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Sajeer Paramabth M, Varma M. Demystifying PCR tests, challenges, alternatives, and future: A quick review focusing on COVID and fungal infections. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2023; 51:719-728. [PMID: 37485773 DOI: 10.1002/bmb.21771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 06/20/2023] [Accepted: 07/12/2023] [Indexed: 07/25/2023]
Abstract
The polymerase chain reaction (PCR) technique is one of the most potent tools in molecular biology. It is extensively used for various applications ranging from medical diagnostics to forensic science and food quality testing. This technique has facilitated to survive COVID-19 pandemic by identifying the virus-infected individuals effortlessly and effectively. This review explores the principles, recent advancements, challenges, and alternatives of PCR technique in the context of COVID-19 and fungal infections. The introduction of PCR technique for anyone new to this field is the primary aim of this review and thereby equips them to understand the science of COVID-19 and related fungal infections in a simplistic manner.
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Affiliation(s)
| | - Manoj Varma
- Center for Nano Science and Engineering (CeNSE), Indian Institute of Science, Bangalore, India
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2
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Prajapati GK, Kumar A, Wany A, Pandey DM. Molecular Beacon Probe (MBP)-Based Real-Time PCR. Methods Mol Biol 2023; 2638:273-287. [PMID: 36781649 DOI: 10.1007/978-1-0716-3024-2_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
In the advancement of molecular biology techniques, several probe-based techniques, like molecular beacon probe (MBP) assay, TaqMan probe, and minor groove binder (MGB) probe assay, have been reported to identify specific sequences through real-time polymerase chain reaction (PCR). All probe-based methods are more sensitive than the conventional PCR for the detection and quantification of target genes. MBP is a hydrolysis probe that emits fluorescence when getting the specific sequences on the gene. Here, we describe the application of MBP for the identification of the motif sequences present in the promoters of differentially expressed genes.
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Affiliation(s)
- Gopal Kumar Prajapati
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India.,R & D Biologics Division, Promea Therapeutics Pvt Ltd, Sultanpur, Hyderabad, India
| | - Ashutosh Kumar
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India.,Department of Biotechnology, School of Sciences, PP Savani University, Kosamba, Surat, Gujarat, India
| | - Aakanksha Wany
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India.,Department of Biotechnology, School of Sciences, PP Savani University, Kosamba, Surat, Gujarat, India
| | - Dev Mani Pandey
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India.
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3
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Leonardi AA, Lo Faro MJ, Fazio B, Spinella C, Conoci S, Livreri P, Irrera A. Fluorescent Biosensors Based on Silicon Nanowires. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:2970. [PMID: 34835735 PMCID: PMC8624671 DOI: 10.3390/nano11112970] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/27/2021] [Accepted: 11/03/2021] [Indexed: 01/05/2023]
Abstract
Nanostructures are arising as novel biosensing platforms promising to surpass current performance in terms of sensitivity, selectivity, and affordability of standard approaches. However, for several nanosensors, the material and synthesis used make the industrial transfer of such technologies complex. Silicon nanowires (NWs) are compatible with Si-based flat architecture fabrication and arise as a hopeful solution to couple their interesting physical properties and surface-to-volume ratio to an easy commercial transfer. Among all the transduction methods, fluorescent probes and sensors emerge as some of the most used approaches thanks to their easy data interpretation, measure affordability, and real-time in situ analysis. In fluorescent sensors, Si NWs are employed as substrate and coupled with several fluorophores, NWs can be used as quenchers in stem-loop configuration, and have recently been used for direct fluorescent sensing. In this review, an overview on fluorescent sensors based on Si NWs is presented, analyzing the literature of the field and highlighting the advantages and drawbacks for each strategy.
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Affiliation(s)
- Antonio Alessio Leonardi
- Dipartimento di Fisica e Astronomia “Ettore Majorana”, Università degli Studi di Catania, Via S. Sofia 64, 95123 Catania, Italy; (A.A.L.); (M.J.L.F.)
- Istituto per i Processi Chimico-Fisici, Consiglio Nazionale delle Ricerche (CNR-IPCF), Viale F. Stagno D’Alcontres 37, 98158 Messina, Italy;
- Istituto per la Microelettronica e Microsistemi, Consiglio Nazionale delle Ricerche (CNR-IMM) UoS Catania, Via S. Sofia 64, 95123 Catania, Italy
- Lab SENS, Beyond NANO, Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche, ed Ambientali, Università Degli Studi di Messina, Viale Ferdinando Stagno d’Alcontres, 98166 Messina, Italy; (C.S.); (S.C.)
| | - Maria José Lo Faro
- Dipartimento di Fisica e Astronomia “Ettore Majorana”, Università degli Studi di Catania, Via S. Sofia 64, 95123 Catania, Italy; (A.A.L.); (M.J.L.F.)
- Istituto per la Microelettronica e Microsistemi, Consiglio Nazionale delle Ricerche (CNR-IMM) UoS Catania, Via S. Sofia 64, 95123 Catania, Italy
| | - Barbara Fazio
- Istituto per i Processi Chimico-Fisici, Consiglio Nazionale delle Ricerche (CNR-IPCF), Viale F. Stagno D’Alcontres 37, 98158 Messina, Italy;
- Lab SENS, Beyond NANO, Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche, ed Ambientali, Università Degli Studi di Messina, Viale Ferdinando Stagno d’Alcontres, 98166 Messina, Italy; (C.S.); (S.C.)
| | - Corrado Spinella
- Lab SENS, Beyond NANO, Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche, ed Ambientali, Università Degli Studi di Messina, Viale Ferdinando Stagno d’Alcontres, 98166 Messina, Italy; (C.S.); (S.C.)
- Istituto per la Microelettronica e Microsistemi, Consiglio Nazionale delle Ricerche (CNR-IMM) Zona Industriale, VIII Strada 5, 95121 Catania, Italy
| | - Sabrina Conoci
- Lab SENS, Beyond NANO, Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche, ed Ambientali, Università Degli Studi di Messina, Viale Ferdinando Stagno d’Alcontres, 98166 Messina, Italy; (C.S.); (S.C.)
- Istituto per la Microelettronica e Microsistemi, Consiglio Nazionale delle Ricerche (CNR-IMM) Zona Industriale, VIII Strada 5, 95121 Catania, Italy
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche, ed Ambientali, Università Degli Studi di Messina, Viale Ferdinando Stagno d’Alcontres, 98166 Messina, Italy
| | - Patrizia Livreri
- Dipartimento di ingegneria, Università degli Studi di Palermo, Viale delle Scienze BLDG 9, 90128 Palermo, Italy;
| | - Alessia Irrera
- Istituto per i Processi Chimico-Fisici, Consiglio Nazionale delle Ricerche (CNR-IPCF), Viale F. Stagno D’Alcontres 37, 98158 Messina, Italy;
- Lab SENS, Beyond NANO, Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche, ed Ambientali, Università Degli Studi di Messina, Viale Ferdinando Stagno d’Alcontres, 98166 Messina, Italy; (C.S.); (S.C.)
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4
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Markey FB, Parashar V, Batish M. Methods for spatial and temporal imaging of the different steps involved in RNA processing at single-molecule resolution. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1608. [PMID: 32543077 DOI: 10.1002/wrna.1608] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 05/06/2020] [Accepted: 05/07/2020] [Indexed: 12/26/2022]
Abstract
RNA plays a quintessential role as a messenger of information from genotype (DNA) to phenotype (proteins), as well as acts as a regulatory molecule (noncoding RNAs). All steps in the journey of RNA from synthesis (transcription), splicing, transport, localization, translation, to its eventual degradation, comprise important steps in gene expression, thereby controlling the fate of the cell. This lifecycle refers to the majority of RNAs (primarily mRNAs), but not other RNAs such as tRNAs. Imaging these processes in fixed cells and in live cells has been an important tool in developing an understanding of the regulatory steps in RNAs journey. Single-cell and single-molecule imaging techniques enable a much deeper understanding of cellular biology, which is not possible with bulk studies involving RNA isolated from a large pool of cells. Classic techniques, such as fluorescence in situ hybridization (FISH), as well as more recent aptamer-based approaches, have provided detailed insights into RNA localization, and have helped to predict the functions carried out by many RNA species. However, there are still certain processing steps that await high-resolution imaging, which is an exciting and upcoming area of research. In this review, we will discuss the methods that have revolutionized single-molecule resolution imaging in general, the steps of RNA processing in which these methods have been used, and new emerging technologies. This article is categorized under: RNA Export and Localization > RNA Localization RNA Methods > RNA Analyses in Cells RNA Interactions with Proteins and Other Molecules > Small Molecule-RNA Interactions.
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Affiliation(s)
- Fatu Badiane Markey
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - Vijay Parashar
- Department of Medical and Molecular Sciences, University of Delaware, Newark, Delaware, USA
| | - Mona Batish
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA.,Department of Medical and Molecular Sciences, University of Delaware, Newark, Delaware, USA
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5
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Simões MF, Ottoni CA, Antunes A. Biogenic Metal Nanoparticles: A New Approach to Detect Life on Mars? Life (Basel) 2020; 10:E28. [PMID: 32245046 PMCID: PMC7151574 DOI: 10.3390/life10030028] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/13/2020] [Accepted: 03/19/2020] [Indexed: 01/02/2023] Open
Abstract
Metal nanoparticles (MNPs) have been extensively studied. They can be produced via different methods (physical, chemical, or biogenic), but biogenic synthesis has become more relevant, mainly for being referred by many as eco-friendly and more advantageous than others. Biogenic MNPs have been largely used in a wide variety of applications, from industry, to agriculture, to health sectors, among others. Even though they are increasingly researched and used, there is still space for exploring further applications and increasing their functionality and our understanding of their synthesis process. Here, we provide an overview of MNPs and biogenic MNPs, and we analyze the potential application of their formation process to astrobiology and the detection of life on Mars and other worlds. According to current knowledge, we suggest that they can be used as potential biosignatures in extra-terrestrial samples. We present the advantages and disadvantages of this approach, suggest further research, and propose its potential use for the search for life in future space exploration.
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Affiliation(s)
- Marta Filipa Simões
- State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau SAR, Hong Kong, China
| | | | - André Antunes
- State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau SAR, Hong Kong, China
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6
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Petrovics R, Söveges B, Egyed A, Knorr G, Kormos A, Imre T, Török G, Zeke A, Kocsmár É, Lotz G, Kele P, Németh K. A rapid and concise setup for the fast screening of FRET pairs using bioorthogonalized fluorescent dyes. Org Biomol Chem 2018; 16:2997-3005. [PMID: 29629719 DOI: 10.1039/c8ob00213d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
One of the most popular means to follow interactions between bio(macro)molecules is Förster resonance energy transfer (FRET). There is large interest in widening the selection of fluorescent FRET pairs especially in the region of the red/far red range, where minimal autofluorescence is encountered. A set of bioorthogonally applicable fluorescent dyes, synthesized recently in our lab, were paired (Cy3T/Cy5T; Cy1A/Cy3T and Cy1A/CBRD1A) based on their spectral characteristics in order to test their potential in FRET applications. For fast elaboration of the selected pairs we have created a bioorthogonalized platform based on complementary 17-mer DNA oligomers. The cyclooctynylated strands were modified nearly quantitatively with the fluorophores via bioorthogonal chemistry steps, using azide- (Cy1; CBRD1) or tetrazine-modified (Cy3; Cy5) dyes. Reactions were followed by capillary electrophoresis using a method specifically developed for this project. FRET efficiencies of the fluorescent dye pairs were compared both in close proximity (5' and 3' matched) and at larger distance (5' and 5' matched). The specificity of FRET signals was further elaborated by denaturation and competition studies. Cy1A/Cy3T and Cy1A/CBRD1A introduced here as novel FRET pairs are highly recommended for FRET applications based on the significant changes in fluorescence intensities of the donor and acceptor peaks. Application of one of the FRET pairs was demonstrated in live cells, transfected with labeled oligos. Furthermore, the concise installation of the dyes allows for efficient fluorescence modification of any selected DNA strands as was demonstrated in the construction of Cy3T labeled oligomers, which were used in the FISH-based detection of Helicobacter pylori.
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Affiliation(s)
- Réka Petrovics
- Research Centre for Natural Sciences of Hungarian Academy of Sciences, Institute of Organic Chemistry, "Lendület" Chemical Biology Research Group, H-1117 Budapest, Magyar tudósok krt. 2, Hungary.
| | - Bianka Söveges
- Research Centre for Natural Sciences of Hungarian Academy of Sciences, Institute of Organic Chemistry, "Lendület" Chemical Biology Research Group, H-1117 Budapest, Magyar tudósok krt. 2, Hungary.
| | - Alexandra Egyed
- Research Centre for Natural Sciences of Hungarian Academy of Sciences, Institute of Organic Chemistry, "Lendület" Chemical Biology Research Group, H-1117 Budapest, Magyar tudósok krt. 2, Hungary.
| | - Gergely Knorr
- Research Centre for Natural Sciences of Hungarian Academy of Sciences, Institute of Organic Chemistry, "Lendület" Chemical Biology Research Group, H-1117 Budapest, Magyar tudósok krt. 2, Hungary.
| | - Attila Kormos
- Research Centre for Natural Sciences of Hungarian Academy of Sciences, Institute of Organic Chemistry, "Lendület" Chemical Biology Research Group, H-1117 Budapest, Magyar tudósok krt. 2, Hungary.
| | - Tímea Imre
- Research Centre for Natural Sciences of Hungarian Academy of Sciences, Instrumentation Center, MS Metabolomics Research Group, H-1117 Budapest, Magyar tudósok krt. 2, Hungary
| | - György Török
- Research Centre for Natural Sciences of Hungarian Academy of Sciences, Institute of Enzymology, Molecular Cell Biology Research Group, H-1117 Budapest, Magyar tudósok krt. 2, Hungary
| | - András Zeke
- Research Centre for Natural Sciences of Hungarian Academy of Sciences, Institute of Enzymology, Protein Research Group, H-1117 Budapest, Magyar tudósok krt. 2, Hungary
| | - Éva Kocsmár
- 2nd Department of Pathology, Semmelweis University, Budapest H-1091 Üllői str. 93, Hungary
| | - Gábor Lotz
- 2nd Department of Pathology, Semmelweis University, Budapest H-1091 Üllői str. 93, Hungary
| | - Péter Kele
- Research Centre for Natural Sciences of Hungarian Academy of Sciences, Institute of Organic Chemistry, "Lendület" Chemical Biology Research Group, H-1117 Budapest, Magyar tudósok krt. 2, Hungary.
| | - Krisztina Németh
- Research Centre for Natural Sciences of Hungarian Academy of Sciences, Institute of Organic Chemistry, "Lendület" Chemical Biology Research Group, H-1117 Budapest, Magyar tudósok krt. 2, Hungary.
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7
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Electronic Detection of DNA Hybridization by Coupling Organic Field-Effect Transistor-Based Sensors and Hairpin-Shaped Probes. SENSORS 2018; 18:s18040990. [PMID: 29584638 PMCID: PMC5948917 DOI: 10.3390/s18040990] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 03/20/2018] [Accepted: 03/23/2018] [Indexed: 11/16/2022]
Abstract
In this paper, the electronic transduction of DNA hybridization is presented by coupling organic charge-modulated field-effect transistors (OCMFETs) and hairpin-shaped probes. These probes have shown interesting properties in terms of sensitivity and selectivity in other kinds of assays, in the form of molecular beacons (MBs). Their integration with organic-transistor based sensors, never explored before, paves the way to a new class of low-cost, easy-to-use, and portable genetic sensors with enhanced performances. Thanks to the peculiar characteristics of the employed sensor, measurements can be performed at relatively high ionic strengths, thus optimizing the probes’ functionality without affecting the detection ability of the device. A complete electrical characterization of the sensor is reported, including calibration with different target concentrations in the measurement environment and selectivity evaluation. In particular, DNA hybridization detection for target concentration as low as 100 pM is demonstrated.
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Dembska A, Kierzek E, Juskowiak B. Studying the influence of stem composition in pH-sensitive molecular beacons onto their sensing properties. Anal Chim Acta 2017; 990:157-167. [PMID: 29029739 DOI: 10.1016/j.aca.2017.07.040] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Revised: 06/21/2017] [Accepted: 07/17/2017] [Indexed: 01/04/2023]
Abstract
Intracellular sensing using fluorescent molecular beacons is a potentially useful strategy for real-time, in vivo monitoring of important cellular events. This work is focused on evaluation of pyrene excimer signaling molecular beacons (MBs) for the monitoring of pH changes in vitro as well as inside living cells. The recognition element in our MB called pHSO (pH-sensitive oligonucleotide) is the loop enclosing cytosine-rich fragment that is able to form i-motif structure in a specific pH range. However, alteration of a sequence of the 6 base pairs containing stem of MB allowed the design of pHSO probes that exhibited different dynamic pH range and possessed slightly different transition midpoint between i-motif and open loop configuration. Moreover, this conformational transition was accompanied by spectral changes showing developed probes different pyrene excimer-monomer emission ratio triggered by pH changes. The potential of these MBs for intracellular pH sensing is demonstrated on the example of HeLa cells line.
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Affiliation(s)
- Anna Dembska
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland.
| | - Elzbieta Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Science, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Bernard Juskowiak
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland
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Wang C, Zhang H, Zeng D, Sun W, Zhang H, Aldalbahi A, Wang Y, San L, Fan C, Zuo X, Mi X. Elaborately designed diblock nanoprobes for simultaneous multicolor detection of microRNAs. NANOSCALE 2015; 7:15822-15829. [PMID: 26359758 DOI: 10.1039/c5nr04618a] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Simultaneous detection of multiple biomarkers has important prospects in the biomedical field. In this work, we demonstrated a novel strategy for the detection of multiple microRNAs (miRNAs) based on gold nanoparticles (Au NPs) and polyadenine (polyA) mediated nanoscale molecular beacon (MB) probes (denoted p-nanoMBs). Novel fluorescent labeled p-nanoMBs bearing consecutive adenines were designed, of which polyA served as an effective anchoring block binding to the surface of Au NPs, and the appended hairpin block formed an upright conformation that favored the hybridization with targets. Using the co-assembling method and the improved hybridization conformation of the hairpin probes, we achieved high selectivity for specifically distinguishing DNA targets from single-base mismatched DNA targets. We also realized multicolor detection of three different synthetic miRNAs in a wide dynamic range from 0.01 nM to 200 nM with a detection limit of 10 pM. What's more, we even detected miRNAs in a simulated serum environment, which indicated that our method could be used in complex media. Compared with the traditional method, our strategy provides a promising alternative method for the qualitative and quantitative detection of miRNAs.
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Affiliation(s)
- Chenguang Wang
- Laboratory of System Biology, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China.
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10
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Martí AA. Metal complexes and time-resolved photoluminescence spectroscopy for sensing applications. J Photochem Photobiol A Chem 2015. [DOI: 10.1016/j.jphotochem.2015.03.020] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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11
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Dembska A, Juskowiak B. Pyrene functionalized molecular beacon with pH-sensitive i-motif in a loop. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 150:928-933. [PMID: 26123509 DOI: 10.1016/j.saa.2015.06.041] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 06/11/2015] [Indexed: 06/04/2023]
Abstract
In this work, we present a spectral characterization of pH-sensitive system, which combines the i-motif properties with the spatially sensitive fluorescence signal of pyrene molecules attached to hairpin ends. The excimer production (fluorescence max. ∼480 nm) by pyrene labels at the ends of the molecular beacon is driven by pH-dependent i-motif formation in the loop. To illustrate the performance and reversible work of our systems, we performed the experiments with repeatedly pH cycling between pH values of 7.5±0.3 and 6.5±0.3. The sensor gives analytical response in excimer-monomer switching mode in narrow pH range (1.5 pH units) and exhibits high pH resolution (0.1 pH unit).
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Affiliation(s)
- Anna Dembska
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland.
| | - Bernard Juskowiak
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland
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12
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Simon AJ, Vallée-Bélisle A, Ricci F, Watkins HM, Plaxco KW. Using the population-shift mechanism to rationally introduce "Hill-type" cooperativity into a normally non-cooperative receptor. Angew Chem Int Ed Engl 2014; 53:9471-5. [PMID: 25044647 PMCID: PMC5660314 DOI: 10.1002/anie.201403777] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Indexed: 12/17/2022]
Abstract
Allosteric cooperativity, which nature uses to improve the sensitivity with which biomolecular receptors respond to small changes in ligand concentration, could likewise be of use in improving the responsiveness of artificial biosystems. Thus motivated, we demonstrate here the rational design of cooperative molecular beacons, a widely employed DNA sensor, using a generalizable population-shift approach in which we engineer receptors that equilibrate between a low-affinity state and a high-affinity state exposing two binding sites. Doing so we achieve cooperativity within error of ideal behavior, greatly steepening the beacon's binding curve relative to that of the parent receptor. The ability to rationally engineer cooperativity should prove useful in applications such as biosensors, synthetic biology and "smart" biomaterials, in which improved responsiveness is of value.
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Affiliation(s)
- Anna J Simon
- Biomolecular Science and Engineering Program, UC Santa Barbara, Santa Barbara, CA 93106 (USA)
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13
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Real-time imaging of the epithelial-mesenchymal transition using microRNA-200a sequence-based molecular beacon-conjugated magnetic nanoparticles. PLoS One 2014; 9:e102164. [PMID: 25048580 PMCID: PMC4105468 DOI: 10.1371/journal.pone.0102164] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 06/16/2014] [Indexed: 12/30/2022] Open
Abstract
The epithelial-mesenchymal transition (EMT) plays important roles in tumor progression to metastasis. Thus, the development of an imaging probe that can monitor transient periods of the EMT process in live cells is required for a better understanding of metastatic process. Inspired by the fact that the mRNA expression levels of zinc finger E-box-binding homeobox 1 (ZEB1) increase when cells adopt mesenchyme characteristics and that microRNA-200a (miR-200a) can bind to ZEB1 mRNA, we conjugated molecular beacon (MB) mimicking mature miR-200a to magnetic nanoparticles (miR-200a-MB-MNPs) and devised an imaging method to observe transitional changes in the cells during EMT. Transforming growth factor-β1 treated epithelial cells and breast cancer cell lines representing both epithelial and mesenchymal phenotypes were used for the validation of miR-200a-MB-MNPs as an EMT imaging probe. The real-time imaging of live cells acquired with the induction of EMT revealed an increase in fluorescence signals by miR-200a-MB-MNPs, cell morphology alterations, and the loss of cell-cell adhesion. Our results suggest that miR-200a-MB-MNPs can be used as an imaging probe for the real-time monitoring of the EMT process in live cells.
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14
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Kim CH, Woo H, Hyun IG, Kim C, Choi JH, Jang SH, Park SM, Kim DG, Lee MG, Jung KS, Hyun J, Kim HS. A comparison between the efficiency of the Xpert MTB/RIF assay and nested PCR in identifying Mycobacterium tuberculosis during routine clinical practice. J Thorac Dis 2014; 6:625-31. [PMID: 24976983 DOI: 10.3978/j.issn.2072-1439.2014.04.12] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 04/02/2014] [Indexed: 11/14/2022]
Abstract
OBJECTIVES Polymerase chain reaction (PCR) for the detection of Mycobacterium tuberculosis (MTB) is more sensitive, specific, and rapid than the conventional methods of acid-fast bacilli (AFB) smear and culture. The aim of this study was to determine if the Xpert MTB/rifampicin (RIF) assay had additional advantages over nested PCR for the detection of MTB in a geographical area with intermediate tuberculosis (TB) incidence. METHODS Between February and December 2013, the Xpert MTB/RIF assay and MTB nested PCR, as well as AFB smear and culture, were simultaneously performed on 198 clinical samples (160 pulmonary and 38 non-pulmonary specimens) collected from 171 patients hospitalized at Hallym University Medical Center for possible TB. The accuracy of the diagnosis of MTB culture-positive TB and the turnaround time of reporting laboratory results were calculated and compared. Rifampin resistance by the Xpert MTB/RIF assay was reviewed with that of conventional drug susceptibility testing (DST). RESULTS The sensitivity, specificity, and positive and negative predictive values of the Xpert MTB/RIF assay and MTB nested PCR for diagnosis of MTB culture-positive pulmonary TB were 86.1% vs. 69.4% (P=0.1563), 97.8% vs. 94.1% (P=0.2173), 91.2% vs. 75.8% (P=0.1695), and 96.4% vs. 92.0% (P=0.2032), respectively. The median turnaround times of the Xpert MTB/RIF assay and MTB nested PCR were 0 [0-4] days and 4 [1-11] days, respectively (P<0.001). Two cases of rifampin resistance, as determined by the Xpert MTB/RIF assay, were found to be multi-drug resistant (MDR) pulmonary TB by DST. CONCLUSIONS The Xpert MTB/RIF assay seemed to be sensitive, specific, and comparable to nested PCR for identifying MTB among clinically suspected TB patients, and the assay can be valuable in giving a timely identification of resistance to rifampin.
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Affiliation(s)
- Cheol-Hong Kim
- 1 Department of Internal Medicine, 2 Lung Research Institute, 3 Department of Laboratory Medicine, Hallym University College of Medicine, Chuncheon, Korea
| | - Heungjeong Woo
- 1 Department of Internal Medicine, 2 Lung Research Institute, 3 Department of Laboratory Medicine, Hallym University College of Medicine, Chuncheon, Korea
| | - In Gyu Hyun
- 1 Department of Internal Medicine, 2 Lung Research Institute, 3 Department of Laboratory Medicine, Hallym University College of Medicine, Chuncheon, Korea
| | - Changhwan Kim
- 1 Department of Internal Medicine, 2 Lung Research Institute, 3 Department of Laboratory Medicine, Hallym University College of Medicine, Chuncheon, Korea
| | - Jeong-Hee Choi
- 1 Department of Internal Medicine, 2 Lung Research Institute, 3 Department of Laboratory Medicine, Hallym University College of Medicine, Chuncheon, Korea
| | - Seung-Hun Jang
- 1 Department of Internal Medicine, 2 Lung Research Institute, 3 Department of Laboratory Medicine, Hallym University College of Medicine, Chuncheon, Korea
| | - Sang Myeon Park
- 1 Department of Internal Medicine, 2 Lung Research Institute, 3 Department of Laboratory Medicine, Hallym University College of Medicine, Chuncheon, Korea
| | - Dong-Gyu Kim
- 1 Department of Internal Medicine, 2 Lung Research Institute, 3 Department of Laboratory Medicine, Hallym University College of Medicine, Chuncheon, Korea
| | - Myung Goo Lee
- 1 Department of Internal Medicine, 2 Lung Research Institute, 3 Department of Laboratory Medicine, Hallym University College of Medicine, Chuncheon, Korea
| | - Ki-Suck Jung
- 1 Department of Internal Medicine, 2 Lung Research Institute, 3 Department of Laboratory Medicine, Hallym University College of Medicine, Chuncheon, Korea
| | - Jeongwon Hyun
- 1 Department of Internal Medicine, 2 Lung Research Institute, 3 Department of Laboratory Medicine, Hallym University College of Medicine, Chuncheon, Korea
| | - Hyun Soo Kim
- 1 Department of Internal Medicine, 2 Lung Research Institute, 3 Department of Laboratory Medicine, Hallym University College of Medicine, Chuncheon, Korea
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Eprobe mediated real-time PCR monitoring and melting curve analysis. PLoS One 2013; 8:e70942. [PMID: 23951046 PMCID: PMC3737233 DOI: 10.1371/journal.pone.0070942] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 06/25/2013] [Indexed: 01/10/2023] Open
Abstract
Real-time monitoring of PCR is one of the most important methods for DNA and RNA detection widely used in research and medical diagnostics. Here we describe a new approach for combined real-time PCR monitoring and melting curve analysis using a 3′ end-blocked Exciton-Controlled Hybridization-sensitive fluorescent Oligonucleotide (ECHO) called Eprobe. Eprobes contain two dye moieties attached to the same nucleotide and their fluorescent signal is strongly suppressed as single-stranded oligonucleotides by an excitonic interaction between the dyes. Upon hybridization to a complementary DNA strand, the dyes are separated and intercalate into the double-strand leading to strong fluorescence signals. Intercalation of dyes can further stabilize the DNA/DNA hybrid and increase the melting temperature compared to standard DNA oligonucleotides. Eprobes allow for specific real-time monitoring of amplification reactions by hybridizing to the amplicon in a sequence-dependent manner. Similarly, Eprobes allow for analysis of reaction products by melting curve analysis. The function of different Eprobes was studied using the L858R mutation in the human epidermal growth factor receptor (EGFR) gene, and multiplex detection was demonstrated for the human EGFR and KRAS genes using Eprobes with two different dyes. Combining amplification and melting curve analysis in a single-tube reaction provides powerful means for new mutation detection assays. Functioning as “sequence-specific dyes”, Eprobes hold great promises for future applications not only in PCR but also as hybridization probes in other applications.
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Bier FF, Schumacher S. Integration in Bioanalysis: Technologies for Point-of-Care Testing. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2013; 133:1-14. [DOI: 10.1007/10_2012_164] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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