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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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Fazelifar P, Cucchiarini A, Khoshbin Z, Mergny JL, Kazemi Noureini S. Strong and selective interactions of palmatine with G-rich sequences in TRF2 promoter; experimental and computational studies. J Biomol Struct Dyn 2023:1-15. [PMID: 38100552 DOI: 10.1080/07391102.2023.2292793] [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: 04/26/2023] [Accepted: 11/25/2023] [Indexed: 12/17/2023]
Abstract
G-rich sequences have the potential to fold into G-quadruplexes (GQs). G-quadruplexes, particularly those positioned in the regulatory regions of proto-oncogenes, have recently garnered attention in anti-cancer drug design. A thermal FRET assay was employed to conduct preliminary screening of various alkaloids, aiming to identify stronger interactions with a specific set of G-rich double-labeled oligonucleotides in both K + and Na + buffers. These oligonucleotides were derived from regions associated with Kit, Myc, Ceb, Bcl2, human telomeres, and potential G-quadruplex forming sequences found in the Nrf2 and Trf2 promoters. Palmatine generally increased the stability of different G-rich sequences into their folded GQ structures, more or less in a concentration dependent manner. The thermal stability and interaction of palmatine was further studied using transition FRET (t-FRET), CD and UV-visible spectroscopy and molecular dynamics simulation methods. Palmatine showed the strongest interaction with T RF2 in both K+ and Na+ buffers even at equimolar concentration ratio. T-FRET studies revealed that palmatine has the potential to disrupt double-strand formation by the T RF2 sequence in the presence of its complementary strand. Palmatine exhibits a stronger interaction with G-rich strand DNA, promoting its folding into G-quadruplex structures. It is noteworthy that palmatine exhibits the strongest interaction with T RF2, which is the shortest sequence among the G-rich oligonucleotides studied, featuring only one nucleotide for two of its loops. Palmatine represents a suitable structure for drug design to develop more specific ligands targeting G-quadruplexes. Whether palmatine can also affect the expression of the T RF2 gene requires further studies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Pegah Fazelifar
- Department of Biology, Faculty of Basic Science, Hakim Sabzevari University, Sabzevar, Iran
| | - Anne Cucchiarini
- Laboratoire d'Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau, France
| | - Zahra Khoshbin
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Jean-Louis Mergny
- Laboratoire d'Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau, France
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Xiao Y, Zhang T, Zhang H. Recent advances in the peptide-based biosensor designs. Colloids Surf B Biointerfaces 2023; 231:113559. [PMID: 37738870 DOI: 10.1016/j.colsurfb.2023.113559] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 09/09/2023] [Accepted: 09/17/2023] [Indexed: 09/24/2023]
Abstract
Biosensors have rapidly emerged as a high-sensitivity and convenient detection method. Among various types of biosensors, optical and electrochemical are the most commonly used. Conventionally, antibodies have been employed to ensure specific interaction between the transmission material and analytes. However, there has been increasing recognition of peptides as a promising recognition element for biosensor development in recent years. The use of peptides as recognition elements provides high level of specificity, sensitivity, and stability for the detection process. The combination of peptide designs and optical or electrochemical detection methods has significantly improved biosensor efficacy. These advancements present opportunities for developing biosensors with diverse functions that can be used to lay a strong scientific foundation for the development of personalized medicine and various other fields. This paper reviews the recent advancements in the development and application of peptide-based optical and electrochemical biosensors, as well as their prospects as a sensor type.
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Affiliation(s)
- Yue Xiao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, MOE Key Laboratory of Molecular Biophysics, Wuhan 430074, China
| | - Ting Zhang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, MOE Key Laboratory of Molecular Biophysics, Wuhan 430074, China
| | - Houjin Zhang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, MOE Key Laboratory of Molecular Biophysics, Wuhan 430074, China.
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Advanced Molecular-Genetic Methods and Prospects for Their Application for the Indication and Identification of <i>Yersinia pestis</i> Strains. PROBLEMS OF PARTICULARLY DANGEROUS INFECTIONS 2023. [DOI: 10.21055/0370-1069-2022-4-29-40] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
The review provides an analysis of the literature data on the use of various modern molecular-genetic methods for the indication and identification of Yersinia pestis strains with different properties and degree of virulence, which is caused by the diverse natural conditions in which they circulate. The methods are also considered from the perspective of their promising application at three levels (territorial, regional and federal) of the system for laboratory diagnosis of infectious diseases at the premises of Rospotrebnadzor organizations to solve the problem of maintaining the sanitary and epidemiological well-being of the country’s population. The main groups of methods considered are as follows: based on the analysis of the lengths of restriction fragments (ribo- and IS-typing, pulse gel electrophoresis); based on the analysis of specific fragments (DFR typing, VNTR typing); based on sequencing (MLST, CRISPR analysis, SNP analysis); PCR methods (including IPCR, SPA); isothermal amplification methods (LAMP, HDA, RPA, SEA, PCA, SHERLOCK); DNA-microarray; methods using aptamer technology; bio- and nano-sensors; DNA origami; methods based on neural networks. We can conclude that the rapid development of molecular diagnostics and genetics is aimed at increasing efficiency, multi-factorial approaches and simplifying the application of techniques with no need for expensive equipment and highly qualified personnel for analysis. At all levels of the system for laboratory diagnosis of infectious diseases at the Rospotrebnadzor organizations, it is possible to use methods based on PCR, isothermal amplification, SHERLOCK, biosensors, and small-sized sequencing devices. At the territorial level, at plague control stations, the use of immuno-PCR and SPA for the indication of Y. pestis is viable. At the regional level, introduction of the technologies based on the use of aptamers and DNA chips looks promising. For the federal level, the use of DNA origami methods and new technologies of whole genome sequencing is a prospect within the framework of advanced identification, molecular typing and sequencing of the genomes of plague agent strains.
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Multifunctional terahertz microscopy for biochemical and chemical imaging and sensing. Biosens Bioelectron 2023; 220:114901. [DOI: 10.1016/j.bios.2022.114901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/11/2022] [Accepted: 11/07/2022] [Indexed: 11/19/2022]
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Bor G, Bulut U, Man E, Balaban Hanoglu S, Evran S, Timur S. Synthetic antibodies for methamphetamine analysis: Design of high affinity aptamers and their use in electrochemical biosensors. J Electroanal Chem (Lausanne) 2022. [DOI: 10.1016/j.jelechem.2022.116686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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Arshavsky‐Graham S, Heuer C, Jiang X, Segal E. Aptasensors versus immunosensors—Which will prevail? Eng Life Sci 2022; 22:319-333. [PMID: 35382545 PMCID: PMC8961048 DOI: 10.1002/elsc.202100148] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/21/2021] [Accepted: 12/24/2021] [Indexed: 12/11/2022] Open
Abstract
Since the invention of the first biosensors 70 years ago, they have turned into valuable and versatile tools for various applications, ranging from disease diagnosis to environmental monitoring. Traditionally, antibodies have been employed as the capture probes in most biosensors, owing to their innate ability to bind their target with high affinity and specificity, and are still considered as the gold standard. Yet, the resulting immunosensors often suffer from considerable limitations, which are mainly ascribed to the antibody size, conjugation chemistry, stability, and costs. Over the past decade, aptamers have emerged as promising alternative capture probes presenting some advantages over existing constraints of immunosensors, as well as new biosensing concepts. Herein, we review the employment of antibodies and aptamers as capture probes in biosensing platforms, addressing the main aspects of biosensor design and mechanism. We also aim to compare both capture probe classes from theoretical and experimental perspectives. Yet, we highlight that such comparisons are not straightforward, and these two families of capture probes should not be necessarily perceived as competing but rather as complementary. We, thus, elaborate on their combined use in hybrid biosensing schemes benefiting from the advantages of each biorecognition element.
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Affiliation(s)
- Sofia Arshavsky‐Graham
- Faculty of Biotechnology and Food Engineering Technion ‐ Israel Institute of Technology Haifa Israel
| | - Christopher Heuer
- Faculty of Biotechnology and Food Engineering Technion ‐ Israel Institute of Technology Haifa Israel
- Institute of Technical Chemistry Leibniz University Hannover Hannover Germany
| | - Xin Jiang
- Faculty of Biotechnology and Food Engineering Technion ‐ Israel Institute of Technology Haifa Israel
| | - Ester Segal
- Faculty of Biotechnology and Food Engineering Technion ‐ Israel Institute of Technology Haifa Israel
- Russell Berrie Nanotechnology Institute Technion ‐ Israel Institute of Technology Haifa Israel
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