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Loop-Mediated Isothermal Amplification-Based Microfluidic Platforms for the Detection of Viral Infections. Curr Infect Dis Rep 2022; 24:205-215. [PMID: 36341307 PMCID: PMC9628606 DOI: 10.1007/s11908-022-00790-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2022] [Indexed: 11/09/2022]
Abstract
Purpose of Review Easy-to-use, fast, and accurate virus detection method is essential for patient management and epidemic surveillance, especially during severe pandemics. Loop-mediated isothermal amplification (LAMP) on a microfluidic platform is suitable for detecting infectious viruses, regardless of the availability of medical resources. The purpose of this review is to introduce LAMP-based microfluidic devices for virus detection, including their detection principles, methods, and application. Recent Findings Facing the uncontrolled spread of viruses, the large-scale deployment of LAMP-based microfluidic platforms at the grassroots level can help expand the coverage of nucleic acid testing and shorten the time to obtain test reports. Microfluidic chip technology is highly integrated and miniaturized, enabling precise fluid control for effective virus detection. Performing LAMP on miniaturized systems can reduce analysis time, reagent consumption and risk of sample contamination, and improve analytical performance. Summary Compared to traditional benchtop protocols, LAMP-based microfluidic devices reduce the testing time, reagent consumption, and the risk of sample contamination. In addition to simultaneous detection of multiple target genes by special channel design, microfluidic chips can also integrate digital LAMP to achieve absolute quantification of target genes.
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2
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Liu H, You Y, Zhu Y, Zheng H. Recent advances in the exonuclease III-assisted target signal amplification strategy for nucleic acid detection. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:5103-5119. [PMID: 34664562 DOI: 10.1039/d1ay01275d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The detection of nucleic acids has become significantly important in molecular diagnostics, gene therapy, mutation analysis, forensic investigations and biomedical development, and so on. In recent years, exonuclease III (Exo III) as an enzyme in the 3'-5' exonuclease family has evolved as a frequently used technique for signal amplification of low level DNA target detection. Different from the traditional target amplification strategies, the Exo III-assisted amplification strategy has been used for target DNA detection through directly amplifying the amounts of signal reagents. The Exo III-assisted amplification strategy has its unique advantages and characters, because the character of non-specific recognition of Exo III can overcome the limitation of a target-to-probe ratio of 1 : 1 in the traditional nucleic acid hybridization assay and acquire higher sensitivity. In this review, we selectively discuss the recent advances in the Exo III-assisted amplification strategy, including the amplification strategy integrated with nanomaterials, biosensors, hairpin probes and other nucleic acid detection methods. We also discuss the strengths and limitations of each strategy and methods to overcome the limitations.
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Affiliation(s)
- Hongyu Liu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, P. R. China.
| | - Yuhao You
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, P. R. China.
| | - Youzhuo Zhu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, P. R. China.
| | - Heng Zheng
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, P. R. China.
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3
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Dovzhenko D, Lednev M, Mochalov K, Vaskan I, Rakovich Y, Karaulov A, Nabiev I. Polariton-assisted manipulation of energy relaxation pathways: donor-acceptor role reversal in a tuneable microcavity. Chem Sci 2021; 12:12794-12805. [PMID: 34703566 PMCID: PMC8494027 DOI: 10.1039/d1sc02026a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 08/29/2021] [Indexed: 11/21/2022] Open
Abstract
Resonant interaction between excitonic transitions of molecules and localized electromagnetic field allows the formation of hybrid light-matter polaritonic states. This hybridization of the light and the matter states has been shown to significantly alter the intrinsic properties of molecular ensembles placed inside the optical cavity. Here, we have observed strong coupling of excitonic transition in a pair of closely located organic dye molecules demonstrating an efficient donor-to-acceptor resonance energy transfer with the mode of a tuneable open-access cavity. Analysing the dependence of the relaxation pathways between energy states in this system on the cavity detuning, we have demonstrated that predominant strong coupling of the cavity photon to the exciton transition in the donor dye molecule can lead not only to an increase in the donor-acceptor energy transfer, but also to an energy shift large enough to cause inversion between the energy states of the acceptor and the mainly donor lower polariton energy state. Furthermore, we have shown that the polariton-assisted donor-acceptor chromophores' role reversal or "carnival effect" not only changes the relative energy levels of the donor-acceptor pair, but also makes it possible to manipulate the energy flow in the systems with resonant dipole-dipole interaction and direct energy transfer from the acceptor to the mainly donor lower polariton state. Our experimental data are the first confirmation of the theoretically predicted possibility of polariton-assisted energy transfer reversal in FRET systems, thus paving the way to new avenues in FRET-imaging, remote-controlled chemistry, and all-optical switching.
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Affiliation(s)
- Dmitriy Dovzhenko
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute) 115409 Moscow Russia .,Department of Physics and Astronomy, University of Southampton Southampton SO17 1BJ UK
| | - Maksim Lednev
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute) 115409 Moscow Russia
| | - Konstantin Mochalov
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute) 115409 Moscow Russia .,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences 117997 Moscow Russia
| | - Ivan Vaskan
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute) 115409 Moscow Russia .,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences 117997 Moscow Russia.,Moscow Institute of Physics and Technology Dolgoprudny 141701 Moscow Russia
| | - Yury Rakovich
- IKERBASQUE, Basque Foundation for Science 48009 Bilbao Spain.,Donostia International Physics Center, Polímeros y Materiales Avanzados: Física, Química y Tecnología, UPV-EHU, Centro de Física de Materiales (MPC, CSIC-UPV/EHU) 20018 Donostia - San Sebastian Spain
| | - Alexander Karaulov
- Sechenov First Moscow State Medical University (Sechenov University) 119146 Moscow Russia
| | - Igor Nabiev
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute) 115409 Moscow Russia .,Sechenov First Moscow State Medical University (Sechenov University) 119146 Moscow Russia.,Laboratoire de Recherche en Nanosciences, LRN-EA4682, Université de Reims Champagne-Ardenne 51100 Reims France
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4
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Uhd J, Miotke L, Ji HP, Dunaeva M, Pruijn GJM, Jørgensen CD, Kristoffersen EL, Birkedal V, Yde CW, Nielsen FC, Hansen J, Astakhova K. Ultra-fast detection and quantification of nucleic acids by amplification-free fluorescence assay. Analyst 2021; 145:5836-5844. [PMID: 32648858 DOI: 10.1039/d0an00676a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Two types of clinically important nucleic acid biomarkers, microRNA (miRNA) and circulating tumor DNA (ctDNA) were detected and quantified from human serum using an amplification-free fluorescence hybridization assay. Specifically, miRNAs hsa-miR-223-3p and hsa-miR-486-5p with relevance for rheumatoid arthritis and cancer related mutations BRAF and KRAS of ctDNA were directly measured. The required oligonucleotide probes for the assay were rationally designed and synthesized through a novel "clickable" approach which is time and cost-effective. With no need for isolating nucleic acid components from serum, the fluoresence-based assay took only 1 hour. Detection and absolute quantification of targets was successfully achieved despite their notoriously low abundance, with a precision down to individual nucleotides. Obtained miRNA and ctDNA amounts showed overall a good correlation with current techniques. With appropriate probes, our novel assay and signal boosting approach could become a useful tool for point-of-care measuring other low abundance nucleic acid biomarkers.
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Affiliation(s)
- Jesper Uhd
- Department of Chemistry, Technical University of Denmark, 207 Kemitorvet, 2800 Kgs. Lyngby, Denmark.
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5
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Dong Z, Xue X, Liang H, Guan J, Chang L. DNA Nanomachines for Identifying Cancer Biomarkers in Body Fluids and Cells. Anal Chem 2020; 93:1855-1865. [PMID: 33325676 DOI: 10.1021/acs.analchem.0c03518] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Identifying molecular biomarkers promises to significantly improve the accuracy in cancer diagnosis at its early stage. DNA nanomachines, which are designable and switchable nanostructures made of DNA, show broad potential to detect tumor biomarkers with noninvasive, inexpensive, highly sensitive, and highly specific advantages. This Feature summarizes the recent DNA nanomachine-based platforms for the early detection of cancer biomarkers, both from body fluids and in cells.
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Affiliation(s)
- Zaizai Dong
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Xinying Xue
- Department of Respiratory and Critical Care, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China.,Department of Respiratory and Critical Care, Chinese PLA General Hospital, Beijing 100853, China
| | - Hailun Liang
- School of Public Administration and Policy, Renmin University of China, Beijing 100872, China
| | - Jingjiao Guan
- Department of Chemical and Biomedical Engineering, FAMU-FSU College of Engineering, Florida State University, Tallahassee, Florida 32310, United States
| | - Lingqian Chang
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China.,School of Biomedical Engineering, Research and Engineering Center of Biomedical Materials, Anhui Medical University, Hefei 230032, China
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6
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Novopashina DS, Semikolenova OA, Venyaminova AG. 5'-Monopyrene and 5'-Bispyrene 2'-O-methyl RNA Probes for Detection of RNA Mismatches. Methods Mol Biol 2020; 2063:45-56. [PMID: 31667762 DOI: 10.1007/978-1-0716-0138-9_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Progress in synthesis of novel fluorescent oligonucleotides has provided effective instruments for nucleic acid detection. Pyrene conjugated oligonucleotides have demonstrated their effectiveness as fluorescent hybridization probes. Here we describe the synthesis, isolation, and analysis of 5'-monopyrene and 5'-bispyrene conjugates of oligo(2'-O-methylribonucleotides) and their application as probes for fluorescent detection of mismatches in RNA targets.
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Affiliation(s)
- D S Novopashina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia. .,Novosibirsk State University, Novosibirsk, Russia.
| | | | - A G Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
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7
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Khatri S, Psaraftis N, Funaro A, Arinuma Y, Fujieda Y, Mader S, Jørgensen CD, Astakhova K. Serological comparison of systemic lupus erythematosus with neuropsychiatric lupus using synthetic nucleic acid antigens. J Transl Autoimmun 2020; 3:100068. [PMID: 33205038 PMCID: PMC7652778 DOI: 10.1016/j.jtauto.2020.100068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/20/2020] [Accepted: 10/23/2020] [Indexed: 12/01/2022] Open
Abstract
Neuropsychiatric systemic lupus erythematosus is an autoimmune disorder characterized by an irregular exchange between the central nervous system and the immune system, leading to the outbreak of neurological conditions with possible disabling effects. Although neuropsychiatric systemic lupus erythematosus is the most common expression of lupus condition, it is still poorly understood. In this study, we focus on the development of an advantageous method based on the application of synthetic nucleic acids and protein-based antigen arrays in order to characterize autoreactive antibodies in neuropsychiatric systemic lupus erythematosus. We confirmed the benefits of using synthetic oligonucleotides such as assay reproducibility, elevated affinity and specificity to autoreactive antibodies. We also demonstrated presence of autoantibodies towards three particular synthetic double stranded antigens and verify similarity of antinuclear antibody patterns in ordinary lupus and neuropsychiatric systemic lupus erythematosus.
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Affiliation(s)
- Sangita Khatri
- Department of Chemistry, Technical University of Denmark, 207 Kemitorvet, 2800, Kgs. Lyngby, Denmark
| | - Nikos Psaraftis
- Department of Chemistry, Technical University of Denmark, 207 Kemitorvet, 2800, Kgs. Lyngby, Denmark
| | - Alessia Funaro
- Department of Chemistry, Technical University of Denmark, 207 Kemitorvet, 2800, Kgs. Lyngby, Denmark
| | - Yoshiyuki Arinuma
- Department of Rheumatology and Infectious Diseases, Kitasato University School of Medicine, 1-15-1, Minamiku, Kitasato, Sagamihara, Kanagawa, 252-0374, Japan
| | - Yuichiro Fujieda
- Department of Rheumatology, Endocrinology and Nephrology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Simone Mader
- Institute of Clinical Neuroimmunology, Biomedical Center and University Hospital, Ludwig-Maximilians University Munich, Martinsried, Germany
| | | | - Kira Astakhova
- Department of Chemistry, Technical University of Denmark, 207 Kemitorvet, 2800, Kgs. Lyngby, Denmark
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Khatri S, Hansen J, Astakhova K. Antibodies to synthetic citrullinated peptide epitope correlate with disease activity and flares in rheumatoid arthritis. PLoS One 2020; 15:e0232010. [PMID: 32324839 PMCID: PMC7179858 DOI: 10.1371/journal.pone.0232010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 04/05/2020] [Indexed: 01/13/2023] Open
Abstract
Rheumatoid arthritis (RA), caused by the abnormal recognition of human joint cells by autoimmune antibodies, remains the world’s most prevalent autoimmune disease, with over five million people affected and as much as 4% of the population at risk of RA. To prevent rapid disease development, hormonal and anti-inflammatory therapies require fast and reliable RA diagnosis. However, difficulty in detecting early specific biomarkers for RA means that it is unclear when treatment needs to begin. Here, we combined synthesis of citrullinated peptide epitopes with molecular diagnostics to verify a new specific biomarker for early RA diagnosis and flare prediction. A fibrinogen-derived 21-amino-acid-long citrullinated peptide showed high reactivity toward autoantibodies in RA samples. Additionally, the level of antibodies to this epitope was elevated prior to flares. In contrast, other citrullinated protein variants had lower reactivity and poorer sensitivity to disease activity. In conclusion, fibrinogen-derived epitope E2 subjected to citrullination facilitated a reliable RA diagnosis with a strong correlation to disease activity. This is of a high value for the diagnosis and management of RA patients who respond poorly to treatment.
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Affiliation(s)
- Sangita Khatri
- Department of Chemistry, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Jonas Hansen
- Department of Chemistry, Technical University of Denmark, Kgs Lyngby, Denmark
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Kira Astakhova
- Department of Chemistry, Technical University of Denmark, Kgs Lyngby, Denmark
- * E-mail:
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9
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Pandey R, Kumar A, Xu Q, Pandey DS. Zinc(ii), copper(ii) and cadmium(ii) complexes as fluorescent chemosensors for cations. Dalton Trans 2020; 49:542-568. [PMID: 31894793 DOI: 10.1039/c9dt03017d] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The fluorescence chemosensing behavior of Zn(ii), Cu(ii), and Cd(ii) based complexes toward cations has been described. Cation detection via conventional mechanisms, metal-metal exchange and chemodosimetric approaches along with the importance of metal ions and the scope, significance, and challenges with regard to the detection of cations by metal complex based probes will be discussed in detail. The fundamentals of photophysical behavior and mechanisms involved in the fluorescence detection of analytes will also be described. This article provides a detailed overview of Zn(ii), Cu(ii), and Cd(ii) based complexes as fluorescent probes for cations, together with essential discussions pertaining to detection mechanisms.
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Affiliation(s)
- Rampal Pandey
- Department of Chemistry, National Institute of Technology Uttarakhand, Srinagar, Garhwal 246174, India
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10
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Sadeghi M, Jahanshahi M, Javadian H. Highly sensitive biosensor for detection of DNA nucleobases: Enhanced electrochemical sensing based on polyaniline/single-layer MoS2 nanosheets nanocomposite modified carbon paste electrode. Microchem J 2020. [DOI: 10.1016/j.microc.2019.104315] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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11
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Dekaliuk M, Qiu X, Troalen F, Busson P, Hildebrandt N. Discrimination of the V600E Mutation in BRAF by Rolling Circle Amplification and Förster Resonance Energy Transfer. ACS Sens 2019; 4:2786-2793. [PMID: 31577130 DOI: 10.1021/acssensors.9b01420] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The quantification of very low concentrations of circulating tumor DNA (ctDNA) biomarkers from liquid biopsies has become an important requirement for clinical diagnostics and personalized medicine. In particular, the simultaneous detection of wild-type (WT) dsDNA and their cancer-related counterparts presenting single-point mutations with simple, sensitive, specific, and reproducible technologies is paramount for ctDNA assays in clinical practice. Here, we present the development and evaluation of an amplified dsDNA assay based on a combination of isothermal rolling circle amplification (RCA) and time-gated Förster resonance energy transfer (TG-FRET) between a Tb donor and two dye (Cy3.5 and Cy5.5) acceptors. The RCA-FRET assay is free of washing and separation steps and can quantify both WT and mutated (MT) (V600E) dsDNA in the BRAF gene from a single sample in the 75 fM to 4.5 pM (4.5 × 105 to 2.7 × 107 copies) concentration range. This assay includes all steps from denaturation of the dsDNA targets to the final duplexed quantification of WT and MT targets. High assay performance at different dsDNA sequence lengths and high target specificity even in the presence of a large excess of nonspecific cell-free DNA from human plasma samples demonstrated the applicability to clinical samples. The RCA-FRET single-point mutation sensor has the potential to become an important complementary technique for analyzing liquid biopsies in advanced cancer diagnostics.
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Affiliation(s)
- Mariia Dekaliuk
- NanoBioPhotonics (nanofret.com), Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, CEA, 91405 Orsay Cedex, France
- Department of Neurochemistry, O. V. Palladin Institute of Biochemistry, Kyiv, 01030, Ukraine
| | - Xue Qiu
- NanoBioPhotonics (nanofret.com), Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, CEA, 91405 Orsay Cedex, France
| | - Frédéric Troalen
- Gustave Roussy, Université Paris-Saclay, CNRS, UMR 8126, 94805 Villejuif, France
| | - Pierre Busson
- Gustave Roussy, Université Paris-Saclay, CNRS, UMR 8126, 94805 Villejuif, France
- Université Paris-Sud, Université Paris-Saclay, 94270 Le Kremlin-Bicêtre, France
| | - Niko Hildebrandt
- NanoBioPhotonics (nanofret.com), Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, CEA, 91405 Orsay Cedex, France
- Laboratoire Chimie Organique, Bioorganique, Réactivité et Analyse (COBRA), Université de Rouen Normandie, CNRS, INSA, 76821 Mont Saint-Aignan, France
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12
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Karadeema RJ, Stancescu M, Steidl TP, Bertot SC, Kolpashchikov DM. The owl sensor: a 'fragile' DNA nanostructure for the analysis of single nucleotide variations. NANOSCALE 2018; 10:10116-10122. [PMID: 29781024 DOI: 10.1039/c8nr01107a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Analysis of single nucleotide variations (SNVs) in DNA and RNA sequences is instrumental in healthcare for the detection of genetic and infectious diseases and drug-resistant pathogens. Here we took advantage of the developments in DNA nanotechnology to design a hybridization sensor, named the 'owl sensor', which produces a fluorescence signal only when it complexes with fully complementary DNA or RNA analytes. The novelty of the owl sensor operation is that the selectivity of analyte recognition is, at least in part, determined by the structural rigidity and stability of the entire DNA nanostructure rather than exclusively by the stability of the analyte-probe duplex, as is the case for conventional hybridization probes. Using two DNA and two RNA analytes we demonstrated that owl sensors differentiate SNVs in a wide temperature range of 5 °C-32 °C, a performance unachievable by conventional hybridization probes including the molecular beacon probe. The owl sensor reliably detects cognate analytes even in the presence of 100 times excess of single base mismatched sequences. The approach, therefore, promises to add to the toolbox for the diagnosis of SNVs at ambient temperatures.
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Affiliation(s)
- Rebekah J Karadeema
- Chemistry Department, University of Central Florida, Orlando, FL 32816, USA.
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Smith AL, Kolpashchikov DM. Divide and Control: Comparison of Split and Switch Hybridization Sensors. ChemistrySelect 2017; 2:5427-5431. [PMID: 29372178 PMCID: PMC5777618 DOI: 10.1002/slct.201701179] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Hybridization probes have been intensively used for nucleic acid analysis in medicine, forensics and fundamental research. Instantaneous hybridization probes (IHPs) enable signalling immediately after binding to a targeted DNA or RNA sequences without the need to isolate the probe-target complex (e. g. by gel electrophoresis). The two most common strategies for IHP design are conformational switches and split approach. A conformational switch changes its conformation and produces signal upon hybridization to a target. Split approach uses two (or more) strands that independently or semi independently bind the target and produce an output signal only if all components associate. Here, we compared the performance of split vs switch designs for deoxyribozyme (Dz) hybridization probes under optimal conditions for each of them. The split design was represented by binary Dz (BiDz) probes; while catalytic molecular beacon (CMB) probes represented the switch design. It was found that BiDz were significantly more selective than CMBs in recognition of single base substitution. CMBs produced high background signal when operated at 55°C. An important advantage of BiDz over CMB is more straightforward design and simplicity of assay optimization.
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Affiliation(s)
- Alexandra L Smith
- Chemistry Department, University of Central Florida, 4000 N. Central Florida Ave, Orlando, FL 32826
| | - Dmitry M Kolpashchikov
- Chemistry Department, Burnett School of Biomedical Sciences, National Center for Forensic Science, University of Central Florida, 4000 N. Central Florida Ave, Orlando, FL 32826
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Astakhova K, Golovin AV, Prokhorenko IA, Ustinov AV, Stepanova IA, Zatsepin TS, Korshun VA. Design of 2′-phenylethynylpyrene excimer forming DNA/RNA probes for homogeneous SNP detection: The attachment manner matters. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.04.045] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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Cox AJ, Bengtson HN, Rohde KH, Kolpashchikov DM. DNA nanotechnology for nucleic acid analysis: multifunctional molecular DNA machine for RNA detection. Chem Commun (Camb) 2016; 52:14318-14321. [PMID: 27886299 PMCID: PMC5645153 DOI: 10.1039/c6cc06889h] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The Nobel prize in chemistry in 2016 was awarded for 'the design and synthesis of molecular machines'. Here we designed and assembled a molecular machine for the detection of specific RNA molecules. An association of several DNA strands, named multifunctional DNA machine for RNA analysis (MDMR1), was designed to (i) unwind RNA with the help of RNA-binding arms, (ii) selectively recognize a targeted RNA fragment, (iii) attract a signal-producing substrate and (iv) amplify the fluorescent signal by catalysis. MDMR1 enabled detection of 16S rRNA at concentrations ∼24 times lower than that by a traditional deoxyribozyme probe.
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Affiliation(s)
- A J Cox
- Chemistry Department, University of Central Florida, Orlando, 32816, Florida, USA and Burnett School of Biomedical Sciences, University of Central Florida, Orlando, 32816, Florida, USA.
| | - H N Bengtson
- Chemistry Department, University of Central Florida, Orlando, 32816, Florida, USA and Burnett School of Biomedical Sciences, University of Central Florida, Orlando, 32816, Florida, USA.
| | - K H Rohde
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, 32816, Florida, USA.
| | - D M Kolpashchikov
- Chemistry Department, University of Central Florida, Orlando, 32816, Florida, USA and Burnett School of Biomedical Sciences, University of Central Florida, Orlando, 32816, Florida, USA.
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