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Rainot A, D'Anna L, Terenzi A, Rouget R, Grandemange S, Piro B, Barone G, Barbault F, Monari A. In Silico Design of a Solution-Gated Graphene Transistor Sensor for the Efficient Detection of Guanine Quadruplexes. J Phys Chem Lett 2024; 15:10881-10887. [PMID: 39441974 DOI: 10.1021/acs.jpclett.4c02796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2024]
Abstract
Guanine quadruplexes (G4s) are nucleic acid structures present in diverse regions of the genome, such as telomeres and transcription initiators. Recently, the different biological roles of G4s have been evidenced as well as their role as biomarkers for tumors or viral infections. However, the fast and efficient detection of G4s in complex matrices remains elusive. In this contribution, by using long-scale molecular dynamics simulations, we propose the design of a biosensor based on organic field-effect transistors recognizing G4s. In particular, we show that the interaction of the G4s with the biosensor is translated into a change in the charge density profile, which correlates with the electrical transduction of the signal, thus allowing the detection of the nucleic acid structure. We also provide rules of thumb for the optimization of the design of the device and more generally for the integration of computationally driven design approaches.
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Affiliation(s)
- Aurianne Rainot
- Université Paris Cité, CNRS, ITODYS, F-75013 Paris, France
- Università degli Studi di Palermo, Department of Biological, Chemical and Pharmaceutical Sciences and Technologies Viale delle Scienze, Edificio 17, 90128 Palermo, Italy
| | - Luisa D'Anna
- Università degli Studi di Palermo, Department of Biological, Chemical and Pharmaceutical Sciences and Technologies Viale delle Scienze, Edificio 17, 90128 Palermo, Italy
| | - Alessio Terenzi
- Università degli Studi di Palermo, Department of Biological, Chemical and Pharmaceutical Sciences and Technologies Viale delle Scienze, Edificio 17, 90128 Palermo, Italy
| | - Raphael Rouget
- Université de Lorraine and CNRS, UMR 7039 CRAN, F-54000 Nancy, France
| | | | - Benoit Piro
- Université Paris Cité, CNRS, ITODYS, F-75013 Paris, France
| | - Giampaolo Barone
- Università degli Studi di Palermo, Department of Biological, Chemical and Pharmaceutical Sciences and Technologies Viale delle Scienze, Edificio 17, 90128 Palermo, Italy
| | | | - Antonio Monari
- Université Paris Cité, CNRS, ITODYS, F-75013 Paris, France
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2
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Wang YP, Eriksson LA, Zhang RB. Mechanism of Dual-Site Recognition in a Classic DNA Aptamer. J Chem Inf Model 2024; 64:7698-7708. [PMID: 39327929 PMCID: PMC11481096 DOI: 10.1021/acs.jcim.4c01389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Revised: 09/09/2024] [Accepted: 09/19/2024] [Indexed: 09/28/2024]
Abstract
Nucleic acid aptamers possess unique advantages in specific recognition. However, the lack of in-depth investigation into their dynamic recognition mechanisms has restricted their rational design and potential applications in fields such as biosensing and targeted therapy. We herein utilized enhanced sampling molecular dynamics to address affinities of adenosine monophosphate (AMP) to the dual binding sites in the DNA aptamer, focusing on the dynamic recognition mechanism and pathways. The present results indicate that in addition to the widely known intermolecular interactions, inequivalence of chemical environments of the two binding sites leads to slightly higher stability of AMP binding to the site proximal to the aptamer terminus. In the presence of two AMPs captured by the two sites, each binding free energy is enhanced. In particular, an additional hydrogen bond of AMP to A10 is introduced in the dual-site binding complex, which increases the binding energy from -4.25 ± 0.47 to -9.48 ± 0.33 kcal mol-1 in the site close to the loop. For the dual-site recognition process, the free energy landscape and minimum free energy pathway calculations elucidate the crucial role of electrostatic interactions between the AMP phosphate groups and Na+ ions in positively cooperative binding mechanisms.
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Affiliation(s)
- Yun-Peng Wang
- School
of Chemistry and Chemical Engineering, Beijing
Institute of Technology, South Street No. 5, Zhongguancun, Haidian District, Beijing 100081, China
| | - Leif A. Eriksson
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Medicinaregatan
7b, Göteborg 405
30, Sweden
| | - Ru-Bo Zhang
- School
of Chemistry and Chemical Engineering, Beijing
Institute of Technology, South Street No. 5, Zhongguancun, Haidian District, Beijing 100081, China
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Zaw O, Noon Shean Aye N, Daduang J, Proungvitaya S, Wongwattanakul M, Ngernyuang N, Daduang S, Shinsuphan N, Phatthanakun R, Jearanaikoon N, Maraming P. DNA aptamer-functionalized PDA nanoparticles: from colloidal chemistry to biosensor applications. Front Bioeng Biotechnol 2024; 12:1427229. [PMID: 39045538 PMCID: PMC11263086 DOI: 10.3389/fbioe.2024.1427229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Accepted: 06/12/2024] [Indexed: 07/25/2024] Open
Abstract
Polydopamine nanoparticles (PDA NPs) are widely utilized in the field of biomedical science for surface functionalization because of their unique characteristics, such as simple and low-cost preparation methods, good adhesive properties, and ability to incorporate amine and oxygen-rich chemical groups. However, challenges in the application of PDA NPs as surface coatings on electrode surfaces and in conjugation with biomolecules for electrochemical sensors still exist. In this work, we aimed to develop an electrochemical interface based on PDA NPs conjugated with a DNA aptamer for the detection of glycated albumin (GA) and to study DNA aptamers on the surfaces of PDA NPs to understand the aptamer-PDA surface interactions using molecular dynamics (MD) simulation. PDA NPs were synthesized by the oxidation of dopamine in Tris buffer at pH 10.5, conjugated with DNA aptamers specific to GA at different concentrations (0.05, 0.5, and 5 μM), and deposited on screen-printed carbon electrodes (SPCEs). The charge transfer resistance of the PDA NP-coated SPCEs decreased, indicating that the PDA NP composite is a conductive bioorganic material. Transmission electron microscopy (TEM) and scanning electron microscopy (SEM) confirmed that the PDA NPs were spherical, and dynamic light scattering (DLS), Fourier transform infrared spectroscopy (FTIR), and Raman spectroscopy data indicated the successful conjugation of the aptamers on the PDA NPs. The as-prepared electrochemical interface was employed for the detection of GA. The detection limit was 0.17 μg/mL. For MD simulation, anti-GA aptamer through the 5'terminal end in a single-stranded DNA-aptamer structure and NH2 linker showed a stable structure with its axis perpendicular to the PDA surface. These findings provide insights into improved biosensor design and have demonstrated the potential for employing electrochemical PDA NP interfaces in point-of-care applications.
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Affiliation(s)
- Ohnmar Zaw
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Nang Noon Shean Aye
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Jureerut Daduang
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Siriporn Proungvitaya
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Molin Wongwattanakul
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
- Center for Innovation and Standard for Medical Technology and Physical Therapy, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Nipaporn Ngernyuang
- Chulabhorn International College of Medicine, Thammasat University, Pathum Thani, Thailand
- Thammasat University Research Unit in Biomedical Science, Thammasat University, Pathum Thani, Thailand
| | - Sakda Daduang
- Division of Pharmacognosy and Toxicology, Faculty of Pharmaceutical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Nikorn Shinsuphan
- Medical Instrument Subsection, Maintenance Section, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | | | - Nichada Jearanaikoon
- Synchrotron Light Research Institute (Public Organization), Nakhon Ratchasima, Thailand
| | - Pornsuda Maraming
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
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Ritz AJ, Stuehr OM, Comer DN, Lazenby RA. Controlling Gold Morphology Using Electrodeposition for the Preparation of Electrochemical Aptamer-Based Sensors. ACS APPLIED BIO MATERIALS 2024; 7:1925-1935. [PMID: 38369768 DOI: 10.1021/acsabm.3c01254] [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: 02/20/2024]
Abstract
Nanostructuring of gold surfaces to enhance electroactive surface area has proven to significantly enhance the performance of electrochemical aptamer-based (E-AB) sensors, particularly for electrodes on the microscale. Unlike for sensors fabricated on polished gold surfaces, predicting the behavior of E-AB sensors on surfaces with varied gold morphologies becomes more intricate due to the effects of surface roughness and the shapes and sizes of surface features on supporting a self-assembled monolayer. In this study, we explored the impact of gold morphology characteristics on sensor performance, evaluating parameters such as signal change in response to the addition of the target analyte, aptamer probe packing density, and continuous sensing ability. Our findings reveal that surface area enhancement can either enhance or diminish sensor performance for gold nanostructured E-AB sensors, contingent upon the surface morphology. In particular, our results indicate that the aptamer packing density and target analyte signal change results are heavily dependent on gold nanostructure size and features. Sensing surfaces with larger nanoparticle diameters, which were prepared using electrodeposition at a constant potential, had a reduced aptamer packing density and exhibited diminished sensor performance. However, the equivalent packing density of polished electrodes did not yield the equivalent signal change. Other surfaces that were prepared using pulsed waveform electrodeposition achieved optimal signal change with a deposition time, tdep, of 120 s, and increased deposition time with enhanced electroactive surface area resulted in minimized signal changes and more rapid sensor degradation. By investigating sensing surfaces with varied morphologies, we have demonstrated that enhancing the electroactive surface does not always enhance the signal change of the sensor, and aptamer packing density alone does not dictate observed signal change trends. We anticipate that understanding how electrodeposition techniques enhance or diminish sensor performance will pave the way for further exploration of nanostructure-aptamer relationships, contributing to the future development of optimized, miniaturized electrochemical aptamer-based sensors for continuous, in vivo sensing.
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Affiliation(s)
- Amanda J Ritz
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| | - Olivia M Stuehr
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| | - Danté N Comer
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| | - Robert A Lazenby
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
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Barbault F, Brémond E, Rey J, Tufféry P, Maurel F. DockSurf: A Molecular Modeling Software for the Prediction of Protein/Surface Adhesion. J Chem Inf Model 2023; 63:5220-5231. [PMID: 37579187 DOI: 10.1021/acs.jcim.3c00569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
The elucidation of structural interfaces between proteins and inorganic surfaces is a crucial aspect of bionanotechnology development. Despite its significance, the interfacial structures between proteins and metallic surfaces are yet to be fully understood, and the lack of experimental investigation has impeded the development of many devices. To overcome this limitation, we suggest considering the generation of protein/surface structures as a molecular docking problem with a homogenous plan as the target. To this extent, we propose a new software, DockSurf, which aims to quickly propose reliable protein/surface structures. Our approach considers the conformational exploration with Euler's angles, which provide a cartography instead of a unique structure. Interaction energies were derived from quantum mechanics computations for a set of small molecules that describe protein atom types and implemented in a Derjaguin, Landau, Verwey, and Overbeek potential for the consideration of large systems such as proteins. The validation of DockSurf software was conducted with molecular dynamics for corona proteins with gold surfaces and provided enthusiastic results. This software is implemented in the RPBS platform to facilitate widespread access to the scientific community.
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Affiliation(s)
| | - Eric Brémond
- Université Paris Cité, CNRS, ITODYS, F-75013 Paris, France
| | - Julien Rey
- Université Paris Cité, CNRS UMR 8251, INSERM U1133, RPBS, 75205 Paris, France
| | - Pierre Tufféry
- Université Paris Cité, CNRS UMR 8251, INSERM U1133, RPBS, 75205 Paris, France
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Sykes KS, White RJ. Effects of Nucleic Acid Structural Heterogeneity on the Electrochemistry of Tethered Redox Molecules. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:7322-7330. [PMID: 35639972 PMCID: PMC10150402 DOI: 10.1021/acs.langmuir.2c00840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The cation condensation-induced collapse of electrode-bound nucleic acids and the resulting change in the electrochemical signal is a useful tool to predict the structure and redox probe location of heterogeneous structures of surface-tethered DNA probes─a common architecture employed in the development of electrochemical sensors. In this paper, we measure the faradaic current of an appended redox molecule at the 3' position of the nucleic acid using cyclic voltammetry before and after nucleic acid collapse for various nucleic acid architectures and heterogeneous mixtures on the same electrode surface. The voltammetric peak current change with collapse correlates with the proximity of the redox molecules from the surface. For stem-loop probes, the terminal methylene blue is initially held closer to the surface, such that inducing collapse, by reducing the dielectric permittivity of the interrogation solution, results in a ∼30% increase in current. However, when incorporating pseudoknot probes that hold methylene blue further away from the electrode surface, the current change is much larger (∼120%), indicating a larger conformation change. Upon a 50:50 ratio of the two, we observe a change in current that relates to the ratiometric distribution of the probe used to make the surfaces. Additionally, using cyclic voltammetry, we find that the change between diffusion-limited and diffusion-independent peak currents is dependent upon the distinct structural characteristics of DNA probes on the surface (stem-loop or pseudoknot), as well as the ratios of different DNA probes on the surface. Thus, we demonstrate that the heterogeneous nature of DNA probes governs the corresponding electrochemical signals, which can lead to a better understanding on how to predict the structures of functional nucleic acids on electrode surfaces and how this affects surface-to-surface variability and electrochemical response.
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Affiliation(s)
- Kiana S. Sykes
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221-0172, United States
| | - Ryan J. White
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221-0172, United States
- Department of Electrical and Computer Engineering, University of Cincinnati, Cincinnati, Ohio 45221-0172, United States
- Corresponding Author:
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