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Moreira MJ, Pintado M, Almeida JMMMD. Are Aptamer-Based Biosensors the Future of the Detection of the Human Gut Microbiome?-A Systematic Review and Meta-Analysis. BIOSENSORS 2024; 14:423. [PMID: 39329798 PMCID: PMC11430143 DOI: 10.3390/bios14090423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Revised: 08/24/2024] [Accepted: 08/29/2024] [Indexed: 09/28/2024]
Abstract
The gut microbiome is shaped early in life by dietary and lifestyle factors. Specific compounds in the gut affect the growth of different bacterial species and the production of beneficial or harmful byproducts. Dysbiosis of the gut microbiome has been linked to various diseases resulting from the presence of harmful bacteria and their byproducts. Existing methods for detecting microbial species, such as microscopic observation and molecular biological techniques, are costly, labor-intensive, and require skilled personnel. Biosensors, which integrate a recognition element, transducer, amplifier, signal processor, and display unit, can convert biological events into electronic signals. This review provides a comprehensive and systematic survey of scientific publications from 2018 to June 2024, obtained from ScienceDirect, PubMed, and Scopus databases. The aim was to evaluate the current state-of-the-art and identify knowledge gaps in the application of aptamer biosensors for the determination of gut microbiota. A total of 13 eligible publications were categorized based on the type of study: those using microbial bioreceptors (category 1) and those using aptamer bioreceptors (category 2) for the determination of gut microbiota. Point-of-care biosensors are being developed to monitor changes in metabolites that may lead to disease. They are well-suited for use in the healthcare system and offer an excellent alternative to traditional methods. Aptamers are gaining attention due to their stability, specificity, scalability, reproducibility, low production cost, and low immunogenicity. While there is limited research on using aptamers to detect human gut microbiota, they show promise for providing accurate, robust, and cost-effective diagnostic methods for monitoring the gut microbiome.
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Affiliation(s)
- Maria João Moreira
- CBQF—Centro de Biotecnologia e Química Fina—Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal; (M.J.M.); (M.P.)
| | - Manuela Pintado
- CBQF—Centro de Biotecnologia e Química Fina—Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal; (M.J.M.); (M.P.)
| | - José M. M. M. De Almeida
- INESC TEC—Institute for Systems and Computer Engineering, Technology and Science, University of Porto, 4169-007 Porto, Portugal
- Department of Physics, School of Sciences and Technology, University of Trás-os-Montes e Alto Douro, 5001-801 Vila Real, Portugal
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2
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Aguirre Rivera J, Mao G, Sabantsev A, Panfilov M, Hou Q, Lindell M, Chanez C, Ritort F, Jinek M, Deindl S. Massively parallel analysis of single-molecule dynamics on next-generation sequencing chips. Science 2024; 385:892-898. [PMID: 39172826 DOI: 10.1126/science.adn5371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 06/12/2024] [Indexed: 08/24/2024]
Abstract
Single-molecule techniques are ideally poised to characterize complex dynamics but are typically limited to investigating a small number of different samples. However, a large sequence or chemical space often needs to be explored to derive a comprehensive understanding of complex biological processes. Here we describe multiplexed single-molecule characterization at the library scale (MUSCLE), a method that combines single-molecule fluorescence microscopy with next-generation sequencing to enable highly multiplexed observations of complex dynamics. We comprehensively profiled the sequence dependence of DNA hairpin properties and Cas9-induced target DNA unwinding-rewinding dynamics. The ability to explore a large sequence space for Cas9 allowed us to identify a number of target sequences with unexpected behaviors. We envision that MUSCLE will enable the mechanistic exploration of many fundamental biological processes.
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Affiliation(s)
- J Aguirre Rivera
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75105 Uppsala, Sweden
| | - G Mao
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75105 Uppsala, Sweden
| | - A Sabantsev
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75105 Uppsala, Sweden
| | - M Panfilov
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75105 Uppsala, Sweden
| | - Q Hou
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75105 Uppsala, Sweden
| | - M Lindell
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, 75144 Uppsala, Sweden
| | - C Chanez
- Department of Biochemistry, University of Zürich, 8057 Zürich, Switzerland
| | - F Ritort
- Small Biosystems Lab, Condensed Matter Physics Department, Universitat de Barcelona, 08028 Barcelona, Spain
- Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona, 08028 Barcelona, Spain
| | - M Jinek
- Department of Biochemistry, University of Zürich, 8057 Zürich, Switzerland
| | - S Deindl
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75105 Uppsala, Sweden
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Tong Y, Yuan J, Li Z, Deng C, Cheng Y. Drug-Loaded Bioscaffolds for Osteochondral Regeneration. Pharmaceutics 2024; 16:1095. [PMID: 39204440 PMCID: PMC11360256 DOI: 10.3390/pharmaceutics16081095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Revised: 07/20/2024] [Accepted: 07/25/2024] [Indexed: 09/04/2024] Open
Abstract
Osteochondral defect is a complex tissue loss disease caused by arthritis, high-energy trauma, and many other reasons. Due to the unique structural characteristics of osteochondral tissue, the repair process is sophisticated and involves the regeneration of both hyaline cartilage and subchondral bone. However, the current clinical treatments often fall short of achieving the desired outcomes. Tissue engineering bioscaffolds, especially those created via three-dimensional (3D) printing, offer promising solutions for osteochondral defects due to their precisely controllable 3D structures. The microstructure of 3D-printed bioscaffolds provides an excellent physical environment for cell adhesion and proliferation, as well as nutrient transport. Traditional 3D-printed bioscaffolds offer mere physical stimulation, while drug-loaded 3D bioscaffolds accelerate the tissue repair process by synergistically combining drug therapy with physical stimulation. In this review, the physiological characteristics of osteochondral tissue and current treatments of osteochondral defect were reviewed. Subsequently, the latest progress in drug-loaded bioscaffolds was discussed and highlighted in terms of classification, characteristics, and applications. The perspectives of scaffold design, drug control release, and biosafety were also discussed. We hope this article will serve as a valuable reference for the design and development of osteochondral regenerative bioscaffolds and pave the way for the use of drug-loaded bioscaffolds in clinical therapy.
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Affiliation(s)
| | | | | | - Cuijun Deng
- Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-like Intelligence, Shanghai Fourth People’s Hospital, School of Medicine, Tongji University, Shanghai 200434, China; (Y.T.); (J.Y.); (Z.L.)
| | - Yu Cheng
- Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-like Intelligence, Shanghai Fourth People’s Hospital, School of Medicine, Tongji University, Shanghai 200434, China; (Y.T.); (J.Y.); (Z.L.)
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Yang T, Duan H, Nian H, Wang P, Yan C, Cao F, Li Q, Cao L. Unraveling the structure-chirality sensing relationship between achiral anthracene-based tetracationic nanotubes and nucleosides in aqueous host-guest complexation. Biosens Bioelectron 2024; 258:116342. [PMID: 38705071 DOI: 10.1016/j.bios.2024.116342] [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: 01/29/2024] [Revised: 03/28/2024] [Accepted: 04/26/2024] [Indexed: 05/07/2024]
Abstract
In biological systems, nucleosides play crucial roles in various physiological processes. In this study, we designed and synthesized four achiral anthracene-based tetracationic nanotubes (1-4) as artificial hosts and chiroptical sensors for nucleosides in aqueous media. Notably, different nanotubes exhibit varied chirality sensing on circular dichroism (CD)/circularly polarized luminescence (CPL) spectra through the host-guest complexation, which prompted us to explore the factors influencing their chiroptical responses. Through systematic host-guest experiments, the structure-chirality sensing relationship between achiral anthracene-based tetracationic nanotubes and nucleosides in the host-guest complexation was unraveled. Firstly, the CD response originates from the anthracene rings situated at the side-wall position, resulting from the right-handed (P)- or left-handed (M)-twisted conformation of the macrocyclic structure. Secondly, the CPL signal is influenced by the presence of anthracene rings at the linking-wall position, which results from intermolecular chiral twisted stacking between these anthracene rings. Therefore, these nanotubes can serve as chiroptical sensor arrays to enhance the accuracy of nucleotide recognition through principal component analysis (PCA) analysis based on the diversified CD spectra. This study provides insights for the construction of adaptive chirality from achiral nanotubes with dynamic conformational nature and might facilitate further design of chiral functional materials for several applications.
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Affiliation(s)
- Ting Yang
- College of Chemistry and Materials Science, Northwest University, Xi'an 710069, China
| | - Honghong Duan
- College of Chemistry and Materials Science, Northwest University, Xi'an 710069, China; Xian North Qinghua Electrical Co., Ltd, Xi'an, 710054, China
| | - Hao Nian
- College of Chemistry and Materials Science, Northwest University, Xi'an 710069, China; Southern University of Science and Technology, Shenzhen, 518055, China
| | - Pingxia Wang
- College of Chemistry and Materials Science, Northwest University, Xi'an 710069, China
| | - Chaochao Yan
- College of Chemistry and Materials Science, Northwest University, Xi'an 710069, China
| | - Fan Cao
- College of Chemistry and Materials Science, Northwest University, Xi'an 710069, China
| | - Qingfang Li
- College of Chemistry and Materials Science, Northwest University, Xi'an 710069, China
| | - Liping Cao
- College of Chemistry and Materials Science, Northwest University, Xi'an 710069, China.
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Qin G, Li H, He J, Wang H, Chen Y, Lao S, Cheng L, Lu W, Luo L, Tang L, Mo R, Wei Y, Zhou Q. A fluorescence aptamer sensor utilizing WS 2 nanosheets for sensitive detection of patulin: enhanced specificity and wide applicability. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:4873-4879. [PMID: 38973381 DOI: 10.1039/d4ay00730a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
A tungsten disulfide (WS2) nanosheet-based aptamer sensor was developed to detect patulin (PAT). The 5'-end of the PAT aptamer was modified with a cyanine 3 (Cy3) fluorophore, which self-assembled on WS2 nanosheets. The interaction between the Cy3 fluorophore at the 5'-end of the PAT aptamer and the WS2 nanosheets resulted in reduced fluorescence (FL) intensity due to fluorescence resonance energy transfer (FRET). The introduction of PAT into this sensing system led to hybridization with the PAT aptamer, forming a G-quadruplex/PAT complex with low affinity for the WS2 nanosheet surface. This hybridization increased the distance between the Cy3 fluorophore and the WS2 nanosheets, inhibiting FRET and producing a strong FL signal. Under optimal experimental conditions, the FL intensity of the sensing system demonstrated an excellent linear correlation with PAT concentrations ranging from 0.5 to 40.0 ng mL-1, and it achieved a detection limit (S/N = 3) of 0.23 ng mL-1. This sensing system offers enhanced specificity for PAT detection and has the potential for broad application in detecting other toxins by substituting the sequence of the recognition aptamer.
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Affiliation(s)
- Guoxin Qin
- Institute for Agricultural Product Quality Safety and Testing Technology, Guangxi Academy of Agricultural Sciences, Nanning 530007, China.
| | - Huiling Li
- Institute for Agricultural Product Quality Safety and Testing Technology, Guangxi Academy of Agricultural Sciences, Nanning 530007, China.
| | - Jie He
- Institute for Agricultural Product Quality Safety and Testing Technology, Guangxi Academy of Agricultural Sciences, Nanning 530007, China.
| | - Haijun Wang
- Institute for Agricultural Product Quality Safety and Testing Technology, Guangxi Academy of Agricultural Sciences, Nanning 530007, China.
| | - Yongxian Chen
- Institute for Agricultural Product Quality Safety and Testing Technology, Guangxi Academy of Agricultural Sciences, Nanning 530007, China.
| | - Shuibing Lao
- Institute for Agricultural Product Quality Safety and Testing Technology, Guangxi Academy of Agricultural Sciences, Nanning 530007, China.
| | - Liang Cheng
- Institute for Agricultural Product Quality Safety and Testing Technology, Guangxi Academy of Agricultural Sciences, Nanning 530007, China.
| | - Weifan Lu
- Institute for Agricultural Product Quality Safety and Testing Technology, Guangxi Academy of Agricultural Sciences, Nanning 530007, China.
| | - Lihong Luo
- Institute for Agricultural Product Quality Safety and Testing Technology, Guangxi Academy of Agricultural Sciences, Nanning 530007, China.
| | - Li Tang
- Institute for Agricultural Product Quality Safety and Testing Technology, Guangxi Academy of Agricultural Sciences, Nanning 530007, China.
| | - Renfu Mo
- Institute for Agricultural Product Quality Safety and Testing Technology, Guangxi Academy of Agricultural Sciences, Nanning 530007, China.
| | - Yuning Wei
- Institute for Agricultural Product Quality Safety and Testing Technology, Guangxi Academy of Agricultural Sciences, Nanning 530007, China.
| | - Qifeng Zhou
- Institute for Agricultural Product Quality Safety and Testing Technology, Guangxi Academy of Agricultural Sciences, Nanning 530007, China.
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Urmi R, Banerjee P, Singh M, Singh R, Chhillar S, Sharma N, Chandra A, Singh N, Qamar I. Revolutionizing biomedicine: Aptamer-based nanomaterials and nanodevices for therapeutic applications. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2024; 42:e00843. [PMID: 38881649 PMCID: PMC11179248 DOI: 10.1016/j.btre.2024.e00843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 04/28/2024] [Accepted: 05/24/2024] [Indexed: 06/18/2024]
Abstract
With the progress in two distinct areas of nanotechnology and aptamer identification technologies, the two fields have merged to what is known as aptamer nanotechnology. Aptamers have varying properties in the biomedical field include their small size, non-toxicity, ease of manufacturing, negligible immunogenicity, ability to identify a wide range of targets, and high immobilizing capacity. Nevertheless, aptamers can utilize the distinct characteristics offered by nanomaterials like optical, magnetic, thermal, electronic properties to become more versatile and function as a novel device in diagnostics and therapeutics. This engineered aptamer conjugated nanomaterials, in turn provides a potentially new and unique properties apart from the pre-existing characteristics of aptamer and nanomaterials, where they act to offer wide array of applications in the biomedical field ranging from drug targeting, delivery of drugs, biosensing, bioimaging. This review gives comprehensive insight of the different aptamer conjugated nanomaterials and their utilization in biomedical field. Firstly, it introduces on the aptamer selection methods and roles of nanomaterials offered. Further, different conjugation strategies are explored in addition, the class of aptamer conjugated nanodevices being discussed. Typical biomedical examples and studies specifically, related to drug delivery, biosensing, bioimaging have been presented.
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Affiliation(s)
- Rajkumari Urmi
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. 201312, India
| | - Pallabi Banerjee
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. 201312, India
| | - Manisha Singh
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. 201312, India
| | - Risha Singh
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. 201312, India
| | - Sonam Chhillar
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. 201312, India
| | - Neha Sharma
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. 201312, India
| | - Anshuman Chandra
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Nagendra Singh
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. 201312, India
| | - Imteyaz Qamar
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. 201312, India
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7
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Wang C, Lan X, Zhu L, Wang Y, Gao X, Li J, Tian H, Liang Z, Xu W. Construction Strategy of Functionalized Liposomes and Multidimensional Application. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2309031. [PMID: 38258399 DOI: 10.1002/smll.202309031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 12/30/2023] [Indexed: 01/24/2024]
Abstract
Liposomes are widely used in the biological field due to their good biocompatibility and surface modification properties. With the development of biochemistry and material science, many liposome structures and their surface functional components have been modified and optimized one by one, pushing the liposome platform from traditional to functionalized and intelligent, which will better satisfy and expand the needs of scientific research. However, a main limiting factor effecting the efficiency of liposomes is the complicated environmental conditions in the living body. Currently, in order to overcome the above problem, functionalized liposomes have become a very promising strategy. In this paper, binding strategies of liposomes with four main functional elements, namely nucleic acids, antibodies, peptides, and stimuli-responsive motif have been summarized for the first time. In addition, based on the construction characteristics of functionalized liposomes, such as drug-carrying, targeting, long-circulating, and stimulus-responsive properties, a comprehensive overview of their features and respective research progress are presented. Finally, the paper critically presents the limitations of these functionalized liposomes in the current applications and also prospectively suggests the future development directions, aiming to accelerate realization of their industrialization.
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Affiliation(s)
- Chengyun Wang
- College of Food Science and Nutritional Engineering, China Agricultural University, No. 17, Qinghua East Road, Beijing, 100083, China
- College of Food Science and Technology, Hebei Agricultural University, Baoding, Hebei, 071000, China
- Key Laboratory of Precision Nutrition and Food Quality, Beijing Laboratory for Food Quality and Safety, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
| | - Xinyue Lan
- Key Laboratory of Precision Nutrition and Food Quality, Beijing Laboratory for Food Quality and Safety, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
| | - Longjiao Zhu
- Key Laboratory of Precision Nutrition and Food Quality, Beijing Laboratory for Food Quality and Safety, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
| | - Yanhui Wang
- Key Laboratory of Precision Nutrition and Food Quality, Beijing Laboratory for Food Quality and Safety, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
| | - Xinru Gao
- College of Food Science and Nutritional Engineering, China Agricultural University, No. 17, Qinghua East Road, Beijing, 100083, China
| | - Jie Li
- College of Food Science and Nutritional Engineering, China Agricultural University, No. 17, Qinghua East Road, Beijing, 100083, China
- Key Laboratory of Precision Nutrition and Food Quality, Beijing Laboratory for Food Quality and Safety, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
| | - Hongtao Tian
- College of Food Science and Technology, Hebei Agricultural University, Baoding, Hebei, 071000, China
| | - Zhihong Liang
- College of Food Science and Nutritional Engineering, China Agricultural University, No. 17, Qinghua East Road, Beijing, 100083, China
| | - Wentao Xu
- College of Food Science and Nutritional Engineering, China Agricultural University, No. 17, Qinghua East Road, Beijing, 100083, China
- Key Laboratory of Precision Nutrition and Food Quality, Beijing Laboratory for Food Quality and Safety, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
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Stevanović M, Filipović N. A Review of Recent Developments in Biopolymer Nano-Based Drug Delivery Systems with Antioxidative Properties: Insights into the Last Five Years. Pharmaceutics 2024; 16:670. [PMID: 38794332 PMCID: PMC11125366 DOI: 10.3390/pharmaceutics16050670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/11/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024] Open
Abstract
In recent years, biopolymer-based nano-drug delivery systems with antioxidative properties have gained significant attention in the field of pharmaceutical research. These systems offer promising strategies for targeted and controlled drug delivery while also providing antioxidant effects that can mitigate oxidative stress-related diseases. Generally, the healthcare landscape is constantly evolving, necessitating the continual development of innovative therapeutic approaches and drug delivery systems (DDSs). DDSs play a pivotal role in enhancing treatment efficacy, minimizing adverse effects, and optimizing patient compliance. Among these, nanotechnology-driven delivery approaches have garnered significant attention due to their unique properties, such as improved solubility, controlled release, and targeted delivery. Nanomaterials, including nanoparticles, nanocapsules, nanotubes, etc., offer versatile platforms for drug delivery and tissue engineering applications. Additionally, biopolymer-based DDSs hold immense promise, leveraging natural or synthetic biopolymers to encapsulate drugs and enable targeted and controlled release. These systems offer numerous advantages, including biocompatibility, biodegradability, and low immunogenicity. The utilization of polysaccharides, polynucleotides, proteins, and polyesters as biopolymer matrices further enhances the versatility and applicability of DDSs. Moreover, substances with antioxidative properties have emerged as key players in combating oxidative stress-related diseases, offering protection against cellular damage and chronic illnesses. The development of biopolymer-based nanoformulations with antioxidative properties represents a burgeoning research area, with a substantial increase in publications in recent years. This review provides a comprehensive overview of the recent developments within this area over the past five years. It discusses various biopolymer materials, fabrication techniques, stabilizers, factors influencing degradation, and drug release. Additionally, it highlights emerging trends, challenges, and prospects in this rapidly evolving field.
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Affiliation(s)
- Magdalena Stevanović
- Group for Biomedical Engineering and Nanobiotechnology, Institute of Technical Sciences of SASA, Kneza Mihaila 35/IV, 11000 Belgrade, Serbia;
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Sitkov N, Ryabko A, Moshnikov V, Aleshin A, Kaplun D, Zimina T. Hybrid Impedimetric Biosensors for Express Protein Markers Detection. MICROMACHINES 2024; 15:181. [PMID: 38398911 PMCID: PMC10890403 DOI: 10.3390/mi15020181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024]
Abstract
Impedimetric biosensors represent a powerful and promising tool for studying and monitoring biological processes associated with proteins and can contribute to the development of new approaches in the diagnosis and treatment of diseases. The basic principles, analytical methods, and applications of hybrid impedimetric biosensors for express protein detection in biological fluids are described. The advantages of this type of biosensors, such as simplicity and speed of operation, sensitivity and selectivity of analysis, cost-effectiveness, and an ability to be integrated into hybrid microfluidic systems, are demonstrated. Current challenges and development prospects in this area are analyzed. They include (a) the selection of materials for electrodes and formation of nanostructures on their surface; (b) the development of efficient methods for biorecognition elements' deposition on the electrodes' surface, providing the specificity and sensitivity of biosensing; (c) the reducing of nonspecific binding and interference, which could affect specificity; (d) adapting biosensors to real samples and conditions of operation; (e) expanding the range of detected proteins; and, finally, (f) the development of biosensor integration into large microanalytical system technologies. This review could be useful for researchers working in the field of impedimetric biosensors for protein detection, as well as for those interested in the application of this type of biosensor in biomedical diagnostics.
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Affiliation(s)
- Nikita Sitkov
- Department of Micro and Nanoelectronics, Saint Petersburg Electrotechnical University “LETI”, 197022 Saint Petersburg, Russia; (V.M.); (T.Z.)
- Engineering Centre for Microtechnology and Diagnostics, Saint Petersburg Electrotechnical University “LETI”, 197022 Saint Petersburg, Russia
| | - Andrey Ryabko
- Laboratory of Nonequilibrium Processes in Semiconductors, Ioffe Institute, 26 Politekhnicheskaya, 194021 Saint Petersburg, Russia;
| | - Vyacheslav Moshnikov
- Department of Micro and Nanoelectronics, Saint Petersburg Electrotechnical University “LETI”, 197022 Saint Petersburg, Russia; (V.M.); (T.Z.)
| | - Andrey Aleshin
- Laboratory of Nonequilibrium Processes in Semiconductors, Ioffe Institute, 26 Politekhnicheskaya, 194021 Saint Petersburg, Russia;
| | - Dmitry Kaplun
- Artificial Intelligence Research Institute, China University of Mining and Technology, 1 Daxue Road, Xuzhou 221116, China;
- Department of Automation and Control Processes, Saint Petersburg Electrotechnical University “LETI”, 197022 Saint Petersburg, Russia
| | - Tatiana Zimina
- Department of Micro and Nanoelectronics, Saint Petersburg Electrotechnical University “LETI”, 197022 Saint Petersburg, Russia; (V.M.); (T.Z.)
- Engineering Centre for Microtechnology and Diagnostics, Saint Petersburg Electrotechnical University “LETI”, 197022 Saint Petersburg, Russia
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Hartung J, McCann N, Doe E, Hayth H, Benkato K, Johnson MB, Viard M, Afonin KA, Khisamutdinov EF. Toehold-Mediated Shape Transition of Nucleic Acid Nanoparticles. ACS APPLIED MATERIALS & INTERFACES 2023; 15:25300-25312. [PMID: 37204867 PMCID: PMC10331730 DOI: 10.1021/acsami.3c01604] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
We introduce a toehold-mediated strand displacement strategy for regulated shape-switching of nucleic acid nanoparticles (NANPs) enabling their sequential transformation from triangular to hexagonal architectures at isothermal conditions. The successful shape transitions were confirmed by electrophoretic mobility shift assays, atomic force microscopy, and dynamic light scattering. Furthermore, implementation of split fluorogenic aptamers allowed for monitoring the individual transitions in real time. Three distinct RNA aptamers─malachite green (MG), broccoli, and mango─were embedded within NANPs as reporter domains to confirm shape transitions. While MG "lights up" within the square, pentagonal, and hexagonal constructs, the broccoli is activated only upon formation of pentagon and hexagon NANPs, and mango reports only the presence of hexagons. Moreover, the designed RNA fluorogenic platform can be employed to construct a logic gate that performs an AND operation with three single-stranded RNA inputs by implementing a non-sequential polygon transformation approach. Importantly, the polygonal scaffolds displayed promising potential as drug delivery agents and biosensors. All polygons exhibited effective cellular internalization followed by specific gene silencing when decorated with fluorophores and RNAi inducers. This work offers a new perspective for the design of toehold-mediated shape-switching nanodevices to activate different light-up aptamers for the development of biosensors, logic gates, and therapeutic devices in the nucleic acid nanotechnology.
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Affiliation(s)
- Jordan Hartung
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Nathan McCann
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Erwin Doe
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Hannah Hayth
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Kheiria Benkato
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - M Brittany Johnson
- Department of Biology, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Mathias Viard
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, United States
- Basic Science Program, Leidos Biomedical Research Inc. National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Kirill A Afonin
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Emil F Khisamutdinov
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
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Duan M, Li K, Zhang L, Zhou Y, Bian L, Wang C. Screening, characterization and specific binding mechanism of aptamers against human plasminogen Kringle 5. Bioorg Chem 2023; 137:106579. [PMID: 37149949 DOI: 10.1016/j.bioorg.2023.106579] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/30/2023] [Accepted: 04/26/2023] [Indexed: 05/09/2023]
Abstract
Plasminogen Kringle 5 is one of the most potent cytokines identified to inhibit the proliferation and migration of vascular endothelial cells. Herein, six aptamer candidates that specifically bind to Kringle 5 were generated by the systematic evolution of ligands by exponential enrichment (SELEX). After 10 rounds of screening against Kringle 5, a highly enriched ssDNA pool was sequenced and the representative aptamers were subjected to binding assays to evaluate their affinity and specificity. The preferred aptamer KG-4, which demonstrated a low dissociation constant (Kd) of ∼ 432 nM and excellent selectivity for Kringle 5. A conserved "motif" of eight bases located at the stem-loop intersection, common to the aptamer, was further confirmed as the recognition element for binding with Kringle 5. The bulge formed by the motif and depression on the lysine binding site of Kringle 5 were both located at the binding interface, and the "induced fit" between their structures played a central role in the recognition process. Kringle 5 interacts KG-4 primarily through enthalpy-driven van der Waals forces and hydrogen bond. The key nucleotides A34 and C35 at motif on KG-4 and the positively charged amino acids in the loop 1 and loop 4 regions on Kringle 5 play a major role in the interaction. Furthermore, KG-4 dose-dependently reduced the proliferation inhibition of vascular endothelial cells by Kringle 5 and had a blocking effect on the function of Kringle 5 in inhibiting migration and promoting apoptosis of vascular endothelial cells in vitro. This study put a new light on protein-aptamer binding mechanism and may provide insight into the treatment of ischemic diseases by target depletion of Kringle 5.
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Affiliation(s)
- Meijiao Duan
- College of Life Science, Northwest University, Xi'an 710069, Shaanxi, China
| | - Kewei Li
- College of Life Science, Northwest University, Xi'an 710069, Shaanxi, China
| | - Ling Zhang
- College of Life Science, Northwest University, Xi'an 710069, Shaanxi, China
| | - Yaqi Zhou
- College of Life Science, Northwest University, Xi'an 710069, Shaanxi, China
| | - Liujiao Bian
- College of Life Science, Northwest University, Xi'an 710069, Shaanxi, China.
| | - Cuiling Wang
- College of Life Science, Northwest University, Xi'an 710069, Shaanxi, China.
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Shishparenok AN, Furman VV, Zhdanov DD. DNA-Based Nanomaterials as Drug Delivery Platforms for Increasing the Effect of Drugs in Tumors. Cancers (Basel) 2023; 15:2151. [PMID: 37046816 PMCID: PMC10093432 DOI: 10.3390/cancers15072151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 04/08/2023] Open
Abstract
DNA nanotechnology has significantly advanced and might be used in biomedical applications, drug delivery, and cancer treatment during the past few decades. DNA nanomaterials are widely used in biomedical research involving biosensing, bioimaging, and drug delivery since they are remarkably addressable and biocompatible. Gradually, modified nucleic acids have begun to be employed to construct multifunctional DNA nanostructures with a variety of architectural designs. Aptamers are single-stranded nucleic acids (both DNAs and RNAs) capable of self-pairing to acquire secondary structure and of specifically binding with the target. Diagnosis and tumor therapy are prospective fields in which aptamers can be applied. Many DNA nanomaterials with three-dimensional structures have been studied as drug delivery systems for different anticancer medications or gene therapy agents. Different chemical alterations can be employed to construct a wide range of modified DNA nanostructures. Chemically altered DNA-based nanomaterials are useful for drug delivery because of their improved stability and inclusion of functional groups. In this work, the most common oligonucleotide nanomaterials were reviewed as modern drug delivery systems in tumor cells.
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Affiliation(s)
- Anastasiya N. Shishparenok
- Laboratory of Medical Biotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121 Moscow, Russia
| | - Vitalina V. Furman
- Center of Chemical Engineering, ITMO University, Kronverkskiy Prospekt 49A, 197101 St. Petersburg, Russia
| | - Dmitry D. Zhdanov
- Laboratory of Medical Biotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121 Moscow, Russia
- Department of Biochemistry, Peoples’ Friendship University of Russia (RUDN University), Miklukho-Maklaya St. 6, 117198 Moscow, Russia
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Bekkouche I, Shishonin AY, Vetcher AA. Recent Development in Biomedical Applications of Oligonucleotides with Triplex-Forming Ability. Polymers (Basel) 2023; 15:858. [PMID: 36850142 PMCID: PMC9964087 DOI: 10.3390/polym15040858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/12/2023] Open
Abstract
A DNA structure, known as triple-stranded DNA, is made up of three oligonucleotide chains that wind around one another to form a triple helix (TFO). Hoogsteen base pairing describes how triple-stranded DNA may be built at certain conditions by the attachment of the third strand to an RNA, PNA, or DNA, which might all be employed as oligonucleotide chains. In each of these situations, the oligonucleotides can be employed as an anchor, in conjunction with a specific bioactive chemical, or as a messenger that enables switching between transcription and replication through the triplex-forming zone. These data are also considered since various illnesses have been linked to the expansion of triplex-prone sequences. In light of metabolic acidosis and associated symptoms, some consideration is given to the impact of several low-molecular-weight compounds, including pH on triplex production in vivo. The review is focused on the development of biomedical oligonucleotides with triplexes.
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Affiliation(s)
- Incherah Bekkouche
- Nanotechnology Scientific and Educational Center, Institute of Biochemical Technology and Nanotechnology, Peoples’ Friendship University of Russia (RUDN), Miklukho-Maklaya Str. 6, Moscow 117198, Russia
| | - Alexander Y. Shishonin
- Complementary and Integrative Health Clinic of Dr. Shishonin, 5, Yasnogorskaya Str., Moscow 117588, Russia
| | - Alexandre A. Vetcher
- Nanotechnology Scientific and Educational Center, Institute of Biochemical Technology and Nanotechnology, Peoples’ Friendship University of Russia (RUDN), Miklukho-Maklaya Str. 6, Moscow 117198, Russia
- Complementary and Integrative Health Clinic of Dr. Shishonin, 5, Yasnogorskaya Str., Moscow 117588, Russia
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