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Gracie K, Smith WE, Yip P, Sutter JU, Birch DJS, Graham D, Faulds K. Interaction of fluorescent dyes with DNA and spermine using fluorescence spectroscopy. Analyst 2015; 139:3735-43. [PMID: 24915043 DOI: 10.1039/c4an00680a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Oligonucleotides labelled with fluorescent dyes are widely used as probes for the identification of DNA sequences in detection methods using optical spectroscopies such as fluorescence and surface enhanced Raman scattering (SERS). Spermine is widely used in surface enhanced based assays as a charge reduction and aggregating agent as it interacts strongly with the phosphate backbone and has shown to enhance the signal of a labelled oligonucleotide. The fluorescence intensity of two commonly used labels, FAM and TAMRA, were compared when spermine was added under different experimental conditions. There was a marked difference upon conjugating the free dye to an oligonucleotide, when FAM was conjugated to an oligonucleotide there was around a six fold decrease in emission, compared to a six fold increase when TAMRA was conjugated to an oligonucleotide. Dye labelled single and double stranded DNA also behaved differently with double stranded DNA labelled with FAM being a much more efficient emitter in the mid pH range, however TAMRA becomes increasingly less efficient as the pH rises. Upon addition of the base spermine, signal enhancement from the FAM labelled oligonucleotide is observed. Increasing probe concentrations of TAMRA oligonucleotide above 0.5 μM led to signal reduction most likely through quenching, either by an interaction with guanine, or through self-quenching. By using different bases for comparison, spermine and triethylamine (TEA), different affects were observed in the measured fluorescence signals. When TEA was added to FAM, a reduction in the pH dependence of fluorescence was observed, which may be useful for mid pH range assays. With the drive to increase information content and decrease time and complexity of DNA assays it is likely that more assays will be carried out in complex media such as extracted DNA fragments and PCR product. This model study indicates that dye DNA and dye spermine interactions are dye specific and that extreme care with conditions is necessary particularly if it is intended to determine the concentrations of multiple analytes using probes labelled with different dyes.
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Affiliation(s)
- K Gracie
- Centre of Molecular Nanometrology, WestChem, Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, UK.
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Ding S, Cargill AA, Das SR, Medintz IL, Claussen JC. Biosensing with Förster Resonance Energy Transfer Coupling between Fluorophores and Nanocarbon Allotropes. SENSORS 2015; 15:14766-87. [PMID: 26110411 PMCID: PMC4507682 DOI: 10.3390/s150614766] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 06/01/2015] [Accepted: 06/05/2015] [Indexed: 01/10/2023]
Abstract
Nanocarbon allotropes (NCAs), including zero-dimensional carbon dots (CDs), one-dimensional carbon nanotubes (CNTs) and two-dimensional graphene, exhibit exceptional material properties, such as unique electrical/thermal conductivity, biocompatibility and high quenching efficiency, that make them well suited for both electrical/electrochemical and optical sensors/biosensors alike. In particular, these material properties have been exploited to significantly enhance the transduction of biorecognition events in fluorescence-based biosensing involving Förster resonant energy transfer (FRET). This review analyzes current advances in sensors and biosensors that utilize graphene, CNTs or CDs as the platform in optical sensors and biosensors. Widely utilized synthesis/fabrication techniques, intrinsic material properties and current research examples of such nanocarbon, FRET-based sensors/biosensors are illustrated. The future outlook and challenges for the research field are also detailed.
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Affiliation(s)
- Shaowei Ding
- Department of Mechanical Engineering, Iowa State University, 2104 Black Engineering, Ames, IA 50011, USA.
| | - Allison A Cargill
- Department of Mechanical Engineering, Iowa State University, 2104 Black Engineering, Ames, IA 50011, USA.
| | - Suprem R Das
- Department of Mechanical Engineering, Iowa State University, 2104 Black Engineering, Ames, IA 50011, USA.
| | - Igor L Medintz
- Center for Bio/Molecular Science & Engineering Code 6900, US Naval Research Laboratory, Washington, DC 20375, USA.
| | - Jonathan C Claussen
- Department of Mechanical Engineering, Iowa State University, 2104 Black Engineering, Ames, IA 50011, USA.
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53
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Lee CC, Liao YC, Lai YH, Lee CCD, Chuang MC. Recognition of dual targets by a molecular beacon-based sensor: subtyping of influenza A virus. Anal Chem 2015; 87:5410-6. [PMID: 25879394 DOI: 10.1021/acs.analchem.5b00810] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A molecular beacon (MB)-based sensor to offer a decisive answer in combination with information originated from dual-target inputs is designed. The system harnesses an assistant strand and thermodynamically favored designation of unpaired nucleotides (UNs) to process the binary targets in "AND-gate" format and report fluorescence in "off-on" mechanism via a formation of a DNA four-way junction (4WJ). By manipulating composition of the UNs, the dynamic fluorescence difference between the binary targets-coexisting circumstance and any other scenario was maximized. Characteristic equilibrium constant (K), change of entropy (ΔS), and association rate constant (k) between the association ("on") and dissociation ("off") states of the 4WJ were evaluated to understand unfolding behavior of MB in connection to its sensing capability. Favorable MB and UNs were furthermore designed toward analysis of genuine genetic sequences of hemagglutinin (HA) and neuraminidase (NA) in an influenza A H5N2 isolate. The MB-based sensor was demonstrated to yield a linear calibration range from 1.2 to 240 nM and detection limit of 120 pM. Furthermore, high-fidelity subtyping of influenza virus was implemented in a sample of unpurified amplicons. The strategy opens an alternative avenue of MB-based sensors for dual targets toward applications in clinical diagnosis.
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Affiliation(s)
- Chun-Ching Lee
- †Department of Chemistry, Tunghai University, Taichung 40704, Taiwan
| | - Yu-Chieh Liao
- ‡Institute of Population Health Science, National Health Research Institutes, Zhunan, Miaoli County 35053, Taiwan
| | - Yu-Hsuan Lai
- †Department of Chemistry, Tunghai University, Taichung 40704, Taiwan
| | | | - Min-Chieh Chuang
- †Department of Chemistry, Tunghai University, Taichung 40704, Taiwan
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54
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Stevaert A, Nurra S, Pala N, Carcelli M, Rogolino D, Shepard C, Domaoal RA, Kim B, Alfonso-Prieto M, Marras SAE, Sechi M, Naesens L. An integrated biological approach to guide the development of metal-chelating inhibitors of influenza virus PA endonuclease. Mol Pharmacol 2015; 87:323-37. [PMID: 25477342 PMCID: PMC11037440 DOI: 10.1124/mol.114.095588] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 12/04/2014] [Indexed: 04/26/2024] Open
Abstract
The influenza virus PA endonuclease, which cleaves capped cellular pre-mRNAs to prime viral mRNA synthesis, is a promising target for novel anti-influenza virus therapeutics. The catalytic center of this enzyme resides in the N-terminal part of PA (PA-Nter) and contains two (or possibly one or three) Mg(2+) or Mn(2+) ions, which are critical for its catalytic function. There is great interest in PA inhibitors that are optimally designed to occupy the active site and chelate the metal ions. We focused here on a series of β-diketo acid (DKA) and DKA-bioisosteric compounds containing different scaffolds, and determined their structure-activity relationship in an enzymatic assay with PA-Nter, in order to build a three-dimensional pharmacophore model. In addition, we developed a molecular beacon (MB)-based PA-Nter assay that enabled us to compare the inhibition of Mn(2+) versus Mg(2+), the latter probably being the biologically relevant cofactor. This real-time MB assay allowed us to measure the enzyme kinetics of PA-Nter or perform high-throughput screening. Several DKA derivatives were found to cause strong inhibition of PA-Nter, with IC50 values comparable to that of the prototype L-742,001 (i.e., below 2 μM). Among the different compounds tested, L-742,001 appeared unique in having equal activity against either Mg(2+) or Mn(2+). Three compounds ( 10: , with a pyrrole scaffold, and 40: and 41: , with an indole scaffold) exhibited moderate antiviral activity in cell culture (EC99 values 64-95 μM) and were proven to affect viral RNA synthesis. Our approach of integrating complementary enzymatic, cellular, and mechanistic assays should guide ongoing development of improved influenza virus PA inhibitors.
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Affiliation(s)
- Annelies Stevaert
- Rega Institute for Medical Research, KU Leuven-University of Leuven, Leuven, Belgium (A.S., L.N.); Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy (S.N., N.P., M.S.); Department of Chemistry, University of Parma, Parma, Italy (M.C., D.R.); Center for Drug Discovery, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia (C.S., R.D., B.K.); Department of Pharmacy, Kyung-Hee University, Seoul, South Korea (B.K.); Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania (M.A.P.); and Public Health Research Institute, Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey (S.M.)
| | - Salvatore Nurra
- Rega Institute for Medical Research, KU Leuven-University of Leuven, Leuven, Belgium (A.S., L.N.); Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy (S.N., N.P., M.S.); Department of Chemistry, University of Parma, Parma, Italy (M.C., D.R.); Center for Drug Discovery, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia (C.S., R.D., B.K.); Department of Pharmacy, Kyung-Hee University, Seoul, South Korea (B.K.); Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania (M.A.P.); and Public Health Research Institute, Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey (S.M.)
| | - Nicolino Pala
- Rega Institute for Medical Research, KU Leuven-University of Leuven, Leuven, Belgium (A.S., L.N.); Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy (S.N., N.P., M.S.); Department of Chemistry, University of Parma, Parma, Italy (M.C., D.R.); Center for Drug Discovery, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia (C.S., R.D., B.K.); Department of Pharmacy, Kyung-Hee University, Seoul, South Korea (B.K.); Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania (M.A.P.); and Public Health Research Institute, Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey (S.M.)
| | - Mauro Carcelli
- Rega Institute for Medical Research, KU Leuven-University of Leuven, Leuven, Belgium (A.S., L.N.); Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy (S.N., N.P., M.S.); Department of Chemistry, University of Parma, Parma, Italy (M.C., D.R.); Center for Drug Discovery, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia (C.S., R.D., B.K.); Department of Pharmacy, Kyung-Hee University, Seoul, South Korea (B.K.); Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania (M.A.P.); and Public Health Research Institute, Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey (S.M.)
| | - Dominga Rogolino
- Rega Institute for Medical Research, KU Leuven-University of Leuven, Leuven, Belgium (A.S., L.N.); Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy (S.N., N.P., M.S.); Department of Chemistry, University of Parma, Parma, Italy (M.C., D.R.); Center for Drug Discovery, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia (C.S., R.D., B.K.); Department of Pharmacy, Kyung-Hee University, Seoul, South Korea (B.K.); Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania (M.A.P.); and Public Health Research Institute, Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey (S.M.)
| | - Caitlin Shepard
- Rega Institute for Medical Research, KU Leuven-University of Leuven, Leuven, Belgium (A.S., L.N.); Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy (S.N., N.P., M.S.); Department of Chemistry, University of Parma, Parma, Italy (M.C., D.R.); Center for Drug Discovery, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia (C.S., R.D., B.K.); Department of Pharmacy, Kyung-Hee University, Seoul, South Korea (B.K.); Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania (M.A.P.); and Public Health Research Institute, Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey (S.M.)
| | - Robert A Domaoal
- Rega Institute for Medical Research, KU Leuven-University of Leuven, Leuven, Belgium (A.S., L.N.); Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy (S.N., N.P., M.S.); Department of Chemistry, University of Parma, Parma, Italy (M.C., D.R.); Center for Drug Discovery, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia (C.S., R.D., B.K.); Department of Pharmacy, Kyung-Hee University, Seoul, South Korea (B.K.); Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania (M.A.P.); and Public Health Research Institute, Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey (S.M.)
| | - Baek Kim
- Rega Institute for Medical Research, KU Leuven-University of Leuven, Leuven, Belgium (A.S., L.N.); Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy (S.N., N.P., M.S.); Department of Chemistry, University of Parma, Parma, Italy (M.C., D.R.); Center for Drug Discovery, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia (C.S., R.D., B.K.); Department of Pharmacy, Kyung-Hee University, Seoul, South Korea (B.K.); Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania (M.A.P.); and Public Health Research Institute, Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey (S.M.)
| | - Mercedes Alfonso-Prieto
- Rega Institute for Medical Research, KU Leuven-University of Leuven, Leuven, Belgium (A.S., L.N.); Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy (S.N., N.P., M.S.); Department of Chemistry, University of Parma, Parma, Italy (M.C., D.R.); Center for Drug Discovery, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia (C.S., R.D., B.K.); Department of Pharmacy, Kyung-Hee University, Seoul, South Korea (B.K.); Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania (M.A.P.); and Public Health Research Institute, Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey (S.M.)
| | - Salvatore A E Marras
- Rega Institute for Medical Research, KU Leuven-University of Leuven, Leuven, Belgium (A.S., L.N.); Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy (S.N., N.P., M.S.); Department of Chemistry, University of Parma, Parma, Italy (M.C., D.R.); Center for Drug Discovery, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia (C.S., R.D., B.K.); Department of Pharmacy, Kyung-Hee University, Seoul, South Korea (B.K.); Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania (M.A.P.); and Public Health Research Institute, Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey (S.M.)
| | - Mario Sechi
- Rega Institute for Medical Research, KU Leuven-University of Leuven, Leuven, Belgium (A.S., L.N.); Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy (S.N., N.P., M.S.); Department of Chemistry, University of Parma, Parma, Italy (M.C., D.R.); Center for Drug Discovery, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia (C.S., R.D., B.K.); Department of Pharmacy, Kyung-Hee University, Seoul, South Korea (B.K.); Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania (M.A.P.); and Public Health Research Institute, Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey (S.M.)
| | - Lieve Naesens
- Rega Institute for Medical Research, KU Leuven-University of Leuven, Leuven, Belgium (A.S., L.N.); Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy (S.N., N.P., M.S.); Department of Chemistry, University of Parma, Parma, Italy (M.C., D.R.); Center for Drug Discovery, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia (C.S., R.D., B.K.); Department of Pharmacy, Kyung-Hee University, Seoul, South Korea (B.K.); Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania (M.A.P.); and Public Health Research Institute, Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey (S.M.)
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55
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Xu C, Zhou R, Zhang R, Yang L, Wang G. Label-Free DNA Sequence Detection through FRET from a Fluorescent Polymer with Pyrene Excimer to SG. ACS Macro Lett 2014; 3:845-848. [PMID: 35596346 DOI: 10.1021/mz500378c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A label-free complex probe composed of a water-soluble fluorescent pyrene-functionalized polymer, ssDNA, and a nucleic acid stain (SG) is presented here, which can detect DNA sequence via FRET from pyrene excimer to SG. Complementary and one-base mismatched strands at nanomolar concentrations can be distinguished by the examination of the FRET fluorescence intensity of SG. This novel strategy for detecting DNA using the fluorescent pyrene-functionalized polymer not only affords a simple label-free method to detect nucleic acid sequence but also endows the detection with high sensitivity and selectivity, which may find wide applications for optical biosensing.
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Affiliation(s)
- Chen Xu
- School
of Materials Science
and Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Ruyi Zhou
- School
of Materials Science
and Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Ruichen Zhang
- School
of Materials Science
and Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Lingye Yang
- School
of Materials Science
and Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Guojie Wang
- School
of Materials Science
and Engineering, University of Science and Technology Beijing, Beijing 100083, China
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56
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Genotyping single nucleotide polymorphisms using different molecular beacon multiplexed within a suspended core optical fiber. SENSORS 2014; 14:14488-99. [PMID: 25111240 PMCID: PMC4179081 DOI: 10.3390/s140814488] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 08/01/2014] [Accepted: 08/05/2014] [Indexed: 11/17/2022]
Abstract
We report a novel approach to genotyping single nucleotide polymorphisms (SNPs) using molecular beacons in conjunction with a suspended core optical fiber (SCF). Target DNA sequences corresponding to the wild- or mutant-type have been accurately recognized by immobilizing two different molecular beacons on the core of a SCF. The two molecular beacons differ by one base in the loop-probe and utilize different fluorescent indicators. Single-color fluorescence enhancement was obtained when the immobilized SCFs were filled with a solution containing either wild-type or mutant-type sequence (homozygous sample), while filling the immobilized SCF with solution containing both wild- and mutant-type sequences resulted in dual-color fluorescence enhancement, indicating a heterozygous sample. The genotyping was realized amplification-free and with ultra low-volume for the required DNA solution (nano-liter). This is, to our knowledge, the first genotyping device based on the combination of optical fiber and molecular beacons.
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57
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Zilbershtein-Shklanovsky L, Kafri P, Shav-Tal Y, Yavin E, Fischer B. Development of fluorescent double-strand probes labeled with 8-(p-CF3-cinnamyl)-adenosine for the detection of cyclin D1 breast cancer marker. Eur J Med Chem 2014; 79:77-88. [DOI: 10.1016/j.ejmech.2014.03.081] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 03/24/2014] [Accepted: 03/29/2014] [Indexed: 12/14/2022]
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58
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Rao AN, Grainger DW. BIOPHYSICAL PROPERTIES OF NUCLEIC ACIDS AT SURFACES RELEVANT TO MICROARRAY PERFORMANCE. Biomater Sci 2014; 2:436-471. [PMID: 24765522 PMCID: PMC3992954 DOI: 10.1039/c3bm60181a] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Both clinical and analytical metrics produced by microarray-based assay technology have recognized problems in reproducibility, reliability and analytical sensitivity. These issues are often attributed to poor understanding and control of nucleic acid behaviors and properties at solid-liquid interfaces. Nucleic acid hybridization, central to DNA and RNA microarray formats, depends on the properties and behaviors of single strand (ss) nucleic acids (e.g., probe oligomeric DNA) bound to surfaces. ssDNA's persistence length, radius of gyration, electrostatics, conformations on different surfaces and under various assay conditions, its chain flexibility and curvature, charging effects in ionic solutions, and fluorescent labeling all influence its physical chemistry and hybridization under assay conditions. Nucleic acid (e.g., both RNA and DNA) target interactions with immobilized ssDNA strands are highly impacted by these biophysical states. Furthermore, the kinetics, thermodynamics, and enthalpic and entropic contributions to DNA hybridization reflect global probe/target structures and interaction dynamics. Here we review several biophysical issues relevant to oligomeric nucleic acid molecular behaviors at surfaces and their influences on duplex formation that influence microarray assay performance. Correlation of biophysical aspects of single and double-stranded nucleic acids with their complexes in bulk solution is common. Such analysis at surfaces is not commonly reported, despite its importance to microarray assays. We seek to provide further insight into nucleic acid-surface challenges facing microarray diagnostic formats that have hindered their clinical adoption and compromise their research quality and value as genomics tools.
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Affiliation(s)
- Archana N. Rao
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, UT 84112 USA
| | - David W. Grainger
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, UT 84112 USA
- Department of Bioengineering, University of Utah, Salt Lake City, UT 84112 USA
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59
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Takei F, Tani H, Matsuura Y, Nakatani K. Detection of hepatitis C virus by single-step hairpin primer RT-PCR. Bioorg Med Chem Lett 2014; 24:394-6. [DOI: 10.1016/j.bmcl.2013.10.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 10/08/2013] [Accepted: 10/10/2013] [Indexed: 11/29/2022]
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60
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Cho YI, Yoon KJ. An overview of calf diarrhea - infectious etiology, diagnosis, and intervention. J Vet Sci 2013; 15:1-17. [PMID: 24378583 PMCID: PMC3973752 DOI: 10.4142/jvs.2014.15.1.1] [Citation(s) in RCA: 324] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 11/20/2013] [Accepted: 11/21/2013] [Indexed: 01/28/2023] Open
Abstract
Calf diarrhea is a commonly reported disease in young animals, and still a major cause of productivity and economic loss to cattle producers worldwide. In the report of the 2007 National Animal Health Monitoring System for U.S. dairy, half of the deaths among unweaned calves was attributed to diarrhea. Multiple pathogens are known or postulated to cause or contribute to calf diarrhea development. Other factors including both the environment and management practices influence disease severity or outcomes. The multifactorial nature of calf diarrhea makes this disease hard to control effectively in modern cow-calf operations. The purpose of this review is to provide a better understanding of a) the ecology and pathogenesis of well-known and potential bovine enteric pathogens implicated in calf diarrhea, b) describe diagnostic tests used to detect various enteric pathogens along with their pros and cons, and c) propose improved intervention strategies for treating calf diarrhea.
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Affiliation(s)
- Yong-Il Cho
- National Institute of Animal Science, Rural Development Administration, Cheonan, Korea
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61
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Idili A, Plaxco KW, Vallée-Bélisle A, Ricci F. Thermodynamic basis for engineering high-affinity, high-specificity binding-induced DNA clamp nanoswitches. ACS NANO 2013; 7:10863-9. [PMID: 24219761 PMCID: PMC4281346 DOI: 10.1021/nn404305e] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Naturally occurring chemoreceptors almost invariably employ structure-switching mechanisms, an observation that has inspired the use of biomolecular switches in a wide range of artificial technologies in the areas of diagnostics, imaging, and synthetic biology. In one mechanism for generating such behavior, clamp-based switching, binding occurs via the clamplike embrace of two recognition elements onto a single target molecule. In addition to coupling recognition with a large conformational change, this mechanism offers a second advantage: it improves both affinity and specificity simultaneously. To explore the physics of such switches we have dissected here the thermodynamics of a clamp-switch that recognizes a target DNA sequence through both Watson-Crick base pairing and triplex-forming Hoogsteen interactions. When compared to the equivalent linear DNA probe (which relies solely on Watson-Crick interactions), the extra Hoogsteen interactions in the DNA clamp-switch increase the probe's affinity for its target by ∼0.29 ± 0.02 kcal/mol/base. The Hoogsteen interactions of the clamp-switch likewise provide an additional specificity check that increases the discrimination efficiency toward a single-base mismatch by 1.2 ± 0.2 kcal/mol. This, in turn, leads to a 10-fold improvement in the width of the "specificity window" of this probe relative to that of the equivalent linear probe. Given these attributes, clamp-switches should be of utility not only for sensing applications but also, in the specific field of DNA nanotechnology, for applications calling for a better control over the building of nanostructures and nanomachines.
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Affiliation(s)
- Andrea Idili
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
- Consorzio Interuniversitario Biostrutture e Biosistemi “INBB”, Rome, Italy
| | - Kevin W. Plaxco
- Center for Bioengineering & Department of Chemistry and Biochemistry, University of California, Santa Barbara CA 93106 USA
- Interdepartmental Program in Biomolecular Science and Engineering, University of California, Santa Barbara CA 93106 USA
| | - Alexis Vallée-Bélisle
- Laboratory of Biosensors and Nanomachines, Département de Chimie, Université de Montréal, Québec, Canada
| | - Francesco Ricci
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
- Consorzio Interuniversitario Biostrutture e Biosistemi “INBB”, Rome, Italy
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62
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Recent Advances in DNA Microarray Technology: an Overview on Production Strategies and Detection Methods. BIONANOSCIENCE 2013. [DOI: 10.1007/s12668-013-0111-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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63
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Riahi R, Dean Z, Wu TH, Teitell MA, Chiou PY, Zhang DD, Wong PK. Detection of mRNA in living cells by double-stranded locked nucleic acid probes. Analyst 2013; 138:4777-85. [PMID: 23772441 PMCID: PMC3736730 DOI: 10.1039/c3an00722g] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Double-stranded probes are homogeneous biosensors for rapid detection of specific nucleotide sequences. These double-stranded probes have been applied in various molecular sensing applications, such as real-time polymerase chain reaction and detection of bacterial 16S rRNA. In this study, we present the design and optimization of double-stranded probes for single-cell gene expression analysis in living cells. With alternating DNA/LNA monomers for optimizing the stability and specificity, we show that the probe is stable in living cells for over 72 hours post-transfection and is capable of detecting changes in gene expression induced by external stimuli. The probes can be delivered to a large number of cells simultaneously by cationic liposomal transfection or to individual cells selectively by photothermal delivery. We also demonstrate that the probe quantifies intracellular mRNA in living cells through the use of an equilibrium analysis. With its effectiveness and performance, the double-stranded probe represents a broadly applicable approach for large-scale single-cell gene expression analysis toward numerous biomedical applications, such as systems biology, cancer, and drug screening.
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Affiliation(s)
- Reza Riahi
- Department of Aerospace and Mechanical Engineering, The University of Arizona, Tucson, AZ 85721-0119, USA
| | - Zachary Dean
- Biomedical Engineering Interdisciplinary Program, The University of Arizona, Tucson, AZ 85721-0119, USA
| | - Ting-Hsiang Wu
- Mechanical and Aerospace Engineering, University of California, Los Angeles, Los Angeles, CA 90095-1597, USA
| | - Michael A. Teitell
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, CA, 90095
| | - Pei-Yu Chiou
- Mechanical and Aerospace Engineering, University of California, Los Angeles, Los Angeles, CA 90095-1597, USA
| | - Donna D. Zhang
- Department of Pharmacology and Toxicology, The University of Arizona, Tucson, AZ 85721-0119, USA
- BIO5 Institute, The University of Arizona, Tucson, AZ 85721-0119, USA
| | - Pak Kin Wong
- Department of Aerospace and Mechanical Engineering, The University of Arizona, Tucson, AZ 85721-0119, USA
- BIO5 Institute, The University of Arizona, Tucson, AZ 85721-0119, USA
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64
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Niederholtmeyer H, Xu L, Maerkl SJ. Real-time mRNA measurement during an in vitro transcription and translation reaction using binary probes. ACS Synth Biol 2013; 2:411-7. [PMID: 23654250 DOI: 10.1021/sb300104f] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In vitro transcription and translation reactions have become popular for a bottom-up approach to synthetic biology. Concentrations of the mRNA intermediate are rarely determined, although knowledge of synthesis and degradation rates could facilitate rational engineering of in vitro systems. We designed binary probes to measure mRNA dynamics during cell-free protein synthesis by fluorescence resonance energy transfer. We tested different mRNA variants and show that the location and sequence environment of the probe target sites are important parameters for probe association kinetics and output signal. Best suited for sensitive real-time quantitation of mRNA was a target site located in the 3' untranslated region, which we designed to reduce secondary structure. We used this probe-target pair to refine our knowledge of mRNA dynamics in the commercially available PURE cell-free protein synthesis system and characterized the effect of TetR repressor on mRNA synthesis rates from a T7 promoter.
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Affiliation(s)
- Henrike Niederholtmeyer
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Ling Xu
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Sebastian J. Maerkl
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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65
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Kovaliov M, Segal M, Fischer B. Fluorescent p-substituted-phenyl-imidazolo-cytidine analogues. Tetrahedron 2013. [DOI: 10.1016/j.tet.2013.03.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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66
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An approach toward SNP detection by modulating the fluorescence of DNA-templated silver nanoclusters. Biosens Bioelectron 2013; 43:419-24. [DOI: 10.1016/j.bios.2012.12.042] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Revised: 12/12/2012] [Accepted: 12/13/2012] [Indexed: 01/29/2023]
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67
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El-Yazbi AF, Loppnow GR. Chimeric RNA–DNA Molecular Beacons for Quantification of Nucleic Acids, Single Nucleotide Polymophisms, and Nucleic Acid Damage. Anal Chem 2013; 85:4321-7. [DOI: 10.1021/ac301669y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Amira F. El-Yazbi
- Department of Chemistry, University of Alberta, Edmonton, AB
T6G 2G2 Canada
| | - Glen R. Loppnow
- Department of Chemistry, University of Alberta, Edmonton, AB
T6G 2G2 Canada
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68
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Kel O, Fürstenberg A, Mehanna N, Nicolas C, Laleu B, Hammarson M, Albinsson B, Lacour J, Vauthey E. Chiral Selectivity in the Binding of [4]Helicene Derivatives to Double-Stranded DNA. Chemistry 2013; 19:7173-80. [DOI: 10.1002/chem.201203915] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Indexed: 11/11/2022]
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69
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Kumar TS, Myznikova A, Samokhina E, Astakhova IK. Rapid genotyping using pyrene-perylene locked nucleic acid complexes. ARTIFICIAL DNA, PNA & XNA 2013; 4:58-68. [PMID: 24044052 PMCID: PMC3771999 DOI: 10.4161/adna.25903] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 07/07/2013] [Accepted: 07/25/2013] [Indexed: 01/27/2023]
Abstract
We have developed an assay for single strand DNA and RNA detection which is based on novel pyrene-perylene FRET pairs attached to short LNA/DNA probes. The assay is based on ratiometric emission upon binding of target DNA/RNA by three combinations of fluorescent LNA/DNA reporter strands. Specific geometry of the pyrene fluorophore attached to the 2'-amino group of 2'-amino-LNA in position 4 allows for the first time to efficiently utilize dipole-dipole orientation parameter for sensing of single-nucleotide polymorphisms (SNPs) in nucleic acid targets by FRET. Using novel probes, SNP detection is achieved with advantages of large Stokes shift (115 nm), high fluorescence quantum yields and low limit of target detection values (< 5 nM). Rapid and accurate genotyping of highly polymorphic HIV Pol cDNA and RNA fragments performed herein proves the possibility for broad application of the novel pyrene-perylene FRET pairs, e.g., in imaging and clinical diagnostics.
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Affiliation(s)
- T. Santhosh Kumar
- Nucleic Acid Center; Department of Physics, Chemistry and Pharmacy; University of Southern Denmark; Odense, Denmark
- National Institute of Diabetes and Digestive and Kidney Diseases; National Institutes of Health; Molecular Recognition Section; Bethesda, MD USA
| | - Anna Myznikova
- Central Research Institute of Epidemiology; Moscow, Russia
| | | | - Irina Kira Astakhova
- Nucleic Acid Center; Department of Physics, Chemistry and Pharmacy; University of Southern Denmark; Odense, Denmark
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70
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Adams NM, Olmsted IR, Haselton FR, Bornhop DJ, Wright DW. The effect of hybridization-induced secondary structure alterations on RNA detection using backscattering interferometry. Nucleic Acids Res 2013; 41:e103. [PMID: 23519610 PMCID: PMC3643578 DOI: 10.1093/nar/gkt165] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Backscattering interferometry (BSI) has been used to successfully monitor molecular interactions without labeling and with high sensitivity. These properties suggest that this approach might be useful for detecting biomarkers of infection. In this report, we identify interactions and characteristics of nucleic acid probes that maximize BSI signal upon binding the respiratory syncytial virus nucleocapsid gene RNA biomarker. The number of base pairs formed upon the addition of oligonucleotide probes to a solution containing the viral RNA target correlated with the BSI signal magnitude. Using RNA folding software mfold, we found that the predicted number of unpaired nucleotides in the targeted regions of the RNA sequence generally correlated with BSI sensitivity. We also demonstrated that locked nucleic acid (LNA) probes improved sensitivity approximately 4-fold compared to DNA probes of the same sequence. We attribute this enhancement in BSI performance to the increased A-form character of the LNA:RNA hybrid. A limit of detection of 624 pM, corresponding to ∼10(5) target molecules, was achieved using nine distinct ∼23-mer DNA probes complementary to regions distributed along the RNA target. Our results indicate that BSI has promise as an effective tool for sensitive RNA detection and provides a road map for further improving detection limits.
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Affiliation(s)
- Nicholas M Adams
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
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71
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Jo SM, Kim Y, Jeong YS, Hee Oh Y, Park K, Kim HS. Rapid detection of exon 2-deleted AIMP2 mutation as a potential biomarker for lung cancer by molecular beacons. Biosens Bioelectron 2013; 46:142-9. [PMID: 23537880 DOI: 10.1016/j.bios.2013.02.037] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 02/24/2013] [Accepted: 02/25/2013] [Indexed: 01/05/2023]
Abstract
Exon 2 deletion in aminoacyl tRNA synthetase complex-interacting multifunctional protein 2 (AIMP2) has been suggested to be associated with the progression of various cancers such as lung and ovarian cancers. However, few studies have been conducted regarding detection and relevance of exon 2-deleted AIMP2 (AIMP2-DX2) mutation to a specific cancer. Here, we demonstrate the rapid and simple detection of the AIMP2-DX2 mutation by molecular beacons and its relation to lung cancer. Real-time PCR with molecular beacons allowed a sensitive detection of the AIMP2-DX2 mutation as low as 0.3 pg initial template. Dual-conjugated liposomes with folate and molecular beacon enabled fluorescence imaging of cancer cells harboring the AIMP2-DX2 mutation with high resolution. Association of the AIMP2-DX2 mutation with lung cancer was shown by analyzing tissue samples from lung cancer patients using real-time PCR. Approximately, 60% of lung cancer patients harbored the AIMP2-DX2 mutation, which implies a potential of the AIMP2-DX2 mutation as a prognostic biomarker for lung cancer. Molecular beacon-based approaches will find applications in the simple and rapid detection of mutations on nucleotides for diagnosing and monitoring the progression of relevant cancer.
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Affiliation(s)
- Seong-Min Jo
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
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72
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Kim T, Reitmair A. Non-Coding RNAs: Functional Aspects and Diagnostic Utility in Oncology. Int J Mol Sci 2013; 14:4934-68. [PMID: 23455466 PMCID: PMC3634484 DOI: 10.3390/ijms14034934] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 02/09/2013] [Accepted: 02/18/2013] [Indexed: 02/06/2023] Open
Abstract
Noncoding RNAs (ncRNAs) have been found to have roles in a large variety of biological processes. Recent studies indicate that ncRNAs are far more abundant and important than initially imagined, holding great promise for use in diagnostic, prognostic, and therapeutic applications. Within ncRNAs, microRNAs (miRNAs) are the most widely studied and characterized. They have been implicated in initiation and progression of a variety of human malignancies, including major pathologies such as cancers, arthritis, neurodegenerative disorders, and cardiovascular diseases. Their surprising stability in serum and other bodily fluids led to their rapid ascent as a novel class of biomarkers. For example, several properties of stable miRNAs, and perhaps other classes of ncRNAs, make them good candidate biomarkers for early cancer detection and for determining which preneoplastic lesions are likely to progress to cancer. Of particular interest is the identification of biomarker signatures, which may include traditional protein-based biomarkers, to improve risk assessment, detection, and prognosis. Here, we offer a comprehensive review of the ncRNA biomarker literature and discuss state-of-the-art technologies for their detection. Furthermore, we address the challenges present in miRNA detection and quantification, and outline future perspectives for development of next-generation biodetection assays employing multicolor alternating-laser excitation (ALEX) fluorescence spectroscopy.
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Affiliation(s)
- Taiho Kim
- Nesher Technologies, Inc., 2100 W. 3rd St. Los Angeles, CA 90057, USA.
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73
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Cornett EM, O’Steen MR, Kolpashchikov DM. Operating Cooperatively (OC) sensor for highly specific recognition of nucleic acids. PLoS One 2013; 8:e55919. [PMID: 23441157 PMCID: PMC3575382 DOI: 10.1371/journal.pone.0055919] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 01/03/2013] [Indexed: 11/18/2022] Open
Abstract
Molecular Beacon (MB) probes have been extensively used for nucleic acid analysis because of their ability to produce fluorescent signal in solution instantly after hybridization. The indirect binding of MB probe to a target analyte offers several advantages, including: improved genotyping accuracy and the possibility to analyse folded nucleic acids. Here we report on a new design for MB-based sensor, called ‘Operating Cooperatively’ (OC), which takes advantage of indirect binding of MB probe to a target analyte. The sensor consists of two unmodified DNA strands, which hybridize to a universal MB probe and a nucleic acid analyte to form a fluorescent complex. OC sensors were designed to analyze two human SNPs and E.coli 16S rRNA. High specificity of the approach was demonstrated by the detection of true analyte in over 100 times excess amount of single base substituted analytes. Taking into account the flexibility in the design and the simplicity in optimization, we conclude that OC sensors may become versatile and efficient tools for instant DNA and RNA analysis in homogeneous solution.
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Affiliation(s)
- Evan M. Cornett
- Chemistry Department, College of Sciences, University of Central Florida, Orlando, Florida, United States of America
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, United States of America
| | - Martin R. O’Steen
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, United States of America
| | - Dmitry M. Kolpashchikov
- Chemistry Department, College of Sciences, University of Central Florida, Orlando, Florida, United States of America
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, United States of America
- * E-mail:
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74
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Miyahata T, Kitamura Y, Futamura A, Matsuura H, Hatakeyama K, Koinuma M, Matsumoto Y, Ihara T. DNA analysis based on toehold-mediated strand displacement on graphene oxide. Chem Commun (Camb) 2013; 49:10139-41. [DOI: 10.1039/c3cc45531a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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75
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Kitamura Y, Yamamoto S, Osawa Y, Matsuura H, Ihara T. Versatile allosteric molecular devices based on reversible formation of luminous lanthanide complexes. Chem Commun (Camb) 2013. [DOI: 10.1039/c2cc36979f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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76
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Kolpashchikov DM. An elegant biosensor molecular beacon probe: challenges and recent solutions. SCIENTIFICA 2012; 2012:928783. [PMID: 24278758 PMCID: PMC3820487 DOI: 10.6064/2012/928783] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 09/10/2012] [Indexed: 05/02/2023]
Abstract
Molecular beacon (MB) probes are fluorophore- and quencher-labeled short synthetic DNAs folded in a stem-loop shape. Since the first report by Tyagi and Kramer, it has become a widely accepted tool for nucleic acid analysis and triggered a cascade of related developments in the field of molecular sensing. The unprecedented success of MB probes stems from their ability to detect specific DNA or RNA sequences immediately after hybridization with no need to wash out the unbound probe (instantaneous format). Importantly, the hairpin structure of the probe is responsible for both the low fluorescent background and improved selectivity. Furthermore, the signal is generated in a reversible manner; thus, if the analyte is removed, the signal is reduced to the background. This paper highlights the advantages of MB probes and discusses the approaches that address the challenges in MB probe design. Variations of MB-based assays tackle the problem of stem invasion, improve SNP genotyping and signal-to-noise ratio, as well as address the challenges of detecting folded RNA and DNA.
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Affiliation(s)
- Dmitry M. Kolpashchikov
- Chemistry Department, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL 32816-2366, USA
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77
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Yang L, Zhao M, Zhang R, Dong J, Zhang T, Zhan X, Wang G. Synthesis and Fluorescence Study of a Quaternized Copolymer Containing Pyrene for DNA-Hybridization Detection. Chemphyschem 2012; 13:4099-104. [DOI: 10.1002/cphc.201200765] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Indexed: 12/27/2022]
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78
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Ricci F, Vallée-Bélisle A, Porchetta A, Plaxco KW. Rational design of allosteric inhibitors and activators using the population-shift model: in vitro validation and application to an artificial biosensor. J Am Chem Soc 2012; 134:15177-80. [PMID: 22924432 PMCID: PMC3523727 DOI: 10.1021/ja304672h] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The population-shift mechanism can be used for rational re-engineering of structure-switching biosensors to enable their allosteric inhibition and activation. As a proof-of-principle example of this, we have introduced distal allosteric sites into molecular beacons, which are optical sensors for the detection of specific nucleic acid sequences. The binding of inhibitors and activators to these sites enabled the rational modulation of the sensor's target affinity-and thus its useful dynamic range-over 3 orders of magnitude. The convenience with which this was done suggests that the population-shift mechanism may prove to be a useful method by which allosteric regulation can be introduced into biosensors, "smart" biomaterials, and other artificial biotechnologies.
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Affiliation(s)
- Francesco Ricci
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
- Consorzio Interuniversitario Biostrutture e Biosistemi “INBB”, Rome, Italy
| | - Alexis Vallée-Bélisle
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106 USA
- Center for Bioengineering, University of California, Santa Barbara, CA 93106 USA
| | - Alessandro Porchetta
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
- Consorzio Interuniversitario Biostrutture e Biosistemi “INBB”, Rome, Italy
| | - Kevin W. Plaxco
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106 USA
- Center for Bioengineering, University of California, Santa Barbara, CA 93106 USA
- Interdepartmental Program in Biomolecular Science and Engineering, University of California, Santa Barbara, CA 93106 USA
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79
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Cornett EM, Campbell EA, Gulenay G, Peterson E, Bhaskar N, Kolpashchikov DM. Molecular logic gates for DNA analysis: detection of rifampin resistance in M. tuberculosis DNA. Angew Chem Int Ed Engl 2012; 51:9075-7. [PMID: 22888076 PMCID: PMC3517149 DOI: 10.1002/anie.201203708] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Indexed: 02/06/2023]
Abstract
Elementary, Dr. Watson! A combination of YES and OR logic gates was applied to differentiate between DNA sequences of wild-type and rifampin-resistant (Rif(r)) Mycobacterium tuberculosis (Mtb) in a multiplex real-time fluorescent assay.
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Affiliation(s)
- Evan M Cornett
- Chemistry Department, University of Central Florida, Orlando, FL 32816, USA
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80
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Huang K, Martí AA. Optimizing the Sensitivity of Photoluminescent Probes Using Time-Resolved Spectroscopy: A Molecular Beacon Case Study. Anal Chem 2012; 84:8075-82. [DOI: 10.1021/ac3019894] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kewei Huang
- Department
of Chemistry, ‡Department of Bioengineering, and §Smalley Institute for Nanoscale Science and
Technology, 6100 South Main Street, Rice University, Houston Texas 77005, United States
| | - Angel A. Martí
- Department
of Chemistry, ‡Department of Bioengineering, and §Smalley Institute for Nanoscale Science and
Technology, 6100 South Main Street, Rice University, Houston Texas 77005, United States
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81
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Design and development of an in-house multiplex RT-PCR assay for simultaneous detection of HIV-1 and HCV in plasma samples. IRANIAN JOURNAL OF MICROBIOLOGY 2012; 52:456-63. [PMID: 22783455 DOI: 10.1007/s12088-012-0271-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2011] [Accepted: 04/26/2012] [Indexed: 01/12/2023]
Abstract
BACKGROUND AND OBJECTIVES HIV-1 and HCV infections are life threatening problems in patients who receive blood products. Serological methods have proven useful in detecting these infections, but there are setbacks that make it challenging to detect these infectious agents. By the advent of Nucleic Acid Testing (NAT) methods, especially in multiplex format, more precise detection is possible. MATERIALS AND METHODS We have developed a multiplex RT-PCR assay for simultaneous detection of HIV-1 and HCV. Primers were designed for highly conserved region of genome of each virus. Using these primers and standard plasmids, we determined the limit of detection, clinical and analytical specificity and sensitivity of the assay. Monoplex and multiplex RT-PCR were performed. RESULTS Analytical sensitivity was considered to be 100 and 200 copies/ml for HIV-1 and HCV, respectively. High concentration of one virus had no significant effect on the detection of the other one with low concentration. By analysis of 40 samples, clinical sensitivity of the assay was determined to be 97.5%. Using different viral and human genome samples, the specificity of the assay was evaluated to be 100%. CONCLUSIONS The aim of this study was to develop a reliable, rapid and cost effective method to detect HIV-1 and HCV simultaneously. Results showed that this simple and rapid method is perfectly capable of detecting two viruses in clinical samples.
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82
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Cornett EM, Campbell EA, Gulenay G, Peterson E, Bhaskar N, Kolpashchikov DM. Molecular Logic Gates for DNA Analysis: Detection of Rifampin Resistance in M. tuberculosis DNA. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201203708] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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83
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Detection of prolactin inducible protein mRNA, a biomarker for breast cancer metastasis, using a molecular beacon-based assay. Anal Bioanal Chem 2012; 404:399-406. [PMID: 22692591 DOI: 10.1007/s00216-012-6162-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 05/24/2012] [Accepted: 05/28/2012] [Indexed: 10/28/2022]
Abstract
Mortality due to breast cancer is increasingly linked to early, undetected metastasis, making methods for earlier detection acutely necessary. We describe the development of an assay based on molecular beacon (MB) chemistry with fluorescence detection to monitor a breast cancer biomarker for the analysis of breast cancer metastasis. The MB assay is based on the complementary base-pairing interactions of the MB nucleic acid with mRNA indicative of breast cancer metastasis. The presence of mRNA is characterized by an increase in the fluorescence intensity of the molecular beacon. The assay gives a linear, reproducible response to prolactin inducible protein mRNA, with a limit of detection in the high picomolar range. This method sensitively and specifically identifies a biomarker directly in serum samples in minimal time and with a straightforward procedure, dramatically reducing the total time for sample analysis over current methods from days to hours. The potential impact of this work in detection and understanding of breast cancer metastasis lies in improvements in simplicity, accuracy, and speed over current methods, which could allow for improved patient treatment and prognoses. Ultimately, additional sample throughput will result in better understanding of disease progression.
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84
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Xuan F, Luo X, Hsing IM. Ultrasensitive solution-phase electrochemical molecular beacon-based DNA detection with signal amplification by exonuclease III-assisted target recycling. Anal Chem 2012; 84:5216-20. [PMID: 22721426 DOI: 10.1021/ac301033w] [Citation(s) in RCA: 186] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Taking advantage of the preferential exodeoxyribonuclease activity of exonuclease III in combination with the difference in diffusivity between an oligonucleotide and a mononucleotide toward a negatively charged ITO electrode, a highly sensitive and selective electrochemical molecular beacon (eMB)-based DNA sensor has been developed. This sensor realizes electrochemical detection of DNA in a homogeneous solution, with sensing signals amplified by an exonuclease III-based target recycling strategy. A hairpin-shaped oligonucleotide containing the target DNA recognition sequence, with a methylene blue tag close to the 3' terminus, is designed as the signaling probe. Hybridization with the target DNA transforms the probe's exonuclease III-inactive protruding 3' terminus into an exonuclease III-active blunt end, triggering the digestion of the probe into mononucleotides including a methylene blue-labeled electro-active mononucleotide (eNT). The released eNT, due to its less negative charge and small size, diffuses easily to the negative ITO electrode, resulting in an increased electrochemical signal. Meanwhile, the intact target DNA returns freely to the solution and hybridizes with other probes, releasing multiple eNTs and thereby further amplifies the electrochemical signal. This new immobilization-free, signal-amplified electrochemical DNA detection strategy shows great potential to be integrated in portable and cost-effective DNA sensing devices.
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Affiliation(s)
- Feng Xuan
- Department of Chemical and Biomolecular Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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85
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Hall LM, Gerowska M, Brown T. A highly fluorescent DNA toolkit: synthesis and properties of oligonucleotides containing new Cy3, Cy5 and Cy3B monomers. Nucleic Acids Res 2012; 40:e108. [PMID: 22495935 PMCID: PMC3413114 DOI: 10.1093/nar/gks303] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Cy3B is an extremely bright and stable fluorescent dye, which is only available for coupling to nucleic acids post-synthetically. This severely limits its use in the fields of genomics, biology and nanotechnology. We have optimized the synthesis of Cy3B, and for the first time produced a diverse range of Cy3B monomers for use in solid-phase oligonucleotide synthesis. This molecular toolkit includes phosphoramidite monomers with Cy3B linked to deoxyribose, to the 5-position of thymine, and to a hexynyl linker, in addition to an oligonucleotide synthesis resin in which Cy3B is linked to deoxyribose. These monomers have been used to incorporate single and multiple Cy3B units into oligonucleotides internally and at both termini. Cy3B Taqman probes, Scorpions and HyBeacons have been synthesized and used successfully in mutation detection, and a dual Cy3B Molecular Beacon was synthesized and found to be superior to the corresponding Cy3B/DABCYL Beacon. Attachment of Cy3, Cy3B and Cy5 to the 5-position of thymidine by an ethynyl linker enabled the synthesis of an oligonucleotide FRET system. The rigid linker between the dye and nucleobase minimizes dye–dye and dye–DNA interactions and reduces fluorescence quenching. These reagents open up new future applications of Cy3B, including more sensitive single-molecule and cell-imaging studies.
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Affiliation(s)
- Lucy M Hall
- School of Chemistry, University of Southampton, SO17 1BJ, UK
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86
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Abstract
We present a quantification method for affinity-based DNA microarrays which is based on the real-time measurements of hybridization kinetics. This method, i.e., real-time DNA microarrays, enhances the detection dynamic range of conventional systems by being impervious to probe saturation, washing artifacts, microarray spot-to-spot variations, and other intensity-affecting impediments. We demonstrate in both theory and practice that the time-constant of target capturing is inversely proportional to the concentration of the target analyte, which we take advantage of as the fundamental parameter to estimate the concentration of the analytes. Furthermore, to experimentally validate the capabilities of this method in practical applications, we present a FRET-based assay which enables the real-time detection in gene expression DNA microarrays.
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Affiliation(s)
- Arjang Hassibi
- Institute for Cellular and Molecular Biology, University of Texas, 1 University Station C8800, Austin, TX 78712-0323, USA.
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87
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Gerasimova YV, Kolpashchikov DM. Connectable DNA Logic Gates: OR and XOR Logics. Chem Asian J 2011; 7:534-40. [DOI: 10.1002/asia.201100664] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Indexed: 01/11/2023]
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88
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Abstract
Fluorescent sensors that make use of DNA structures have become widely useful in monitoring enzymatic activities. Early studies focused primarily on enzymes that naturally use DNA or RNA as the substrate. However, recent advances in molecular design have enabled the development of nucleic acid sensors for a wider range of functions, including enzymes that do not normally bind DNA or RNA. Nucleic acid sensors present some potential advantages over classical small-molecule sensors, including water solubility and ease of synthesis. An overview of the multiple strategies under recent development is presented in this critical review, and expected future developments in microarrays, single molecule analysis, and in vivo sensing are discussed (160 references).
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Affiliation(s)
- Nan Dai
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Eric T. Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
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89
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Kolpashchikov DM, Gerasimova YV, Khan MS. DNA nanotechnology for nucleic acid analysis: DX motif-based sensor. Chembiochem 2011; 12:2564-7. [PMID: 22006680 PMCID: PMC3221779 DOI: 10.1002/cbic.201100545] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2011] [Indexed: 11/09/2022]
Abstract
A light on the tiles: A sensor that fluoresces in the presence of specific nucleic acids was designed and characterized. The sensor uses a molecular beacon probe and three adaptor strands to form a five-stranded assembly, a DX-tile, with a specific analyte. This sensor is a highly selective and affordable tool for the real-time analysis of DNA and RNA.
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90
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Astakhova IV, Kumar TS, Wengel J. Fluorescent oligonucleotides containing a novel perylene 2′-amino-α-L-LNA monomer: Synthesis and analytical potential. ACTA ACUST UNITED AC 2011. [DOI: 10.1135/cccc2011096] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Herein, a novel fluorescent nucleotide analogue, perylene-2′-amino-α-L-LNA, has been prepared and studied within synthetic oligonucleotides of different sequences. The phosphoramidite reagent was synthesized in 85% overall yield starting from 2′-amino-α-L-LNA nucleoside. Incorporation efficiency of the resulting perylene-2′-amino-α-L-LNA monomer (T*) into synthetic oligonucleotides was significantly improved by replacement of the typically used 1H-tetrazole activator with pyridine hydrochloride. Generally, oligonucleotides containing monomerT* showed high binding affinity towards complementary DNA and RNA targets, batochromically shifted excitation/emission wavelengths with respect to the often applied polyaromatic hydrocarbon pyrene, high fluorescent quantum yields and very low target detection limits (5–10 nM). Fluorescence of single stranded LNA/DNA mixmer oligonucleotide having two incorporations of monomersT* was quenched (quantum yield ΦF= 0.21) relative to duplexes of this probe with complementary DNA and RNA (ΦF= 0.42 and 0.35, respectively). On the contrary, a strong fluorescence quenching upon target binding was demonstrated by two short oligonucleotides of analogues sequences containing monomersT* at 5′- and 3′-terminal positions. We explain the hybridization-induced light-up effect observed for double-labeled probe by a reduction of fluorescence quenching due to precise positioning of the fluorophores within the double-stranded complexes. Furthermore, we propose that a covalent link between twoT* monomers in the double-labeled probe provides a remarkable degree of rigidity in the double helix which enforces positioning of the bulky perylene moieties in the nonpolar groove resulting in reduced fluorescence quenching.
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91
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Lambertucci C, Buccioni M, Cacciari B, Dal Ben D, Federico S, Klotz KN, Marucci G, Volpini R, Spalluto G, Cristalli G. New 9-methyl-8-(4-hydroxyphenyl)adenine derivatives as A1 adenosine receptor antagonists. ACTA ACUST UNITED AC 2011. [DOI: 10.1135/cccc2011091] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
A new series of 9-methyladenines, bearing different bulky groups at the 8-position, were prepared and their affinity for the four human adenosine receptor subtypes were evaluated. All the synthesized compounds showed affinities at the A1, A2A, and A3AR subtypes ranging from nanomolar to micromolar levels with different degrees of A1selectivity, while they resulted nearly inactive at A2BAR. In particular, 9-methyl-8-[4-(4-methylbenzyloxy)phenyl]- adenine showed A1AR affinity in the nanomolar range and good levels of selectivity versus the other receptor subtypes. Furthermore, a functional assay at mouse ileum allowed to assess the potency of selected compounds at A1AR subtype. Results showed that all the tested derivatives are neutral antagonists and theirKbvalues are in good agreement with theKivalues from radioligand binding assay at human A1AR, confirming that the effect is due to inhibition of this subtype.
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92
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Nguyen C, Grimes J, Gerasimova YV, Kolpashchikov DM. Molecular-beacon-based tricomponent probe for SNP analysis in folded nucleic acids. Chemistry 2011; 17:13052-8. [PMID: 21956816 PMCID: PMC3221966 DOI: 10.1002/chem.201101987] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Indexed: 01/13/2023]
Abstract
Hybridization probes are often inefficient in the analysis of single-stranded DNA or RNA that are folded in stable secondary structures. A molecular beacon (MB) probe is a short DNA hairpin with a fluorophore and a quencher attached to opposite sides of the oligonucleotide. The probe is widely used in real-time analysis of specific DNA and RNA sequences. This study demonstrates how a conventional MB probe can be used for the analysis of nucleic acids that form very stable (T(m) > 80 °C) hairpin structures. Here we demonstrate that the MB probe is not efficient in direct analysis of secondary structure-folded analytes, whereas a MB-based tricomponent probe is suitable for these purposes. The tricomponent probe takes advantage of two oligonucleotide adaptor strands f and m. Each adaptor strand contains a fragment complementary to the analyte and a fragment complementary to a MB probe. In the presence of a specific analyte, the two adaptor strands hybridize to the analyte and the MB probe, thus forming a quadripartite complex. DNA strand f binds to the analyte with high affinity and unwinds its secondary structure. Strand m forms a stable complex only with the fully complementary analyte. The MB probe fluorescently reports the formation of the quadripartite associate. It was demonstrated that the DNA analytes folded in hairpin structures with stems containing 5, 6, 7, 8, 9, 11, or 13 base pairs can be detected in real time with the limit of detection (LOD) lying in the nanomolar range. The stability of the stem region in the DNA analyte did not affect the LOD. Analytes containing single base substitutions in the stem or in the loop positions were discriminated from the fully complementary DNA at room temperature. The tricomponent probe promises to simplify nucleic acid analysis at ambient temperatures in such applications as in vivo RNA monitoring, detection of pathogens, and single nucleotide polymorphism (SNP) genotyping by DNA microarrays.
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Affiliation(s)
- Camha Nguyen
- Camha Nguyen, Jeffrey Grimes, Dr. Y. V. Gerasimova, Dr. D. M. Kolpashchikov Chemistry Department University of Central Florida 4000 Central Florida Blvd., Orlando, FL 32816, USA
| | - Jeffrey Grimes
- Camha Nguyen, Jeffrey Grimes, Dr. Y. V. Gerasimova, Dr. D. M. Kolpashchikov Chemistry Department University of Central Florida 4000 Central Florida Blvd., Orlando, FL 32816, USA
| | - Yulia V. Gerasimova
- Camha Nguyen, Jeffrey Grimes, Dr. Y. V. Gerasimova, Dr. D. M. Kolpashchikov Chemistry Department University of Central Florida 4000 Central Florida Blvd., Orlando, FL 32816, USA
| | - Dmitry M. Kolpashchikov
- Camha Nguyen, Jeffrey Grimes, Dr. Y. V. Gerasimova, Dr. D. M. Kolpashchikov Chemistry Department University of Central Florida 4000 Central Florida Blvd., Orlando, FL 32816, USA
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93
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Biner SM, Häner R. A two-color, self-controlled molecular beacon. Chembiochem 2011; 12:2733-6. [PMID: 22076865 DOI: 10.1002/cbic.201100651] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Indexed: 12/22/2022]
Abstract
Control yourself! A two-color molecular beacon with non-nucleosidic chromophores in a triplex stem is presented. Pyrene and PDI fluorophores act as mutual quenchers by formation of a donor-acceptor complex in the closed form. Hybridization with the target results in two independent fluorescence signals. The two-color read-out provides a "self-control" feature, which helps to eliminate false positive signals in imaging and screening applications.
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Affiliation(s)
- Sarah M Biner
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
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94
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Chen Q, Sun Y, Zhang L, Deng K, Xia H, Xing H, Xiang Y, Ran B, Zhang M, Xu X, Fu W. Detection of C677T mutation of MTHFR in subject with coronary heart disease by hairpin probe with enzymatic color on microarray. Biosens Bioelectron 2011; 28:84-90. [PMID: 21802936 DOI: 10.1016/j.bios.2011.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Revised: 06/10/2011] [Accepted: 07/04/2011] [Indexed: 12/17/2022]
Abstract
Molecular beacon (MB) is especially suited for detection of single nucleotide polymorphism (SNP), and the type of MB immobilized on the surface of microarray in particular, may detect multi-sample and multi-locus. However, the majority of MB needs to be labeled with fluorescence and quenching molecules on the two ends of the probe, and observed the reaction of fluorescence or complicated electrochemical signal produced hybridization of MB and target sequence by complex and expensive instruments. The "molecular beacon" and microarray designed appropriately in our study can produce visible light response signal induced by amplification effect of enzymatic color, and are avoided with the marker of fluorescence and quenching molecules and expensive instruments. The "molecular beacon" without fluorescence and quenching molecules is entitled as "hairpin DNA probe" by us for only the "hairpin" structure of traditional molecular beacon is adopted. The merits of two techniques, molecular beacon and amplification effect of enzymatic color, are successfully combined, and the technique is simple, sensitive and specific, to detect and compare the methylenetetrahydrofolate reductase (MTHFR) Gene C677T mutation of subjects between coronary heart disease (CHD) and control group. The results showed that MTHFR Gene C677T polymorphism is an independent risk factor for CHD.
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Affiliation(s)
- Qinghai Chen
- Laboratory, Clinical Experimental Base of Biosensor and Microarray, and Center of Molecule and Gene Diagnosis, Southwest Hospital, Third Military Medical University, Chongqing 400038, PR China
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95
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Ricci F, Vallée-Bélisle A, Plaxco KW. High-precision, in vitro validation of the sequestration mechanism for generating ultrasensitive dose-response curves in regulatory networks. PLoS Comput Biol 2011; 7:e1002171. [PMID: 21998566 PMCID: PMC3188500 DOI: 10.1371/journal.pcbi.1002171] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Accepted: 07/10/2011] [Indexed: 01/20/2023] Open
Abstract
Our ability to recreate complex biochemical mechanisms in designed, artificial systems provides a stringent test of our understanding of these mechanisms and opens the door to their exploitation in artificial biotechnologies. Motivated by this philosophy, here we have recapitulated in vitro the “target sequestration” mechanism used by nature to improve the sensitivity (the steepness of the input/output curve) of many regulatory cascades. Specifically, we have employed molecular beacons, a commonly employed optical DNA sensor, to recreate the sequestration mechanism and performed an exhaustive, quantitative study of its key determinants (e.g., the relative concentrations and affinities of probe and depletant). We show that, using sequestration, we can narrow the pseudo-linear range of a traditional molecular beacon from 81-fold (i.e., the transition from 10% to 90% target occupancy spans an 81-fold change in target concentration) to just 1.5-fold. This narrowing of the dynamic range improves the sensitivity of molecular beacons to that equivalent of an oligomeric, allosteric receptor with a Hill coefficient greater than 9. Following this we have adapted the sequestration mechanism to steepen the binding-site occupancy curve of a common transcription factor by an order of magnitude over the sensitivity observed in the absence of sequestration. Given the success with which the sequestration mechanism has been employed by nature, we believe that this strategy could dramatically improve the performance of synthetic biological systems and artificial biosensors. Here we recreate in vitro the sequestration mechanism thought to underlie the extraordinary sensitivity (the steepness of the input/output function) of a number of genetic networks. We do so first using fluorescent molecular beacons, a well-established, DNA-based biosensor architecture, as our model system. The experimental parameters that define this in vitro model can be controlled with great precision, allowing us to dissect and test a quantitative model of sequestration in unprecedented detail. Following on this we employ the sequestration mechanism to steepen the binding-site occupancy curve of a common transcription factor by an order of magnitude over the sensitivity observed in the absence of sequestration. Our study thus highlights the versatility with which this approach can be used to improve the performance of both synthetic biological systems and artificial biosensors.
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Affiliation(s)
- Francesco Ricci
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, United States of America
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome, Tor Vergata, Rome, Italy
- Consorzio Interuniversitario Biostrutture e Biosistemi “INBB”, Rome, Italy
| | - Alexis Vallée-Bélisle
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, United States of America
| | - Kevin W. Plaxco
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, United States of America
- Interdepartmental Program in Biomolecular Science and Engineering, University of California, Santa Barbara, California, United States of America
- * E-mail:
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96
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Zilbershtein L, Silberman A, Fischer B. 8-(p-CF3-cinnamyl)-modified purine nucleosides as promising fluorescent probes. Org Biomol Chem 2011; 9:7763-73. [PMID: 21960279 DOI: 10.1039/c1ob05681f] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Natural nucleotides are not useful as fluorescent probes because of their low quantum yields. Therefore, a common methodology for the detection of RNA and DNA is the application of extrinsic fluorescent dyes coupled to bases in oligonucleotides. To overcome the many limitations from which fluorescent nucleotide-dye conjugates suffer, we have developed novel purine nucleosides with intrinsic fluorescence to be incorporated into oligonucleotide probes. For this purpose we synthesized adenosine and guanosine fluorescent analogues 7-25, conjugated at the C8 position with aryl/heteroaryl moieties either directly, or via alkenyl/alkynyl linkers. Directly conjugated analogues 7-14, exhibited high quantum yields, φ >0.1, and short λ(em) (<385 nm). Alkynyl conjugated analogues 22-25, exhibited low quantum yields, φ <0.075, and λ(em)<385 nm. The alkenyl conjugated analogues 15-21, exhibited λ(em) 408-459 nm. While analogues 15,16, and 20 bearing an EDG on the aryl moiety, exhibited φ <0.02, analogues 17, and 21 with EWG on the aryl moiety, exhibited extremely high quantum yields, φ ≈ 0.8, suggesting better intramolecular charge transfer. We determined the conformation of selected adenosine analogues. Directly conjugated analogue 8 and alkynyl conjugated analogue 22, adapted the syn conformation, whereas alkenyl conjugated analogue 15 adapted the anti conformation. Based on the long emission wavelengths, high quantum yields, anti conformation and base-paring compatibility, we suggest analogues 17 and 21 for further development as fluorescent probes for the sensitive detection of genetic material.
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Affiliation(s)
- Lital Zilbershtein
- Department of Chemistry, Gonda-Goldschmied Medical Research Center, Bar-Ilan University, Ramat-Gan, 52900, Israel
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97
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Sato Y, Nishizawa S, Teramae N. Label-Free Molecular Beacon System Based on DNAs Containing Abasic Sites and Fluorescent Ligands That Bind Abasic Sites. Chemistry 2011; 17:11650-6. [DOI: 10.1002/chem.201100384] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Revised: 05/31/2011] [Indexed: 01/13/2023]
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98
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Dobosy JR, Rose SD, Beltz KR, Rupp SM, Powers KM, Behlke MA, Walder JA. RNase H-dependent PCR (rhPCR): improved specificity and single nucleotide polymorphism detection using blocked cleavable primers. BMC Biotechnol 2011; 11:80. [PMID: 21831278 PMCID: PMC3224242 DOI: 10.1186/1472-6750-11-80] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 08/10/2011] [Indexed: 12/13/2022] Open
Abstract
Background The polymerase chain reaction (PCR) is commonly used to detect the presence of nucleic acid sequences both in research and diagnostic settings. While high specificity is often achieved, biological requirements sometimes necessitate that primers are placed in suboptimal locations which lead to problems with the formation of primer dimers and/or misamplification of homologous sequences. Results Pyrococcus abyssi (P.a.) RNase H2 was used to enable PCR to be performed using blocked primers containing a single ribonucleotide residue which are activated via cleavage by the enzyme (rhPCR). Cleavage occurs 5'-to the RNA base following primer hybridization to the target DNA. The requirement of the primer to first hybridize with the target sequence to gain activity eliminates the formation of primer-dimers and greatly reduces misamplification of closely related sequences. Mismatches near the scissile linkage decrease the efficiency of cleavage by RNase H2, further increasing the specificity of the assay. When applied to the detection of single nucleotide polymorphisms (SNPs), rhPCR was found to be far more sensitive than standard allele-specific PCR. In general, the best discrimination occurs when the mismatch is placed at the RNA:DNA base pair. Conclusion rhPCR eliminates the formation of primer dimers and markedly improves the specificity of PCR with respect to off-target amplification. These advantages of the assay should find utility in challenging qPCR applications such as genotyping, high level multiplex assays and rare allele detection.
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Affiliation(s)
- Joseph R Dobosy
- Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA 5224, USA
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99
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Feng K, Qiu LP, Yang Y, Wu ZS, Shen GL, Yu RQ. Label-free optical bifunctional oligonucleotide probe for homogeneous amplification detection of disease markers. Biosens Bioelectron 2011; 29:66-75. [PMID: 21872459 DOI: 10.1016/j.bios.2011.07.068] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2011] [Revised: 07/19/2011] [Accepted: 07/27/2011] [Indexed: 02/02/2023]
Abstract
Oligonucleotide-based detection schemes that avoid chemical modification possess significant advantages, including simplified design, intrinsic affinity for targets, low cost and ease to extend applications. In this contribution, we developed a label-free self-locked bifunctional oligonucleotide probe (signaling probe) for the detection of different disease markers in parallel. Two signal enhancement techniques based on isothermal circular strand-displacement polymerization reaction, cyclical nucleic acid strand-displacement polymerization (CNDP) and cyclical common (nonnucleic acid) target-displacement polymerization (CCDP), were employed to implement the amplification assay for p53 gene and PDGF-BB, respectively. The attractive assay properties confirmed the effectiveness of isothermal polymerization in common biosensing systems without evolving any chemical modification: PDGF could be detected down to 0.87ng/mL, and a dynamic response range of 8-5000ng/mL was achieved; The capability to screen the p53 gene was also considerably improved, including the detection limit, sensitivity, dynamic range and so on. Moreover, because no any chemical modification of the signaling probe was acquired and different targets were separately detected in homogeneous solution. This interrogating platform exhibits the design flexibility, convenience, simplicity and cost-effectiveness. The success achieved here is expected to serve as a significant step toward the development of robust label-free oligonucleotide probes in biomarker profiling and disease diagnostics.
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Affiliation(s)
- Kejun Feng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Chemistry and Chemical Engineering College, Hunan University, Changsha 410082, PR China
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100
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Morihiro K, Kodama T, Obika S. Benzylidene acetal type bridged nucleic acids: changes in properties upon cleavage of the bridge triggered by external stimuli. Chemistry 2011; 17:7918-26. [PMID: 21644240 DOI: 10.1002/chem.201100541] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Indexed: 11/07/2022]
Abstract
Four classes of benzylidene acetal type bridged nucleic acids (BA-BNAs) were designed with 2',4'-bridged structures that cleaved upon exposure to appropriate external stimuli. Cleavage of 6-nitroveratrylidene and 2-nitrobenzylidene acetal type BNA bridges occurred upon photoirradiation and subsequent treatment with thiol caused changes in secondary structure to afford 4'-C-hydroxymethyl RNA. Benzylidene and 4-nitrobenzylidene acetal type BNA responded to acids and reducing agents, respectively, resulting in hydrolysis of the acetal-bridged structure. Cleavage of the bridge removed sugar conformational restrictions and changed the duplex- and triplex-forming properties of the BNA-modified oligonucleotides. Moreover, oligonucleotides incorporating a single BA-BNA modification had considerably improved stability toward 3'-exonuclease, which was lost upon cleavage of the bridge. Thus, these new BNAs may be useful as therapeutic and detection tools by sensing various environments.
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Affiliation(s)
- Kunihiko Morihiro
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
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