1
|
Huang S, Wang Y, Liu S, Li H, Yang M, Fang Y, Xiao Q. Triblock polyadenine-based electrochemical aptasensor for ultra-sensitive detection of carcinoembryonic antigen via exonuclease III-assisted target recycling and hybridization chain reaction. Bioelectrochemistry 2024; 159:108749. [PMID: 38823375 DOI: 10.1016/j.bioelechem.2024.108749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Revised: 05/18/2024] [Accepted: 05/26/2024] [Indexed: 06/03/2024]
Abstract
Carcinoembryonic antigen (CEA), a key colon biomarker, demands a precise detection method for cancer diagnosis and prognosis. This study introduces a novel electrochemical aptasensor using a triblock polyadenine probe for ultra-sensitive detection of CEA. The method leverages Exonuclease III (Exo III)-assisted target recycling and hybridization chain reaction. The triblock polyadenine probe self-assembles on the bare gold electrode through the strong affinity between adenine and gold electrode, blocking CEA diffusion and providing a large immobilization surface. CEA binding to hairpin probe 1 (HP1), followed by the hybridization between HP1 and hairpin probe 2 (HP2), triggers DNA cleavage by Exo III, amplifying the signal via a hybridization chain reaction and producing numerous dsDNA walkers that generates a dramatic electrochemical impedance signal. Under optimized conditions, the aptasensor achieved two ultra-low detection limits: 0.39 ag∙mL-1 within the concentration range of 5 ag∙mL-1 to 5 × 106 ag∙mL-1, and 1.5 ag∙mL-1 within the concentration range of 5 × 106 ag∙mL-1 to 1 × 1010 ag∙mL-1. Its performance in human serum samples meets the practical standards, offering a promising new tool for ultrasensitive tumor marker detection, potentially revolutionizing early cancer diagnosis.
Collapse
Affiliation(s)
- Shan Huang
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning 530001, PR China
| | - Yali Wang
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning 530001, PR China
| | - Shuai Liu
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning 530001, PR China
| | - Huihao Li
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning 530001, PR China
| | - Mingli Yang
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning 530001, PR China
| | - Yi Fang
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning 530001, PR China
| | - Qi Xiao
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning 530001, PR China.
| |
Collapse
|
2
|
Huang S, Li B, Mu P, Zhang W, Liu Y, Xiao Q. Highly sensitive detection of microRNA-21 by nitrogen-doped carbon dots-based ratio fluorescent probe via nuclease-assisted rolling circle amplification strategy. Anal Chim Acta 2023; 1273:341533. [PMID: 37423665 DOI: 10.1016/j.aca.2023.341533] [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: 01/17/2023] [Revised: 04/27/2023] [Accepted: 06/14/2023] [Indexed: 07/11/2023]
Abstract
Highly sensitive and selective detection of microRNA-21 (miRNA-21) in biological samples is critical for the disease diagnosis and cancer treatment. In this study, a nitrogen-doped carbon dots (N-CDs)-based ratio fluorescence sensing strategy was constructed for miRNA-21 detection with high sensitivity and excellent specificity. Bright-blue N-CDs (λex/λem = 378 nm/460 nm) were synthesized by facile one-step microwave-assisted pyrolysis method by using uric acid as the single precursor, and the absolute fluorescence quantum yield and fluorescence lifetime of N-CDs were 35.8% and 5.54 ns separately. The padlock probe hybridized with miRNA-21 firstly and then was cyclized by T4 RNA ligase 2 to form a circular template. At the present of dNTPs and phi29 DNA polymerase, the oligonucleotide sequence in miRNA-21 was prolonged to hybridize with the surplus oligonucleotide sequences in circular template, generating long and reduplicated oligonucleotide sequences containing abundant guanine nucleotides. Separate G-quadruplex sequences were generated after the addition of Nt.BbvCI nicking endonuclease, and then hemin bound with G-quadruplex sequence to construct the G-quadruplex DNAzyme. Such G-quadruplex DNAzyme catalyzed the redox reaction of o-phenylenediamine (OPD) with H2O2, finally producing the yellowish-brown 2,3-diaminophenazine (DAP) (λem = 562 nm). Due to the inner filter effect between N-CDs and DAP, the ratio fluorescence signal of DAP with N-CDs was utilized for sensitive detection of miRNA-21 with detection limit of 0.87 pM. Such approach has practical feasibility and excellent specificity for miRNA-21 analysis during highly homological miRNA family in HeLa cell lysates and human serum samples.
Collapse
Affiliation(s)
- Shan Huang
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning, 530001, PR China.
| | - Bo Li
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning, 530001, PR China
| | - Pingping Mu
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning, 530001, PR China
| | - Wenqian Zhang
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning, 530001, PR China
| | - Yi Liu
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning, 530001, PR China; State Key Laboratory of Separation Membranes and Membrane Processes, School of Chemistry and Chemical Engineering, Tiangong University, Tianjin, 300387, PR China.
| | - Qi Xiao
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning, 530001, PR China.
| |
Collapse
|
3
|
Wang Y, Liu S, Zhang D, Xiao Q, Huang S. Ultrasensitive electrochemical platform for the p53 gene via molecular beacon-mediated circular strand displacement and terminal deoxynucleotidyl transferase-mediated signal amplification strategy. Analyst 2023; 148:1005-1015. [PMID: 36723078 DOI: 10.1039/d2an01676a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
As an important tumor suppressor gene, the p53 gene is considered to be a typical biomarker for the early diagnosis and prognosis evaluation of severe cancer. Herein, an electrochemical biosensor was proposed for the ultrasensitive detection of the p53 gene based on molecular beacon-mediated circular strand displacement polymerization combined with terminal deoxynucleotide transferase-mediated template-free DNA extension. Firstly, the p53 gene opened the hairpin structure of the molecular beacon, thereby exposing the binding sequence region of the primer DNA. The circular strand displacement polymerization occurred in the presence of the primer DNA and phi29 DNA polymerase, subsequently resulting in the circulation of the p53 gene. With the catalysis of the terminal deoxynucleotide transferase, the 3'-OH terminal sequence of the molecular beacon elongated to produce long single-stranded DNA under the template-free DNA extension. Methylene blue bound with such DNA strands generated a strong differential pulse voltammetry (DPV) signal with a peak potential of -0.28 V. Under the optimal detection conditions, the DPV signal of methylene blue showed good linear relationships with the logarithm value of the p53 gene in two concentration ranges of 0.05 fM to 3 pM and 5 fM to 100 fM, and the detection limit of the p53 gene was as low as 0.018 fM. This electrochemical biosensor possessed high recognition ability for the p53 gene in its analogues and was successfully applied for p53 gene analysis in human serum samples.
Collapse
Affiliation(s)
- Yali Wang
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning 530001, P. R. China.
| | - Shuai Liu
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning 530001, P. R. China.
| | - Dongyou Zhang
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning 530001, P. R. China.
| | - Qi Xiao
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning 530001, P. R. China.
| | - Shan Huang
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning 530001, P. R. China.
| |
Collapse
|
4
|
Liu J, Xie G, Lv S, Xiong Q, Xu H. Recent applications of rolling circle amplification in biosensors and DNA nanotechnology. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
|
5
|
Screening of hepatitis B virus DNA in the serum sample by a new sensitive electrochemical genosensor-based Pd-Al LDH substrate. J Solid State Electrochem 2022. [DOI: 10.1007/s10008-022-05176-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
6
|
Babaei A, Pouremamali A, Rafiee N, Sohrabi H, Mokhtarzadeh A, de la Guardia M. Genosensors as an alternative diagnostic sensing approaches for specific detection of various certain viruses: a review of common techniques and outcomes. Trends Analyt Chem 2022; 155:116686. [PMID: 35611316 PMCID: PMC9119280 DOI: 10.1016/j.trac.2022.116686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 05/08/2022] [Accepted: 05/15/2022] [Indexed: 12/19/2022]
Abstract
Viral infections are responsible for the deaths of millions of people throughout the world. Since outbreak of highly contagious and mutant viruses such as contemporary sars-cov-2 pandemic, has challenged the conventional diagnostic methods, the entity of a thoroughly sensitive, specific, rapid and inexpensive detecting technique with minimum level of false-positivity or -negativity, is desperately needed more than any time in the past decades. Biosensors as minimized devices could detect viruses in simple formats. So far, various nucleic acid, immune- and protein-based biosensors were designed and tested for recognizing the genome, antigen, or protein level of viruses, respectively; however, nucleic acid-based sensing techniques, which is the foundation of constructing genosensors, are preferred not only because of their ultra-sensitivity and applicability in the early stages of infections but also for their ability to differentiate various strains of the same virus. To date, the review articles related to genosensors are just confined to particular pathogenic diseases; In this regard, the present review covers comprehensive information of the research progress of the electrochemical, optical, and surface plasmon resonance (SPR) genosensors that applied for human viruses' diseases detection and also provides a well description of viruses' clinical importance, the conventional diagnosis approaches of viruses and their disadvantages. This review would address the limitations in the current developments as well as the future challenges involved in the successful construction of sensing approaches with the functionalized nanomaterials and also allow exploring into core-research works regarding this area.
Collapse
Affiliation(s)
- Abouzar Babaei
- Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Amir Pouremamali
- Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Nastaran Rafiee
- Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Hessamaddin Sohrabi
- Department of Analytical Chemistry, Faculty of Chemistry, University of Tabriz, Tabriz, Iran
| | - Ahad Mokhtarzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Miguel de la Guardia
- Department of Analytical Chemistry, University of Valencia, Dr. Moliner 50, 46100, Burjassot, Valencia, Spain
| |
Collapse
|
7
|
Tamiya E. Portable Electrochemical DNA Sensors Based on Gene Amplification Reactions to Screen and Identify Pathogen and SNPs. SENSORS 2022; 22:s22051865. [PMID: 35271014 PMCID: PMC8914808 DOI: 10.3390/s22051865] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/16/2022] [Accepted: 02/22/2022] [Indexed: 02/04/2023]
Abstract
In this paper, we introduce portable sensors based on genetic measurements that can be used in the field for the diagnosis of infectious diseases and disease risk based on SNPs (single nucleotide polymorphisms). In particular, the sensors are based on electrochemical measurements that can be performed with printed electrodes and small measuring devices. Indicator molecules that can bind to nucleic acid molecules in various ways are already known, and some of these molecules have electrochemical activity. First, we investigated the change in their electrochemical responses in a solution system. As a result, we searched for nucleic acid-binding molecules whose current value changes in the presence of DNA. In addition, when we measured the change in the current value, associated with the amplification of specific genes, such as PCR (polymerase chain reaction) and LAMP (loop-mediated isothermal amplification), we found that the current value decreased with the number of amplifications, indicating that specific genes can be monitored electrochemically. Based on this principle, we showed that pathogenic microorganisms and viruses, such as Salmonella, O157 E. coli, hepatitis B virus, periodontal disease bacteria, antibiotic-resistant bacteria and influenza virus, were able to be measured. The method was also applied to the diagnosis of SNPs, such as ApoE (apolipoprotein E), which is a risk factor for Alzheimer’s disease. Rapid PCR was available with a microfluidic device, and a simple method was also presented with the isothermal amplification of LAMP.
Collapse
Affiliation(s)
- Eiichi Tamiya
- Advanced Photonics and Biosensing Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan;
- Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| |
Collapse
|
8
|
Zhang D, Wang Y, Jin X, Xiao Q, Huang S. A label-free and ultrasensitive electrochemical biosensor for oral cancer overexpressed 1 gene via exonuclease III-assisted target recycling and dual enzyme-assisted signal amplification strategies. Analyst 2022; 147:2412-2424. [DOI: 10.1039/d2an00367h] [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
A label-free and ultrasensitive electrochemical biosensor for ORAOV1 gene via exonuclease III-assisted target recycling and dual enzyme-assisted signal amplification strategies. The detection limit of ORAOV1 gene was as low as 0.019 fM.
Collapse
Affiliation(s)
- Dongyou Zhang
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning 530001, P. R. China
| | - Yali Wang
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning 530001, P. R. China
| | - Xiaoyu Jin
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning 530001, P. R. China
| | - Qi Xiao
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning 530001, P. R. China
| | - Shan Huang
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning 530001, P. R. China
| |
Collapse
|
9
|
Usha SP, Manoharan H, Deshmukh R, Álvarez-Diduk R, Calucho E, Sai VVR, Merkoçi A. Attomolar analyte sensing techniques (AttoSens): a review on a decade of progress on chemical and biosensing nanoplatforms. Chem Soc Rev 2021; 50:13012-13089. [PMID: 34673860 DOI: 10.1039/d1cs00137j] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Detecting the ultra-low abundance of analytes in real-life samples, such as biological fluids, water, soil, and food, requires the design and development of high-performance biosensing modalities. The breakthrough efforts from the scientific community have led to the realization of sensing technologies that measure the analyte's ultra-trace level, with relevant sensitivity, selectivity, response time, and sampling efficiency, referred to as Attomolar Analyte Sensing Techniques (AttoSens) in this review. In an AttoSens platform, 1 aM detection corresponds to the quantification of 60 target analyte molecules in 100 μL of sample volume. Herein, we review the approaches listed for various sensor probe design, and their sensing strategies that paved the way for the detection of attomolar (aM: 10-18 M) concentration of analytes. A summary of the technological advances made by the diverse AttoSens trends from the past decade is presented.
Collapse
Affiliation(s)
- Sruthi Prasood Usha
- Biomedical Engineering, Department of Applied Mechanics, Indian Institute of Technology Madras (IITM), India.
| | - Hariharan Manoharan
- Biomedical Engineering, Department of Applied Mechanics, Indian Institute of Technology Madras (IITM), India.
| | - Rehan Deshmukh
- Biomedical Engineering, Department of Applied Mechanics, Indian Institute of Technology Madras (IITM), India.
| | - Ruslan Álvarez-Diduk
- Nanobioelectronics & Biosensors Group, Institut Català de Nanociència i Nanotecnologia (ICN2), Campus UAB, Barcelona, Spain.
| | - Enric Calucho
- Nanobioelectronics & Biosensors Group, Institut Català de Nanociència i Nanotecnologia (ICN2), Campus UAB, Barcelona, Spain.
| | - V V R Sai
- Biomedical Engineering, Department of Applied Mechanics, Indian Institute of Technology Madras (IITM), India.
| | - Arben Merkoçi
- Nanobioelectronics & Biosensors Group, Institut Català de Nanociència i Nanotecnologia (ICN2), Campus UAB, Barcelona, Spain. .,ICREA, Institució Catalana de Recercai Estudis Avançats, Barcelona, Spain
| |
Collapse
|
10
|
Rolling Circle Amplification as an Efficient Analytical Tool for Rapid Detection of Contaminants in Aqueous Environments. BIOSENSORS-BASEL 2021; 11:bios11100352. [PMID: 34677308 PMCID: PMC8533700 DOI: 10.3390/bios11100352] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/16/2021] [Accepted: 09/21/2021] [Indexed: 12/16/2022]
Abstract
Environmental contaminants are a global concern, and an effective strategy for remediation is to develop a rapid, on-site, and affordable monitoring method. However, this remains challenging, especially with regard to the detection of various contaminants in complex water environments. The application of molecular methods has recently attracted increasing attention; for example, rolling circle amplification (RCA) is an isothermal enzymatic process in which a short nucleic acid primer is amplified to form a long single-stranded nucleic acid using a circular template and special nucleic acid polymerases. Furthermore, this approach can be further engineered into a device for point-of-need monitoring of environmental pollutants. In this paper, we describe the fundamental principles of RCA and the advantages and disadvantages of RCA assays. Then, we discuss the recently developed RCA-based tools for environmental analysis to determine various targets, including heavy metals, organic small molecules, nucleic acids, peptides, proteins, and even microorganisms in aqueous environments. Finally, we summarize the challenges and outline strategies for the advancement of this technique for application in contaminant monitoring.
Collapse
|
11
|
Jin X, Zhang D, Zhang W, Wang Y, Xiao Q, Huang S. Ratiometric electrochemical biosensor for ultrasensitive and highly selective detection of p53 gene based on nicking endonuclease-assisted target recycling and rolling circle amplification. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106461] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
12
|
Spring SA, Goggins S, Frost CG. Ratiometric Electrochemistry: Improving the Robustness, Reproducibility and Reliability of Biosensors. Molecules 2021; 26:2130. [PMID: 33917231 PMCID: PMC8068091 DOI: 10.3390/molecules26082130] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 12/21/2022] Open
Abstract
Electrochemical biosensors are an increasingly attractive option for the development of a novel analyte detection method, especially when integration within a point-of-use device is the overall objective. In this context, accuracy and sensitivity are not compromised when working with opaque samples as the electrical readout signal can be directly read by a device without the need for any signal transduction. However, electrochemical detection can be susceptible to substantial signal drift and increased signal error. This is most apparent when analysing complex mixtures and when using small, single-use, screen-printed electrodes. Over recent years, analytical scientists have taken inspiration from self-referencing ratiometric fluorescence methods to counteract these problems and have begun to develop ratiometric electrochemical protocols to improve sensor accuracy and reliability. This review will provide coverage of key developments in ratiometric electrochemical (bio)sensors, highlighting innovative assay design, and the experiments performed that challenge assay robustness and reliability.
Collapse
Affiliation(s)
- Sam A. Spring
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK;
| | - Sean Goggins
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road, Avonmouth, Bristol BS11 9QD, UK;
| | | |
Collapse
|
13
|
Bellassai N, D'Agata R, Spoto G. Novel nucleic acid origami structures and conventional molecular beacon-based platforms: a comparison in biosensing applications. Anal Bioanal Chem 2021; 413:6063-6077. [PMID: 33825006 PMCID: PMC8440263 DOI: 10.1007/s00216-021-03309-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/05/2021] [Accepted: 03/23/2021] [Indexed: 12/20/2022]
Abstract
Nucleic acid nanotechnology designs and develops synthetic nucleic acid strands to fabricate nanosized functional systems. Structural properties and the conformational polymorphism of nucleic acid sequences are inherent characteristics that make nucleic acid nanostructures attractive systems in biosensing. This review critically discusses recent advances in biosensing derived from molecular beacon and DNA origami structures. Molecular beacons belong to a conventional class of nucleic acid structures used in biosensing, whereas DNA origami nanostructures are fabricated by fully exploiting possibilities offered by nucleic acid nanotechnology. We present nucleic acid scaffolds divided into conventional hairpin molecular beacons and DNA origami, and discuss some relevant examples by focusing on peculiar aspects exploited in biosensing applications. We also critically evaluate analytical uses of the synthetic nucleic acid structures in biosensing to point out similarities and differences between traditional hairpin nucleic acid sequences and DNA origami.
Collapse
Affiliation(s)
- Noemi Bellassai
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale Andrea Doria 6, 95125, Catania, Italy
| | - Roberta D'Agata
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale Andrea Doria 6, 95125, Catania, Italy
| | - Giuseppe Spoto
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale Andrea Doria 6, 95125, Catania, Italy.
- Consorzio Interuniversitario "Istituto Nazionale Biostrutture e Biosistemi", c/o Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale Andrea Doria 6, 95125, Catania, Italy.
| |
Collapse
|
14
|
Bidar N, Amini M, Oroojalian F, Baradaran B, Hosseini SS, Shahbazi MA, Hashemzaei M, Mokhtarzadeh A, Hamblin MR, de la Guardia M. Molecular beacon strategies for sensing purpose. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2020.116143] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
15
|
Xu L, Duan J, Chen J, Ding S, Cheng W. Recent advances in rolling circle amplification-based biosensing strategies-A review. Anal Chim Acta 2020; 1148:238187. [PMID: 33516384 DOI: 10.1016/j.aca.2020.12.062] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/09/2020] [Accepted: 12/28/2020] [Indexed: 01/12/2023]
Abstract
Rolling circle amplification (RCA) is an efficient enzymatic isothermal reaction that using circular probe as a template to generate long tandem single-stranded DNA or RNA products under the initiation of short DNA or RNA primers. As a simplified derivative of natural rolling circle replication which synthesizes copies of circular nucleic acids molecules such as plasmids, RCA amplifies the circular template rapidly without thermal cycling and finds various applications in molecular biology. Compared with other amplification strategies, RCA has many obvious advantages. Firstly, because of the strict complementarity required in ligation of a padlock probe, it endows the RCA reaction with high specificity and can even be utilized to distinguish single base mismatches. Secondly, through the introduction of multiple primers, exponential amplification can be achieved easily and leads to a good sensitivity. Thirdly, RCA products can be customized by manipulating circular templates to generate functional nucleic acids such as aptamer, DNAzymes and restriction enzyme sites. Moreover, the RCA has good biocompatibility and is especially suitable for in situ detection. Therefore, RCA has attracted considerable attention as an efficient and potential tool for highly sensitive detection of biomarkers. Herein, we comprehensively introduce the fundamental principles of RCA technology, summarize it from three aspects including initiation mode, amplification mode and signal output mode, and discuss the recent application of RCA-based biosensor in this review.
Collapse
Affiliation(s)
- Lulu Xu
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Jiaxin Duan
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Junman Chen
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China.
| | - Wei Cheng
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China.
| |
Collapse
|
16
|
Bai X, Ma X, Li M, Li X, Fan G, Zhang R, Wang R, Duan Q, Shen X, Xie Y, Rong X. Field applicable detection of hepatitis B virus using internal controlled duplex recombinase-aided amplification assay and lateral flow dipstick assay. J Med Virol 2020; 92:3344-3353. [PMID: 32190907 DOI: 10.1002/jmv.25778] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 03/17/2020] [Indexed: 12/12/2022]
Abstract
Hepatitis B virus (HBV) is a widespread blood-borne pathogen associated with the complication of liver cirrhosis and hepatocellular carcinoma, particularly in south-east Asian and African countries where HBV is highly endemic and the budget and resources are limited. Therefore, simple, rapid, and portable field detection methods are crucial to efficiently control HBV infection. In this study, using heat-treated DNA, we developed two-field applicable detection assays for HBV based on recombinase-aided amplification (RAA). One was an internal controlled duplex RAA assay using a portable real-time fluorescence detection device, another was an instrument-free visual observation assay using lateral flow dipsticks. The entire experimental time was greatly shortened to less than 40 minutes at 39.0°C. The sensitivities, specificities, and clinical performance of both assays were evaluated. Compared with quantitative polymerase chain reaction assay as a reference, our results demonstrated that the two RAA-based assay obtained 97.18% and 95.77% of sensitivity, respectively, and the specificity was 100%, by testing a total of 157 serum samples with HBsAg positive. We conclude that the advantages of rapidity, simplicity, portability, and visualization of proposed two assays make them great potentials in point-of-care testing of HBV infection by untrained people in resource-limited situations.
Collapse
Affiliation(s)
- Xueding Bai
- North China University of Science and Technology, Tangshan, China
- Tangshan Gongren Hospital, Tangshan, China
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xuejun Ma
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Minghui Li
- Department of Hepatology Division 2, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Xinna Li
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Guohao Fan
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ruiqing Zhang
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ruihuan Wang
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qingxia Duan
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xinxin Shen
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yao Xie
- Department of Hepatology Division 2, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Xiuge Rong
- Tangshan Gongren Hospital, Tangshan, China
| |
Collapse
|
17
|
DNA/RNA Electrochemical Biosensing Devices a Future Replacement of PCR Methods for a Fast Epidemic Containment. SENSORS 2020; 20:s20164648. [PMID: 32824787 PMCID: PMC7472328 DOI: 10.3390/s20164648] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 08/16/2020] [Accepted: 08/17/2020] [Indexed: 12/28/2022]
Abstract
Pandemics require a fast and immediate response to contain potential infectious carriers. In the recent 2020 Covid-19 worldwide pandemic, authorities all around the world have failed to identify potential carriers and contain it on time. Hence, a rapid and very sensitive testing method is required. Current diagnostic tools, reverse transcription PCR (RT-PCR) and real-time PCR (qPCR), have its pitfalls for quick pandemic containment such as the requirement for specialized professionals and instrumentation. Versatile electrochemical DNA/RNA sensors are a promising technological alternative for PCR based diagnosis. In an electrochemical DNA sensor, a nucleic acid hybridization event is converted into a quantifiable electrochemical signal. A critical challenge of electrochemical DNA sensors is sensitive detection of a low copy number of DNA/RNA in samples such as is the case for early onset of a disease. Signal amplification approaches are an important tool to overcome this sensitivity issue. In this review, the authors discuss the most recent signal amplification strategies employed in the electrochemical DNA/RNA diagnosis of pathogens.
Collapse
|
18
|
A robust host-guest interaction controlled probe immobilization strategy for the ultrasensitive detection of HBV DNA using hollow HP5-Au/CoS nanobox as biosensing platform. Biosens Bioelectron 2020; 153:112051. [PMID: 32056664 DOI: 10.1016/j.bios.2020.112051] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/23/2020] [Accepted: 01/24/2020] [Indexed: 01/15/2023]
Abstract
The combination of supramolecular chemistry and nanotechnology has potentially applied in the construction of biosensors, and thus improves the analytical performance and robustness of electron devices. Herein, a new sandwich-type DNA sensor was constructed for ultrasensitive determination of hepatitis B virus (HBV) DNA, a recognized marker for chronic hepatitis B. The water-soluble pillar[5]arene stabilized Pd NPs combined with reduced graphene oxide nanosheet (WP5-Pd/RGO) was synthesized and employed as supporting material for the modification of electrode surface. The probe DNA was immobilized onto the electrode surface through a new strategy based on the host-guest interaction between WP5 and methylene blue labeled DNA (MB-DNA). Moreover, MOF-derived cobalt sulfide nanobox was prepared to anchor the hydroxylatopillar[5]arene stabilized Au NPs (HP5-Au/CoS), which had superior electrocatalytic performance towards H2O2 reduction to achieve signal amplification. Under the optimized conditions, the proposed sensor displayed a linear relationship between amperometric currents and the logarithm of tDNA solution from 1 × 10-15 mol/L to 1 × 10-9 mol/L, and a low detection limit of 0.32 fmol/L. What's more, the DNA sensor had remarkable behaviors of stability, reproducibility, specificity, and accuracy, which provided a potential and promising prospect for clinical diagnosis and analysis.
Collapse
|
19
|
Ozer T, Geiss BJ, Henry CS. Review-Chemical and Biological Sensors for Viral Detection. JOURNAL OF THE ELECTROCHEMICAL SOCIETY 2020; 167:037523. [PMID: 32287357 PMCID: PMC7106559 DOI: 10.1149/2.0232003jes] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 11/25/2019] [Indexed: 05/19/2023]
Abstract
Infectious diseases commonly occur in contaminated water, food, and bodily fluids and spread rapidly, resulting in death of humans and animals worldwide. Among infectious agents, viruses pose a serious threat to public health and global economy because they are often difficult to detect and their infections are hard to treat. Since it is crucial to develop rapid, accurate, cost-effective, and in-situ methods for early detection viruses, a variety of sensors have been reported so far. This review provides an overview of the recent developments in electrochemical sensors and biosensors for detecting viruses and use of these sensors on environmental, clinical and food monitoring. Electrochemical biosensors for determining viruses are divided into four main groups including nucleic acid-based, antibody-based, aptamer-based and antigen-based electrochemical biosensors. Finally, the drawbacks and advantages of each type of sensors are identified and discussed.
Collapse
Affiliation(s)
- Tugba Ozer
- Department of Chemistry, Colorado State University, USA
- Yildiz Technical University, Faculty of Chemistry-Metallurgy, Department of Bioengineering, Istanbul, Turkey
| | - Brian J Geiss
- Department of Microbiology, Immunology & Pathology, Colorado State University, USA
- School of Biomedical Engineering, Colorado State University, USA
| | - Charles S Henry
- Department of Chemistry, Colorado State University, USA
- School of Biomedical Engineering, Colorado State University, USA
| |
Collapse
|
20
|
Lv MM, Fan SF, Wang QL, Lv QY, Song X, Cui HF. An enzyme-free electrochemical sandwich DNA assay based on the use of hybridization chain reaction and gold nanoparticles: application to the determination of the DNA of Helicobacter pylori. Mikrochim Acta 2019; 187:73. [PMID: 31863213 DOI: 10.1007/s00604-019-3999-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 11/03/2019] [Indexed: 01/27/2023]
Abstract
An ultrasensitive enzyme-free electrochemical sandwich DNA biosensor is described for the detection of ssDNA oligonucleotides. A DNA sequence derived from the genom of Helicobacter pylori was selected as a model target DNA. The DNA assay was realized through catching target DNA on capture DNA immobilized gold electrode; then labeling the target DNA with reporter DNA (rpDNA) and initiator DNA (iDNA) co-modified gold nanoparticles (AuNPs). The high density of iDNAs serves as one of the amplification strategies. The iDNA triggers hybridization chain reaction (HCR) between two hairpins. This leads to the formation of a long dsDNA concatamer strand and represents one amplification strategy. The electrochemical probe [Ru(NH3)5L]2+, where L stands for 3-(2-phenanthren-9-ylvinyl)pyridine, intercalated into dsDNA chain. Multiple probe molecules intercalate into one dsDNA chain, serving as one amplification strategy. The electrode was subjected to differential pulse voltammetry for signal acquisition, and the oxidation peak current at -0.28 V was recorded. On each AuNP, 240 iDNA and 25 rpDNA molecules were immobilized. Successful execution of HCR at the DNA-modified AuNPs was confirmed by gel electrophoresis and hydrodynamic diameter measurements. Introduction of HCR significantly enhances the DNA detection signal intensity. The assay has two linear ranges of different slopes, one from 0.01 fM to 0.5 fM; and one from 1 fM to 100 fM. The detection limit is as low as 0.68 aM. Single mismatch DNA can be differentiated from the fully complementary DNA. Conceivably, this highly sensitive and selective assay provides a general method for detection of various kinds of DNA. Graphical abstractSchematic representation of the detection and the amplification principles of the electrochemical sandwich DNA assay. Purple curl: Captured DNA; Green curl: Reporter DNA; Orange curl: HCR initiator DNA; Yellow solid-circle: Gold nanoparticle; H1 and H2: Two hairpin DNA; [Ru(NH3)5L]2+: Signal probe.
Collapse
Affiliation(s)
- Man-Man Lv
- Department of Bioengineering, School of Life Sciences, Zhengzhou University, 100# Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Shuang-Fei Fan
- Department of Bioengineering, School of Life Sciences, Zhengzhou University, 100# Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Qiong-Lin Wang
- Department of Bioengineering, School of Life Sciences, Zhengzhou University, 100# Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Qi-Yan Lv
- Department of Bioengineering, School of Life Sciences, Zhengzhou University, 100# Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Xiaojie Song
- Department of Bioengineering, School of Life Sciences, Zhengzhou University, 100# Science Avenue, Zhengzhou, 450001, People's Republic of China.
| | - Hui-Fang Cui
- Department of Bioengineering, School of Life Sciences, Zhengzhou University, 100# Science Avenue, Zhengzhou, 450001, People's Republic of China.
| |
Collapse
|
21
|
Xiao Q, Feng J, Feng M, Li J, Liu Y, Wang D, Huang S. A ratiometric electrochemical aptasensor for ultrasensitive determination of adenosine triphosphate via a triple-helix molecular switch. Mikrochim Acta 2019; 186:478. [DOI: 10.1007/s00604-019-3630-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 06/19/2019] [Indexed: 12/18/2022]
|
22
|
Salimian R, Shahrokhian S, Panahi S. Enhanced Electrochemical Activity of a Hollow Carbon Sphere/Polyaniline-Based Electrochemical Biosensor for HBV DNA Marker Detection. ACS Biomater Sci Eng 2019; 5:2587-2594. [DOI: 10.1021/acsbiomaterials.8b01520] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Razieh Salimian
- Department of Chemistry, Sharif University of Technology, Azadi Ave., Tehran 11155−9516, Iran
| | - Saeed Shahrokhian
- Department of Chemistry, Sharif University of Technology, Azadi Ave., Tehran 11155−9516, Iran
- Institute for Nanoscience and Technology, Sharif University of Technology, Azadi Ave., Tehran 11155−9516, Iran
| | - Saba Panahi
- Department of Chemistry, Sharif University of Technology, Azadi Ave., Tehran 11155−9516, Iran
| |
Collapse
|
23
|
Hassanpour S, Baradaran B, de la Guardia M, Baghbanzadeh A, Mosafer J, Hejazi M, Mokhtarzadeh A, Hasanzadeh M. Diagnosis of hepatitis via nanomaterial-based electrochemical, optical or piezoelectrical biosensors: a review on recent advancements. Mikrochim Acta 2018; 185:568. [DOI: 10.1007/s00604-018-3088-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 11/09/2018] [Indexed: 12/21/2022]
|
24
|
Liu M, Xu Y, Huang C, Jia T, Zhang X, Yang DP, Jia N. Hyaluronic acid-grafted three-dimensional MWCNT array as biosensing interface for chronocoulometric detection and fluorometric imaging of CD44-overexpressing cancer cells. Mikrochim Acta 2018; 185:338. [DOI: 10.1007/s00604-018-2861-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 06/04/2018] [Indexed: 12/18/2022]
|