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Pan W, Niu H, Luo S, Chen L, Wu ZS. Intelligent Reconfiguration-Promoted Cellular Internalization of Core-Shell DNA Nanoprobe Equipped with Successive Dual Stimuli-Responsive Protective Satellites for Amplification Fluorescence Imaging of Tumor Cells. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2311388. [PMID: 38282377 DOI: 10.1002/smll.202311388] [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: 12/07/2023] [Indexed: 01/30/2024]
Abstract
Although DNA probes have attracted increasing interest for precise tumor cell identification by imaging intracellular biomarkers, the requirement of commercial transfection reagents, limited targeting ligands, and/or non-biocompatible inorganic nanostructures has hampered the clinic translation. To circumvent these shortcomings, a reconfigurable ES-NC (Na+-dependent DNAzyme (E)-based substrate (S) cleavage core/shell DNA nanocluster (NC)) entirely from DNA strands is assembled for precise imaging of cancerous cells in a successive dual-stimuli-responsive manner. This nanoprobe is composed of a strung DNA tetrahedral satellites-based protective (DTP) shell, parallelly aligned target-responsive sensing (PTS) interlayer, and hydrophobic cholesterol-packed innermost layer (HCI core). Tetrahedral axial rotation-activated reconfiguration of DTP shell promotes the exposure of interior hydrophobic moieties, enabling cholesterol-mediated cellular internalization without auxiliary elements. Within cells, over-expressed glutathione triggers the disassembly of the DTP protective shell (first stimulus), facilitating target-stimulated signal transduction/amplification process (second stimuli). Target miRNA-21 is detected down to 10.6 fM without interference from coexisting miRNAs. Compared with transfection reagent-mediated counterpart, ES-NC displays a higher imaging ability, resists nuclease degradation, and has no detectable damage to healthy cells. The blind test demonstrates that the ES-NC is suitable for the identification of cancerous cells from healthy cells, indicating a promising tool for early diagnosis and prediction of cancer.
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Affiliation(s)
- Wenhao Pan
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, and Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, 325035, China
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, China
| | - Huimin Niu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, China
- Fujian Key Laboratory of Aptamers Technology, The 900th Hospital of Joint Logistics Support Force, Fuzhou, 350025, China
| | - Shasha Luo
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, China
| | - Linhuan Chen
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, China
| | - Zai-Sheng Wu
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, and Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, 325035, China
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, China
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2
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Marpaung DSS, Sinaga AOY, Damayanti D, Taharuddin T. Bridging biological samples to functional nucleic acid biosensor applications: current enzymatic-based strategies for single-stranded DNA generation. ANAL SCI 2024; 40:1225-1237. [PMID: 38607600 DOI: 10.1007/s44211-024-00566-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/13/2024] [Indexed: 04/13/2024]
Abstract
The escalating threat of emerging diseases, often stemming from contaminants and lethal pathogens, has precipitated a heightened demand for sophisticated diagnostic tools. Within this landscape, the functional nucleic acid (FNA) biosensor, harnessing the power of single-stranded DNA (ssDNA), has emerged as a preeminent choice for target analyte detection. However, the dependence on ssDNA has raised difficulties in realizing it in biological samples. Therefore, the production of high-quality ssDNA from biological samples is critical. This review aims to discuss strategies for generating ssDNA from biological samples for integration into biosensors. Several innovative strategies for ssDNA generation have been deployed, encompassing techniques, such as asymmetric PCR, Exonuclease-PCR, isothermal amplification, biotin-streptavidin PCR, transcription-reverse transcription, ssDNA overhang generation, and urea denaturation PAGE. These approaches have been seamlessly integrated with biosensors for biological sample analysis, ushering in a new era of disease detection and monitoring. This amalgamation of ssDNA generation techniques with biosensing applications holds significant promise, not only in improving the speed and accuracy of diagnostic processes but also in fortifying the global response to deadly diseases, thereby underlining the pivotal role of cutting-edge biotechnology in public health and disease prevention.
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Affiliation(s)
- David Septian Sumanto Marpaung
- Department of Biosystems Engineering, Institut Teknologi Sumatera, Jl. Terusan Ryacudu, Way Huwi, Kec. Jati Agung, Lampung Selatan, Lampung, 35365, Indonesia.
| | - Ayu Oshin Yap Sinaga
- Department of Biology, Institut Teknologi Sumatera, Jl. Terusan Ryacudu, Way Huwi, Kec. Jati Agung, Lampung Selatan, Lampung, 35365, Indonesia
| | - Damayanti Damayanti
- Department of Chemical Engineering, Institut Teknologi Sumatera, Jl. Terusan Ryacudu, Way Huwi, Kec. Jati Agung, Lampung Selatan, Lampung, 35365, Indonesia
| | - Taharuddin Taharuddin
- Department of Chemical Engineering, University of Lampung, Jl. Prof. Dr. Ir. Sumantri Brojonegoro No.1, Gedong Meneng, Kec. Rajabasa, Kota Bandar Lampung, Lampung, 35141, Indonesia
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3
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Fang L, Jin J, Zhang Z, Yu S, Tian C, Luo F, Long M, Zuo H, Lou S. Antidote-controlled DNA aptamer modulates human factor IXa activity. Bioorg Chem 2024; 148:107463. [PMID: 38776649 DOI: 10.1016/j.bioorg.2024.107463] [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: 03/07/2024] [Revised: 04/24/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024]
Abstract
Thrombosis leads to elevated mortality rates and substantial medical expenses worldwide. Human factor IXa (HFIXa) protease is pivotal in tissue factor (TF)-mediated thrombin generation, and represents a promising target for anticoagulant therapy. We herein isolated novel DNA aptamers that specifically bind to HFIXa through systematic evolution of ligands by exponential enrichment (SELEX) method. We identified two distinct aptamers, seq 5 and seq 11, which demonstrated high binding affinity to HFIXa (Kd = 74.07 ± 2.53 nM, and 4.93 ± 0.15 nM, respectively). Computer software was used for conformational simulation and kinetic analysis of DNA aptamers and HFIXa binding. These aptamers dose-dependently prolonged activated partial thromboplastin time (aPTT) in plasma. We further rationally optimized the aptamers by truncation and site-directed mutation, and generated the truncated forms (Seq 5-1t, Seq 11-1t) and truncated-mutated forms (Seq 5-2tm, Seq 11-2tm). They also showed good anticoagulant effects. The rationally and structurally designed antidotes (seq 5-2b and seq 11-2b) were competitively bound to the DNA aptamers and effectively reversed the anticoagulant effect. This strategy provides DNA aptamer drug-antidote pair with effective anticoagulation and rapid reversal, developing advanced therapies by safe, regulatable aptamer drug-antidote pair.
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Affiliation(s)
- Liang Fang
- Department of Hematology, the Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
| | - Jin Jin
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Zhe Zhang
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Shuang Yu
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Cheng Tian
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Fukang Luo
- Department of Laboratory Medicine, The Ninth People's Hospital of Chongqing, Chongqing 400700, China
| | - Mengfei Long
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Hua Zuo
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Shifeng Lou
- Department of Hematology, the Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China.
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4
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Zhu F, Yu H, Zhao Q. CRISPR/Cas12a-Amplified Aptamer Switch Microplate Assay for Small Molecules. Anal Chem 2024; 96:6853-6859. [PMID: 38646918 DOI: 10.1021/acs.analchem.4c01452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
The presence of small molecule contaminants such as mycotoxins and heavy metals in foods and the environment causes a serious threat to human health and huge economic losses. The development of simple, rapid, sensitive, and on-site methods for small molecule pollutant detection is highly demanded. Here, combining the advantages of structure-switchable aptamer-mediated signal conversion and CRISPR/Cas12a-based signal amplification, we developed a CRISPR/Cas12a-amplified aptamer switch assay on a microplate for sensitive small molecule detection. In this assay, a short DNA strand complementary to the aptamer (cDNA) is immobilized on a microplate, which can capture the aptamer-linked active DNA probe (Apt-acDNA) in the sample solution when the target is absent. With the addition of the Cas12a reporter system, the captured Apt-acDNA probes activate Cas12a to indiscriminately cleave fluorescent DNA substrates, producing a high fluorescence signal. When the target is present, the Apt-acDNA probe specifically binds to the target rather than hybridizing with cDNA on the microplate, and the fluorescence signal is reduced. The analytical performance of our method was demonstrated by the detection of two highly toxic pollutants, aflatoxin B1 (AFB1) and cadmium ion (Cd2+), as examples. The assay exhibited good selectivity and high sensitivity, with detection limits of 31 pM AFB1 and 3.9 nM Cd2+. It also allowed the detection of targets in the actual sample matrix. With the general signal conversion strategy, this method can be used to detect other targets by simply changing the aptamer and cDNA, showing potential practical applications in broad fields.
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Affiliation(s)
- Fengxi Zhu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hao Yu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiang Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
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5
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Tian Z, Yan H, Zeng Y. Solid-Phase Extraction and Enhanced Amplification-Free Detection of Pathogens Integrated by Multifunctional CRISPR-Cas12a. ACS APPLIED MATERIALS & INTERFACES 2024; 16:14445-14456. [PMID: 38472096 DOI: 10.1021/acsami.3c17039] [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] [Indexed: 03/14/2024]
Abstract
Public healthcare demands effective and pragmatic diagnostic tools to address the escalating challenges in infection management in resource-limited areas. Recent advances in clustered regularly interspaced short palindromic repeat (CRISPR)-based biosensing promise the development of next-generation tools for disease diagnostics, including point-of-care (POC) testing for infectious diseases. The currently prevailing strategy of developing CRISPR/Cas-based diagnostics exploits only the target identification and trans-cleavage activity of a CRISPR-Cas12a/Cas13a system to provide diagnostic results, and they need to be combined with an additional preamplification reaction to enhance sensitivity. In contrast to this dual-function strategy, here, we present a new approach that collaboratively integrates the triple functions of CRISPR-Cas12a: target identification, sequence-specific enrichment, and signal generation. With this approach, we develop a nucleic acid assay termed Solid-Phase Extraction and Enhanced Detection Assay integrated by CRISPR-Cas12a (SPEEDi-CRISPR) that negates the need for preamplification but significantly improves the detection of limit (LOD) from the pM to fM level. Specifically, using Cas12a-coated magnetic beads, this assay combines efficient solid-phase extraction and enrichment of DNA targets enabled by the sequence-specific affinity of CRISPR-Cas12a with fluorogenic detection by activated Cas12a on beads. SPEEDi-CRISPR, for the first time, leverages the possibility of employing CRISPR/Cas12a in nucleic acid extraction and integrates the ability of both enrichment and detection of CRISPR/Cas into a single platform. Our proof-of-concept studies revealed that the SPEEDi-CRISPR assay has great specificity to distinguish HPV-18 from HPV-16, and Parvovirus B19, in addition to being able to detect HPV-18 at a concentration as low as 2.3 fM in 100 min and 4.7 fM in 60 min. Furthermore, we proved that this assay can be coupled with two point-of-care testing strategies: the smartphone-based fluorescence detector and the lateral flow assay. Overall, these results suggested that our assay could pave a new way for developing CRISPR diagnostics.
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Affiliation(s)
- Zimu Tian
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - He Yan
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Yong Zeng
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, Florida 32611, United States
- University of Florida Health Cancer Center, Gainesville, Florida 32611, United States
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6
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Han Y, Li DL, Han Q, Ma F, Zhang CY. Integration of Demethylation-Activated DNAzyme with a Single Quantum Dot Nanosensor for Sensitive Detection of O 6-Methylguanine DNA Methyltransferase in Breast Tissues. Anal Chem 2024; 96:4487-4494. [PMID: 38451469 DOI: 10.1021/acs.analchem.3c05090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
O6-Methylguanine-DNA-methyltransferase (MGMT) is a demethylation protein that dynamically regulates the O6-methylguanine modification (O6 MeG), and dysregulated MGMT is implicated in various malignant tumors. Herein, we integrate demethylation-activated DNAzyme with a single quantum dot nanosensor to sensitively detect MGMT in breast tissues. The presence of MGMT induces the demethylation of the O6 MeG-caged DNAzyme and the restoration of catalytic activity. The activated DNAzyme then specifically cleaves the ribonucleic acid site of hairpin DNA to expose toehold sequences. The liberated toehold sequence may act as a primer to trigger a cyclic exponential amplification reaction for the generation of enormous signal strands that bind with the Cy5/biotin-labeled probes to form sandwich hybrids. The assembly of sandwich hybrids onto 605QD obtains 605QD-dsDNA-Cy5 nanostructures, inducing efficient FRET between the 605QD donor and Cy5 acceptor. Notably, the introduction of a mismatched base in hairpin DNA can greatly minimize the background and improve the signal-to-noise ratio. This nanosensor achieves a dynamic range of 1.0 × 10-8 to 0.1 ng/μL and a detection limit of 155.78 aM, and it can screen MGMT inhibitors and monitor cellular MGMT activity with single-cell sensitivity. Moreover, it can distinguish the MGMT level in tissues of breast cancer patients and healthy persons, holding great potential in clinical diagnostics and epigenetic research studies.
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Affiliation(s)
- Yun Han
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Dong-Ling Li
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Qian Han
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Fei Ma
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Chun-Yang Zhang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
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7
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Yu H, Zhao Q. Profiling Additional Effects of Aptamer Fluorophore Modification on Microscale Thermophoresis Characterization of Aptamer-Target Binding. Anal Chem 2023; 95:17011-17019. [PMID: 37946406 DOI: 10.1021/acs.analchem.3c03603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Aptamers are promising affinity ligands with considerable applications, such as biosensors, disease diagnosis, therapy, etc. Characterization of aptamer-target binding is important in aptamer selection and aptamer applications. Microscale thermophoresis (MST) is an emerging optical technique for molecular interactions, which monitors fluorescence responses of fluorescent molecules in a microscopic temperature gradient. Harnessing merits in trace sample consumption, high speed, free separation, free immobilization, and ratiometric analysis, MST draws intense wide attention. MST is often applied for aptamer-target binding studies using fluorescently labeled aptamers. However, the MST signal is strongly dependent on fluorophore modifications at aptamers, which brings additional challenges and effects for MST analyzing aptamer affinity. Here, we systematically explored effects of fluorophore modifications (e.g., fluorophore types, fluorophore positions, etc.) of aptamer probes on MST characterizing aptamer-target interactions and identified gaps of MST analysis in aptamer affinity determination, taking aptamers against cadmium ions and aflatoxin B1 as two representatives. The same aptamers with different fluorophore modifications showed distinct MST signals in response magnitudes and signs as well as determined affinities, and some of them failed to respond to target binding and gave false affinity information in MST. A competitive MST method can be used to extract the affinity of unmodified aptamers, excluding effects of fluorophore modification. This work highlights that appropriate fluorophore modification is crucial in MST analysis of aptamer affinity, and caution is needed in MST applications, providing a basis for rational design of the MST method for the reliable molecular interaction study.
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Affiliation(s)
- Hao Yu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiang Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
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8
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Wu Y, Chang D, Chang Y, Zhang Q, Liu Y, Brennan JD, Li Y, Liu M. Nucleic Acid Enzyme-Activated CRISPR-Cas12a With Circular CRISPR RNA for Biosensing. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2303007. [PMID: 37294164 DOI: 10.1002/smll.202303007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 06/01/2023] [Indexed: 06/10/2023]
Abstract
clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems are increasingly used in biosensor development. However, directly translating recognition events for non-nucleic acid targets by CRISPR into effective measurable signals represents an important ongoing challenge. Herein, it is hypothesized and confirmed that CRISPR RNAs (crRNAs) in a circular topology efficiently render Cas12a incapable of both site-specific double-stranded DNA cutting and nonspecific single-stranded DNA trans cleavage. Importantly, it is shown that nucleic acid enzymes (NAzymes) with RNA-cleaving activity can linearize the circular crRNAs, activating CRISPR-Cas12a functions. Using ligand-responsive ribozymes and DNAzymes as molecular recognition elements, it is demonstrated that target-triggered linearization of circular crRNAs offers great versatility for biosensing. This strategy is termed as "NAzyme-Activated CRISPR-Cas12a with Circular CRISPR RNA (NA3C)." Use of NA3C for clinical evaluation of urinary tract infections using an Escherichia coli-responsive RNA-cleaving DNAzyme to test 40 patient urine samples, providing a diagnostic sensitivity of 100% and specificity of 90%, is further demonstrated.
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Affiliation(s)
- Yunping Wu
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian POCT Laboratory, Dalian, 116024, China
| | - Dingran Chang
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S4K1, Canada
| | - Yangyang Chang
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian POCT Laboratory, Dalian, 116024, China
| | - Qiang Zhang
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Yi Liu
- Department of Neurology, Dalian Municipal Central Hospital, Affiliated Hospital of Dalian Medical University, Dalian, 116033, China
| | - John D Brennan
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S4O3, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S4K1, Canada
| | - Meng Liu
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian POCT Laboratory, Dalian, 116024, China
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9
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Feng Q, Zakaria S, Morrison D, Tram K, Gu J, Salena BJ, Li Y. A Fluorogenic DNAzyme for A Thermally Stable Protein Biomarker from Fusobacterium nucleatum, a Human Bacterial Pathogen. Angew Chem Int Ed Engl 2023; 62:e202306272. [PMID: 37404195 DOI: 10.1002/anie.202306272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 07/06/2023]
Abstract
Fusobacterium nucleatum has been correlated to many poor human conditions including oral infections, adverse pregnancies and cancer, and thus molecular tools capable of detecting this human pathogen can be used to develop diagnostic tests for them. Using a new selection method targeting thermally stable proteins without a counter-selection step, we derived an fluorogenic RNA-cleaving DNAzyme, named RFD-FN1, that can be activated by a thermally stable protein target that is unique to F. nucleatum subspecies. High thermal stability of protein targets is a very desirable attribute for DNAzyme-based biosensing directly with biological samples because nucleases found inherently in these samples can be heat-inactivated. We further demonstrate that RFD-FN1 can function as a fluorescent sensor in both human saliva and human stool samples. The discovery of RFD-FN1 paired with a highly thermal stable protein target presents opportunities for developing simpler diagnostic tests for this important pathogen.
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Affiliation(s)
- Qian Feng
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4 K1, Canada
| | - Sandy Zakaria
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4 K1, Canada
| | - Devon Morrison
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4 K1, Canada
| | - Kha Tram
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4 K1, Canada
| | - Jim Gu
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4 K1, Canada
| | - Bruno J Salena
- Department of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4 K1, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4 K1, Canada
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4 K1, Canada
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10
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Yu H, Zhao Q. Sensitive microscale thermophoresis assay for rapid ochratoxin A detection with fluorescently labeled engineered aptamer. Analyst 2023. [PMID: 37439690 DOI: 10.1039/d3an00867c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
Ochratoxin A (OTA) is a widespread mycotoxin that causes contamination in a variety of foodstuffs and environments, inducing great health risks to humans and animals. Rapid and sensitive detection of OTA is necessary for food safety, environmental health, and risk assessment. Herein, we report an aptamer microscale thermophoresis (MST) assay for OTA, with the unique merits of ratiometric analysis, rapid measurement, simple operation, high sensitivity, low sample consumption, and high throughput. A fluorescein (FAM)-labeled high-affinity DNA aptamer with a G-quadruplex and duplex structure was used as the recognition element for OTA, and MST, which measures the fluorescence responses of the sample solution inside capillaries to a mild temperature increase generated by infrared laser heating, was employed for signal generation. Upon OTA binding, the FAM-labeled aptamer probe underwent changes in conformation and stability, and the bound and unbound aptamer probes showed significant differences in their MST signals. To achieve sensitive detection of OTA with a large signal change, we systematically characterized aptamers with different stem lengths, which had large effects on the MST responses of the aptamer probes to OTA. We found that a 32-mer aptamer with FAM label at the 3' end gave a sensitive MST response to OTA, allowing OTA detection within seconds with a detection limit of 0.98 nM under optimal experimental conditions. This aptamer MST assay shows potential in real sample analysis and broad applications.
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Affiliation(s)
- Hao Yu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiang Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China
- School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310000, China
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11
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Hu Z, Jiang Z, Yang Z, Liu L, Zhu Z, Jin Y, Yin Y. Development of a modularized aptamer targeting the nuclear T-cell suppressor PAC1. Analyst 2023; 148:2616-2625. [PMID: 37191022 DOI: 10.1039/d3an00011g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Aptamers associated with cancer targeting therapy are commonly focused on cell membrane proteins; however, the study of intracellular, particularly, nuclear proteins is limited. The nuclear phosphatase PAC1 has been reported to be a potential T cell-related immunotherapeutic target. Here, we identified an aptamer, designated as PA5, with high affinity and specificity for PAC1 through the systematic evolution of ligands by exponential enrichment (SELEX) procedure. We then developed a dual-module aptamer PAC1-AS consisting of a cell-internalizing module and a targeting module, which can recognize PAC1 in the nucleus under physiological conditions. This modularized aptamer raises the possibility of manipulating endosomes and provides insights into the exploration and development of an efficient cancer immunotherapy approach.
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Affiliation(s)
- Zixi Hu
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Peking-Tsinghua Center for Life Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing 100191, China.
| | - Zhongyu Jiang
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Peking-Tsinghua Center for Life Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing 100191, China.
| | - Zeliang Yang
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Peking-Tsinghua Center for Life Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing 100191, China.
| | - Liang Liu
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Peking-Tsinghua Center for Life Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing 100191, China.
| | - Zhenyu Zhu
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Peking-Tsinghua Center for Life Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing 100191, China.
| | - Yan Jin
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Peking-Tsinghua Center for Life Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing 100191, China.
| | - Yuxin Yin
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Peking-Tsinghua Center for Life Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing 100191, China.
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12
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Tian Z, Yan H, Zeng Y. Solid-Phase Extraction and Enhanced Amplification-Free Detection of Pathogens Integrated by Dual-Functional CRISPR-Cas12a. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.04.28.23289279. [PMID: 37162995 PMCID: PMC10168481 DOI: 10.1101/2023.04.28.23289279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Public healthcare demands effective and pragmatic diagnostic tools to address the escalating challenges in infection management in resource-limited areas. Recent advance in CRISPR-based biosensing promises the development of next-generation tools for disease diagnostics, including point-of-care (POC) testing for infectious diseases. Currently prevailing strategy of developing CRISPR assays exploits only the non-specific trans-cleavage function of a CRISPR-Cas12a/Cas13a system for detection and combines it with an additional pre-amplification reaction to enhance the sensitivity. In contrast to this single-function strategy, here we present a new approach that collaboratively integrates the dual functions of CRISPR-Cas12a: sequence-specific binding and trans-cleavage activity. With this approach, we developed a POC nucleic acid assay termed Solid-Phase Extraction and Enhanced Detection assay Integrated by CRISPR-Cas12a (SPEEDi-CRISPR) that negates the need for preamplification but significantly improves the detection of limit (LOD) from the pM to fM level. Specifically, using Cas12a-coated magnetic beads, this assay combines efficient solid-phase extraction and enrichment of DNA targets enabled by the sequence-specific affinity of CRISPR-Cas12a with the fluorogenic detection by the activated Cas12a on beads. Our proof-of-concept study demonstrated that the SPEEDi-CRISPR assay affords an improved detection sensitivity for human papillomavirus (HPV)-18 with a LOD of 2.3 fM and excellent specificity to discriminate HPV-18 from HPV-16, Parvovirus B19, and scramble HPV-18. Furthermore, this robust assay was readily coupled with a portable smartphone-based fluorescence detector and a lateral flow assay for quantitative detection and visualized readout, respectively. Overall, these results should suggest that our dual-function strategy could pave a new way for developing the next-generation CRISPR diagnostics and that the SPEEDi-CRISPR assay provides a potentially useful tool for point-of-care testing.
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13
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Iwaniuk EE, Adebayo T, Coleman S, Villaros CG, Nesterova IV. Activatable G-quadruplex based catalases for signal transduction in biosensing. Nucleic Acids Res 2023; 51:1600-1607. [PMID: 36727464 PMCID: PMC9976883 DOI: 10.1093/nar/gkad031] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 01/05/2023] [Accepted: 01/10/2023] [Indexed: 02/03/2023] Open
Abstract
Discovery of oxidative catalysis with G-quadruplex•hemin constructs prompted a range of exciting developments in the field of biosensor design. Thus, G-quadruplex based DNAzymes with peroxidase activity found a niche as signal transduction modules in a wide range of analytical applications. The ability of nucleic acid scaffolds to recognise a variety of practically meaningful markers and to translate the recognition events into conformational changes powers numerous sensor design possibilities. In this work, we establish a catalase activity of G-quadruplex•hemin scaffolds. Catalase activated hydrogen peroxide decomposition generates molecular oxygen that forms bubbles. Observation of bubbles is a truly equipment free signal readout platform that is highly desirable in limited resources or do-it-yourself environments. We take a preliminary insight into a G-quadruplex structure-folding topology-catalase activity correlation and establish efficient operating conditions. Further, we demonstrate the platform's potential as a signal transduction modality for reporting on biomolecular recognition using an oligonucleotide as a proof-of-concept target. Ultimately, activatable catalases based on G-quadruplex•hemin scaffolds promise to become valuable contributors towards accessible molecular diagnostics applications.
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Affiliation(s)
- Elzbieta E Iwaniuk
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
| | - Thuwebat Adebayo
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
| | - Seth Coleman
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
| | - Caitlin G Villaros
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
| | - Irina V Nesterova
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
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14
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Discovery and translation of functional nucleic acids for clinically diagnosing infectious diseases: Opportunities and challenges. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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15
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Yu H, Zhao Q. Sensitive Microscale Thermophoresis Assay Using Aptamer Thermal Switch. Anal Chem 2022; 94:16685-16691. [DOI: 10.1021/acs.analchem.2c03068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Hao Yu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiang Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310000, China
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16
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Wang W, Gunasekaran S. MXene-Based Nucleic Acid Biosensors for Agricultural and Food Systems. BIOSENSORS 2022; 12:bios12110982. [PMID: 36354491 PMCID: PMC9688781 DOI: 10.3390/bios12110982] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/02/2022] [Accepted: 11/04/2022] [Indexed: 05/04/2023]
Abstract
MXene is a two-dimensional (2D) nanomaterial that exhibits several superior properties suitable for fabricating biosensors. Likewise, the nucleic acid (NA) in oligomerization forms possesses highly specific biorecognition ability and other features amenable to biosensing. Hence the combined use of MXene and NA is becoming increasingly common in biosensor design and development. In this review, MXene- and NA-based biosensors are discussed in terms of their sensing mechanisms and fabrication details. MXenes are introduced from their definition and synthesis process to their characterization followed by their use in NA-mediated biosensor fabrication. The emphasis is placed on the detection of various targets relevant to agricultural and food systems, including microbial pathogens, chemical toxicants, heavy metals, organic pollutants, etc. Finally, current challenges and future perspectives are presented with an eye toward the development of advanced biosensors with improved detection performance.
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17
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Liu L, Yu H, Zhao Q. The Characterization of Binding between Aptamer and Bisphenol A and Developing Electrochemical Aptasensors for Bisphenol A with Rationally Engineered Aptamers. BIOSENSORS 2022; 12:bios12110913. [PMID: 36354422 PMCID: PMC9688307 DOI: 10.3390/bios12110913] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/16/2022] [Accepted: 10/17/2022] [Indexed: 06/12/2023]
Abstract
Bisphenol A (BPA) is widely used in the manufacture of polycarbonate and epoxy-resin-based products, and BPA contamination often happens in a variety of types of environment and food stuffs. BPA can cause many harmful effects to health due to its high toxicity. The rapid detection of BPA is of great significance in environmental monitoring and food safety. Nucleic acid aptamers show advantages in biosensors due to good chemical stability, the ease of labeling functional groups, and target binding that induces conformation change. Here, we performed a thorough characterization of the binding performance of one 60-nt anti-BPA DNA aptamer with isothermal titration calorimetry (ITC). We found the crucial region of the aptamer sequence for affinity binding with BPA, and the aptamer was able to be truncated to 29-nt DNA without losing affinity. We then developed a simple reagent-less electrochemical aptamer-based sensor for rapid BPA detection with this engineered aptamer. The truncated aptamer with a redox tag methylene blue (MB) was immobilized on a gold electrode. BPA-binding induced the conformation change of the MB-labeled aptamer, moving the MB close to the electrode surface and causing a significant current increase in MB in square wave voltammetry (SWV). Under optimized conditions, we achieved the quantitative detection of BPA with a detection limit of BPA at 0.1 μM. This sensor showed quick response to BPA and could be regenerated by washing with deionized water. This sensor was selective, and it allowed detecting BPA in complex samples, showing its potential in practice. This study will help in further applications of the aptamers of BPA.
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Affiliation(s)
- Liying Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hao Yu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiang Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
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18
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Ma X, Xu J, Zhou F, Ye J, Yang D, Wang H, Wang P, Li M. Recent advances in PCR-free nucleic acid detection for SARS-COV-2. Front Bioeng Biotechnol 2022; 10:999358. [PMID: 36277389 PMCID: PMC9585218 DOI: 10.3389/fbioe.2022.999358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 09/26/2022] [Indexed: 11/13/2022] Open
Abstract
As the outbreak of Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory disease coronavirus 2 (SARS-COV-2), fast, accurate, and economic detection of viral infection has become crucial for stopping the spread. Polymerase chain reaction (PCR) of viral nucleic acids has been the gold standard method for SARS-COV-2 detection, which, however, generally requires sophisticated facilities and laboratory space, and is time consuming. This review presents recent advances in PCR-free nucleic acid detection methods for SARS-CoV-2, including emerging methods of isothermal amplification, nucleic acid enzymes, electrochemistry and CRISPR.
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Affiliation(s)
| | | | | | | | | | - Hua Wang
- *Correspondence: Hua Wang, ; Pengfei Wang, ; Min Li,
| | - Pengfei Wang
- *Correspondence: Hua Wang, ; Pengfei Wang, ; Min Li,
| | - Min Li
- *Correspondence: Hua Wang, ; Pengfei Wang, ; Min Li,
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19
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Victorious A, Zhang Z, Chang D, Maclachlan R, Pandey R, Xia J, Gu J, Hoare T, Soleymani L, Li Y. A DNA Barcode‐Based Aptasensor Enables Rapid Testing of Porcine Epidemic Diarrhea Viruses in Swine Saliva Using Electrochemical Readout. Angew Chem Int Ed Engl 2022; 61:e202204252. [DOI: 10.1002/anie.202204252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Amanda Victorious
- School of Biomedical Engineering McMaster University 1280 Main Street West, Hamilton Ontario L8S 4K1 Canada
| | - Zijie Zhang
- Department of Biochemistry and Biomedical Sciences McMaster University Canada
| | - Dingran Chang
- Department of Biochemistry and Biomedical Sciences McMaster University Canada
| | | | - Richa Pandey
- School of Biomedical Engineering McMaster University 1280 Main Street West, Hamilton Ontario L8S 4K1 Canada
| | - Jianrun Xia
- Department of Biochemistry and Biomedical Sciences McMaster University Canada
| | - Jimmy Gu
- Department of Biochemistry and Biomedical Sciences McMaster University Canada
| | - Todd Hoare
- School of Biomedical Engineering McMaster University 1280 Main Street West, Hamilton Ontario L8S 4K1 Canada
- Department of Chemical Engineering McMaster University Canada
| | - Leyla Soleymani
- School of Biomedical Engineering McMaster University 1280 Main Street West, Hamilton Ontario L8S 4K1 Canada
- Department of Engineering Physics McMaster University Canada
- Michael G. DeGroote Institute for Infectious Disease Research McMaster University Canada
| | - Yingfu Li
- School of Biomedical Engineering McMaster University 1280 Main Street West, Hamilton Ontario L8S 4K1 Canada
- Department of Biochemistry and Biomedical Sciences McMaster University Canada
- Michael G. DeGroote Institute for Infectious Disease Research McMaster University Canada
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20
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Victorious A, Zhang Z, Chang D, Malachlan R, Pandey R, Xia J, Gu J, Hoare T, Soleymani L, Li Y. A DNA Barcode‐Based Aptasensor Enables Rapid Testing of Porcine Epidemic Diarrhea Viruses in Swine Saliva Using Electrochemical Readout. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202204252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | - Zijie Zhang
- McMaster University Biochemistry and Biomedical Sciences CANADA
| | - Dingran Chang
- McMaster University Biochemistry and Biomedical Sciences CANADA
| | | | | | - Jianrun Xia
- McMaster University Biochemistry and Biomedical Sciences CANADA
| | - Jimmy Gu
- McMurry University Biochemistry and Biomedical Sciences CANADA
| | - Todd Hoare
- McMurry University Chemical Engineering CANADA
| | - Leyla Soleymani
- McMastser University Engineering Physics 1280 Main Street W. L8S 4M1 Hamilton CANADA
| | - Yingfu Li
- McMaster University Biochemistry and Biomedical Sciences CANADA
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21
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Li J, Zhang Z, Amini R, Li Y. One Solution for All: Searching for Universal Aptamers for Constantly Mutating Spike Proteins of SARS‐CoV‐2. ChemMedChem 2022; 17:e202200166. [PMID: 35491395 PMCID: PMC9347811 DOI: 10.1002/cmdc.202200166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/28/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Jiuxing Li
- McMaster University Biochemistry and Biomedical Sciences CANADA
| | - Zijie Zhang
- McMaster University Biochemistry and Biomedical Sciences CANADA
| | - Ryan Amini
- McMaster University Biochemistry and Biomedical Sciences CANADA
| | - Yingfu Li
- McMaster University Biochemistry and Biomedical Sciences 1280 Main Street West L8S4K1 Hamilton CANADA
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22
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Pandey R, Lu Y, Osman E, Saxena S, Zhang Z, Qian S, Pollinzi A, Smieja M, Li Y, Soleymani L, Hoare T. DNAzyme-Immobilizing Microgel Magnetic Beads Enable Rapid, Specific, Culture-Free, and Wash-Free Electrochemical Quantification of Bacteria in Untreated Urine. ACS Sens 2022; 7:985-994. [PMID: 35384648 DOI: 10.1021/acssensors.1c02440] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Rapid, ultrasensitive, and specific detection and identification of bacteria in unprocessed clinical specimens is critically needed to enable point-of-care diagnosis of infectious diseases. However, existing systems require sample processing and/or analyte enrichment for direct bacterial analysis in clinical samples, which significantly adds to the assay time and complexity. Herein, we integrate RNA-cleaving DNAzymes specific to Escherichia coli (E. coli) and programmed for electrochemical signal transduction, multifunctional microgel magnetic beads for immobilizing the DNAzyme into a hydrated and three-dimensional scaffold, and hierarchical electrodes for ultrasensitive electrochemical readout to achieve rapid bacterial analysis in undiluted and unprocessed urine collected from symptomatic patients suspected of having urinary tract infections (UTIs). The microgel magnetic bead assay enables highly efficient conjugation and hydration of the immobilized DNAzymes, resulting in low limits-of-detection of 6 CFU/mL in buffer and 138 CFU/mL in unprocessed urine with high specificity against multiple urinary pathogens within a 1 hour assay time. The assay successfully identifies which patients are infected with E. coli as the causative organism for their UTI symptoms, indicating the clinical relevance of this assay.
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Affiliation(s)
- Richa Pandey
- Department of Engineering Physics, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
| | - Yang Lu
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
| | - Enas Osman
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
| | - Survanshu Saxena
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
| | - Zijie Zhang
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
| | - Shuwen Qian
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
| | - Angela Pollinzi
- Department of Chemical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L7, Canada
| | - Marek Smieja
- Department of Medicine, Pathology and Molecular Medicine, Research St. Joseph’s Hamilton, McMaster University, Hamilton, Ontario L8S 4L8, Canada
| | - Yingfu Li
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
| | - Leyla Soleymani
- Department of Engineering Physics, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
| | - Todd Hoare
- Department of Engineering Physics, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
- Department of Chemical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L7, Canada
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23
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Amini R, Zhang Z, Li J, Gu J, Brennan J, Li Y. Aptamers for SARS-CoV-2: Isolation, Characterization, and Diagnostic and Therapeutic Developments. ANALYSIS & SENSING 2022; 2:e202200012. [PMID: 35574520 PMCID: PMC9082509 DOI: 10.1002/anse.202200012] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/19/2022] [Indexed: 12/17/2022]
Abstract
The SARS‐CoV‐2 virus and COVID‐19 pandemic continue to demand effective diagnostic and therapeutic solutions. Finding these solutions requires highly functional molecular recognition elements. Nucleic acid aptamers represent a possible solution. Characterized by their high affinity and specificity, aptamers can be rapidly identified from random‐sequence nucleic acid libraries. Over the past two years, many labs around the world have rushed to create diverse aptamers that target two important structural proteins of SARS‐CoV‐2: the spike (S) protein and nucleocapsid (N) protein. These have led to the identification of many aptamers that show real promise for the development of diagnostic tests and therapeutic agents for SARS‐CoV‐2. Herein we review all these developments, with a special focus on the development of diverse aptasensors for detecting SARS‐CoV‐2. These include electrochemical and optical sensors, lateral flow devices, and aptamer‐linked immobilized sorbent assays.
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Affiliation(s)
- Ryan Amini
- McMaster University Biochemistry and Biomedical Sciences CANADA
| | - Zijie Zhang
- McMaster University Biochemistry and Biomedical Sciences CANADA
| | - Jiuxing Li
- McMaster University Biochemistry and Biomedical Sciences CANADA
| | - Jimmy Gu
- McMaster University Biochemistry and Biomedical Sciences CANADA
| | - John Brennan
- McMaster University Biointerfaces Institute CANADA
| | - Yingfu Li
- McMaster University Biochemistry and Biomedical Sciences 1280 Main Street West L8S4K1 Hamilton CANADA
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24
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Zhou M, Yin Y, Shi Y, Huang Z, Shi Y, Chen M, Ke G, Zhang XB. Spherical nucleic acid reporter-based cascade CRISPR/Cas12a amplifier for stable and sensitive biosensing of circulating tumor DNA. Chem Commun (Camb) 2022; 58:4508-4511. [PMID: 35302126 DOI: 10.1039/d2cc00960a] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Stable and sensitive ctDNA biosensing in complex biological fluid is highly important but still remains a challenge. Herein, we develop a spherical nucleic acid reporter-based cascade CRISPR/Cas12a amplifier with improved stability and sensitivity (5 orders of magnitude).
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Affiliation(s)
- Min Zhou
- College of Materials Science and Engineering, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Yao Yin
- College of Materials Science and Engineering, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Yuyan Shi
- College of Materials Science and Engineering, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Zhaoxin Huang
- College of Materials Science and Engineering, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Yu Shi
- College of Materials Science and Engineering, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Mei Chen
- College of Materials Science and Engineering, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Guoliang Ke
- College of Materials Science and Engineering, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Xiao-Bing Zhang
- College of Materials Science and Engineering, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
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25
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Recent advances in the construction of functional nucleic acids with isothermal amplification for heavy metal ions sensor. Microchem J 2022. [DOI: 10.1016/j.microc.2021.107077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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26
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Zhang Z, Li J, Gu J, Amini R, Stacey HD, Ang JC, White D, Filipe CDM, Mossman K, Miller MS, Salena BJ, Yamamura D, Sen P, Soleymani L, Brennan JD, Li Y. A Universal DNA Aptamer that Recognizes Spike Proteins of Diverse SARS‐CoV‐2 Variants of Concern. Chemistry 2022; 28:e202200078. [PMID: 35084794 PMCID: PMC9015322 DOI: 10.1002/chem.202200078] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Indexed: 12/15/2022]
Abstract
We report on a unique DNA aptamer, denoted MSA52, that displays universally high affinity for the spike proteins of wildtype SARS‐CoV‐2 as well as the Alpha, Beta, Gamma, Epsilon, Kappa, Delta and Omicron variants. Using an aptamer pool produced from round 13 of selection against the S1 domain of the wildtype spike protein, we carried out one‐round SELEX experiments using five different trimeric spike proteins from variants, followed by high‐throughput sequencing and sequence alignment analysis of aptamers that formed complexes with all proteins. A previously unidentified aptamer, MSA52, showed Kd values ranging from 2 to 10 nM for all variant spike proteins, and also bound similarly to variants not present in the reselection experiments. This aptamer also recognized pseudotyped lentiviruses (PL) expressing eight different spike proteins of SARS‐CoV‐2 with Kd values between 20 and 50 pM, and was integrated into a simple colorimetric assay for detection of multiple PL variants. This discovery provides evidence that aptamers can be generated with high affinity to multiple variants of a single protein, including emerging variants, making it well‐suited for molecular recognition of rapidly evolving targets such as those found in SARS‐CoV‐2.
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Affiliation(s)
- Zijie Zhang
- Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
| | - Jiuxing Li
- Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
| | - Jimmy Gu
- Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
| | - Ryan Amini
- Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
| | - Hannah D. Stacey
- Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
- Michael G. DeGroote Institute of Infectious Disease Research McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
- McMaster Immunology Research Centre McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
| | - Jann C. Ang
- Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
- Michael G. DeGroote Institute of Infectious Disease Research McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
- McMaster Immunology Research Centre McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
| | - Dawn White
- Biointerfaces Institute McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
| | - Carlos D. M. Filipe
- Department of Chemical Engineering McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
| | - Karen Mossman
- Department of Medicine McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
| | - Matthew S. Miller
- Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
- Michael G. DeGroote Institute of Infectious Disease Research McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
- McMaster Immunology Research Centre McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
| | - Bruno J. Salena
- Department of Medicine McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
| | - Deborah Yamamura
- Michael G. DeGroote Institute of Infectious Disease Research McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
- Department of Pathology and Molecular Medicine McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
| | - Payel Sen
- School of Biomedical Engineering McMaster University 1280 Main Street West Hamilton, Ontario Canada L8S 4K1
| | - Leyla Soleymani
- School of Biomedical Engineering McMaster University 1280 Main Street West Hamilton, Ontario Canada L8S 4K1
| | - John D. Brennan
- Biointerfaces Institute McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
- Biointerfaces Institute McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
- Michael G. DeGroote Institute of Infectious Disease Research McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
- School of Biomedical Engineering McMaster University 1280 Main Street West Hamilton, Ontario Canada L8S 4K1
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HASEBE Y, WANG Y. Electrochemical Flow Injection Analysis Biosensors Using Biomolecules-immobilized Carbon Felt. BUNSEKI KAGAKU 2022. [DOI: 10.2116/bunsekikagaku.71.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Yasushi HASEBE
- Department of Life Science and Green Chemistry, Faculty of Engineering, Saitama Institute of Technology
| | - Yue WANG
- School of Chemical Engineering, University of Science and Technology Liaoning
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28
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Sande MG, Rodrigues JL, Ferreira D, Silva CJ, Rodrigues LR. Novel Biorecognition Elements against Pathogens in the Design of State-of-the-Art Diagnostics. BIOSENSORS 2021; 11:bios11110418. [PMID: 34821636 PMCID: PMC8615483 DOI: 10.3390/bios11110418] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 05/21/2023]
Abstract
Infectious agents, especially bacteria and viruses, account for a vast number of hospitalisations and mortality worldwide. Providing effective and timely diagnostics for the multiplicity of infectious diseases is challenging. Conventional diagnostic solutions, although technologically advanced, are highly complex and often inaccessible in resource-limited settings. An alternative strategy involves convenient rapid diagnostics which can be easily administered at the point-of-care (POC) and at low cost without sacrificing reliability. Biosensors and other rapid POC diagnostic tools which require biorecognition elements to precisely identify the causative pathogen are being developed. The effectiveness of these devices is highly dependent on their biorecognition capabilities. Naturally occurring biorecognition elements include antibodies, bacteriophages and enzymes. Recently, modified molecules such as DNAzymes, peptide nucleic acids and molecules which suffer a selective screening like aptamers and peptides are gaining interest for their biorecognition capabilities and other advantages over purely natural ones, such as robustness and lower production costs. Antimicrobials with a broad-spectrum activity against pathogens, such as antibiotics, are also used in dual diagnostic and therapeutic strategies. Other successful pathogen identification strategies use chemical ligands, molecularly imprinted polymers and Clustered Regularly Interspaced Short Palindromic Repeats-associated nuclease. Herein, the latest developments regarding biorecognition elements and strategies to use them in the design of new biosensors for pathogens detection are reviewed.
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Affiliation(s)
- Maria G. Sande
- CEB—Centre of Biological Engineering, Campus de Gualtar, Universidade do Minho, 4710-057 Braga, Portugal; (M.G.S.); (J.L.R.); (D.F.)
| | - Joana L. Rodrigues
- CEB—Centre of Biological Engineering, Campus de Gualtar, Universidade do Minho, 4710-057 Braga, Portugal; (M.G.S.); (J.L.R.); (D.F.)
| | - Débora Ferreira
- CEB—Centre of Biological Engineering, Campus de Gualtar, Universidade do Minho, 4710-057 Braga, Portugal; (M.G.S.); (J.L.R.); (D.F.)
| | - Carla J. Silva
- CENTI—Center for Nanotechnology and Smart Materials, Rua Fernando Mesquita 2785, 4760-034 Vila Nova de Famalicão, Portugal;
- CITEVE—Technological Center for the Textile and Clothing Industries of Portugal, Rua Fernando Mesquita 2785, 4760-034 Vila Nova de Famalicão, Portugal
| | - Ligia R. Rodrigues
- CEB—Centre of Biological Engineering, Campus de Gualtar, Universidade do Minho, 4710-057 Braga, Portugal; (M.G.S.); (J.L.R.); (D.F.)
- Correspondence: ; Tel.: +351-253601978
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29
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Chang D, Zakaria S, Esmaeili Samani S, Chang Y, Filipe CDM, Soleymani L, Brennan JD, Liu M, Li Y. Functional Nucleic Acids for Pathogenic Bacteria Detection. Acc Chem Res 2021; 54:3540-3549. [PMID: 34478272 DOI: 10.1021/acs.accounts.1c00355] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Pathogens have long presented a significant threat to human lives, and hence the rapid detection of infectious pathogens is vital for improving human health. Current detection methods lack the means to detect infectious pathogens in a simple, rapid, and reliable manner at the time and point of need. Functional nucleic acids (FNAs) have the potential to overcome these limitations by acting as key components for point-of-care (POC) biosensors due to their distinctive advantages that include high binding affinities and specificities, excellent chemical stability, ease of synthesis and modification, and compatibility with a variety of signal-amplification and signal-transduction mechanisms.This Account summarizes the work completed in our groups toward developing FNA-based biosensors for detecting bacteria. In vitro selection has led to the isolation of many RNA-cleaving fluorogenic DNAzymes (RFDs) and DNA aptamers that can recognize infectious pathogens, including Escherichia coli, Clostridium difficile, Helicobacter pylori, and Legionella pneumophila. In most cases, a "many-against-many" approach was employed using a DNA library against a crude cellular mixture of an infectious pathogen containing diverse biomarkers as the target to isolate RFDs, with combined counter and positive selections ensuring high specificity toward the desired target. This procedure allows for the isolation of pathogen-specific FNAs without first identifying a suitable biomarker. Multiple target-specific DNA aptamers, including anti-glutamate dehydrogenase (GDH) circular aptamers, anti-degraded toxin B aptamers, and anti-RNase HII aptamers, have also been isolated for the detection of bacteria such as Clostridium difficile. The isolated FNAs have been integrated into fluorescent, colorimetric, and electrochemical biosensors using various signal transduction mechanisms. Both simple-to-use paper-based analytical devices and hand-held electrical devices with integrated FNAs have been developed for POC applications. In addition, signal-amplification strategies, including DNA catenane enabled rolling circle amplification (RCA), DNAzyme feedback RCA, and an all-DNA amplification system using a four-way junction and catalytic hairpin assembly (CHA), have been designed and applied to these systems to further increase their detection sensitivity. The use of these FNA-based biosensors to detect pathogens directly in clinical samples, such as urine, blood, and stool, has now been demonstrated with an outstanding sensitivity of as low as 10 cells per milliliter, highlighting the tremendous potential of using FNA-based sensors in clinical applications. We further describe strategies to overcome the challenges of using FNA-based biosensors in clinical applications, including strategies to improve the stability of FNAs in biological samples and prevent their nonspecific degradation from nucleases and strategies to deal with issues such as signal loss caused by nonspecific binding and biofouling. Finally, the remaining roadblocks for employing FNA-based biosensors in clinical applications are discussed.
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Affiliation(s)
| | | | | | - Yangyang Chang
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian, 116024, China
| | | | | | | | - Meng Liu
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian, 116024, China
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30
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Zhang F, Liu Z, Han Y, Fan L, Guo Y. Sandwich electrochemical carcinoembryonic antigen aptasensor based on signal amplification of polydopamine functionalized graphene conjugate Pd-Pt nanodendrites. Bioelectrochemistry 2021; 142:107947. [PMID: 34507161 DOI: 10.1016/j.bioelechem.2021.107947] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/16/2021] [Accepted: 08/29/2021] [Indexed: 02/09/2023]
Abstract
Carcinoembryonic antigen (CEA) is considered as a disease biomarker, which is related to various cancers and tumors in the human bodies. Sensitive detection of CEA is significant for clinical diagnosis and treatment. Herein, we proposed an electrochemical aptasensor for CEA detection based on the amplification driven by polydopamine functional graphene and Pd-Pt nanodendrites (PDA@Gr/Pd-PtNDs), conjugated hemin/G-quadruplex (hemin/G4), which possess mimicking peroxidases activity. Firstly, PDA@Gr was modified on the electrode surface for fixing CEA aptamer 1 (Apt1). Then, PDA@Gr/Pd-PtNDs with large surface area served as matrix for immobilization of hemin/G4 to obtain the secondary aptamer. In virtue of the sandwich-type specific reaction between CEA and the corresponding aptamers, the second aptamer was captured on the sensing interface, which can catalyze the oxidation of signal probe hydroquinone (HQ) with H2O2 and amplify current signal. Furthermore, the electrochemical signals of HQ were proportional with CEA concentrations. Under the optimal conditions, a dynamic response range from 50 pg/mL to 1.0 μg/mL and a detection limit of 6.3 pg/mL for CEA were obtained. Moreover, the proposed strategy represented satisfactory sensitivity and stability, and showed a good precision in real samples application.
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Affiliation(s)
- Fenglin Zhang
- Institute of Environmental Science, Shanxi University, Taiyuan 030006, China
| | - Zhiguang Liu
- Institute of Environmental Science, Shanxi University, Taiyuan 030006, China
| | - Yujie Han
- Institute of Environmental Science, Shanxi University, Taiyuan 030006, China
| | - Lifang Fan
- Institute of Environmental Science, Shanxi University, Taiyuan 030006, China
| | - Yujing Guo
- Institute of Environmental Science, Shanxi University, Taiyuan 030006, China.
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31
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Abstract
This article provides a comprehensive review of biosensing with DNAzymes, providing an overview of different sensing applications while highlighting major progress and seminal contributions to the field of portable biosensor devices and point-of-care diagnostics. Specifically, the field of functional nucleic acids is introduced, with a specific focus on DNAzymes. The incorporation of DNAzymes into bioassays is then described, followed by a detailed overview of recent advances in the development of in vivo sensing platforms and portable sensors incorporating DNAzymes for molecular recognition. Finally, a critical perspective on the field, and a summary of where DNAzyme-based devices may make the biggest impact are provided.
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Affiliation(s)
- Erin M McConnell
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada.
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32
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Li J, Zhang Z, Gu J, Stacey HD, Ang JC, Capretta A, Filipe CDM, Mossman KL, Balion C, Salena BJ, Yamamura D, Soleymani L, Miller MS, Brennan JD, Li Y. Diverse high-affinity DNA aptamers for wild-type and B.1.1.7 SARS-CoV-2 spike proteins from a pre-structured DNA library. Nucleic Acids Res 2021; 49:7267-7279. [PMID: 34232998 PMCID: PMC8287928 DOI: 10.1093/nar/gkab574] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/14/2021] [Accepted: 06/18/2021] [Indexed: 12/12/2022] Open
Abstract
We performed in vitro selection experiments to identify DNA aptamers for the S1 subunit of the SARS-CoV-2 spike protein (S1 protein). Using a pool of pre-structured random DNA sequences, we obtained over 100 candidate aptamers after 13 cycles of enrichment under progressively more stringent selection pressure. The top 10 sequences all exhibited strong binding to the S1 protein. Two aptamers, named MSA1 (Kd = 1.8 nM) and MSA5 (Kd = 2.7 nM), were assessed for binding to the heat-treated S1 protein, untreated S1 protein spiked into 50% human saliva and the trimeric spike protein of both the wildtype and the B.1.1.7 variant, demonstrating comparable affinities in all cases. MSA1 and MSA5 also recognized the pseudotyped lentivirus of SARS-CoV-2 with respective Kd values of 22.7 pM and 11.8 pM. Secondary structure prediction and sequence truncation experiments revealed that both MSA1 and MSA5 adopted a hairpin structure, which was the motif pre-designed into the original library. A colorimetric sandwich assay was developed using MSA1 as both the recognition element and detection element, which was capable of detecting the pseudotyped lentivirus in 50% saliva with a limit of detection of 400 fM, confirming the potential of these aptamers as diagnostic tools for COVID-19 detection.
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Affiliation(s)
- Jiuxing Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Zijie Zhang
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Jimmy Gu
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Hannah D Stacey
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada.,McMaster Immunology Research Centre, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Jann C Ang
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada.,McMaster Immunology Research Centre, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Alfredo Capretta
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada.,Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
| | - Carlos D M Filipe
- Department of Chemical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
| | - Karen L Mossman
- Department of Medicine, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
| | - Cynthia Balion
- Department of Pathology and Molecular Medicine, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Bruno J Salena
- Department of Medicine, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Deborah Yamamura
- Department of Pathology and Molecular Medicine, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
| | - Leyla Soleymani
- Department of Engineering Physics, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L7, Canada.,School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
| | - Matthew S Miller
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada.,McMaster Immunology Research Centre, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - John D Brennan
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada.,Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada.,Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada.,Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada.,School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
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33
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Xu X, Xiao L, Gu C, Shang J, Xiang Y. Wavelength-Selective Activation of Photocaged DNAzymes for Metal Ion Sensing in Live Cells. ACS OMEGA 2021; 6:13153-13160. [PMID: 34056465 PMCID: PMC8158819 DOI: 10.1021/acsomega.1c00976] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 04/28/2021] [Indexed: 05/09/2023]
Abstract
RNA-cleaving DNAzymes are widely applied as sensors for detecting metal ions in environmental samples owing to their high sensitivity and selectivity, but their use for sensing biological metal ions in live cells is challenging because constitutive sensors fail to report the spatiotemporal heterogeneity of biological processes. Photocaged DNAzymes can be activated by light for sensing purposes that need spatial and temporal resolution. Studying complex biological processes requires logic photocontrol, but unfortunately all the literature-reported photocaged DNAzymes working in live cells cannot be selectively controlled by light irradiation at different wavelengths. In this work, we developed photocaged DNAzymes responsive to UV and visible light using a general synthetic method based on phosphorothioate chemistry. Taking the Zn2+-dependent DNAzyme sensor as a model, we achieved wavelength-selective activation of photocaged DNAzymes in live human cells by UV and visible light, laying the groundwork for the logic activation of DNAzyme-based sensors in biological systems.
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34
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Minasyan AS, Chakravarthy S, Vardelly S, Joseph M, Nesterov EE, Nesterova IV. Rational design of guiding elements to control folding topology in i-motifs with multiple quadruplexes. NANOSCALE 2021; 13:8875-8883. [PMID: 33949568 PMCID: PMC8210535 DOI: 10.1039/d1nr00611h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Nucleic acids are versatile scaffolds that accommodate a wide range of precisely defined operational characteristics. Rational design of sensing, molecular computing, nanotechnology, and other nucleic acid devices requires precise control over folding conformations in these macromolecules. Here, we report a new approach that empowers well-defined conformational transitions in DNA molecular devices. Specifically, we develop tools for precise folding of multiple DNA quadruplexes (i-motifs) within the same oligonucleotide strand. To accomplish this task, we modify a DNA strand with kinetic control elements (hairpins and double stranded stems) that fold on a much faster timescale and consequently guide quadruplexes toward the targeted folding topology. To demonstrate that such guiding elements indeed facilitate formation of the targeted folding topology, we thoroughly characterize the folding/unfolding transitions through a combination of thermodynamic techniques, size exclusion chromatography (SEC) and small-angle X-ray scattering (SAXS). Furthermore, we extend SAXS capabilities to produce a direct insight on the shape and dimensions of the folded quadruplexes by computing their electron density maps from solution scattering data.
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Affiliation(s)
- Alexander S Minasyan
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA.
| | | | - Suchitra Vardelly
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA.
| | - Mark Joseph
- Department of Natural Science, University of Maryland Eastern Shore, Princess Anne, MD 21853, USA
| | - Evgueni E Nesterov
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA.
| | - Irina V Nesterova
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA.
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35
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Chang T, He S, Amini R, Li Y. Functional Nucleic Acids Under Unusual Conditions. Chembiochem 2021; 22:2368-2383. [PMID: 33930229 DOI: 10.1002/cbic.202100087] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/24/2021] [Indexed: 02/06/2023]
Abstract
Functional nucleic acids (FNAs), including naturally occurring ribozymes and riboswitches as well as artificially created DNAzymes and aptamers, have been popular molecular toolboxes for diverse applications. Given the high chemical stability of nucleic acids and their ability to fold into diverse sequence-dependent structures, FNAs are suggested to be highly functional under unusual reaction conditions. This review will examine the progress of research on FNAs under conditions of low pH, high temperature, freezing conditions, and the inclusion of organic solvents and denaturants that are known to disrupt nucleic acid structures. The FNA species to be discussed include ribozymes, riboswitches, G-quadruplex-based peroxidase mimicking DNAzymes, RNA-cleaving DNAzymes, and aptamers. Research within this space has not only revealed the hidden talents of FNAs but has also laid important groundwork for pursuing these intriguing functional macromolecules for unique applications.
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Affiliation(s)
- Tianjun Chang
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada.,Department of Biology, Institute of Resources and Environment, Henan Polytechnic University, Jiaozuo, 454000, Henan, P. R. China
| | - Sisi He
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada.,School of Science, Harbin Institute of Technology (Shenzhen), University Town, Shenzhen, 518055, Guangdong, P. R. China
| | - Ryan Amini
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
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36
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Guo WY, Fu YX, Liu SY, Mei LC, Sun Y, Yin J, Yang WC, Yang GF. Multienzyme-Targeted Fluorescent Probe as a Biosensing Platform for Broad Detection of Pesticide Residues. Anal Chem 2021; 93:7079-7085. [PMID: 33906355 DOI: 10.1021/acs.analchem.1c00553] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Pesticide residues, significantly hampering the overall environmental and human health, have become an increasingly severe issue. Thus, developing rapid, cost-effective, and sensitive tools for monitoring the pesticide residues in food and water is extremely important. Compared to the conventional and chromatographic techniques, enzyme inhibition-based biosensors conjugated with the fluorogenic probes provide effective alternative methods for detecting pesticide residues due to the inherent advantages including high selectivity and sensitivity, simple operation, and capability of providing in situ and real-time information. However, the detection efficiency of a single enzyme-targeted biosensor in practical samples is strongly impeded by the structural diversity of pesticides and their distinct targets. In this work, we developed a strategy of multienzyme-targeted fluorescent probe design and accordingly obtained a novel fluorescent probe (named as 3CP) for detecting the presence of wide variety of pesticides. The designed probe 3CP, targeting cholinesterases, carboxylesterases, and chymotrypsin simultaneously, yielded intense fluorescence in the solid state upon the enzyme-catalyzed hydrolysis. It showed excellent sensitivity against organophosphorus and carbamate pesticides, and the detection limit for dichlorvos achieved 1.14 pg/L. Moreover, it allowed for the diffusion-resistant in situ visualization of pesticides in live cells and zebrafish and the sensitive measurement of organophosphorus pesticides in fresh vegetables, demonstrating the promising potential for tracking the pesticide residues in environment and biological systems.
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Affiliation(s)
- Wu-Yingzheng Guo
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Yi-Xuan Fu
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Shi-Yu Liu
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Long-Can Mei
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Yao Sun
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Jun Yin
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Wen-Chao Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
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37
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Clifford A, Das J, Yousefi H, Mahmud A, Chen JB, Kelley SO. Strategies for Biomolecular Analysis and Continuous Physiological Monitoring. J Am Chem Soc 2021; 143:5281-5294. [PMID: 33793215 DOI: 10.1021/jacs.0c13138] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Portable devices capable of rapid disease detection and health monitoring are crucial to decentralizing diagnostics from clinical laboratories to the patient point-of-need. Although technologies have been developed targeting this challenge, many require the use of reporter molecules or reagents that complicate the automation and autonomy of sensors. New work in the field has targeted reagentless approaches to enable breakthroughs that will allow personalized monitoring of a wide range of biomarkers on demand. This Perspective focuses on the ability of reagentless platforms to revolutionize the field of sensing by allowing rapid and real-time analysis in resource-poor settings. First, we will highlight advantages of reagentless sensing techniques, specifically electrochemical detection strategies. Advances in this field, including the development of wearable and in situ sensors capable of real-time monitoring of biomarkers such as nucleic acids, proteins, viral particles, bacteria, therapeutic agents, and metabolites, will be discussed. Reagentless platforms which allow for wash-free, calibration free-detection with increased dynamic range are highlighted as a key technological advance for autonomous sensing applications. Furthermore, we will highlight remaining challenges which must be overcome to enable widespread use of reagentless devices. Finally, future prospects and potential breakthroughs in precision medicine that will arise as a result of further development of reagentless sensing approaches are discussed.
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Affiliation(s)
- Amanda Clifford
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Jagotamoy Das
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Hanie Yousefi
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Alam Mahmud
- The Edward S. Rogers Sr. Department of Electrical and Computer Engineering, University of Toronto, Toronto, Ontario M5S 3G4, Canada
| | - Jenise B Chen
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Shana O Kelley
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada.,Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada.,Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3G9, Canada
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38
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Fu X, Shi Y, Peng F, Zhou M, Yin Y, Tan Y, Chen M, Yin X, Ke G, Zhang XB. Exploring the Trans-Cleavage Activity of CRISPR/Cas12a on Gold Nanoparticles for Stable and Sensitive Biosensing. Anal Chem 2021; 93:4967-4974. [PMID: 33703873 DOI: 10.1021/acs.analchem.1c00027] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Taking advantage of the excellent trans-cleavage activity, CRISPR-based diagnostics (CRISPR-Dx) has shown great promise in molecular diagnostics. However, the single-stranded DNA reporter of the current CRISPR-Dx suffers from poor stability and limited sensitivity, which make their application in complex biological environments difficult. Herein, we, for the first time, explore the trans-cleavage activity of CRISPR/Cas12a toward the substrate on gold nanoparticles and apply the new phenomenon to develop a spherical nucleic acid (SNA) reporter for stable and sensitive CRISPR-Dx biosensing. By anchoring the DNA substrate on gold nanoparticles, we discovered different trans-cleavage activities of different types of the Cas12a system (e.g., LbCas12a and AsCas12a) on a nanoparticle surface. The further study suggests that the trans-cleavage activity of LbCas12a on the nanoparticle surface is highly dependent on the density and length of DNA strands. Based on these interesting discoveries, we furthermore develop SNA reporter-based fluorescent CRISPR-Dx for stable and sensitive biosensing application. Compared to traditional ssDNA reporters, the SNA reporter exhibits improved stability, which enables the stable application in a complex serum environment. In addition, the SNA reporter system with tunable density exhibits high sensitivity with a detection limit of 10 fM, which is about 2 orders of magnitude lower than that of the ssDNA reporter system. Finally, the practical application of SNA reporter-based CRISPR-Dx in clinical serum was successfully achieved. These results indicate their significant potential in future research on biology science and medical diagnoses.
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Affiliation(s)
- Xiaoyi Fu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Yuyan Shi
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Fangqi Peng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Min Zhou
- College of Materials Science and Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Yao Yin
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Yin Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Mei Chen
- College of Materials Science and Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Xia Yin
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Guoliang Ke
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Xiao-Bing Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
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Wang T, Chen L, Chikkanna A, Chen S, Brusius I, Sbuh N, Veedu RN. Development of nucleic acid aptamer-based lateral flow assays: A robust platform for cost-effective point-of-care diagnosis. Theranostics 2021; 11:5174-5196. [PMID: 33859741 PMCID: PMC8039946 DOI: 10.7150/thno.56471] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 01/29/2021] [Indexed: 02/07/2023] Open
Abstract
Lateral flow assay (LFA) has made a paradigm shift in the in vitro diagnosis field due to its rapid turnaround time, ease of operation and exceptional affordability. Currently used LFAs predominantly use antibodies. However, the high inter-batch variations, error margin and storage requirements of the conventional antibody-based LFAs significantly impede its applications. The recent progress in aptamer technology provides an opportunity to combine the potential of aptamer and LFA towards building a promising platform for highly efficient point-of-care device development. Over the past decades, different forms of aptamer-based LFAs have been introduced for broad applications ranging from disease diagnosis, agricultural industry to environmental sciences, especially for the detection of antibody-inaccessible small molecules such as toxins and heavy metals. But commercial aptamer-based LFAs are still not used widely compared with antibodies. In this work, by analysing the key issues of aptamer-based LFA design, including immobilization strategies, signalling methods, and target capturing approaches, we provide a comprehensive overview about aptamer-based LFA design strategies to facilitate researchers to develop optimised aptamer-based LFAs.
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Affiliation(s)
- Tao Wang
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth 6150, Australia
- Perron Institute for Neurological and Translational Science, Perth 6009, Australia
| | - Lanmei Chen
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth 6150, Australia
- Guangdong Key Laboratory for Research and Development of Nature Drugs, School of Pharmacy, Guangdong Medical University, Zhanjiang 524023, China
| | - Arpitha Chikkanna
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth 6150, Australia
| | - Suxiang Chen
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth 6150, Australia
| | - Isabell Brusius
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth 6150, Australia
| | - Nabayet Sbuh
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth 6150, Australia
| | - Rakesh N. Veedu
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth 6150, Australia
- Perron Institute for Neurological and Translational Science, Perth 6009, Australia
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Feng W, Newbigging AM, Tao J, Cao Y, Peng H, Le C, Wu J, Pang B, Li J, Tyrrell DL, Zhang H, Le XC. CRISPR technology incorporating amplification strategies: molecular assays for nucleic acids, proteins, and small molecules. Chem Sci 2021; 12:4683-4698. [PMID: 34163728 PMCID: PMC8179559 DOI: 10.1039/d0sc06973f] [Citation(s) in RCA: 114] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/19/2021] [Indexed: 12/19/2022] Open
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated (Cas) protein systems have transformed the field of genome editing and transcriptional modulation. Progress in CRISPR-Cas technology has also advanced molecular detection of diverse targets, ranging from nucleic acids to proteins. Incorporating CRISPR-Cas systems with various nucleic acid amplification strategies enables the generation of amplified detection signals, enrichment of low-abundance molecular targets, improvements in analytical specificity and sensitivity, and development of point-of-care (POC) diagnostic techniques. These systems take advantage of various Cas proteins for their particular features, including RNA-guided endonuclease activity, sequence-specific recognition, multiple turnover trans-cleavage activity of Cas12 and Cas13, and unwinding and nicking ability of Cas9. Integrating a CRISPR-Cas system after nucleic acid amplification improves detection specificity due to RNA-guided recognition of specific sequences of amplicons. Incorporating CRISPR-Cas before nucleic acid amplification enables enrichment of rare and low-abundance nucleic acid targets and depletion of unwanted abundant nucleic acids. Unwinding of dsDNA to ssDNA using CRISPR-Cas9 at a moderate temperature facilitates techniques for achieving isothermal exponential amplification of nucleic acids. A combination of CRISPR-Cas systems with functional nucleic acids (FNAs) and molecular translators enables the detection of non-nucleic acid targets, such as proteins, metal ions, and small molecules. Successful integrations of CRISPR technology with nucleic acid amplification techniques result in highly sensitive and rapid detection of SARS-CoV-2, the virus that causes the COVID-19 pandemic.
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Affiliation(s)
- Wei Feng
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta Edmonton Alberta T6G 2G3 Canada +1-780-492-7800 +1-780-492-6416
| | - Ashley M Newbigging
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta Edmonton Alberta T6G 2G3 Canada +1-780-492-7800 +1-780-492-6416
| | - Jeffrey Tao
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta Edmonton Alberta T6G 2G3 Canada +1-780-492-7800 +1-780-492-6416
| | - Yiren Cao
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta Edmonton Alberta T6G 2G3 Canada +1-780-492-7800 +1-780-492-6416
| | - Hanyong Peng
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta Edmonton Alberta T6G 2G3 Canada +1-780-492-7800 +1-780-492-6416
| | - Connie Le
- Li Ka Shing Institute of Virology, Department of Medical Microbiology and Immunology, Faculty of Medicine and Dentistry, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - Jinjun Wu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta Edmonton Alberta T6G 2G3 Canada +1-780-492-7800 +1-780-492-6416
| | - Bo Pang
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta Edmonton Alberta T6G 2G3 Canada +1-780-492-7800 +1-780-492-6416
- School of Public Health, Jilin University 1163 Xinmin Street Changchun Jilin 130021 China
| | - Juan Li
- School of Public Health, Jilin University 1163 Xinmin Street Changchun Jilin 130021 China
| | - D Lorne Tyrrell
- Li Ka Shing Institute of Virology, Department of Medical Microbiology and Immunology, Faculty of Medicine and Dentistry, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - Hongquan Zhang
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta Edmonton Alberta T6G 2G3 Canada +1-780-492-7800 +1-780-492-6416
| | - X Chris Le
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta Edmonton Alberta T6G 2G3 Canada +1-780-492-7800 +1-780-492-6416
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Rothenbroker M, McConnell EM, Gu J, Urbanus ML, Samani SE, Ensminger AW, Filipe CDM, Li Y. Selection and Characterization of an RNA‐Cleaving DNAzyme Activated by
Legionella pneumophila. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202012444] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Meghan Rothenbroker
- Michael G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - Erin M. McConnell
- Michael G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - Jimmy Gu
- Michael G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | | | | | | | | | - Yingfu Li
- Michael G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton ON L8S 4K1 Canada
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Selection and applications of functional nucleic acids for infectious disease detection and prevention. Anal Bioanal Chem 2021; 413:4563-4579. [PMID: 33506341 PMCID: PMC7840224 DOI: 10.1007/s00216-020-03124-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 11/30/2020] [Accepted: 12/14/2020] [Indexed: 02/07/2023]
Abstract
Infectious diseases caused by pathogenic microorganisms such as viruses and bacteria pose a great threat to human health. Although a significant progress has been obtained in the diagnosis and prevention of infectious diseases, it still remains challenging to develop rapid and cost-effective detection approaches and overcome the side effects of therapeutic agents and pathogen resistance. Functional nucleic acids (FNAs), especially the most widely used aptamers and DNAzymes, hold the advantages of high stability and flexible design, which make them ideal molecular recognition tools for bacteria and viruses, as well as potential therapeutic drugs for infectious diseases. This review summarizes important advances in the selection and detection of bacterial- and virus-associated FNAs, along with their potential prevention ability of infectious disease in recent years. Finally, the challenges and future development directions are concluded.
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Rothenbroker M, McConnell EM, Gu J, Urbanus ML, Samani SE, Ensminger AW, Filipe CDM, Li Y. Selection and Characterization of an RNA‐Cleaving DNAzyme Activated by
Legionella pneumophila. Angew Chem Int Ed Engl 2021; 60:4782-4788. [DOI: 10.1002/anie.202012444] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 10/22/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Meghan Rothenbroker
- Michael G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - Erin M. McConnell
- Michael G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - Jimmy Gu
- Michael G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | | | | | | | | | - Yingfu Li
- Michael G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton ON L8S 4K1 Canada
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Li W, Ma Y, Guo Z, Xing R, Liu Z. Efficient Screening of Glycan-Specific Aptamers Using a Glycosylated Peptide as a Scaffold. Anal Chem 2020; 93:956-963. [PMID: 33300777 DOI: 10.1021/acs.analchem.0c03675] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Abnormal glycan structures are valuable biomarkers for disease states; the development of glycan-specific binders is thereby significantly important. However, the structural homology and weak immunogenicity of glycans pose major hurdles in the evolution of antibodies, while the poor availability of complex glycans also has extremely hindered the selection of anti-glycan aptamers. Herein, we present a new approach to efficiently screen aptamers toward specific glycans with a complex structure, using a glycosylated peptide as a scaffold. In this method, using peptide-imprinted magnetic nanoparticles (MNPs) as a versatile platform, a glycopeptide tryptically digested from a native glycoprotein was selectively entrapped for positive selection, while a nonglycosylated analogue with an identical peptide sequence was synthesized for negative selection. Alternating positive and negative selection steps were carried out to guide the directed evolution of glycan-binding aptamers. As proof of the principle, the biantennary digalactosylated disialylated N-glycan A2G2S2, against which there have been no antibodies and lectins so far, was employed as the target. With the glycoprotein transferrin as a source of target glycan, two satisfied anti-A2G2S2 aptamers were selected within seven rounds. Since A2G2S2 is upregulated in cancerous liver cells, carboxyfluorescein (FAM)-labeled aptamers were prepared as fluorescent imaging reagents, and successful differentiation of cancerous liver cells over normal liver cells was achieved, which demonstrated the application feasibility of the selected aptamers. This approach obviated a tedious glycan preparation process and allowed favorable expose of the intrinsic flexible conformation of natural glycans. Therefore, it holds great promise for developing glycan-specific aptamers for challenging applications such as cancer targeting.
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Affiliation(s)
- Wei Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yanyan Ma
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Zhanchen Guo
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Rongrong Xing
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Zhen Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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Wang C, Liu L, Zhao Q. Low Temperature Greatly Enhancing Responses of Aptamer Electrochemical Sensor for Aflatoxin B1 Using Aptamer with Short Stem. ACS Sens 2020; 5:3246-3253. [PMID: 33052655 DOI: 10.1021/acssensors.0c01572] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Aflatoxin B1 (AFB1), one of the most toxic mycotoxins, poses great health risks. Rapid and sensitive detection of AFB1 is important for food safety, environment monitoring, and health risk assessment. We report here the development of a simple and reusable electrochemical aptasensor for rapid and sensitive detection of AFB1. Main improvements were achieved through engineering an aptamer containing a short stem-loop structure and enhancing the binding affinity at a lower temperature. The DNA aptamer with a methylene blue (MB) label at one end was immobilized on a gold electrode. Upon AFB1 binding, the aptamer folded into a stem-loop structure and brought MB close to the electrode surface, resulting in increases in electric current. The aptamer having a shorter stem (2-4 bp) underwent a larger conformation change upon target binding. The sensors built with the aptamer containing a 2 bp stem generated much higher signal-on responses to AFB1 at 4 °C than at room temperature (25 °C). The improvements resulted in a detection limit of 6 pM, enabling the determination of trace AFB1 in a complex sample matrix. This study demonstrates that low temperature greatly enhances the performance of aptamer electrochemical sensors. This aptasensor is simple to construct and readily regenerated by washing with deionized water for reuse. This aptasensor strategy could be applied to the development of an electrochemical aptasensor for other targets.
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Affiliation(s)
- Chao Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liying Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiang Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310000, China
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46
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Liu R, He L, Hu Y, Luo Z, Zhang J. A serological aptamer-assisted proximity ligation assay for COVID-19 diagnosis and seeking neutralizing aptamers. Chem Sci 2020; 11:12157-12164. [PMID: 34123223 PMCID: PMC8162504 DOI: 10.1039/d0sc03920a] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Rapid and accurate diagnosis of COVID-19 plays an essential role in the current epidemic prevention and control. Despite the promise of nucleic acid and antibody tests, there is still a great challenge to reduce the misdiagnosis, especially for asymptomatic individuals. Here we report a generalizable method for highly specific and ultrasensitive detection of serum COVID-19-associated antigens based on an aptamer-assisted proximity ligation assay. The sensor is based on binding two aptamer probes to the same protein target that brings the ligation DNA region into close proximity, thereby initiating ligation-dependent qPCR amplification. Using this system, serum nucleocapsid protein has been detected quantitatively by converting protein recognition into a detectable qPCR signal using a simple, homogeneous and fast detection workflow in ∼2 hours. In addition, this system has also been transformed into a universal platform for measuring specific interactions between spike S1 and its receptor ACE2, and more importantly demonstrated the feasibility for screening and investigation of potential neutralizing aptamers. Since in vitro selection can obtain aptamers selective for many COVID-19-associated antigens, the method demonstrated here will serve as an important tool for the diagnosis and therapeutics of COVID-19.
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Affiliation(s)
- Ran Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Lei He
- Hefei National Laboratory for Physical Science at the Microscale, Core Facility Center for Life Sciences, School of Life Sciences, University of Science and Technology of China Hefei 230026 China
| | - Yuansheng Hu
- The Third Affiliated Hospital of Anhui Medical University, Binhu Hospital of Hefei City Hefei 230022 China
| | - Zhaofeng Luo
- Hefei National Laboratory for Physical Science at the Microscale, Core Facility Center for Life Sciences, School of Life Sciences, University of Science and Technology of China Hefei 230026 China
| | - Jingjing Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
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Ming T, Luo J, Liu J, Sun S, Xing Y, Wang H, Xiao G, Deng Y, Cheng Y, Yang Z, Jin H, Cai X. Paper-based microfluidic aptasensors. Biosens Bioelectron 2020; 170:112649. [PMID: 33022516 DOI: 10.1016/j.bios.2020.112649] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/21/2020] [Accepted: 09/22/2020] [Indexed: 12/14/2022]
Abstract
For in-situ disease markers detection, point-of-care (POC) diagnosis has great advantages in speed and cost compared with traditional techniques. The rapid diagnosis, prognosis, and surveillance of diseases can significantly reduce disease-related mortality and trauma. Therefore, increasing attention has been paid to the POC diagnosis devices due to their excellent diagnosis speed and portability. Over the past ten years, paper-based microfluidic aptasensors have emerged as a class of critical POC diagnosis devices and various aptasensors have been proposed to detect various disease markers. However, most aptasensors need further improvement before they can actually enter the market and be widely used. There is thus an urgent need to sort out the key points of preparing the aptasensors and the direction that needs to be invested in. This review summarizes the representative articles in the development of paper-based microfluidic aptasensors. These works can be divided into paper-based optical aptasensors and paper-based electrochemical aptasensors according to their output signals. Significant focus is applied to these works according to the following three parts: (1) The ingenious design of device structure; (2) Application and synthesis of nanomaterial; (3) The detection principle of the proposed aptasensor. This is a detailed and comprehensive review of paper-based microfluidic aptasensors. The accomplishments and shortcomings of the current aptasensors are outlined, the development direction and the future prospective are given. It is hoped that the research in this review can provide a reference for further development of more advanced, more effective paper-based microfluidic aptasensors for POC disease markers diagnosis.
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Affiliation(s)
- Tao Ming
- Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing, 100094, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Jinping Luo
- Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing, 100094, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Juntao Liu
- Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing, 100094, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Shuai Sun
- Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing, 100094, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Yu Xing
- Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing, 100094, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Hao Wang
- Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing, 100094, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Guihua Xiao
- Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing, 100094, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Yu Deng
- Obstetrics and Gynecology Department, Peking University First Hospital, Beijing, 100034, PR China
| | - Yan Cheng
- Obstetrics and Gynecology Department, Peking University First Hospital, Beijing, 100034, PR China
| | - Zhugen Yang
- Cranfield Water Science Institute, Cranfield University, Cranfield, MK43 0AL, United Kingdom
| | - Hongyan Jin
- Obstetrics and Gynecology Department, Peking University First Hospital, Beijing, 100034, PR China.
| | - Xinxia Cai
- Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing, 100094, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China.
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Geng F, Wang D, Feng L, Li G, Xu M. An improved structure-switch aptamer-based fluorescent Pb 2+ biosensor utilizing the binding induced quenching of AMT to G-quadruplex. Chem Commun (Camb) 2020; 56:10517-10520. [PMID: 32779681 DOI: 10.1039/d0cc03669b] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
An improved aptamer-based fluorescent Pb2+ biosensor utilizing the binding induced quenching of AMT to G-quadruplex has been rationally designed with a LOD of 3.6 nM. The utility of the developed biosensor was demonstrated by the successful detection of Pb2+ in real complex clinical samples with satisfactory recovery and good reproducibility.
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Affiliation(s)
- Fenghua Geng
- National Engineering Research Center of Coal Preparation and Purification, Key Laboratory of Coal Processing and Efficient Utilization of Ministry of Education, School of Chemical Engineering and Technology, China University of Mining & Technology, Xuzhou, 221116, China.
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Wang C, Zhao Q. A reagentless electrochemical sensor for aflatoxin B1 with sensitive signal-on responses using aptamer with methylene blue label at specific internal thymine. Biosens Bioelectron 2020; 167:112478. [PMID: 32810704 DOI: 10.1016/j.bios.2020.112478] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 06/21/2020] [Accepted: 07/25/2020] [Indexed: 12/21/2022]
Abstract
Aptamer electrochemical sensors using immobilized aptamers with redox tag rely on the target binding-induced changes of current signal on electrode, offering advantages in operation convenience, no separation, rapidity, and sensitivity. Usually, the redox tag is placed on aptamer terminal, however, sometimes the terminal label may be insensitive to target-binding and fail to generate sensitive responses. The redox tag methylene blue (MB) labeled on different sites of aptamer may experience distinct changes in local environment, distance to electrode, or interactions with aptamer bases during affinity binding, which affect the current signal. Thus, it is possible to construct aptamer electrochemical sensors with sensitive and significant responses to targets by screening a series of sites (e.g., internal thymine T) of the aptamer and placing MB tag on a specific site of the aptamer. With this strategy, we successfully fabricated an electrochemical sensor on gold electrode for rapid, reagentless, and sensitive detection of aflatoxin B1 (AFB1), an important mycotoxin causing great health risks, by using a 26-mer DNA aptamer with MB on an internal T site (e.g., 18th T) and a thiol moiety at 5' terminal. This sensor generated remarkable signal-on responses to AFB1, allowed a detection limit of 6 pM, and enabled detection of AFB1 in wine, milk and corn flour samples. This sensor can be well regenerated by rinsing with deionized water and reused, and shows good stability. This sensor and the demonstrated strategy are promising in wide applications.
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Affiliation(s)
- Chao Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiang Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China; School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310000, China.
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50
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Label-free and self-assembled fluorescent DNA nanopompom for determination of miRNA-21. Mikrochim Acta 2020; 187:432. [PMID: 32638088 DOI: 10.1007/s00604-020-04377-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 06/07/2020] [Indexed: 02/07/2023]
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