiung 80424, Taiwan
| | - Wei-Lung Tseng
- Department of Chemistry
- National Sun Yat-sen University
- Kaohsiung 80424, Taiwan
- School of Pharmacy
- College of Pharmacy
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36
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Boonlua C, Ditmangklo B, Reenabthue N, Suparpprom C, Poomsuk N, Siriwong K, Vilaivan T. Pyrene-labeled pyrrolidinyl peptide nucleic acid as a hybridization-responsive DNA probe: comparison between internal and terminal labeling. RSC Adv 2014. [DOI: 10.1039/c3ra47997h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Internally pyrene-labeled pyrrolidinyl PNA yields much larger fluorescence increase than terminally labeled PNA upon hybridization with complementary DNA.
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Affiliation(s)
- Chalothorn Boonlua
- Organic Synthesis Research Unit
- Department of Chemistry
- Faculty of Science
- Chulalongkorn University
- Bangkok 10330, Thailand
| | - Boonsong Ditmangklo
- Organic Synthesis Research Unit
- Department of Chemistry
- Faculty of Science
- Chulalongkorn University
- Bangkok 10330, Thailand
| | - Nisanath Reenabthue
- Department of Chemistry
- Faculty of Science
- Naresuan University
- Phitsanulok 65000, Thailand
| | - Chaturong Suparpprom
- Department of Chemistry
- Faculty of Science
- Naresuan University
- Phitsanulok 65000, Thailand
| | - Nattawee Poomsuk
- Materials Chemistry Research Unit
- Department of Chemistry
- Faculty of Science
- Khon Kaen University
- Khon Kaen 40002, Thailand
| | - Khatcharin Siriwong
- Materials Chemistry Research Unit
- Department of Chemistry
- Faculty of Science
- Khon Kaen University
- Khon Kaen 40002, Thailand
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit
- Department of Chemistry
- Faculty of Science
- Chulalongkorn University
- Bangkok 10330, Thailand
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37
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Onasanya A, Onasanya RO, Ojo AA, Adewale BO. Genetic Analysis and Molecular Identification of Virulence in Xanthomonas oryzae pv. oryzae Isolates. ISRN MOLECULAR BIOLOGY 2013; 2013:160157. [PMID: 27335673 PMCID: PMC4890910 DOI: 10.1155/2013/160157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Accepted: 08/04/2013] [Indexed: 11/18/2022]
Abstract
Bacterial leaf blight (BLB) of rice is a very destructive disease worldwide and is caused by Xanthomonas oryzae pv. oryzae (Xoo). The aim of the present study was to examine if the Xoo virulence pathotypes obtained using phenotypic pathotyping could be confirmed using molecular approach. After screening of 60 Operon primers with genomic DNA of two Xoo isolates (virulent pathotype, Vr, and mildly virulent pathotype, MVr), 12 Operon primers that gave reproducible and useful genetic information were selected and used to analyze 50 Xoo isolates from 7 West African countries. Genetic analysis revealed two major Xoo virulence genotypes (Mta and Mtb) with Mta having two subgroups (Mta1 and Mta2). Mta1 (Vr1) subgroup genotype has occurrence in six countries and Mta2 (Vr2) in three countries while Mtb genotype characterized mildly virulence (MVr) Xoo isolates present in five countries. The study revealed possible linkage and correlation between phenotypic pathotyping and molecular typing of Xoo virulence. Xoo virulence genotypes were known to exist within country and there was evidence of Xoo pathogen migration between countries. Durable resistance rice cultivars would need to overcome both Mta and Mtb Xoo virulence genotypes in order to survive after their deployment into different rice ecologies in West Africa.
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Affiliation(s)
- Amos Onasanya
- Department of Chemical Sciences, College of Sciences, Afe Babalola University, PMB 5454, Ado Ekiti, Nigeria
| | - R. O. Onasanya
- Federal College of Agriculture Ibadan, PMB 502, Ibadan, Nigeria
| | - Abiodun A. Ojo
- Department of Chemical Sciences, College of Sciences, Afe Babalola University, PMB 5454, Ado Ekiti, Nigeria
| | - B. O. Adewale
- Department of Chemical Sciences, College of Sciences, Afe Babalola University, PMB 5454, Ado Ekiti, Nigeria
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38
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Porchetta A, Vallée-Bélisle A, Plaxco KW, Ricci F. Allosterically tunable, DNA-based switches triggered by heavy metals. J Am Chem Soc 2013; 135:13238-41. [PMID: 23971651 DOI: 10.1021/ja404653q] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Here we demonstrate the rational design of allosterically controllable, metal-ion-triggered molecular switches. Specifically, we designed DNA sequences that adopt two low energy conformations, one of which does not bind to the target ion and the other of which contains mismatch sites serving as specific recognition elements for mercury(II) or silver(I) ions. Both switches contain multiple metal binding sites and thus exhibit homotropic allosteric (cooperative) responses. As heterotropic allosteric effectors we employ single-stranded DNA sequences that either stabilize or destabilize the nonbinding state, enabling dynamic range tuning over several orders of magnitude. The ability to rationally introduce these effects into target-responsive switches could be of value in improving the functionality of DNA-based nanomachines.
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Affiliation(s)
- Alessandro Porchetta
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome , Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
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39
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Ditmangklo B, Boonlua C, Suparpprom C, Vilaivan T. Reductive alkylation and sequential reductive alkylation-click chemistry for on-solid-support modification of pyrrolidinyl peptide nucleic acid. Bioconjug Chem 2013; 24:614-25. [PMID: 23517168 DOI: 10.1021/bc3005914] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A methodology for the site-specific attachment of fluorophores to the backbone of pyrrolidinyl peptide nucleic acids (PNAs) with an α/β-backbone derived from D-prolyl-(1S,2S)-2-aminocyclopentanecarboxylic acid (acpcPNA) has been developed. The strategy involves a postsynthetic reductive alkylation of the aldehyde-containing labels onto the acpcPNA that was previously modified with (3R,4S)-3-aminopyrrolidine-4-carboxylic acid on the solid support. The reductive alkylation reaction is remarkably efficient and compatible with a range of reactive functional groups including Fmoc-protected amino, azide, and alkynes. This allows further attachment of readily accessible carboxyl-, alkyne-, or azide-containing labels via amide bond formation or Cu-catalyzed azide-alkyne cycloaddition (CuAAC, also known as click chemistry). The label attached in this way does not negatively affect the affinity and specificity of the pairing of the acpcPNA to its DNA target. Applications of this methodology in creating self-reporting pyrene- and thiazole orange-labeled acpcPNA probes that can yield a change in fluorescence in response to the presence of the correct DNA target have also been explored. A strong fluorescence enhancement was observed with thiazole orange-labeled acpcPNA in the presence of DNA. The specificity could be further improved by enzymatic digestion with S1 nuclease, providing a 9- to 60-fold fluorescence enhancement with fully complementary DNA and a less than 3.5-fold enhancement with mismatched DNA targets.
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Affiliation(s)
- Boonsong Ditmangklo
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Naresuan University, Phitsanulok 65000, Thailand
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40
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41
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Anisenko A, Agapkina J, Zatsepin T, Yanvarev D, Gottikh M. A new fluorometric assay for the study of DNA-binding and 3'-processing activities of retroviral integrases and its use for screening of HIV-1 integrase inhibitors. Biochimie 2012; 94:2382-90. [PMID: 22728110 DOI: 10.1016/j.biochi.2012.06.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Accepted: 06/07/2012] [Indexed: 11/24/2022]
Abstract
Fluorometry using a substrate DNA labeled with a single fluorophore (6-carboxyfluorescein) at the 3'-end of the processed strand was shown to be a useful tool for monitoring DNA-binding and 3'-processing activities of HIV-1 and PFV integrases (INs). The DNA binding to either of the INs resulted in a fluorescence signal decrease, which is likely due to the fluorescence quenching by aromatic amino acids located near the 3'-end of the processed strand. The fluorescence deviations upon the 3'-processing strongly depended on the sequence of the fluorescein-labeled terminus of the substrate DNA. In the case of HIV-1 IN, a time-dependent fluorescence decrease was detected. Since it correlated with the rate of 3'-processing resulted in the labeled GT dinucleotide accumulation, it might be explained by the fluorescein quenching by a guanosine residue in the single-stranded dinucleotide. The 3'-processing catalyzed by PFV IN led to the fluorescence enhancement. We ascribed it to the migration of the cleaved AT dinucleotide conjugated with fluorescein away from the amino acids that could quench its fluorescence. The fluorescence-based assay was used for the search of new HIV-1 IN inhibitors. Some bisphosphonate derivatives, which are known to block the phosphorolytic activity of HIV-1 reverse transcriptase, were shown to inhibit HIV-1 IN at micromolar concentrations. This property makes bisphosphonates promising agents for the development of HIV-1 inhibitors affecting two viral enzymes.
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Affiliation(s)
- Andrey Anisenko
- Lomonosov Moscow State University, Chemistry Department and Belozersky Institute of Physical and Chemical Biology, Leninskie gory 1/40, Moscow 119991, Russia
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42
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Asanuma H, Fujii T, Kato T, Kashida H. Coherent interactions of dyes assembled on DNA. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2012. [DOI: 10.1016/j.jphotochemrev.2012.04.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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43
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Abstract
Recent technical advances have begun to realize the potential of molecular beacons to test for diverse infections in clinical diagnostic laboratories. These include the ability to test for, and quantify, multiple pathogens in the same clinical sample, and to detect antibiotic resistant strains within hours. The design principles of molecular beacons have also spawned a variety of allied technologies.
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Affiliation(s)
- Sanjay Tyagi
- Public Health Research Institute, New Jersey Medical School, University of Medicine and Dentistry of New Jersey225 Warren Street, Newark, NJ 07103USA
| | - Fred Russell Kramer
- Public Health Research Institute, New Jersey Medical School, University of Medicine and Dentistry of New Jersey225 Warren Street, Newark, NJ 07103USA
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, University of Medicine and Dentistry of New Jersey225 Warren Street, Newark, NJ 07103USA
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44
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Mizukami S, Watanabe S, Akimoto Y, Kikuchi K. No-Wash Protein Labeling with Designed Fluorogenic Probes and Application to Real-Time Pulse-Chase Analysis. J Am Chem Soc 2012; 134:1623-9. [DOI: 10.1021/ja208290f] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Shin Mizukami
- Division of Advanced Science
and Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- Immunology Frontier Research
Center (IFReC), Osaka University, 3-1 Yamadaoka,
Suita, Osaka 565-0871, Japan
| | - Shuji Watanabe
- Division of Advanced Science
and Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yuri Akimoto
- Division of Advanced Science
and Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kazuya Kikuchi
- Division of Advanced Science
and Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- Immunology Frontier Research
Center (IFReC), Osaka University, 3-1 Yamadaoka,
Suita, Osaka 565-0871, Japan
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45
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Asanuma H, Akahane M, Kondo N, Osawa T, Kato T, Kashida H. Quencher-free linear probe with multiple fluorophores on an acyclic scaffold. Chem Sci 2012. [DOI: 10.1039/c2sc20732j] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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46
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Zhou S, Acquaah-Harrison G, Jack KD, Bergmeier SC, Hines JV. Ligand-induced changes in T box antiterminator RNA stability. Chem Biol Drug Des 2011; 79:202-8. [PMID: 22117759 DOI: 10.1111/j.1747-0285.2011.01274.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The T box antiterminator RNA element is an important component of the T box riboswitch that controls the transcription of vital genes in many Gram-positive bacteria. A series of 1,4-disubstituted 1,2,3-triazoles was screened in a fluorescence-monitored thermal denaturation assay to identify ligands that altered the stability of antiterminator model RNA. Several ligands were identified that significantly increased or decreased the melting temperature (T(m) ) of the RNA. The results indicate that this series of triazole ligands can alter the stability of antiterminator model RNA in a structure-dependent manner.
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Affiliation(s)
- Shu Zhou
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701, USA
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47
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Kimoto M, Mitsui T, Yamashige R, Sato A, Yokoyama S, Hirao I. A new unnatural base pair system between fluorophore and quencher base analogues for nucleic acid-based imaging technology. J Am Chem Soc 2011; 132:15418-26. [PMID: 20939572 DOI: 10.1021/ja1072383] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the development of orthogonal extra base pairs for expanding the genetic alphabet, we created novel, unnatural base pairs between fluorophore and quencher nucleobase analogues. We found that the nucleobase analogue, 2-nitropyrrole (denoted by Pn), and its 4-substitutions, such as 2-nitro-4-propynylpyrrole (Px) and 4-[3-(6-aminohexanamido)-1-propynyl]-2-nitropyrrole (NH(2)-hx-Px), act as fluorescence quenchers. The Pn and Px bases specifically pair with their pairing partner, 7-(2,2'-bithien-5-yl)imidazo[4,5-b]pyridine (Dss), which is strongly fluorescent. Thus, these unnatural Dss-Pn and Dss-Px base pairs function as reporter-quencher base pairs, and are complementarily incorporated into DNA by polymerase reactions as a third base pair in combination with the natural A-T and G-C pairs. Due to the static contact quenching, the Pn and Px quencher bases significantly decreased the fluorescence intensity of Dss by the unnatural base pairings in DNA duplexes. In addition, the Dss-Px pair exhibited high efficiency and selectivity in PCR amplification. Thus, this new unnatural base pair system would be suitable for detection methods of target nucleic acid sequences, and here we demonstrated the applications of the Dss-Pn and Dss-Px pairs as molecular beacons and in real-time PCR. The genetic alphabet expansion system with the replicable, unnatural fluorophore-quencher base pair will be a useful tool for sensing and diagnostic applications, as well as an imaging tool for basic research.
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Affiliation(s)
- Michiko Kimoto
- RIKEN Systems and Structural Biology Center and TagCyx Biotechnologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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48
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Kopecky K, Novakova V, Miletin M, Kucera R, Zimcik P. Solid-phase synthesis of azaphthalocyanine-oligonucleotide conjugates and their evaluation as new dark quenchers of fluorescence. Bioconjug Chem 2011; 21:1872-9. [PMID: 20853840 DOI: 10.1021/bc100226x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrophobic nonaggregating metal-free azaphthalocyanines (AzaPc) of the tetrapyrazinoporphyrazine type were synthesized, characterized, and used for oligonucleotide labeling. Both 3'-end and 5'-end labeling methods using solid phase synthesis suitable for automatic processes in the DNA/RNA synthesizer were developed. The hydrophobic character of AzaPc enabled the anchoring of the conjugates on reverse phase of the oligonucleotide purification cartridge, thus enabling their simple purification. AzaPc did not show any fluorescence and extremely low singlet oxygen quantum yields (Φ(Δ) = 0.015-0.018 in DMF) in a monomeric state due to ultrafast intramolecular charge transfer. That is why they were investigated as a new dark quencher structural type. They profit particularly from absorption in a wide range of wavelengths (300-740 nm) that covers all fluorophores used in hybridization assays nowadays. As an example, quenching efficiency was evaluated in a simple hybridization assay using monolabeled probes. AzaPc-based probes efficiently quenched both fluorescein and Cy5 fluorescence by both resonance energy transfer and contact quenching. The results were compared with three established dark quenchers, and the AzaPc exerted better (BHQ-1 and BHQ-2) or comparable (BBQ-650) quenching efficiencies for both fluorophores.
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Affiliation(s)
- Kamil Kopecky
- Department of Pharmaceutical Chemistry and Drug Control, Faculty of Pharmacy in Hradec Kralove, Charles University in Prague, Hradec Kralove, Czech Republic
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49
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Yamashige R, Kimoto M, Mitsui T, Yokoyama S, Hirao I. Monitoring the site-specific incorporation of dual fluorophore-quencher base analogues for target DNA detection by an unnatural base pair system. Org Biomol Chem 2011; 9:7504-9. [DOI: 10.1039/c1ob06118f] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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50
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Sato Y, Tian J, Ichihashi T, Chinda Y, Xu Z, Pang Y, Nishizawa S, Teramae N. Enhancement in fluorescence response by a quencher for amiloride upon binding to thymine opposite an abasic site in a DNA duplex. Anal Chim Acta 2010; 675:49-52. [DOI: 10.1016/j.aca.2010.06.042] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Revised: 06/28/2010] [Accepted: 06/29/2010] [Indexed: 11/27/2022]
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