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Johnson RE, Murray MT, Roby DJ, Bycraft LJ, Churcher ZR, Yadav S, Johnson PE, Wetmore SD, Manderville RA. Unlocking Pb 2+ Sensing Potential in a DNA G-Quadruplex via Loop Modification with Fluorescent Chalcone Surrogates. ACS Sens 2023; 8:4756-4764. [PMID: 38063049 DOI: 10.1021/acssensors.3c01866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
The ability of guanine (G)-rich DNA to bind toxic lead (Pb2+) ions within a G-quadruplex (GQ) motif is a leading DNA biosensor strategy. A major analytical hurdle for GQ detection of Pb2+ is competitive GQ templating by potassium (K+) ions. We employ the on-strand DNA synthesis of internal fluorescent chalcone surrogates within the 15-mer thrombin binding aptamer (TBA15) to address this challenge. Replacement of thymidine at the 3-position (T3) within TBA15 with an indole-4-hydroxy-indanone (Ind4HI) chalcone strongly decreases K+-GQ stability while enhancing Pb2+-GQ stability to increase Pb2+ binding specificity. The new T3-Ind4HI probe exhibits a 15-fold increase in fluorescence intensity upon binding of Pb2+ by the modified TBA15 and can detect 6.4 nM Pb2+ in the presence of 10 mM K+. Thus, replacement of the T3 residue of TBA15 with the new Ind4HI probe modulates metal ion affinity by native TBA15 to solve the analytical challenge posed by K+ in real water samples for detecting Pb2+ to meet regulatory guidelines by using a GQ biosensor.
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Affiliation(s)
- Ryan E Johnson
- Departments of Chemistry and Toxicology, University of Guelph, Guelph N1G 2W1, Ontario, Canada
| | - Makay T Murray
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge T1K 3M4, Alberta, Canada
| | - Dylan J Roby
- Departments of Chemistry and Toxicology, University of Guelph, Guelph N1G 2W1, Ontario, Canada
| | - Lucas J Bycraft
- Departments of Chemistry and Toxicology, University of Guelph, Guelph N1G 2W1, Ontario, Canada
| | - Zachary R Churcher
- Department of Chemistry, York University, Toronto M3J 1P3, Ontario, Canada
| | - Saanya Yadav
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge T1K 3M4, Alberta, Canada
| | - Philip E Johnson
- Department of Chemistry, York University, Toronto M3J 1P3, Ontario, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge T1K 3M4, Alberta, Canada
| | - Richard A Manderville
- Departments of Chemistry and Toxicology, University of Guelph, Guelph N1G 2W1, Ontario, Canada
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Zhu T, Loyez M, Chah K, Caucheteur C. Gold-coated tilted fiber Bragg gratings for lead ion sensing. OPTICS EXPRESS 2023; 31:32478-32487. [PMID: 37859050 DOI: 10.1364/oe.498571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 07/31/2023] [Indexed: 10/21/2023]
Abstract
Surface plasmon resonance sensor based on gold-coated tilted fiber Bragg gratings (SPR-TFBGs) are perfectly suited for fine refractometry. Thanks to the functionalization of the gold layer, they can be used for label-free biosensing. They have been largely used for the specific detection of proteins and cells. In this work, we experimentally demonstrate that they are enough sensitive to detect a very small entity like an environmental pollutant. In this context, we report here a bio-functionalization of the SPR-TFBG with thrombin aptamers for lead ion detection. We used aqueous solutions of lead ions with increasing concentrations from 0.001 ppb to 10 ppb. Based on the affinity bending of Pb2+ ions to the thrombin aptamer, we experimentally demonstrated low detection level of lead ion concentration (0.001 ppb) while the saturation limit is meanly fixed by the physical dimension of the sensor and the binding efficiency.
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Alfinito E. TBA for Sensing Toxic Cations: A Critical Analysis of Structural and Electrical Properties. Int J Mol Sci 2023; 24:14492. [PMID: 37833940 PMCID: PMC10572628 DOI: 10.3390/ijms241914492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/19/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
Food and drinks can be contaminated with pollutants such as lead and strontium, which poses a serious danger to human health. For this reason, a number of effective sensors have been developed for the rapid and highly selective detection of such contaminants. TBA, a well-known aptamer developed to selectively target and thereby inhibit the protein of clinical interest α-thrombin, is receiving increasing attention for sensing applications, particularly for the sensing of different cations. Indeed, TBA, in the presence of these cations, folds into the stable G-quadruplex structure. Furthermore, different cations produce small but significant changes in this structure that result in changes in the electrical responses that TBA can produce. In this article, we give an overview of the expected data regarding the use of TBA in the detection of lead and strontium, calculating the expected electrical response using different measurement techniques. Finally, we conclude that TBA should be able to detect strontium with a sensitivity approximately double that achievable for lead.
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Affiliation(s)
- Eleonora Alfinito
- Dipartimento di Matematica e Fisica 'Ennio De Giorgi', Università del Salento, I-73100 Lecce, Italy
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Demers SME, Kuhne WW, Swindle AR, Dick DD, Coopersmith KJ. Quantum Dot-DNA FRET Conjugates for Direct Analysis of Methylphosphonic Acid in Complex Media. ACS OMEGA 2023; 8:23017-23023. [PMID: 37396263 PMCID: PMC10308513 DOI: 10.1021/acsomega.3c02173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/22/2023] [Indexed: 07/04/2023]
Abstract
Rapid detection of nerve agents from complex matrices with minimal sample preparation is essential due to their high toxicity and bioavailability. In this work, quantum dots (QDs) were functionalized with oligonucleotide aptamers that specifically targeted a nerve agent metabolite, methylphosphonic acid (MePA). These QD-DNA bioconjugates were covalently linked to quencher molecules to form Förster resonance energy transfer (FRET) donor-acceptor pairs that quantitatively measure the presence of MePA. Using the FRET biosensor, the MePA limit of detection was 743 nM in artificial urine. A decrease in the QD lifetime was measured upon DNA binding and was recovered with MePA. The biosensor's flexible design makes it a strong candidate for the rapid detection of chemical and biological agents for deployable, in-field detectors.
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Mathivanan J, Liu H, Gan J, Chandrasekaran AR, Sheng J. Fluorescent Aptaswitch for Detection of Lead Ions. ACS APPLIED BIO MATERIALS 2022; 5:5089-5093. [PMID: 35652916 DOI: 10.1021/acsabm.2c00368] [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: 01/25/2023]
Abstract
Detection of metal ions has essential roles in biology, food industry, and environmental sciences. In this work, we developed a Pb2+ detection strategy based on a fluorophore-tagged Pb2+-binding aptamer. The DNA aptamer changes its conformation on binding Pb2+, switching from an "off" state (low fluorescence) to an "on" state (high fluorescence). This method provides a quantitative readout with a detection limit of 468 nM, is highly specific to Pb2+ when tested against other metal ions, and is functional in complex biofluids. Such metal sensing DNA aptamers could be coupled with other biomolecules for sense-and-actuate mechanisms in biomedical and environmental applications.
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Affiliation(s)
- Johnsi Mathivanan
- Department of Chemistry, University of Albany, State University of New York, Albany, New York 12222, United States.,The RNA Institute, University of Albany, State University of New York, Albany, New York 12222, United States
| | - Hehua Liu
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, P. R. China
| | - Jianhua Gan
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, P. R. China
| | - Arun Richard Chandrasekaran
- The RNA Institute, University of Albany, State University of New York, Albany, New York 12222, United States
| | - Jia Sheng
- Department of Chemistry, University of Albany, State University of New York, Albany, New York 12222, United States.,The RNA Institute, University of Albany, State University of New York, Albany, New York 12222, United States
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R O'Steen M, M Kolpashchikov D. A self-assembling split aptamer multiplex assay for SARS-COVID19 and miniaturization of a malachite green DNA-based aptamer. SENSORS AND ACTUATORS REPORTS 2022; 4:100125. [PMID: 36373144 PMCID: PMC9635949 DOI: 10.1016/j.snr.2022.100125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 09/30/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
Multiplex assays often rely on expensive sensors incorporating covalently linked fluorescent dyes. Herein, we developed a self-assembling aptamer-based multiplex assay. This multiplex approach utilizes a previously established split aptamer sensor in conjugation with a novel split aptamer sensor based upon a malachite green DNA aptamer. This system was capable of simultaneous fluorescent detection of two SARS COVID-19-related sequences in one sample with individual sensors that possesses a limit of detection (LOD) in the low nM range. Optimization of the Split Malachite Green (SMG) sensor yielded a minimized aptamer construct, Mini-MG, capable of inducing fluorescence of malachite green in both a DNA hairpin and sensor format.
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Affiliation(s)
- Martin R O'Steen
- Chemistry Department, University of Central Florida, Orlando, FL, USA
| | - Dmitry M Kolpashchikov
- Chemistry Department, University of Central Florida, Orlando, FL, USA
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, USA
- National Center for Forensic Science, University of Central Florida, Orlando, FL, USA
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