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Kumar S, Mohan A, Sharma NR, Kumar A, Girdhar M, Malik T, Verma AK. Computational Frontiers in Aptamer-Based Nanomedicine for Precision Therapeutics: A Comprehensive Review. ACS OMEGA 2024; 9:26838-26862. [PMID: 38947800 PMCID: PMC11209897 DOI: 10.1021/acsomega.4c02466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/09/2024] [Accepted: 05/28/2024] [Indexed: 07/02/2024]
Abstract
In the rapidly evolving landscape of nanomedicine, aptamers have emerged as powerful molecular tools, demonstrating immense potential in targeted therapeutics, diagnostics, and drug delivery systems. This paper explores the computational features of aptamers in nanomedicine, highlighting their advantages over antibodies, including selectivity, low immunogenicity, and a simple production process. A comprehensive overview of the aptamer development process, specifically the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) process, sheds light on the intricate methodologies behind aptamer selection. The historical evolution of aptamers and their diverse applications in nanomedicine are discussed, emphasizing their pivotal role in targeted drug delivery, precision medicine and therapeutics. Furthermore, we explore the integration of artificial intelligence (AI), machine learning (ML), Internet of Things (IoT), Internet of Medical Things (IoMT), and nanotechnology in aptameric development, illustrating how these cutting-edge technologies are revolutionizing the selection and optimization of aptamers for tailored biomedical applications. This paper also discusses challenges in computational methods for advancing aptamers, including reliable prediction models, extensive data analysis, and multiomics data incorporation. It also addresses ethical concerns and restrictions related to AI and IoT use in aptamer research. The paper examines progress in computer simulations for nanomedicine. By elucidating the importance of aptamers, understanding their superiority over antibodies, and exploring the historical context and challenges, this review serves as a valuable resource for researchers and practitioners aiming to harness the full potential of aptamers in the rapidly evolving field of nanomedicine.
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Affiliation(s)
- Shubham Kumar
- School
of Bioengineering and Biosciences, Lovely
Professional University, Phagwara, Punjab 144001, India
| | - Anand Mohan
- School
of Bioengineering and Biosciences, Lovely
Professional University, Phagwara, Punjab 144001, India
| | - Neeta Raj Sharma
- School
of Bioengineering and Biosciences, Lovely
Professional University, Phagwara, Punjab 144001, India
| | - Anil Kumar
- Gene
Regulation Laboratory, National Institute
of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Madhuri Girdhar
- Division
of Research and Development, Lovely Professional
University, Phagwara 144401, Punjab, India
| | - Tabarak Malik
- Department
of Biomedical Sciences, Institute of Health, Jimma University, MVJ4+R95 Jimma, Ethiopia
| | - Awadhesh Kumar Verma
- School
of Bioengineering and Biosciences, Lovely
Professional University, Phagwara, Punjab 144001, India
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2
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Davydova AS, Vorobyeva MA. Aptasensors Based on Non-Enzymatic Peroxidase Mimics: Current Progress and Challenges. BIOSENSORS 2023; 14:1. [PMID: 38275302 PMCID: PMC10813519 DOI: 10.3390/bios14010001] [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: 11/20/2023] [Revised: 12/12/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024]
Abstract
Immunoassays based on antibodies as recognizing elements and enzymes as signal-generating modules are extensively used now in clinical lab diagnostics, food, and environmental analyses. However, the application of natural enzymes and antibodies has some drawbacks, such as relatively high manufacturing costs, thermal instability, and lot-to-lot variations that lower the reproducibility of results. Oligonucleotide aptamers are able to specifically bind their targets with high affinity and selectivity, so they represent a prospective alternative to protein antibodies for analyte recognition. Their main advantages include thermal stability and long shelf life, cost-efficient chemical synthesis, and negligible batch-to-batch variations. At the same time, a wide variety of non-protein peroxidase mimics are now available that show strong potential to replace protein enzymes. Here, we review and analyze non-protein biosensors that represent a nexus of these two concepts: aptamer-based sensors (aptasensors) with optical detection (colorimetric, luminescent, or fluorescent) based on different peroxidase mimics, such as DNAzymes, nanoparticles, or metal-organic frameworks.
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Affiliation(s)
- Anna S. Davydova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Akad. Lavrentiev, 8, 630090 Novosibirsk, Russia;
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3
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Hu Y, Li C, Hu M, Zhang Z, Fu R, Tang X, Wu T. Allosteric Nucleic Acid Enzyme: A Versatile Stimuli-Responsive Tool for Molecular Computing and Biosensing Nanodevices. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023:e2300207. [PMID: 36978231 DOI: 10.1002/smll.202300207] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/09/2023] [Indexed: 06/18/2023]
Abstract
Allostery is a naturally occurring mechanism in which effector binding induces the modulation and fine control of a related biomolecule function. Deoxyribozyme (DNAzyme) with catalytic activity and substrate recognition ability is ideal to be regulated by allosteric strategies. However, the current regulations frequently confront various obstacles, such as severe activity decay, signal leakage, and limited effectors. In this work, a rational regulation strategy for developing versatile effectors-responsive allosteric nucleic acid enzyme (ANAzyme) by introducing an allosteric domain in response to diverse effectors is established. The enzyme-like activity of this re-engineered ANAzyme can be modulated in a more predictable and fine way compared with the previous DNAzyme regulation strategies. Based on the allosteric strategy, the construction of allosterically coregulatory nanodevices and a series of basic logic gates and logic circuits are achieved, demonstrating that the proposed ANAzyme-regulated strategy showed great potential in molecular computing. Given these facts, the rational design of ANAzyme with the allosteric domain presented here can expand the available toolbox to develop a variety of stimuli-responsive allosteric DNA materials, including molecular machines, computing systems, biosensing platforms, and gene-silencing tools.
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Affiliation(s)
- Yuqiang Hu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P. R. China
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, P. R. China
| | - Changjiang Li
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P. R. China
| | - Minghao Hu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P. R. China
| | - Zhen Zhang
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P. R. China
| | - Ruolan Fu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P. R. China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, P. R. China
| | - Tongbo Wu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P. R. China
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4
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Pandey R, Lu Y, McConnell EM, Osman E, Scott A, Gu J, Hoare T, Soleymani L, Li Y. Electrochemical DNAzyme-based biosensors for disease diagnosis. Biosens Bioelectron 2023; 224:114983. [PMID: 36640547 DOI: 10.1016/j.bios.2022.114983] [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: 09/10/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 01/01/2023]
Abstract
DNAzyme-based electrochemical biosensors provide exceptional analytical sensitivity and high target recognition specificity for disease diagnosis. This review provides a critical perspective on the fundamental and applied impact of incorporating DNAzymes in the field of electrochemical biosensing. Specifically, we highlight recent advances in creating DNAzyme-based electrochemical biosensors for diagnosing infectious diseases, cancer and regulatory diseases. We also develop an understanding of challenges around translating the research in the field of DNAzyme-based electrochemical biosensors from labs to clinics, followed by a discussion on different strategies that can be applied to enhance the performance of the currently existing technologies to create truly point-of-care electrochemical DNAzyme biosensors.
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Affiliation(s)
- Richa Pandey
- Department of Engineering Physics, McMaster University, Hamilton, Ontario, L8S 4K1, Canada; Department of Biomedical Engineering, University of Calgary, Calgary, Alberta, T2N 1N4, Canada.
| | - Yang Lu
- School of Biomedical Engineering, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Erin M McConnell
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Enas Osman
- School of Biomedical Engineering, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Alexander Scott
- School of Biomedical Engineering, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Jimmy Gu
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Todd Hoare
- School of Biomedical Engineering, McMaster University, Hamilton, Ontario, L8S 4K1, Canada; Department of Chemical Engineering, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Leyla Soleymani
- Department of Engineering Physics, McMaster University, Hamilton, Ontario, L8S 4K1, Canada; School of Biomedical Engineering, McMaster University, Hamilton, Ontario, L8S 4K1, Canada; Michael G. DeGroot Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4K1, Canada.
| | - Yingfu Li
- School of Biomedical Engineering, McMaster University, Hamilton, Ontario, L8S 4K1, Canada; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4K1, Canada; Michael G. DeGroot Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4K1, Canada.
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5
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Hua Y, Ma J, Li D, Wang R. DNA-Based Biosensors for the Biochemical Analysis: A Review. BIOSENSORS 2022; 12:bios12030183. [PMID: 35323453 PMCID: PMC8945906 DOI: 10.3390/bios12030183] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 03/09/2022] [Accepted: 03/16/2022] [Indexed: 05/21/2023]
Abstract
In recent years, DNA-based biosensors have shown great potential as the candidate of the next generation biomedical detection device due to their robust chemical properties and customizable biosensing functions. Compared with the conventional biosensors, the DNA-based biosensors have advantages such as wider detection targets, more durable lifetime, and lower production cost. Additionally, the ingenious DNA structures can control the signal conduction near the biosensor surface, which could significantly improve the performance of biosensors. In order to show a big picture of the DNA biosensor's advantages, this article reviews the background knowledge and recent advances of DNA-based biosensors, including the functional DNA strands-based biosensors, DNA hybridization-based biosensors, and DNA templated biosensors. Then, the challenges and future directions of DNA-based biosensors are discussed and proposed.
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Harding BI, Pollak NM, Stefanovic D, Macdonald J. Complexing deoxyribozymes with RNA aptamers for detection of the small molecule theophylline. Biosens Bioelectron 2022; 198:113774. [PMID: 34823962 DOI: 10.1016/j.bios.2021.113774] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 10/17/2021] [Accepted: 11/05/2021] [Indexed: 11/28/2022]
Abstract
Biointegrative information processing systems offer a great advantage to autonomous biodevices, as their capacity for biological computation provides the ability to sense the state of more complex environments and better integrate with downstream biological regulation systems. Deoxyribozymes (DNAzymes) and aptamers are of interest to such computational biosensing systems due to the enzymatic properties of DNAzymes and the ligand-inducible conformational structures of aptamers. Herein, we describe a novel method for providing ligand-responsive allosteric control to a DNAzyme using an RNA aptamer. We designed a NOT-logic-compliant E6 DNAzyme to be complementary to an RNA aptamer targeting theophylline, such that the aptamer competitively interacted with either theophylline or the DNAzyme, and disabled the DNAzyme only when theophylline concentration was below a given threshold. Out of our seven designed "complexing aptazymes," three demonstrated effective theophylline-responsive allosteric regulation (2.84 ± 3.75%, 4.97 ± 2.92%, and 8.91 ± 4.19% activity in the absence of theophylline; 46.29 ± 3.36%, 50.70 ± 10.15%, and 61.26 ± 6.18% activity in the presence of theophylline). Moreover, the same three complexing aptazymes also demonstrated the ability to semi-quantitatively determine the concentration of theophylline present in solution, successfully discriminating between therapeutically ineffective (<20 μM), safe (20-100 μM), and toxic (>100 μM) theophylline concentrations. Our method of using an RNA aptamer for ligand-responsive allosteric control of a DNAzyme expands the way aptamers can be configured for biosensing, and suggests a pathway for embedding DNAzymes to provide enhanced information processing and control of biological systems.
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Affiliation(s)
- Bradley I Harding
- Genecology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland, 4556, Australia; School of Science and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, 4556, Australia
| | - Nina M Pollak
- Genecology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland, 4556, Australia; School of Science and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, 4556, Australia; CSIRO Synthetic Biology Future Science Platform, GPO Box 1700, Canberra, Australian Capital Territory, 2601, Australia
| | - Darko Stefanovic
- Department of Computer Science, University of New Mexico, Albuquerque, NM, 87131, United States; Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, NM, 87131, United States; Center for Biomedical Engineering, University of New Mexico, Albuquerque, NM, 87131, United States
| | - Joanne Macdonald
- Genecology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland, 4556, Australia; School of Science and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, 4556, Australia.
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Dillen A, Lammertyn J. Paving the way towards continuous biosensing by implementing affinity-based nanoswitches on state-dependent readout platforms. Analyst 2022; 147:1006-1023. [DOI: 10.1039/d1an02308j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Combining affinity-based nanoswitches with state-dependent readout platforms allows for continuous biosensing and acquisition of real-time information about biochemical processes occurring in the environment of interest.
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Affiliation(s)
- Annelies Dillen
- KU Leuven, Department of Biosystems – Biosensors Group, Willem de Croylaan 42, Box 2428, 3001, Leuven, Belgium
| | - Jeroen Lammertyn
- KU Leuven, Department of Biosystems – Biosensors Group, Willem de Croylaan 42, Box 2428, 3001, Leuven, Belgium
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8
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Yang L, Cao Y, Pei R. Selection of Aptamer for N-Methyl Mesoporphyrin IX to Develop Porphyrin Metalation DNAzyme. Methods Mol Biol 2022; 2439:15-26. [PMID: 35226312 DOI: 10.1007/978-1-0716-2047-2_2] [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: 06/14/2023]
Abstract
Mesoporphyrin IX (MPIX) contains a planar macrocycle center that can interact with various divalent metal ions through the exposed binding sites, leading to the metalation of MPIX. The DNA aptamers for porphyrin molecules usually display different catalytic functions (termed deoxyribozymes or DNAzymes), which can accelerate such chemical reactions. Inspired by this, an affinity chromatography selection approach was designed for identifying a porphyrin metalation DNAzyme. In our experiment, N-methyl mesoporphyrin IX (NMM), an analog of MPIX, is used as the target molecule, owing to its stable and high fluorescence enhancement after combining with specific oligonucleotides. Our results showed that the selected aptamer Nm1 is capable of binding to NMM with a low micromolar dissociation constant (0.75 ± 0.08 μM) and displays a catalytic activity for MPIX metalation with 3.3-fold rate enhancement. The protocol for isolation of such a porphyrin metalation DNAzyme is described in detail here.
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Affiliation(s)
- Luyan Yang
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, China
| | - Yanwei Cao
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, China
| | - Renjun Pei
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, China.
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei, China.
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9
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Hybridization chain reaction and its applications in biosensing. Talanta 2021; 234:122637. [PMID: 34364446 DOI: 10.1016/j.talanta.2021.122637] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 06/17/2021] [Accepted: 06/21/2021] [Indexed: 12/30/2022]
Abstract
To pursue the sensitive and efficient detection of informative biomolecules for bioanalysis and disease diagnosis, a series of signal amplification techniques have been put forward. Among them, hybridization chain reaction (HCR) is an isothermal and enzyme-free process where the cascade reaction of hybridization events is initiated by a target analyte, yielding a long nicked dsDNA molecule analogous to alternating copolymers. Compared with conventional polymerase chain reaction (PCR) that can proceed only with the aid of polymerases and complicated thermal cycling, HCR has attracted increasing attention because it can occur under mild conditions without using enzymes. As a powerful signal amplification tool, HCR has been employed to construct various simple, sensitive and economic biosensors for detecting nucleic acids, small molecules, cells, and proteins. Moreover, HCR has also been applied to assemble complex nanostructures, some of which even act as the carriers to execute the targeted delivery of anticancer drugs. Recently, HCR has engendered tremendous progress in RNA imaging applications, which can not only achieve endogenous RNA imaging in living cells or even living animals but also implement imaging-guided photodynamic therapy, paving a promising path to promote the development of theranostics. In this review, we begin with the fundamentals of HCR and then focus on summarizing the recent advances in HCR-based biosensors for biosensing and RNA imaging strategies. Further, the challenges and future perspective of HCR-based signal amplification in biosensing and theranostic application are discussed.
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10
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Li Q, Wu JT, Liu Y, Qi XM, Jin HG, Yang C, Liu J, Li GL, He QG. Recent advances in black phosphorus-based electrochemical sensors: A review. Anal Chim Acta 2021; 1170:338480. [PMID: 34090586 DOI: 10.1016/j.aca.2021.338480] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 03/30/2021] [Accepted: 03/31/2021] [Indexed: 12/11/2022]
Abstract
Since the discovery of liquid-phase-exfoliated black phosphorus (BP) as a field-effect transistor in 2014, BP, with its 2D layered structure, has attracted significant attention, owing to its anisotropic electroconductivity, tunable direct bandgap, extraordinary surface activity, moderate switching ratio, high hole mobility, good biocompatibility, and biodegradability. Several pioneering research efforts have explored the application of BP in different types of electrochemical sensors. This review summarizes the latest synthesis methods, protection strategies, and electrochemical sensing applications of BP and its derivatives. The typical synthesis methods for BP-based crystals, nanosheets, and quantum dots are discussed in detail; the degradation of BP under ambient conditions is introduced; and state-of-the-art protection methodologies for enhancing BP stability are explored. Various electrochemical sensing applications, including chemically modified electrodes, electrochemiluminescence sensors, enzyme electrodes, electrochemical aptasensors, electrochemical immunosensors, and ion-selective electrodes are discussed in detail, along with the mechanisms of BP functionalization, sensing strategies, and sensing properties. Finally, the major challenges in this field are outlined and future research avenues for BP-based electrochemical sensors are highlighted.
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Affiliation(s)
- Qing Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou, 412007, China
| | - Jing-Tao Wu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou, 412007, China
| | - Ying Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou, 412007, China
| | - Xiao-Man Qi
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou, 412007, China
| | - Hong-Guang Jin
- College of Materials Science and Engineering, Changsha University of Science and Technology, Changsha, 410114, China
| | - Chun Yang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou, 412007, China
| | - Jun Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou, 412007, China
| | - Guang-Li Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou, 412007, China.
| | - Quan-Guo He
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou, 412007, China
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Ahmadi Y, Soldo R, Rathammer K, Eibler L, Barišić I. Analyzing Criteria Affecting the Functionality of G-Quadruplex-Based DNA Aptazymes as Colorimetric Biosensors and Development of Quinine-Binding Aptazymes. Anal Chem 2021; 93:5161-5169. [PMID: 33724777 DOI: 10.1021/acs.analchem.0c05052] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A DNA aptazyme consists of an aptamer domain and a DNAzyme module, in which the DNAzyme activity can be regulated by the aptamer-target interaction. The complex of G-quadruplex (GQ) and hemin is a peroxidase-mimicking DNAzyme and has become increasingly popular as a reporter system for biosensing applications. The development of GQ-based aptazymes is of high interest as they can be used as label-free biosensors for the real-time detection of pathogens. Herein, we rationally designed ca. 200 GQ-based aptazyme candidates and evaluated the suitability of 14 aptamers targeting quinine, Protein A, Staphylococcus enterotoxin B, and ATP for this detection concept. As a result, six novel aptazymes were developed for the specific detection of quinine based on two quinine-binding aptamers. The rest of designed probes, however, hardly showed significant functionality. To uncover the reasons, we performed enzyme-linked oligonucleotide assays to find how the affinity of aptamers is affected once conjugated to the DNAzyme sequence or upon integration into the aptazyme probe. Furthermore, we investigated the impact of the structure-switching functionality in the parent aptamer and the effect of the reaction matrix on the efficiency of probes.
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Affiliation(s)
- Yasaman Ahmadi
- Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria
| | - Regina Soldo
- Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria
| | - Krista Rathammer
- Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria
| | - Laura Eibler
- Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria
| | - Ivan Barišić
- Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria
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12
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Abstract
Aptamers are single-stranded DNA or RNA molecules that can be identified through an iterative in vitro selection–amplification process. Among them, fluorogenic aptamers in response to small molecules have been of great interest in biosensing and bioimaging due to their rapid fluorescence turn-on signals with high target specificity and low background noise. In this review, we report recent advances in fluorogenic aptasensors and their applications to in vitro diagnosis and cellular imaging. These aptasensors modulated by small molecules have been implemented in different modalities that include duplex or molecular beacon-type aptasensors, aptazymes, and fluorogen-activating aptamer reporters. We highlight the working principles, target molecules, modifications, and performance characteristics of fluorogenic aptasensors, and discuss their potential roles in the field of biosensor and bioimaging with future directions and challenges.
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Sorrentino D, Ranallo S, Ricci F. Rational Control of the Activity of a Cu 2+-Dependent DNAzyme by Re-engineering Purely Entropic Intrinsically Disordered Domains. ACS APPLIED MATERIALS & INTERFACES 2021; 13:9300-9305. [PMID: 33001621 DOI: 10.1021/acsami.0c09472] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The function and activity of many proteins is finely controlled by the modulation of the entropic contribution of intrinsically disordered domains that are not directly involved in any recognition event. Inspired by this mechanism, we demonstrate here that we could finely regulate the catalytic activity of a model DNAzyme (i.e., a synthetic DNA sequence with enzyme-like properties) by rationally introducing intrinsically disordered nucleic acid portions in its original sequence. More specifically, we have re-engineered here the well-characterized Cu2+-dependent DNAzyme that catalyzes a self-cleavage reaction by introducing a poly(T) linker domain in its sequence. The linker is not directly involved in the recognition event and connects the two domains that fold to form the catalytic core. We demonstrate that the enzyme-like activity of this re-engineered DNAzyme can be modulated in a predictable and fine way by changing the length, and thus entropy, of such a linker domain. Given these attributes, the rational design of intrinsically disordered domains could expand the available toolbox to achieve a control of the activity of DNAzymes and, in analogy, ribozymes through a purely entropic contribution.
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Affiliation(s)
- Daniela Sorrentino
- Chemistry Department, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Simona Ranallo
- Chemistry Department, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Francesco Ricci
- Chemistry Department, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
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Liu LS, Wang F, Ge Y, Lo PK. Recent Developments in Aptasensors for Diagnostic Applications. ACS APPLIED MATERIALS & INTERFACES 2021; 13:9329-9358. [PMID: 33155468 DOI: 10.1021/acsami.0c14788] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Aptamers are exciting smart molecular probes for specific recognition of disease biomarkers. A number of strategies have been developed to convert target-aptamer binding into physically detectable signals. Since the aptamer sequence was first discovered, a large variety of aptamer-based biosensors have been developed, with considerable attention paid to their potential applications in clinical diagnostics. So far, a variety of techniques in combination with a wide range of functional nanomaterials have been used for the design of aptasensors to further improve the sensitivity and detection limit of target determination. In this paper, the advantages of aptamers over traditional antibodies as the molecular recognition components in biosensors for high-throughput screening target molecules are highlighted. Aptamer-target pairing configurations are predominantly single- or dual-site binding; the design of recognition modes of each aptamer-target pairing configuration is described. Furthermore, signal transduction strategies including optical, electrical, mechanical, and mass-sensitive modes are clearly explained together with examples. Finally, we summarize the recent progress in the development of aptamer-based biosensors for clinical diagnosis, including detection of cancer and disease biomarkers and in vivo molecular imaging. We then conclude with a discussion on the advanced development and challenges of aptasensors.
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Affiliation(s)
- Ling Sum Liu
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Fei Wang
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Yonghe Ge
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Pik Kwan Lo
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, China
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15
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Shahsavar K, Shokri E, Hosseini M. A fluorescence-readout method for miRNA-155 detection with double-hairpin molecular beacon based on quadruplex DNA structure. Microchem J 2020. [DOI: 10.1016/j.microc.2020.105277] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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16
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LIU Z, LIU T, TAO CA, CHEN X, HUANG J, WANG F, WANG J. Amplified Analysis of DNA or Proteins by TdT-generated DNAzyme. ANAL SCI 2020; 36:835-840. [DOI: 10.2116/analsci.19p387] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Zhuoliang LIU
- College of Liberal Arts and Sciences, National University of Defense Technology
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University
| | - Tianxiong LIU
- College of Liberal Arts and Sciences, National University of Defense Technology
| | - Cheng-an TAO
- College of Liberal Arts and Sciences, National University of Defense Technology
| | - Xianzhe CHEN
- College of Liberal Arts and Sciences, National University of Defense Technology
| | - Jian HUANG
- College of Liberal Arts and Sciences, National University of Defense Technology
| | - Fang WANG
- College of Liberal Arts and Sciences, National University of Defense Technology
| | - Jianfang WANG
- College of Liberal Arts and Sciences, National University of Defense Technology
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17
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Tao Z, Zhou Y, Li X, Wang Z. Competitive HRP-Linked Colorimetric Aptasensor for the Detection of Fumonisin B1 in Food based on Dual Biotin-Streptavidin Interaction. BIOSENSORS 2020; 10:E31. [PMID: 32235423 PMCID: PMC7235773 DOI: 10.3390/bios10040031] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/19/2020] [Accepted: 03/25/2020] [Indexed: 02/07/2023]
Abstract
Fumonisin B1 (FB1) is the most prevalent and toxic form among fumonisin homologues which are produced by fusarium species and it contaminates various types of food products, posing serious health hazards for humans and animals. In this work, a colorimetric assay for the detection of FB1 has been developed based on competitive horseradish peroxidase (HRP)-linked aptamer and dual biotin-streptavidin interaction. In short, a biotinylated aptamer of FB1 was immobilized on the microplate by biotin-streptavidin binding; the complementary strand (csDNA) of the aptamer was ligated with HRP by biotin-streptavidin binding again to form a csDNA-HRP sensing probe, competing with FB1 to bind to the aptamer. The color change can be observed after the addition of chromogenic and stop solution, thereby realizing the visual detection of FB1. Under optimal conditions, good linearity was observed within the concentration range of 0.5 to 300 ng/mL, with a detection of limit of 0.3 ng/mL. This assay is further validated by spike recovery tests towards beer and corn samples, it provides a simple, sensitive and reliable method for the screening of FB1 in food samples and may be potentially used as an alternative to conventional assays.
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Affiliation(s)
- Zui Tao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (Z.T.); (Y.Z.); (X.L.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - You Zhou
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (Z.T.); (Y.Z.); (X.L.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Xiang Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (Z.T.); (Y.Z.); (X.L.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Zhouping Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (Z.T.); (Y.Z.); (X.L.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
- Collaborative Innovation Center of Food safety and Quality Control of Jiangsu Province, Jiangnan University, Wuxi 214122, China
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18
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LIU ZL, TAO CA, WANG JF. Progress on Applications of G-quadruplex in Biochemical Analysis. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2020. [DOI: 10.1016/s1872-2040(19)61212-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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19
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Mao X, Li Q, Zuo X, Fan C. Catalytic Nucleic Acids for Bioanalysis. ACS APPLIED BIO MATERIALS 2019; 3:2674-2685. [PMID: 35025402 DOI: 10.1021/acsabm.9b00928] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Xiuhai Mao
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Chunhai Fan
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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20
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Wang J, Song Q, Guo X, Cui X, Tan L, Dong L. Precise Cross-Dimensional Regulation of the Structure of a Photoreversible DNA Nanoswitch. Anal Chem 2019; 91:14530-14537. [PMID: 31617350 DOI: 10.1021/acs.analchem.9b03547] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this study, an accurately and digitally regulated allosteric nanoswitch based on the conformational control of two DNA hairpins was developed. By switching between UV irradiation and blue light conditions, the second molecular beacon (H#2) would bind/separate with a repression sequence (RES) via the introduced PTG molecules (a photosensitive azobenzene derivative), resulting in the target aptamer sequence in the first molecular beacon (H#1) not being able/being able to hold the stem-loop configuration, hence losing/regaining the ability to bind with the target. Importantly, we successfully monitor conformation changes of the nanoswitch by an elegant mathematical model for connecting Ki (the dissociation constant between RES and H#2) with Kd (the overall equilibrium constant of the nanoswitch binding the target), hence realizing "observing" DNA structure across dimensions from "structural visualization" to digitization and, accurately, digitally regulating DNA structure from digitization to "structural visualization".
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Affiliation(s)
- Jing Wang
- College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China.,School of Chemistry and Chemical Engineering , Chongqing University , Chongqing 400044 , China.,Key Laboratory of Low-grade Energy Utilization Technologies & Systems of the Ministry of Education , Chongqing University , Chongqing 40004 , China
| | - Qitao Song
- College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China.,Peking-Tsinghua Center for Life Sciences , Peking University , 100871 Beijing , China
| | - Xiaogang Guo
- College of Chemistry and Chemical Engineering , Yangtze Normal. University , Chongqing 408100 , China
| | - Xun Cui
- School of Materials Science and Engineering , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
| | - Luxi Tan
- School of Chemistry and Chemical Engineering , Chongqing University , Chongqing 400044 , China.,Key Laboratory of Low-grade Energy Utilization Technologies & Systems of the Ministry of Education , Chongqing University , Chongqing 40004 , China
| | - Lichun Dong
- School of Chemistry and Chemical Engineering , Chongqing University , Chongqing 400044 , China.,Key Laboratory of Low-grade Energy Utilization Technologies & Systems of the Ministry of Education , Chongqing University , Chongqing 40004 , China
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21
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Díaz-Cartagena D, Hernández-Cancel G, Bracho-Rincón DP, González-Feliciano JA, Cunci L, González CI, Cabrera CR. Label-Free Telomerase Activity Detection via Electrochemical Impedance Spectroscopy. ACS OMEGA 2019; 4:16724-16732. [PMID: 31646217 PMCID: PMC6796945 DOI: 10.1021/acsomega.9b00783] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 05/16/2019] [Indexed: 05/14/2023]
Abstract
In the last decade, researchers have been searching for innovative platforms, methods, and techniques able to address recurring problems with the current cancer detection methods. Early disease detection, fast results, point-of-care sensing, and cost are among the most prevalent issues that need further exploration in this field. Herein, studies are focused on overcoming these problems by developing an electrochemical device able to detect telomerase as a cancer biomarker. Electrochemical platforms and techniques are more appealing for cancer detection, offering lower costs than the established cancer detection methods, high sensitivity inherent to the technique, rapid signal processing, and their capacity of being miniaturized. Therefore, Au interdigital electrodes and electrochemical impedance spectroscopy were used to detect telomerase activity in acute T cell leukemia. Different cancer cell concentrations were evaluated, and a detection limit of 1.9 × 105 cells/mL was obtained. X-ray photoelectron spectroscopy was used to characterize the telomerase substrate (TS) DNA probe self-assembled monolayer on gold electrode surfaces. Atomic force microscopy displayed three-dimensional images of the surface to establish a height difference of 9.0 nm between the bare electrode and TS-modified Au electrodes. The TS probe is rich in guanines, thus forming secondary structures known as G-quadruplex that can be triggered with a fluorescence probe. Confocal microscopy fluorescence images showed the formation of DNA G-quadruplex because of TS elongation by telomerase on the Au electrode surface. Moreover, electrodes exposed to telomerase containing 2',3'-dideoxyguanosine-5'-triphosphate (ddGTP) did not exhibit high fluorescence, as ddGTP is a telomerase inhibitor, thus making this device suitable for telomerase inhibitors capacity studies. The electrochemical method and Au microchip device may be developed as a biosensor for a point-of-care medical device.
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Affiliation(s)
- Diana
C. Díaz-Cartagena
- Department
of Chemistry, University of Puerto Rico, Río Piedras Campus, San Juan, Puerto Rico 00925-2537, United States
- Molecular
Sciences Research Center, University of
Puerto Rico, San Juan, Puerto Rico 00926, United States
| | - Griselle Hernández-Cancel
- Molecular
Sciences Research Center, University of
Puerto Rico, San Juan, Puerto Rico 00926, United States
| | - Dina P. Bracho-Rincón
- Molecular
Sciences Research Center, University of
Puerto Rico, San Juan, Puerto Rico 00926, United States
- Department
of Biology, University of Puerto Rico, Río Piedras Campus, San Juan, Puerto Rico 00931, United States
| | - José A. González-Feliciano
- Molecular
Sciences Research Center, University of
Puerto Rico, San Juan, Puerto Rico 00926, United States
| | - Lisandro Cunci
- School
of Natural Sciences and Technology, Universidad
Ana G. Méndez, Gurabo Campus, Gurabo, Puerto
Rico 00778, United
States
| | - Carlos I. González
- Molecular
Sciences Research Center, University of
Puerto Rico, San Juan, Puerto Rico 00926, United States
- Department
of Biology, University of Puerto Rico, Río Piedras Campus, San Juan, Puerto Rico 00931, United States
| | - Carlos R. Cabrera
- Department
of Chemistry, University of Puerto Rico, Río Piedras Campus, San Juan, Puerto Rico 00925-2537, United States
- Molecular
Sciences Research Center, University of
Puerto Rico, San Juan, Puerto Rico 00926, United States
- E-mail:
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22
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Kosman J, Juskowiak B. Bioanalytical Application of Peroxidase-Mimicking DNAzymes: Status and Challenges. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2019; 170:59-84. [PMID: 28474157 DOI: 10.1007/10_2017_7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
DNAzymes with peroxidase-mimicking activity are a new class of catalytically active DNA molecules. This system is formed as a complex of hemin and a G-quadruplex structure created by oligonucleotides rich in guanine. Considering catalytic activity, this DNAzyme mimics horseradish peroxidase, the enzyme most commonly used for signal generation in bioassays. Because DNAzymes exhibit many advantages over protein enzymes (thermal stability, easy and cheap synthesis and purification) they can successfully replace HRP in bioanalytical applications. HRP-like DNAzymes have been applied in the detection of several DNA sequences. Many amplification techniques have been conjugated with DNAzyme systems, resulting in ultrasensitive bioassays. On the other hand, the combination of aptamers and DNAzymes has led to the development of aptazymes for specific targets. An up-to-date summary of the most interesting DNAzyme-based assays is presented here. The elaborated systems can be used in medical diagnosis or chemical and biological studies.
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Affiliation(s)
- J Kosman
- Laboratory of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Poznan, Poland.
| | - B Juskowiak
- Laboratory of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Poznan, Poland
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23
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Li J, Lin L, Yu J, Zhai S, Liu G, Tian L. Fabrication and Biomedical Applications of “Polymer-Like” Nucleic Acids Enzymatically Produced by Rolling Circle Amplification. ACS APPLIED BIO MATERIALS 2019; 2:4106-4120. [DOI: 10.1021/acsabm.9b00622] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jing Li
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Boulevard, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
| | - Li Lin
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Boulevard, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
| | - Jiantao Yu
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Boulevard, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
| | - Shiyao Zhai
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Boulevard, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
| | - Guoyuan Liu
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Boulevard, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
| | - Leilei Tian
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Boulevard, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
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24
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Chen YH, Chien WC, Lee DC, Tan KT. Signal Amplification and Detection of Small Molecules via the Activation of Streptavidin and Biotin Recognition. Anal Chem 2019; 91:12461-12467. [DOI: 10.1021/acs.analchem.9b03144] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
| | | | | | - Kui-Thong Tan
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan (ROC)
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25
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Li S, Li G, Du Z, Zhu L, Tian J, Luo Y, Huang K, Xu W. The ultra-sensitive visual biosensor based on thermostatic triple step functional nucleic acid cascade amplification for detecting Zn2+. Food Chem 2019; 290:95-100. [DOI: 10.1016/j.foodchem.2019.03.134] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 03/21/2019] [Accepted: 03/25/2019] [Indexed: 12/29/2022]
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26
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Ramalingam S, Chand R, Singh CB, Singh A. Phosphorene-gold nanocomposite based microfluidic aptasensor for the detection of okadaic acid. Biosens Bioelectron 2019; 135:14-21. [PMID: 30981975 DOI: 10.1016/j.bios.2019.03.056] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/21/2019] [Accepted: 03/26/2019] [Indexed: 11/25/2022]
Abstract
Okadaic acid (OA) is one of the most prevalent and largely distributed bio-toxin in the world. Consumption of OA results in a series of digestive ailments such as nausea and diarrhea. This study demonstrates the preparation and functioning of an electrochemical microfluidic biochip for the detection of OA. The screen-printed carbon electrode (SPCE) was modified by phosphorene-gold nanocomposite onto which an aptamer specific to OA was immobilized. BP-Au nanocomposites were synthesized by an in-situ, one-step method without the use of a reducing agent. Potassium ferro-ferri cyanide was used as a redox pair to quantify signal strength. To improve reaction time, increase sensitivity and portability, a microfluidic platform was designed and developed. This device comprised of channels identified for specific purposes such as sample mixing and incubation. Overall, the integrated system consisted of a polydimethylsiloxane microfluidic chip housing an aptamer modified SPCE, as a single detection module for Okadaic acid. The nanomaterials and the microfluidic channels prepared were spectroscopically and electrochemically analyzed. Differential pulse voltammograms revealed a detection limit of 8 pM, while a linear range was found between 10 nM-250 nM. Selectivity studies were also performed with spiked mussel samples and other interfering species. This point-of-care device can be deployed to perform on-farm assays in fishing units.
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Affiliation(s)
| | - Rohit Chand
- W. Booth School of Engineering Practice and Technology, McMaster University, Hamilton, ON, L8S 4L8, Canada
| | - Chandra B Singh
- Stored Grains Engineering, School of Engineering, University of South Australia, Adelaide, SA, 5001, Australia
| | - Ashutosh Singh
- School of Engineering, University of Guelph, Guelph, ON, N1G 2W1, Canada.
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27
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Munzar JD, Ng A, Juncker D. Duplexed aptamers: history, design, theory, and application to biosensing. Chem Soc Rev 2019; 48:1390-1419. [PMID: 30707214 DOI: 10.1039/c8cs00880a] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Nucleic acid aptamers are single stranded DNA or RNA sequences that specifically bind a cognate ligand. In addition to their widespread use as stand-alone affinity binding reagents in analytical chemistry, aptamers have been engineered into a variety of ligand-specific biosensors, termed aptasensors. One of the most common aptasensor formats is the duplexed aptamer (DA). As defined herein, DAs are aptasensors containing two nucleic acid elements coupled via Watson-Crick base pairing: (i) an aptamer sequence, which serves as a ligand-specific receptor, and (ii) an aptamer-complementary element (ACE), such as a short DNA oligonucleotide, which is designed to hybridize to the aptamer. The ACE competes with ligand binding, such that DAs generate a signal upon ligand-dependent ACE-aptamer dehybridization. DAs possess intrinsic advantages over other aptasensor designs. For example, DA biosensing designs generalize across DNA and RNA aptamers, DAs are compatible with many readout methods, and DAs are inherently tunable on the basis of nucleic acid hybridization. However, despite their utility and popularity, DAs have not been well defined in the literature, leading to confusion over the differences between DAs and other aptasensor formats. In this review, we introduce a framework for DAs based on ACEs, and use this framework to distinguish DAs from other aptasensor formats and to categorize cis- and trans-DA designs. We then explore the ligand binding dynamics and chemical properties that underpin DA systems, which fall under conformational selection and induced fit models, and which mirror classical SN1 and SN2 models of nucleophilic substitution reactions. We further review a variety of in vitro and in vivo applications of DAs in the chemical and biological sciences, including riboswitches and riboregulators. Finally, we present future directions of DAs as ligand-responsive nucleic acids. Owing to their tractability, versatility and ease of engineering, DA biosensors bear a great potential for the development of new applications and technologies in fields ranging from analytical chemistry and mechanistic modeling to medicine and synthetic biology.
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Affiliation(s)
- Jeffrey D Munzar
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada.
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28
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Fu B, Park Y, Kim KT, Chen K, Zou G, Wei Q, Peng S, Chen Y, Kim BH, Zhou X. A novel nucleic acid aptamer tag: a rapid fluorescence strategy using a self-constructing G-quadruplex from AGG trinucleotide repeats. Chem Commun (Camb) 2018; 54:11487-11490. [PMID: 30256356 DOI: 10.1039/c8cc05197f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Herein, we have developed a novel fluorescence labeling strategy for nucleic acid aptamers based on self-assembling between AGG tri-nucleotide repeats and a pyrene-modified oligonucleotide. This strategy could be an effective tool for developing targeting-imaging systems and biosensor systems to detect target molecules.
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Affiliation(s)
- Boshi Fu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan, Hubei 430072, P. R. China.
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29
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An Aptamer-Based Biosensor for Direct, Label-Free Detection of Melamine in Raw Milk. SENSORS 2018; 18:s18103227. [PMID: 30257498 PMCID: PMC6210019 DOI: 10.3390/s18103227] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 09/19/2018] [Accepted: 09/20/2018] [Indexed: 01/19/2023]
Abstract
Melamine, a nitrogen-rich compound, has been used as a food and milk additive to falsely increase the protein content. However, melamine is toxic, and high melamine levels in food or in milk can cause kidney and urinary problems, or even death. Hence, the detection of melamine in food and milk is desirable, for which numerous detection methods have been developed. Several methods have successfully detected melamine in raw milk; however, they require a sample preparation before the analyses. This study aimed to develop an aptamer-DNAzyme conjugated biosensor for label-free detection of melamine, in raw milk, without any sample preparation. An aptamer-DNAzyme conjugated biosensor was developed via screening using microarray analysis to identify the candidate aptamers followed by an optimization, to reduce the background noise and improve the aptamer properties, thereby, enhancing the signal-to-noise (S/N) ratio of the screened biosensor. The developed biosensor was evaluated via colorimetric detection and tested with raw milk without any sample preparation, using N-methylmesoporphyrin IX for fluorescence detection. The biosensor displayed significantly higher signal intensity at 2 mM melamine (S/N ratio, 20.2), which was sufficient to detect melamine at high concentrations, in raw milk.
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30
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Sensitive and rapid aptasensing of chloramphenicol by colorimetric signal transduction with a DNAzyme-functionalized gold nanoprobe. Food Chem 2018; 270:287-292. [PMID: 30174048 DOI: 10.1016/j.foodchem.2018.07.127] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 05/13/2018] [Accepted: 07/18/2018] [Indexed: 01/03/2023]
Abstract
By combination of the aptamer biorecognition with the colorimetric signal transduction of a DNAzyme-functionalized nanoprobe, a new biosensing method was developed for the rapid and sensitive detection of chloramphenicol (CAP). The nanoprobe was prepared through the functionalization of gold nanoparticles with the complementary oligonucleotide against aptamer and high-content hemin/G-quadruplex DNAzyme. When one-step incubating the nanoprobe and CAP at a constructed aptamer-magnetic bead (MB) biosensing platform, due to the competitive biorecognition reaction, the nanoprobes related with CAP amounts were quantitative captured onto the MB surface. Based on the catalytic reaction of the peroxidase-mimicking DNAzyme, a colored substance was produced for the colorimetric signal transduction of the method. Due to the great signal amplification of the nanoprobe, a very low detection limit down to 0.13 pg/mL was obtained. Considering the excellent performance of the aptasensing method and satisfactory results for milk sample experiments, it indicates good reliability for practical applications.
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31
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Wang Y, Shan D, Wu G, Wang H, Ru F, Zhang X, Li L, Qian Y, Lu X. A novel “dual-potential” ratiometric electrochemiluminescence DNA sensor based on enhancing and quenching effect by G-quadruplex / hemin and Au-Luminol bifunctional nanoparticles. Biosens Bioelectron 2018; 106:64-70. [DOI: 10.1016/j.bios.2018.01.052] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 01/22/2018] [Accepted: 01/23/2018] [Indexed: 11/26/2022]
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32
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Sato H, Shimada N, Masuda T, Maruyama A. Allosteric Control of Peroxidase-Mimicking DNAzyme Activity with Cationic Copolymers. Biomacromolecules 2018; 19:2082-2088. [DOI: 10.1021/acs.biomac.8b00201] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Hiroki Sato
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 B-57 Nagatsuta Midori-ku, Yokohama, Kanagawa, Japan 226-8501
| | - Naohiko Shimada
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 B-57 Nagatsuta Midori-ku, Yokohama, Kanagawa, Japan 226-8501
| | - Tsukuru Masuda
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 B-57 Nagatsuta Midori-ku, Yokohama, Kanagawa, Japan 226-8501
| | - Atsushi Maruyama
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 B-57 Nagatsuta Midori-ku, Yokohama, Kanagawa, Japan 226-8501
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33
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Castillo RR, Baeza A, Vallet-Regí M. Recent applications of the combination of mesoporous silica nanoparticles with nucleic acids: development of bioresponsive devices, carriers and sensors. Biomater Sci 2018; 5:353-377. [PMID: 28105473 DOI: 10.1039/c6bm00872k] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The discovery and control of the biological roles mediated by nucleic acids have turned them into a powerful tool for the development of advanced biotechnological materials. Such is the importance of these gene-keeping biomacromolecules that even nanomaterials have succumbed to the claimed benefits of DNA and RNA. Currently, there could be found in the literature a practically intractable number of examples reporting the use of combination of nanoparticles with nucleic acids, so boundaries are demanded. Following this premise, this review will only cover the most recent and powerful strategies developed to exploit the possibilities of nucleic acids as biotechnological materials when in combination with mesoporous silica nanoparticles. The extensive research done on nucleic acids has significantly incremented the technological possibilities for those biomacromolecules, which could be employed in many different applications, where substrate or sequence recognition or modulation of biological pathways due to its coding role in living cells are the most promising. In the present review, the chosen counterpart, mesoporous silica nanoparticles, also with unique properties, became a reference material for drug delivery and biomedical applications due to their high biocompatibility and porous structure suitable for hosting and delivering small molecules. Although most of the reviews dealt with significant advances in the use of nucleic acid and mesoporous silica nanoparticles in biotechnological applications, a rational classification of these new generation hybrid materials is still uncovered. In this review, there will be covered promising strategies for the development of living cell and biological sensors, DNA-based molecular gates with targeting, transfection or silencing properties, which could provide a significant advance in current nanomedicine.
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Affiliation(s)
- Rafael R Castillo
- Dpto. Química Inorgánica y Bioinorgánica. Facultad de Farmacia, Universidad Complutense de Madrid. Plaza Ramon y Cajal s/n. Instituto de Investigación Sanitaria Hospital 12 de Octubre i+12, Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain.
| | - Alejandro Baeza
- Dpto. Química Inorgánica y Bioinorgánica. Facultad de Farmacia, Universidad Complutense de Madrid. Plaza Ramon y Cajal s/n. Instituto de Investigación Sanitaria Hospital 12 de Octubre i+12, Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain.
| | - María Vallet-Regí
- Dpto. Química Inorgánica y Bioinorgánica. Facultad de Farmacia, Universidad Complutense de Madrid. Plaza Ramon y Cajal s/n. Instituto de Investigación Sanitaria Hospital 12 de Octubre i+12, Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain.
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Rossetti M, Porchetta A. Allosterically regulated DNA-based switches: From design to bioanalytical applications. Anal Chim Acta 2018; 1012:30-41. [PMID: 29475471 DOI: 10.1016/j.aca.2017.12.046] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 12/10/2017] [Accepted: 12/28/2017] [Indexed: 02/07/2023]
Abstract
DNA-based switches are structure-switching biomolecules widely employed in different bioanalytical applications. Of particular interest are DNA-based switches whose activity is regulated through the use of allostery. Allostery is a naturally occurring mechanism in which ligand binding induces the modulation and fine control of a connected biomolecule function as a consequence of changes in concentration of the effector. Through this general mechanism, many different allosteric DNA-based switches able to respond in a highly controlled way at the presence of a specific molecular effector have been engineered. Here, we discuss how to design allosterically regulated DNA-based switches and their applications in the field of molecular sensing, diagnostic and drug release.
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Affiliation(s)
- Marianna Rossetti
- Chemistry Department, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Alessandro Porchetta
- Chemistry Department, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy.
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Fluorescence Sensing Using DNA Aptamers in Cancer Research and Clinical Diagnostics. Cancers (Basel) 2017; 9:cancers9120174. [PMID: 29261171 PMCID: PMC5742822 DOI: 10.3390/cancers9120174] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 12/14/2017] [Accepted: 12/16/2017] [Indexed: 12/12/2022] Open
Abstract
Among the various advantages of aptamers over antibodies, remarkable is their ability to tolerate a large number of chemical modifications within their backbone or at the termini without losing significant activity. Indeed, aptamers can be easily equipped with a wide variety of reporter groups or coupled to different carriers, nanoparticles, or other biomolecules, thus producing valuable molecular recognition tools effective for diagnostic and therapeutic purposes. This review reports an updated overview on fluorescent DNA aptamers, designed to recognize significant cancer biomarkers both in soluble or membrane-bound form. In many examples, the aptamer secondary structure switches induced by target recognition are suitably translated in a detectable fluorescent signal using either fluorescently-labelled or label-free aptamers. The fluorescence emission changes, producing an enhancement (“signal-on”) or a quenching (“signal-off”) effect, directly reflect the extent of the binding, thereby allowing for quantitative determination of the target in bioanalytical assays. Furthermore, several aptamers conjugated to fluorescent probes proved to be effective for applications in tumour diagnosis and intraoperative surgery, producing tumour-type specific, non-invasive in vivo imaging tools for cancer pre- and post-treatment assessment.
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Centola M, Valero J, Famulok M. Allosteric Control of Oxidative Catalysis by a DNA Rotaxane Nanostructure. J Am Chem Soc 2017; 139:16044-16047. [DOI: 10.1021/jacs.7b08839] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Mathias Centola
- LIMES
Chemical Biology Unit, Universität Bonn, Gerhard-Domagk-Straße
1, 53121 Bonn, Germany
| | - Julián Valero
- LIMES
Chemical Biology Unit, Universität Bonn, Gerhard-Domagk-Straße
1, 53121 Bonn, Germany
- Center of Advanced European Studies and Research, Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Michael Famulok
- LIMES
Chemical Biology Unit, Universität Bonn, Gerhard-Domagk-Straße
1, 53121 Bonn, Germany
- Center of Advanced European Studies and Research, Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
- Center
of Aptamer Research and Development, University of Bonn, Gerhard-Domagk-Straße
1, 53121 Bonn, Germany
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Ma H, Li W, Zhou W, Liu J. Site-Selective Labeling of Chromium(III) as a Quencher on DNA for Molecular Beacons. Chempluschem 2017; 82:1224-1230. [DOI: 10.1002/cplu.201700361] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Huan Ma
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
| | - Wang Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
- Department of Chemistry; Water Institute and Waterloo Institute for Nanotechnology; University of Waterloo; Waterloo ON N2L 3G1 Canada
| | - Wenhu Zhou
- Department of Chemistry; Water Institute and Waterloo Institute for Nanotechnology; University of Waterloo; Waterloo ON N2L 3G1 Canada
- Xiangya School of Pharmaceutical Sciences; Central South University; Changsha Hunan 410013 P. R. China
| | - Juewen Liu
- Department of Chemistry; Water Institute and Waterloo Institute for Nanotechnology; University of Waterloo; Waterloo ON N2L 3G1 Canada
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Li X, Zhang H, Tang Y, Wu P, Xu S, Zhang X. A Both-End Blocked Peroxidase-Mimicking DNAzyme for Low-Background Chemiluminescent Sensing of miRNA. ACS Sens 2017; 2:810-816. [PMID: 28723123 DOI: 10.1021/acssensors.7b00178] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
G-quadruplex DNAzymes that exhibited peroxidase-like activity have been shown to be appealing reporters for amplified readout of biosensing events simply by their formation or dissociation in the presence of analytes. For low background signaling, the efficient preblock of DNAzymes is critically important. Herein, we report a both-end blocked DNAzyme beacon strategy for chemiluminescent biosensing. The catalytic activity of peroxidase-mimicking DNAzyme can be inactivated fully by fixing both ends of the DNAzyme sequence, and easily recovered via a strand displace reaction between the miRNA and the block DNA. The efficient block and recovery of DNAzymes provide the both-end blocked beacon the highest signal-to-background ratio (over 25) among the reported DNAzymes for amplification-free detection of miRNA. As a result, the beacon allowed detection of subpicomolar miRNA without any labeling and amplification procedures, which is about 40-fold more sensitive than the traditional hairpin fluorescence beacon. Also, it exhibited excellent discrimination ability that can distinguish single-base mismatch miRNA. The simplicity, high sensitivity, and selectivity provided by the beacon make it a promising alternative tool for nucleic acid detection.
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Affiliation(s)
- Xianming Li
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, China
| | - Houchun Zhang
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, China
| | - Yurong Tang
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, China
| | - Peng Wu
- Analytical & Testing Center, Sichuan University, Chengdu 610064, China
| | - Shuxia Xu
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, China
| | - Xinfeng Zhang
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, China
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Chen L, Chao J, Qu X, Zhang H, Zhu D, Su S, Aldalbahi A, Wang L, Pei H. Probing Cellular Molecules with PolyA-Based Engineered Aptamer Nanobeacon. ACS APPLIED MATERIALS & INTERFACES 2017; 9:8014-8020. [PMID: 28221021 DOI: 10.1021/acsami.6b16764] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Adenosine triphosphate (ATP) is a central metabolite that is of critical importance in many cellular processes. The development of sensitive and selective methods for the detection of ATP level in vivo is crucial in diagnostic and theranostic applications. In this work, we have developed a polyA-based aptamer nanobeacon (PAaptNB) with improved efficiency and speed of ATP analysis. We found that the dissociation constants and competitive binding kinetics of the PAaptNB could be programmably regulated by adjusting the polyA length. When the polyA length reached to 30 bases, a 10 μM detection limit for ATP assay with PAaptNB can be achieved (∼10-fold improvement compared with the conventional thiol-based aptamer nanobeacon). The feasibility of the PAaptNB for in vivo assay was further demonstrated by imaging intracellular ATP molecules. This study provides a new strategy to construct high-efficiency and high-speed biosensors for cellular molecules analysis, which holds great potential in bioanalysis and theranostic applications.
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Affiliation(s)
- Lizhen Chen
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University , 500 Dongchuan Road, Shanghai 200241, PR China
| | - Jie Chao
- Institute of Advanced Materials, Nanjing University of Posts and Telecommunications , Nanjing 210023, PR China
| | - Xiangmeng Qu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University , 500 Dongchuan Road, Shanghai 200241, PR China
| | - Hongbo Zhang
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki , FI-00014 Helsinki, Finland
| | - Dan Zhu
- Institute of Advanced Materials, Nanjing University of Posts and Telecommunications , Nanjing 210023, PR China
| | - Shao Su
- Institute of Advanced Materials, Nanjing University of Posts and Telecommunications , Nanjing 210023, PR China
| | - Ali Aldalbahi
- Chemistry Department, King Saud University , Riyadh 11451, Saudi Arabia
| | - Lianhui Wang
- Institute of Advanced Materials, Nanjing University of Posts and Telecommunications , Nanjing 210023, PR China
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University , 500 Dongchuan Road, Shanghai 200241, PR China
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Minagawa H, Onodera K, Fujita H, Sakamoto T, Akitomi J, Kaneko N, Shiratori I, Kuwahara M, Horii K, Waga I. Selection, Characterization and Application of Artificial DNA Aptamer Containing Appended Bases with Sub-nanomolar Affinity for a Salivary Biomarker. Sci Rep 2017; 7:42716. [PMID: 28256555 PMCID: PMC5335659 DOI: 10.1038/srep42716] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 01/12/2017] [Indexed: 12/21/2022] Open
Abstract
We have attained a chemically modified DNA aptamer against salivary α-amylase (sAA), which attracts researchers’ attention as a useful biomarker for assessing human psychobiological and social behavioural processes, although high affinity aptamers have not been isolated from a random natural DNA library to date. For the selection, we used the base-appended base (BAB) modification, that is, a modified-base DNA library containing (E)-5-(2-(N-(2-(N6-adeninyl)ethyl))carbamylvinyl)-uracil in place of thymine. After eight rounds of selection, a 75 mer aptamer, AMYm1, which binds to sAA with extremely high affinity (Kd < 1 nM), was isolated. Furthermore, we have successfully determined the 36-mer minimum fragment, AMYm1-3, which retains target binding activity comparable to the full-length AMYm1, by surface plasmon resonance assays. Nuclear magnetic resonance spectral analysis indicated that the minimum fragment forms a specific stable conformation, whereas the predicted secondary structures were suggested to be disordered forms. Thus, DNA libraries with BAB-modifications can achieve more diverse conformations for fitness to various targets compared with natural DNA libraries, which is an important advantage for aptamer development. Furthermore, using AMYm1, a capillary gel electrophoresis assay and lateral flow assay with human saliva were conducted, and its feasibility was demonstrated.
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Affiliation(s)
- Hirotaka Minagawa
- Innovation Laboratory, NEC Solution Innovators, Ltd., 1-18-7, Shinkiba, Koto-Ku, Tokyo 136-8627, Japan
| | - Kentaro Onodera
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Hiroto Fujita
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Taiichi Sakamoto
- Department of Life and Environmental Sciences, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino 275-0016, Japan
| | - Joe Akitomi
- Innovation Laboratory, NEC Solution Innovators, Ltd., 1-18-7, Shinkiba, Koto-Ku, Tokyo 136-8627, Japan
| | - Naoto Kaneko
- Innovation Laboratory, NEC Solution Innovators, Ltd., 1-18-7, Shinkiba, Koto-Ku, Tokyo 136-8627, Japan
| | - Ikuo Shiratori
- Innovation Laboratory, NEC Solution Innovators, Ltd., 1-18-7, Shinkiba, Koto-Ku, Tokyo 136-8627, Japan
| | - Masayasu Kuwahara
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Katsunori Horii
- Innovation Laboratory, NEC Solution Innovators, Ltd., 1-18-7, Shinkiba, Koto-Ku, Tokyo 136-8627, Japan
| | - Iwao Waga
- Innovation Laboratory, NEC Solution Innovators, Ltd., 1-18-7, Shinkiba, Koto-Ku, Tokyo 136-8627, Japan
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41
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Liang G, Man Y, Li A, Jin X, Liu X, Pan L. DNAzyme-based biosensor for detection of lead ion: A review. Microchem J 2017. [DOI: 10.1016/j.microc.2016.12.010] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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42
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Integrating Deoxyribozymes into Colorimetric Sensing Platforms. SENSORS 2016; 16:s16122061. [PMID: 27918487 PMCID: PMC5191042 DOI: 10.3390/s16122061] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 11/30/2016] [Accepted: 11/30/2016] [Indexed: 01/05/2023]
Abstract
Biosensors are analytical devices that have found a variety of applications in medical diagnostics, food quality control, environmental monitoring and biodefense. In recent years, functional nucleic acids, such as aptamers and nucleic acid enzymes, have shown great potential in biosensor development due to their excellent ability in target recognition and catalysis. Deoxyribozymes (or DNAzymes) are single-stranded DNA molecules with catalytic activity and can be isolated to recognize a wide range of analytes through the process of in vitro selection. By using various signal transduction mechanisms, DNAzymes can be engineered into fluorescent, colorimetric, electrochemical and chemiluminescent biosensors. Among them, colorimetric sensors represent an attractive option as the signal can be easily detected by the naked eye. This reduces reliance on complex and expensive equipment. In this review, we will discuss the recent progress in the development of colorimetric biosensors that make use of DNAzymes and the prospect of employing these sensors in a range of chemical and biological applications.
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43
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Lin S, Kang TS, Lu L, Wang W, Ma DL, Leung CH. A G-quadruplex-selective luminescent probe with an anchor tail for the switch-on detection of thymine DNA glycosylase activity. Biosens Bioelectron 2016; 86:849-857. [DOI: 10.1016/j.bios.2016.07.082] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 07/23/2016] [Accepted: 07/23/2016] [Indexed: 11/25/2022]
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Mishra RK, Nath S, Kumar S. Rupture of DNA aptamer: New insights from simulations. J Chem Phys 2016; 143:164902. [PMID: 26520549 DOI: 10.1063/1.4933948] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Base-pockets (non-complementary base-pairs) in a double-stranded DNA play a crucial role in biological processes. Because of thermal fluctuations, it can lower the stability of DNA, whereas, in case of DNA aptamer, small molecules, e.g., adenosinemonophosphate and adenosinetriphosphate, form additional hydrogen bonds with base-pockets termed as "binding-pockets," which enhance the stability. Using the Langevin dynamics simulations of coarse grained model of DNA followed by atomistic simulations, we investigated the influence of base-pocket and binding-pocket on the stability of DNA aptamer. Striking differences have been reported here for the separation induced by temperature and force, which require further investigation by single molecule experiments.
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Affiliation(s)
| | - Shesh Nath
- Department of Physics, Banaras Hindu University, Varanasi 221 005, India
| | - Sanjay Kumar
- Department of Physics, Banaras Hindu University, Varanasi 221 005, India
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45
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Colorimetric detection of proteins based on target-induced activation of aptazyme. Anal Chim Acta 2016; 942:68-73. [PMID: 27720123 DOI: 10.1016/j.aca.2016.09.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 09/04/2016] [Accepted: 09/07/2016] [Indexed: 11/20/2022]
Abstract
The detection of protein is vital to fundamental research as well as practical applications. However, most detection methods depend on antibody-based assays which are faced with many shortcomings. Herein, we propose a colorimetric method for protein assays based on target-triggered activation of aptazyme, which may offer simple, rapid and cost-effective detection of the target protein. In this method, the conformation change of aptazyme induced by target protein is designed to be associated with aptazyme activation. Consequently, in the presence of the target protein, the designed DNA linkers will be cleaved into two fragments that fail to cross-link gold nanoparticles (GNPs), thus the color of GNP solution remains red, while the color will be changed in the absence of the target. Because of the advantages of aptazyme such as economic synthesis, stable, easy modification and its ability to accomplish signal recognition and signal amplification simultaneously, the method is thermostable, simple and cost-efficient. In this work, we have taken the detection of vascular endothelial growth factor (VEGF) as an example, which can present an analytical performance with as low as 0.1 nM detection limit, spanning a detection range of 3 orders of magnitude. What is more, the principle of this proposed new method can be extended as a universal assay method not only for the detection of analytes which have an aptamer but also for those analytes that have ligands.
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46
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Bazin I, Tria SA, Hayat A, Marty JL. New biorecognition molecules in biosensors for the detection of toxins. Biosens Bioelectron 2016; 87:285-298. [PMID: 27568847 DOI: 10.1016/j.bios.2016.06.083] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 06/17/2016] [Accepted: 06/28/2016] [Indexed: 12/24/2022]
Abstract
Biological and synthetic recognition elements are at the heart of the majority of modern bioreceptor assays. Traditionally, enzymes and antibodies have been integrated in the biosensor designs as a popular choice for the detection of toxin molecules. But since 1970s, alternative biological and synthetic binders have been emerged as a promising alternative to conventional biorecognition elements in detection systems for laboratory and field-based applications. Recent research has witnessed immense interest in the use of recombinant enzymatic methodologies and nanozymes to circumvent the drawbacks associated with natural enzymes. In the area of antibody production, technologies based on the modification of in vivo synthesized materials and in vitro approaches with development of "display "systems have been introduced in the recent years. Subsequently, molecularly-imprinted polymers and Peptide nucleic acid (PNAs) were developed as an attractive receptor with applications in the area of sample preparation and detection systems. In this article, we discuss all alternatives to conventional biomolecules employed in the detection of various toxin molecules We review recent developments in modified enzymes, nanozymes, nanobodies, aptamers, peptides, protein scaffolds and DNazymes. With the advent of nanostructures and new interface materials, these recognition elements will be major players in future biosensor development.
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Affiliation(s)
- Ingrid Bazin
- École des Mines d'Alès, 6 Avenuede Clavières, 30100 Alès Cedex, France.
| | - Scherrine A Tria
- École des Mines d'Alès, 6 Avenuede Clavières, 30100 Alès Cedex, France
| | - Akhtar Hayat
- BAE (Biocapteurs-Analyses-Environnement), Universite de Perpignan Via Domitia, 52 Avenue Paul Alduy, Perpignan Cedex 66860, France; Interdisciplinary Research Centre in Biomedical Materials (IRCBM), COMSATS Institute of Information Technology (CIIT), Lahore, Pakistan
| | - Jean-Louis Marty
- BAE (Biocapteurs-Analyses-Environnement), Universite de Perpignan Via Domitia, 52 Avenue Paul Alduy, Perpignan Cedex 66860, France
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47
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Tomita Y, Morita Y, Suga H, Fujiwara D. DNA module platform for developing colorimetric aptamer sensors. Biotechniques 2016; 60:285-92. [PMID: 27286805 DOI: 10.2144/000114425] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 03/11/2016] [Indexed: 11/23/2022] Open
Abstract
Here we present a DNA module platform for developing simple aptamer sensors based on a microarray format combined with secondary structure prediction in silico. The platform comprises four parts: (i) aptamer, (ii) joint module, (iii) terminal stem, and (iv) a DNAzyme that catalyzes a redox reaction controlled by a structural change induced by aptamer/target binding. First, we developed a joint module, capable of sensing a conformational change in the aptamer region, that was linked to the signal transmission activity of a DNAzyme as the reporter in a concentration-dependent manner with the AMP aptamer. This module design was then used to generate an arginine sensor simply by replacing the AMP aptamer region with a previously reported arginine aptamer. Using this DNA module platform, we were also able to customize a microarray containing >10,000 sequences designed by in silico secondary structure prediction and successfully identify a new aptamer against patulin. Our results show that the DNA module platform can be used to readily devise sensors based on known aptamers as well as create new aptamer sensors by array-based screening.
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Affiliation(s)
- Yasuyuki Tomita
- Central Laboratories for Key Technologies, KIRIN Company, Ltd, Yokohama, Japan
| | - Yuji Morita
- Central Laboratories for Key Technologies, KIRIN Company, Ltd, Yokohama, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Daisuke Fujiwara
- Central Laboratories for Key Technologies, KIRIN Company, Ltd, Yokohama, Japan
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48
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Trends in the Design and Development of Specific Aptamers Against Peptides and Proteins. Protein J 2016; 35:81-99. [DOI: 10.1007/s10930-016-9653-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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49
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Yang B, Li J, Deng H, Zhang L. Progress of Mimetic Enzymes and Their Applications in Chemical Sensors. Crit Rev Anal Chem 2016; 46:469-81. [PMID: 26907867 DOI: 10.1080/10408347.2016.1151767] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The need to develop innovative and reformative approaches to synthesize chemical sensors has increased in recent years because of demands for selectivity, stability, and reproducibility. Mimetic enzymes provide an efficient and convenient method for chemical sensors. This review summarizes the application of mimetic enzymes in chemical sensors. Mimetic enzymes can be classified into five categories: hydrolases, oxidoreductases, transferases, isomerases, and induced enzymes. Potential and recent applications of mimetic enzymes in chemical sensors are reviewed in detail, and the outlook of profound development has been illustrated.
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Affiliation(s)
- Bin Yang
- a Guangxi Key laboratory of Electrochemical and Magnetochemical Function Materials, College of Chemistry and Bioengineering , Guilin University of Technology , Guilin , China
| | - Jianping Li
- a Guangxi Key laboratory of Electrochemical and Magnetochemical Function Materials, College of Chemistry and Bioengineering , Guilin University of Technology , Guilin , China
| | - Huan Deng
- a Guangxi Key laboratory of Electrochemical and Magnetochemical Function Materials, College of Chemistry and Bioengineering , Guilin University of Technology , Guilin , China
| | - Lianming Zhang
- a Guangxi Key laboratory of Electrochemical and Magnetochemical Function Materials, College of Chemistry and Bioengineering , Guilin University of Technology , Guilin , China
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50
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Wu Q, Shen H, Shen H, Sun Y, Song L. Study on sensing strategy and performance of a microfluidic chemiluminescence aptazyme sensor. Talanta 2015; 150:531-8. [PMID: 26838440 DOI: 10.1016/j.talanta.2015.12.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 12/04/2015] [Accepted: 12/10/2015] [Indexed: 11/30/2022]
Abstract
Aptamers are analogous to antibodies in their range of target recognition. G-quadruplex DNAzymes exhibit peroxidase-like activity toward certain specific reactions. Despite aptazyme sensors, based on aptamer and DNAzyme conjugates, have the potential to replace many conventional immune-biosensors; the mechanism concerning high background interference has scarcely been discussed. In this work, by taking a couple of aptazyme sensors with oligonucleotide sequences of adenosine aptamer and CatG4 DNAzyme, the sensing strategy dealing with the thermodynamic equilibrium of the functional oligonucleotide distribution had been studied. Oligonucleotide arrangement and cation condition were found important in modulating the shifting between Watson-Crick duplex and Hoogsteen G-quadruplex, which ultimately influenced sample and background signals. Notably, benefit from the microfluidic chemiluminescence detection, the developed aptazyme sensor achieved an absolute detection limit of 12 pmol adenosine with just 2 μL of pretreated sample solution consumption and satisfactory selectivity. The results have implication for better design of aptazyme sensor in the future.
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Affiliation(s)
- Qiwang Wu
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Haihui Shen
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Hong Shen
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China.
| | - Yue Sun
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Lifang Song
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
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