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Osman EA, Rynes TP, Wang YL, Mruk K, McKeague M. Non-invasive single cell aptasensing in live cells and animals. Chem Sci 2024; 15:4770-4778. [PMID: 38550682 PMCID: PMC10967030 DOI: 10.1039/d3sc05735f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 02/18/2024] [Indexed: 04/04/2024] Open
Abstract
We report a genetically encoded aptamer biosensor platform for non-invasive measurement of drug distribution in cells and animals. We combined the high specificity of aptamer molecular recognition with the easy-to-detect properties of fluorescent proteins. We generated six encoded aptasensors, showcasing the platform versatility. The biosensors display high sensitivity and specificity for detecting their specific drug target over related analogs. We show dose dependent response of biosensor performance reaching saturating drug uptake levels in individual live cells. We designed our platform for integration into animal genomes; thus, we incorporated aptamer biosensors into zebrafish, an important model vertebrate. The biosensors enabled non-invasive drug biodistribution imaging in whole animals across different timepoints. To our knowledge, this is the first example of an aptamer biosensor-expressing transgenic vertebrate that is carried through generations. As such, our encoded platform addresses the need for non-invasive whole animal biosensing ideal for pharmacokinetic-pharmacodynamic analyses that can be expanded to other organisms and to detect diverse molecules of interest.
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Affiliation(s)
- Eiman A Osman
- Department of Chemistry, Faculty of Science, McGill University Montreal QC H3A 0B8 Canada
| | - Thomas P Rynes
- Department of Pharmacology and Toxicology, Brody School of Medicine, East Carolina University Greenville NC 27834 USA
| | - Y Lucia Wang
- Pharmacology and Therapeutics, Faculty of Medicine and Health Sciences, McGill University Montreal QC H3G 1Y6 Canada
| | - Karen Mruk
- Department of Pharmacology and Toxicology, Brody School of Medicine, East Carolina University Greenville NC 27834 USA
| | - Maureen McKeague
- Department of Chemistry, Faculty of Science, McGill University Montreal QC H3A 0B8 Canada
- Pharmacology and Therapeutics, Faculty of Medicine and Health Sciences, McGill University Montreal QC H3G 1Y6 Canada
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Saftics A, Kurunczi S, Peter B, Szekacs I, Ramsden JJ, Horvath R. Data evaluation for surface-sensitive label-free methods to obtain real-time kinetic and structural information of thin films: A practical review with related software packages. Adv Colloid Interface Sci 2021; 294:102431. [PMID: 34330074 DOI: 10.1016/j.cis.2021.102431] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 04/16/2021] [Accepted: 04/18/2021] [Indexed: 02/07/2023]
Abstract
Interfacial layers are important in a wide range of applications in biomedicine, biosensing, analytical chemistry and the maritime industries. Given the growing number of applications, analysis of such layers and understanding their behavior is becoming crucial. Label-free surface sensitive methods are excellent for monitoring the formation kinetics, structure and its evolution of thin layers, even at the nanoscale. In this paper, we review existing and commercially available label-free techniques and demonstrate how the experimentally obtained data can be utilized to extract kinetic and structural information during and after formation, and any subsequent adsorption/desorption processes. We outline techniques, some traditional and some novel, based on the principles of optical and mechanical transduction. Our special focus is the current possibilities of combining label-free methods, which is a powerful approach to extend the range of detected and deduced parameters. We summarize the most important theoretical considerations for obtaining reliable information from measurements taking place in liquid environments and, hence, with layers in a hydrated state. A thorough treamtmaent of the various kinetic and structural quantities obtained from evaluation of the raw label-free data are provided. Such quantities include layer thickness, refractive index, optical anisotropy (and molecular orientation derived therefrom), degree of hydration, viscoelasticity, as well as association and dissociation rate constants and occupied area of subsequently adsorbed species. To demonstrate the effect of variations in model conditions on the observed data, simulations of kinetic curves at various model settings are also included. Based on our own extensive experience with optical waveguide lightmode spectroscopy (OWLS) and the quartz crystal microbalance (QCM), we have developed dedicated software packages for data analysis, which are made available to the scientific community alongside this paper.
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Huang S, Chen R, Zhao S, Wang C, Jia Q, Wang M, Zhang Z, He L, Zhang Z. Diverse metal ions-doped titanium-based metal-organic frameworks as novel bioplatforms for sensitively detecting bisphenol A. Electrochim Acta 2021. [DOI: 10.1016/j.electacta.2021.138403] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Lee W, Han K. Constructive Prediction of Potential RNA Aptamers for a Protein Target. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020; 17:1476-1482. [PMID: 31689200 DOI: 10.1109/tcbb.2019.2951114] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Aptamers are short single-stranded nucleic acids that bind to target molecules with high affinity and selectivity. Aptamers are generally identified in vitro by performing SELEX (systematic evolution of ligands by exponential enrichment). Complementing the SELEX process, several computational methods have been proposed in the search for aptamers. However, many of these methods cannot be applied for finding new aptamers, either because they are classifiers for determining whether an RNA and protein interact with each other, or because they are limited to a specific target only. Hence, we developed a new random forest (RF) model for finding potential RNA aptamers for a protein target. From an extensive analysis of protein-RNA complexes including RNA aptamers-protein complexes, we identified key features of interacting RNA and protein molecules, and structural constraints on RNA aptamers. The potential RNA aptamers predicted by our method reveal similar secondary and protein-binding structures as the actual RNA aptamers. The RF model showed a reliable performance in both cross validations and independent testing. The key features of interacting RNA and protein molecules and the structural constraints identified in our study were effective in finding potential aptamers for a protein target. Although preliminary, our results are promising, and we believe this approach will be useful in reducing time and money spent on in vitro experiments by substantially limiting the size of the initial pool of nucleic acid sequences.
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Xue CS, Erika G, Jiří H. Surface plasmon resonance biosensor for the ultrasensitive detection of bisphenol A. Anal Bioanal Chem 2019; 411:5655-5658. [DOI: 10.1007/s00216-019-01996-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/15/2019] [Accepted: 06/19/2019] [Indexed: 02/04/2023]
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Zhou C, Yu Z, Yu W, Liu H, Zhang H, Guo C. Split aptamer-based detection of adenosine triphosphate using surface enhanced Raman spectroscopy and two kinds of gold nanoparticles. Mikrochim Acta 2019; 186:251. [PMID: 30895481 DOI: 10.1007/s00604-019-3356-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 02/02/2019] [Indexed: 12/17/2022]
Abstract
An ultrasensitive and highly selective method is described for the determination of adenosine triphosphate (ATP) via surface-enhanced Raman scattering (SERS). Two split aptamers are used for specific recognition of ATP. They were attached to two SERS substrates. The first was placed on a nanolayer of gold nanoparticle-decorated graphene oxide (GO/Au3), and the other on gold nanoparticles (Au2). When ATP is introduced, it will interact with the split aptamers on the gold nanostructures to form a sandwich structure that brings the GO/Au3 nanolayer and the Au2 nanoparticle in close proximity. Consequently, the SERS signal, best measured at 1072 cm-1, is strongly enhanced. The sandwich structure also displays good water solubility and stability. Under optimized conditions, the SERS signal increases in the 10 pM - 10 nM ATP concentration range, and the limit of detection (LOD) is 0.85 pM. The method was applied to the determination of ATP in spiked human serum, and the LODs in serum and buffer are comparable. In our perception, the method has a wide scope in that numerous other aptamers may be used. This may result in a variety of other highly sensitive aptasensors for use in in-vitro diagnostics. Graphical abstract Schematic presentation of a self-assembly sandwich nanostructure as unique SERS assay platform for the sensitive detection of ATP.
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Affiliation(s)
- Chunyang Zhou
- The Guo China-US Photonics Laboratory, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, Jilin, 130033, People's Republic of China.
| | - Zhi Yu
- The Guo China-US Photonics Laboratory, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, Jilin, 130033, People's Republic of China
| | - Weili Yu
- The Guo China-US Photonics Laboratory, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, Jilin, 130033, People's Republic of China
| | - Huiwen Liu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, People's Republic of China
| | - Hao Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, People's Republic of China
| | - Chunlei Guo
- The Guo China-US Photonics Laboratory, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, Jilin, 130033, People's Republic of China. .,The Institute of Optics, University of Rochester, Rochester, New York, 14627, USA.
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Peltomaa R, Glahn-Martínez B, Benito-Peña E, Moreno-Bondi MC. Optical Biosensors for Label-Free Detection of Small Molecules. SENSORS (BASEL, SWITZERLAND) 2018; 18:E4126. [PMID: 30477248 PMCID: PMC6308632 DOI: 10.3390/s18124126] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 11/20/2018] [Accepted: 11/21/2018] [Indexed: 12/12/2022]
Abstract
Label-free optical biosensors are an intriguing option for the analyses of many analytes, as they offer several advantages such as high sensitivity, direct and real-time measurement in addition to multiplexing capabilities. However, development of label-free optical biosensors for small molecules can be challenging as most of them are not naturally chromogenic or fluorescent, and in some cases, the sensor response is related to the size of the analyte. To overcome some of the limitations associated with the analysis of biologically, pharmacologically, or environmentally relevant compounds of low molecular weight, recent advances in the field have improved the detection of these analytes using outstanding methodology, instrumentation, recognition elements, or immobilization strategies. In this review, we aim to introduce some of the latest developments in the field of label-free optical biosensors with the focus on applications with novel innovations to overcome the challenges related to small molecule detection. Optical label-free methods with different transduction schemes, including evanescent wave and optical fiber sensors, surface plasmon resonance, surface-enhanced Raman spectroscopy, and interferometry, using various biorecognition elements, such as antibodies, aptamers, enzymes, and bioinspired molecularly imprinted polymers, are reviewed.
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Affiliation(s)
- Riikka Peltomaa
- Departamento de Química Analítica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain.
| | - Bettina Glahn-Martínez
- Departamento de Química Analítica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain.
| | - Elena Benito-Peña
- Departamento de Química Analítica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain.
| | - María C Moreno-Bondi
- Departamento de Química Analítica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain.
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Abnous K, Danesh NM, Ramezani M, Alibolandi M, Taghdisi SM. A novel electrochemical sensor for bisphenol A detection based on nontarget-induced extension of aptamer length and formation of a physical barrier. Biosens Bioelectron 2018; 119:204-208. [DOI: 10.1016/j.bios.2018.08.024] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 08/10/2018] [Accepted: 08/10/2018] [Indexed: 12/20/2022]
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