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Mirza AH, Akhtar M, Aguren J, Marino J, Bruno JG. Advancements in Rapid and Affordable Diagnostic Testing for Respiratory Infectious Diseases: Evaluation of Aptamer Beacon Technology for Rapid and Sensitive Detection of SAR-CoV-2 in Breath Condensate. J Fluoresc 2023:10.1007/s10895-023-03453-3. [PMID: 37864614 DOI: 10.1007/s10895-023-03453-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/26/2023] [Indexed: 10/23/2023]
Abstract
The demand for rapid and efficient diagnostic point-of-care tests for respiratory infectious diseases has become increasingly critical in the current landscape. The emphasis on accessibility has been underscored over the past year, making it crucial to have biological components that exhibit fast and accurate kinetics. The foundation for precise, swift, and effective testing relies on the availability of highly responsive biological agents. Two published aptamer DNA sequences designated Song and MSA52 and their truncated internal stem-loop structures were studied for their potential to serve as aptamer beacons for rapid COVID detection. The candidate beacons were covalently labeled with Atto 633 dye attached to their 5' ends and Iowa Black quencher attached to their 3' ends. The whole aptamer structures exhibited the greatest fluorescence signal intensities and higher fluorescence background than their truncated internal stem-loop beacon structures suggesting that the distance between fluorophores and quenchers was greater for the whole aptamer beacon candidates versus the isolated stem-loop structures. Beacon candidates were tested against two heat- or gamma radiation-killed SARS-CoV-2 Washington 1/2020 virus samples and three different COVID spike (S) proteins to test their effectiveness. Despite the higher background fluorescence, the whole aptamer beacons showed better signal-to-noise ratios and were selected for further investigation. Limit of detection (LOD) studies revealed that both the whole Song and whole MSA52 aptamer beacon candidates had a LOD of 9.61 × 103 genome equivalents in phosphate-buffered saline using the red channel of a Promega Quantus™ fluorometer which correlated well with confirmatory spectrofluorometry. Cross-reactivity studies using numerous COVID variants, related coronaviruses, and other common respiratory pathogens suggested greater COVID selectivity for the whole MSA52 versus the whole Song aptamer beacon candidate, indicating promise for specific COVID detection. Importantly, both whole aptamer beacon candidates exhibited very rapid "bind and detect" fluorescence increases within the first 1-2 min of mixing the beacons with killed SARS-CoV-2 viruses in 100 µl samples. Overall, this work illustrates the strong potential for aptamer beacons for rapid, on-site detection and presumptive diagnosis of COVID in breath condensates or other small liquid samples. This research highlights the strong potential of aptamer beacons for addressing the need for fast and convenient diagnostic tools in global health contexts, especially in resource-limited settings.
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Affiliation(s)
- Asma H Mirza
- Steradian Technologies, Inc, 2450 Holcombe Street Suite J, Houston, TX, 77021, USA
| | - Moneeb Akhtar
- Steradian Technologies, Inc, 2450 Holcombe Street Suite J, Houston, TX, 77021, USA
| | - Jerry Aguren
- Steradian Technologies, Inc, 2450 Holcombe Street Suite J, Houston, TX, 77021, USA
| | - John Marino
- Steradian Technologies, Inc, 2450 Holcombe Street Suite J, Houston, TX, 77021, USA
| | - John G Bruno
- Nanohmics, Inc, 6201 E. Oltorf Street Suite 400, Austin, TX, 78741, USA.
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Yoshikawa AM, Rangel AE, Zheng L, Wan L, Hein LA, Hariri AA, Eisenstein M, Soh HT. A massively parallel screening platform for converting aptamers into molecular switches. Nat Commun 2023; 14:2336. [PMID: 37095144 PMCID: PMC10126150 DOI: 10.1038/s41467-023-38105-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 04/14/2023] [Indexed: 04/26/2023] Open
Abstract
Aptamer-based molecular switches that undergo a binding-induced conformational change have proven valuable for a wide range of applications, such as imaging metabolites in cells, targeted drug delivery, and real-time detection of biomolecules. Since conventional aptamer selection methods do not typically produce aptamers with inherent structure-switching functionality, the aptamers must be converted to molecular switches in a post-selection process. Efforts to engineer such aptamer switches often use rational design approaches based on in silico secondary structure predictions. Unfortunately, existing software cannot accurately model three-dimensional oligonucleotide structures or non-canonical base-pairing, limiting the ability to identify appropriate sequence elements for targeted modification. Here, we describe a massively parallel screening-based strategy that enables the conversion of virtually any aptamer into a molecular switch without requiring any prior knowledge of aptamer structure. Using this approach, we generate multiple switches from a previously published ATP aptamer as well as a newly-selected boronic acid base-modified aptamer for glucose, which respectively undergo signal-on and signal-off switching upon binding their molecular targets with second-scale kinetics. Notably, our glucose-responsive switch achieves ~30-fold greater sensitivity than a previously-reported natural DNA-based switch. We believe our approach could offer a generalizable strategy for producing target-specific switches from a wide range of aptamers.
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Affiliation(s)
- Alex M Yoshikawa
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
| | | | - Liwei Zheng
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA
| | - Leighton Wan
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Linus A Hein
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Amani A Hariri
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA
| | - Michael Eisenstein
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - H Tom Soh
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA.
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
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Moutsiopoulou A, Broyles D, Dikici E, Daunert S, Deo SK. Molecular Aptamer Beacons and Their Applications in Sensing, Imaging, and Diagnostics. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1902248. [PMID: 31313884 PMCID: PMC6715520 DOI: 10.1002/smll.201902248] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 05/31/2019] [Indexed: 05/07/2023]
Abstract
The ability to monitor types, concentrations, and activities of different biomolecules is essential to obtain information about the molecular processes within cells. Successful monitoring requires a sensitive and selective tool that can respond to these molecular changes. Molecular aptamer beacon (MAB) is a molecular imaging and detection tool that enables visualization of small or large molecules by combining the selectivity and sensitivity of molecular beacon and aptamer technologies. MAB design leverages structure switching and specific recognition to yield an optical on/off switch in the presence of the target. Various donor-quencher pairs such as fluorescent dyes, quantum dots, carbon-based materials, and metallic nanoparticles have been employed in the design of MABs. In this work, the diverse biomedical applications of MAB technology are focused on. Different conjugation strategies for the energy donor-acceptor pairs are addressed, and the overall sensitivities of each detection system are discussed. The future potential of this technology in the fields of biomedical research and diagnostics is also highlighted.
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Affiliation(s)
- Angeliki Moutsiopoulou
- Leonard M. Miller School of Medicine, Department of Biochemistry and Molecular Biology, University of Miami, Miami, FL, 33136, USA
- Dr. J. T. Macdonald Foundation Biomedical Nanotechnology Institute, University of Miami, Miami, FL, 33136, USA
- Department of Chemistry Coral Gables, University of Miami, FL, 33146, USA
| | - David Broyles
- Leonard M. Miller School of Medicine, Department of Biochemistry and Molecular Biology, University of Miami, Miami, FL, 33136, USA
- Dr. J. T. Macdonald Foundation Biomedical Nanotechnology Institute, University of Miami, Miami, FL, 33136, USA
| | - Emre Dikici
- Leonard M. Miller School of Medicine, Department of Biochemistry and Molecular Biology, University of Miami, Miami, FL, 33136, USA
- Dr. J. T. Macdonald Foundation Biomedical Nanotechnology Institute, University of Miami, Miami, FL, 33136, USA
| | - Sylvia Daunert
- Leonard M. Miller School of Medicine, Department of Biochemistry and Molecular Biology, University of Miami, Miami, FL, 33136, USA
- Dr. J. T. Macdonald Foundation Biomedical Nanotechnology Institute, University of Miami, Miami, FL, 33136, USA
- University of Miami Clinical and Translational Science Institute, Miami, FL, 33136, USA
| | - Sapna K Deo
- Leonard M. Miller School of Medicine, Department of Biochemistry and Molecular Biology, University of Miami, Miami, FL, 33136, USA
- Dr. J. T. Macdonald Foundation Biomedical Nanotechnology Institute, University of Miami, Miami, FL, 33136, USA
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Hu J, Xiao K, Jin B, Zheng X, Ji F, Bai D. Paper-based point-of-care test with xeno nucleic acid probes. Biotechnol Bioeng 2019; 116:2764-2777. [PMID: 31282991 DOI: 10.1002/bit.27106] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 06/20/2019] [Accepted: 06/24/2019] [Indexed: 01/09/2023]
Abstract
Bridging the unmet need of efficient point-of-care testing (POCT) in biomedical engineering research and practice with the emerging development in artificial synthetic xeno nucleic acids (XNAs), this review summarized the recent development in paper-based POCT using XNAs as sensing probes. Alongside the signal transducing mode and immobilization methods of XNA probes, a detailed evaluation of probe performance was disclosed. With these new aspects, both researchers in synthetic chemistry / biomedical engineering and physicians in clinical practice could gain new insights in designing, manufacturing and choosing suitable reagents and techniques for POCT.
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Affiliation(s)
- Jie Hu
- Singapore Institute of Manufacturing Technology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Kang Xiao
- Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, P. R. China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, P. R. China
| | - Birui Jin
- School of Materials and Chemical Engineering, Xi'an Technological University, Xi'an, P. R. China
| | - Xuyang Zheng
- Department of Infectious Diseases, Tangdu Hospital, The Fourth Military Medical University, Xi'an, Shaanxi, P. R. China
| | - Fanpu Ji
- Department of Infectious Diseases, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Dan Bai
- Xi'an Institute of Flexible Electronics (IFE) & Xi'an Key Laboratory of Flexible Electronics (KLoFE), MIIT Key Laboratory of Flexible Electronics (KLoFE), Shaanxi Key Laboratory of Flexible Electronics (KLoFE), Northwestern Polytechnical University (NPU), Xi'an, Shaanxi, P. R. China.,Xi'an Institute of Biomedical Materials and Engineering (IBME) & Xi'an Key Laboratory of Biomedical Materials and Engineering (KLBME), Northwestern Polytechnical University (NPU), Xi'an, Shaanxi, P. R. China
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Tachallait H, Safir Filho M, Marzag H, Bougrin K, Demange L, Martin AR, Benhida R. A straightforward and versatile FeCl3 catalyzed Friedel–Crafts C-glycosylation process. Application to the synthesis of new functionalized C-nucleosides. NEW J CHEM 2019. [DOI: 10.1039/c8nj06300a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Rapid and straightforward access to C-nucleosides using an inexpensive FeCl3 catalyst.
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Affiliation(s)
- Hamza Tachallait
- Laboratoire de Chimie des Plantes et de Synthèse Organique et Bioorganique
- URAC23
- Faculté des Sciences
- 1014 Rabat
- Morocco
| | - Mauro Safir Filho
- Université Côte d’Azur
- CNRS
- Institut de Chimie de Nice UMR 7272
- 06108 Nice
- France
| | - Hamid Marzag
- Université Côte d’Azur
- CNRS
- Institut de Chimie de Nice UMR 7272
- 06108 Nice
- France
| | - Khalid Bougrin
- Laboratoire de Chimie des Plantes et de Synthèse Organique et Bioorganique
- URAC23
- Faculté des Sciences
- 1014 Rabat
- Morocco
| | - Luc Demange
- Université Côte d’Azur
- CNRS
- Institut de Chimie de Nice UMR 7272
- 06108 Nice
- France
| | - Anthony R. Martin
- Université Côte d’Azur
- CNRS
- Institut de Chimie de Nice UMR 7272
- 06108 Nice
- France
| | - Rachid Benhida
- Université Côte d’Azur
- CNRS
- Institut de Chimie de Nice UMR 7272
- 06108 Nice
- France
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Zhang H, Li F, Dever B, Li XF, Le XC. DNA-mediated homogeneous binding assays for nucleic acids and proteins. Chem Rev 2012; 113:2812-41. [PMID: 23231477 DOI: 10.1021/cr300340p] [Citation(s) in RCA: 339] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Hongquan Zhang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
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Hong H, Goel S, Zhang Y, Cai W. Molecular imaging with nucleic acid aptamers. Curr Med Chem 2012; 18:4195-205. [PMID: 21838686 DOI: 10.2174/092986711797189691] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Revised: 06/22/2011] [Accepted: 06/22/2011] [Indexed: 01/16/2023]
Abstract
With many desirable properties such as ease of synthesis, small size, lack of immunogenicity, and versatile chemistry, aptamers represent a class of targeting ligands that possess tremendous potential in molecular imaging applications. Non-invasive imaging of various disease markers with aptamer-based probes has many potential clinical applications such as lesion detection, patient stratification, treatment monitoring, etc. In this review, we will summarize the current status of molecular imaging with aptamer-based probes. First, fluorescence imaging will be described which include both direct targeting and activatable probes. Next, we discuss molecular magnetic resonance imaging and targeted ultrasound investigations using aptamer-based agents. Radionuclide-based imaging techniques (single-photon emission computed tomography and positron emission tomography) will be summarized as well. In addition, aptamers have also been labeled with various tags for computed tomography, surface plasmon resonance, dark-field light scattering microscopy, transmission electron microscopy, and surface-enhanced Raman spectroscopy imaging. Among all molecular imaging modalities, no single modality is perfect and sufficient to obtain all the necessary information for a particular question. Thus, a multimodality probe has also been constructed for concurrent fluorescence, gamma camera, and magnetic resonance imaging in vivo. Although the future of aptamer-based molecular imaging is becoming increasingly bright and many proof-of-principle studies have already been reported, much future effort needs to be directed towards the development of clinically translatable aptamer-based imaging agents which will eventually benefit patients.
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Affiliation(s)
- H Hong
- Department of Radiology, University of Wisconsin-Madison, 1111 Highland Ave, Madison, WI 53705-2275, USA
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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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Zhou J, Battig MR, Wang Y. Aptamer-based molecular recognition for biosensor development. Anal Bioanal Chem 2010; 398:2471-80. [PMID: 20644915 DOI: 10.1007/s00216-010-3987-y] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Revised: 06/21/2010] [Accepted: 06/29/2010] [Indexed: 11/30/2022]
Abstract
Nucleic acid aptamers are an emerging class of synthetic ligands and have recently attracted significant attention in numerous fields. One is in biosensor development. In principle, nucleic acid aptamers can be discovered to recognize any molecule of interest with high affinity and specificity. In addition, unlike most ligands evolved in nature, synthetic nucleic acid aptamers are usually tolerant of harsh chemical, physical, and biological conditions. These distinguished characteristics make aptamers attractive molecular recognition ligands for biosensing applications. This review first concisely introduces methods for aptamer discovery including upstream selection and downstream truncation, then discusses aptamer-based biosensor development from the viewpoint of signal production.
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Affiliation(s)
- Jing Zhou
- Department of Chemical, Materials and Biomolecular Engineering, University of Connecticut, 191 Auditorium Road, Storrs, CT 06269-3222, USA
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