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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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2
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Ji S, Wang X, Wang Y, Sun Y, Su Y, Lv X, Song X. Advances in Cas12a-Based Amplification-Free Nucleic Acid Detection. CRISPR J 2023; 6:405-418. [PMID: 37751223 DOI: 10.1089/crispr.2023.0023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023] Open
Abstract
In biomedicine, rapid and sensitive nucleic acid detection technology plays an important role in the early detection of infectious diseases. However, most traditional nucleic acid detection methods require the amplification of nucleic acids, resulting in problems such as long detection time, complex operation, and false-positive results. In recent years, clustered regularly interspaced short palindromic repeats (CRISPR) systems have been widely used in nucleic acid detection, especially the CRISPR-Cas12a system, which can trans cleave single-stranded DNA and can realize the detection of DNA targets. But, amplification of nucleic acids is still required to further improve detection sensitivity, which makes Cas12a-based amplification-free nucleic acid detection methods a great challenge. This article reviews the recent progress of Cas12a-based amplification-free detection methods for nucleic acids. These detection methods apply electrochemical detection methods, fluorescence detection methods, noble metal nanomaterial detection methods, and lateral flow assay. Under various optimization strategies, unamplified nucleic acids have the same sensitivity as amplified nucleic acids. At the same time, the article discusses the advantages and disadvantages of each method and further discusses the current challenges such as off-target effects and the ability to achieve high-throughput detection. Amplification-free nucleic acid detection technology based on CRISPR-Cas12a has great potential in the biomedical field.
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Affiliation(s)
- Shixin Ji
- School of Life Sciences, Changchun Normal University, Changchun, China; and Jilin Business and Technology College, Changchun, China
| | - Xueli Wang
- School of Grain, Jilin Business and Technology College, Changchun, China
| | - Yangkun Wang
- School of Life Sciences, Changchun Normal University, Changchun, China; and Jilin Business and Technology College, Changchun, China
| | - Yingqi Sun
- School of Life Sciences, Changchun Normal University, Changchun, China; and Jilin Business and Technology College, Changchun, China
| | - Yingying Su
- School of Life Sciences, Changchun Normal University, Changchun, China; and Jilin Business and Technology College, Changchun, China
| | - Xiaosong Lv
- School of Life Sciences, Changchun Normal University, Changchun, China; and Jilin Business and Technology College, Changchun, China
| | - Xiangwei Song
- School of Life Sciences, Changchun Normal University, Changchun, China; and Jilin Business and Technology College, Changchun, China
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3
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Luo P, Huang X, Luo F, Chen Z, Chen Y, Lin C, Wang J, Qiu B, Lin Z. Low-Background Signal-On Homogeneous Electrochemiluminescence Biosensor for Hepatitis B Virus Detection Based on the Regulation of the Length of DNA Modified on the Nanoparticles by CRISPR/Cas12a and Hybridization Chain Reaction. Anal Chem 2023; 95:14127-14134. [PMID: 37676272 DOI: 10.1021/acs.analchem.3c03141] [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: 09/08/2023]
Abstract
In this work, combined with the high amplification efficiency of hybridization chain reaction (HCR), high specificity of the CRISPR/Cas12a system, and convenience of the homogeneous electrochemiluminescence (ECL) assay based on the regulation of negative charge on the reporting probes, a sensitive ECL biosensor for hepatitis B virus DNA (chosen as a model target) had been developed. The initiator chain trigger DNA that can induce HCR amplification is modified on the surface of ruthenium bipyridine-doped silica nanoparticles (Ru@SiO2 NPs) first, and large amounts of negative charges modified on the particles were achieved through the HCR amplification reaction. The efficiency of the nanoparticles reaching the negatively charged working electrode can be regulated and realize the change of the ECL signal. In addition, long DNA on the surface of the luminescent body may prevent the coreactant from entering the pore to react with ruthenium bipyridine. These factors combine to produce a low-background system. The presence of the target can activate the CRISPR/Cas12a system and make trigger DNA disappear from the nanoparticle surface, and strong ECL can be detected. The sensor does not require a complex electrode modification; therefore, it has better reproducibility. Additionally, due to dual signal amplification, the sensor has a high sensitivity. In the range of 10 fM to 10 nM, the ECL intensity exhibits a strong linear relationship with the logarithm of the target concentration, and the detection limit is 7.41 fM. This sensor has shown high accuracy in detecting clinical samples, which holds significant potential for application in clinical testing.
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Affiliation(s)
- Peiqing Luo
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, 2 Xue Yuan Road, Fuzhou, Fujian 350116, China
| | - Xiaocui Huang
- Department of Science Research and Training, Fujian Institute of Education, Fuzhou, Fujian 350001, China
| | - Fang Luo
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, 2 Xue Yuan Road, Fuzhou, Fujian 350116, China
| | - Zhonghui Chen
- Affiliated Hospital of Putian University, Putian University, Putian, Fujian 351100, China
| | - Yu Chen
- Central Laboratory, Affiliated Hospital of Putian University, Putian University, Putian 351100, China
| | - Cuiying Lin
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, 2 Xue Yuan Road, Fuzhou, Fujian 350116, China
| | - Jian Wang
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, 2 Xue Yuan Road, Fuzhou, Fujian 350116, China
| | - Bin Qiu
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, 2 Xue Yuan Road, Fuzhou, Fujian 350116, China
| | - Zhenyu Lin
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, 2 Xue Yuan Road, Fuzhou, Fujian 350116, China
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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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Khuda N, Somasundaram S, Urgunde AB, Easley CJ. Ionic Strength and Hybridization Position near Gold Electrodes Can Significantly Improve Kinetics in DNA-Based Electrochemical Sensors. ACS APPLIED MATERIALS & INTERFACES 2023; 15:5019-5027. [PMID: 36661270 PMCID: PMC10370289 DOI: 10.1021/acsami.2c22741] [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: 06/16/2023]
Abstract
A variety of electrochemical (EC) biosensors play critical roles in disease diagnostics. More recently, DNA-based EC sensors have been established as promising for detecting a wide range of analyte classes. Since most of these sensors rely on the high specificity of DNA hybridization for analyte binding or structural control, it is crucial to understand the kinetics of hybridization at the electrode surface. In this work, we have used methylene blue-labeled DNA strands to monitor the kinetics of DNA hybridization at the electrode surface with square-wave voltammetry. By varying the position of the double-stranded DNA segment relative to the electrode surface as well as the bulk solution's ionic strength (0.125-1.00 M), we observed significant interferences with DNA hybridization closer to the surface, with more substantial interference at lower ionic strength. As a demonstration of the effect, toehold-mediated strand displacement reactions were slowed and diminished close to the surface, while strategic placement of the DNA binding site improved reaction rates and yields. This work manifests that both the salt concentration and DNA hybridization site relative to the electrode are important factors to consider when designing DNA-based EC sensors that measure hybridization directly at the electrode surface.
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Affiliation(s)
- Niamat Khuda
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849, USA
| | | | - Ajay B. Urgunde
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849, USA
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Yang X, Liu X, Kang Q, Qi Y, Du Y, Xiang H. A novel DNA detection using spherical identification probe and strand displacement reaction-initiated silver nanocluster switch. ANAL SCI 2023; 39:275-284. [PMID: 36607557 PMCID: PMC9816546 DOI: 10.1007/s44211-022-00243-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/23/2022] [Indexed: 01/07/2023]
Abstract
Herein, we developed a novel fluorescent assay using spherical identification probes and toehold-mediated strand displacement reaction-initiated silver nanoclusters (AgNCs) "on-off" signal switch. In this strategy, the target was captured by the spherical probes to induce the activity of exonuclease III (Exo III), catalyzing the cyclic cleavage of substrates to produce a mass of trigger strands. After magnetic bead separation, the intermediates in the supernatant activated downstream toehold-mediated strand displacement reaction to change the structure of silver nanocluster templates, leading to fluorescence intensity reduction. Furthermore, it is demonstrated that the application of spherical identification probes could reduce the signal leakage and the limit of detection. In addition, AgNCs with perfect optical property were ingeniously combined to realize signal output, which reduced the cost and time of synthesis. Under the optimal conditions, the sensing method displayed a good linear range from 250 pM to 25 nM with a detectable minimum concentration of 250 pM. And the practical application potential in complex biological matrices was also evaluated. Considering these advantages, this constructed strategy opens a new path for nucleic acid detection with better performance. A simple, label- and hairpin-free fluorescent system based on spherical identification probe and toehold-mediated strand displacement reaction-initiated silver nanoclusters (AgNCs) "on-off" signal switch was successfully constructed to detect target DNA.
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Affiliation(s)
- Xiaoyan Yang
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016 People’s Republic of China
| | - Xiaoyu Liu
- Department of Clinical Laboratory, Guang’an People’ Hospital, Guang’an, People’s Republic of China
| | - Qi Kang
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016 People’s Republic of China
| | - Yinxiao Qi
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016 People’s Republic of China
| | - Yumin Du
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016 People’s Republic of China
| | - Hua Xiang
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, People's Republic of China.
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7
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Zhu Q, Yan T, Yang Y, Song Y, Lu J, Luo Y, Xu LP, Xu T. Programmable Microparticle Array for In Situ Modification and Multiple miRNA Detection. ACS Sens 2022; 7:3654-3659. [PMID: 36448914 DOI: 10.1021/acssensors.2c02158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Simultaneous detection of multiple miRNAs of one disease can greatly reduce misdiagnosis and improve the detection rate, which is helpful for early cancer diagnosis. Here, a programmable microparticle-array-based acoustic microchip for in situ simultaneous multiple miRNAs detection is developed. On this microchip, the multiple probes-labeled microparticle array can be procedurally arranged in a microfluidic reaction chamber when four orthogonally piezoelectric transducers are applied. The probes-labeled microparticle array offers a platform for full molecular contact under dynamic ultrasonic streaming, and the array supplies a multipoint data correction to reduce the false positive of the detection results for more precisely visible fluorescence multiple target miRNAs sensing. We employed miRNA-21, miRNA-210, and miRNA-155 as specific biomarkers of pancreatic cancer and successfully finished the multiple miRNAs simultaneous detection in the microchip with a detection limit of 139.1, 179.9, and 111.4 pM, respectively. Such a device is programmable by adjusting the imputing frequency and voltage, and target biomarkers can be easily collected when the ultrasound force is released for further analysis, which shows great potential in multiple miRNAs enrichment and simultaneous detection for cancer clinical diagnosis.
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Affiliation(s)
- Qinglin Zhu
- Research Center for Bioengineering and Sensing Technology, University of Science and Technology Beijing, Beijing100083, People's Republic of China
| | - Tingxiu Yan
- Research Center for Bioengineering and Sensing Technology, University of Science and Technology Beijing, Beijing100083, People's Republic of China
| | - Yuemeng Yang
- Research Center for Bioengineering and Sensing Technology, University of Science and Technology Beijing, Beijing100083, People's Republic of China
| | - Yongchao Song
- Intelligent Wearable Engineering Research Center of Qingdao, Research Center for Intelligent and Wearable Technology, College of Textiles and Clothing, State Key Laboratory of Bio-Fibers and Eco-Textiles, Qingdao University, Qingdao266071, People's Republic of China
| | - Jingwei Lu
- Research Center for Bioengineering and Sensing Technology, University of Science and Technology Beijing, Beijing100083, People's Republic of China
| | - Yong Luo
- Research Center for Bioengineering and Sensing Technology, University of Science and Technology Beijing, Beijing100083, People's Republic of China
| | - Li-Ping Xu
- Research Center for Bioengineering and Sensing Technology, University of Science and Technology Beijing, Beijing100083, People's Republic of China
| | - Tailin Xu
- Research Center for Bioengineering and Sensing Technology, University of Science and Technology Beijing, Beijing100083, People's Republic of China.,School of Biomedical Engineering, Shenzhen University, Shenzhen, Guangdong518060, People's Republic of China
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8
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Zhang W, Mu Y, Dong K, Zhang L, Yan B, Hu H, Liao Y, Zhao R, Shu W, Ye Z, Lu Y, Wan C, Sun Q, Li L, Wang H, Xiao X. PAM-independent ultra-specific activation of CRISPR-Cas12a via sticky-end dsDNA. Nucleic Acids Res 2022; 50:12674-12688. [PMID: 36484104 PMCID: PMC9825152 DOI: 10.1093/nar/gkac1144] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 11/04/2022] [Accepted: 11/18/2022] [Indexed: 12/13/2022] Open
Abstract
Although CRISPR-Cas12a [clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 12a] combining pre-amplification technology has the advantage of high sensitivity in biosensing, its generality and specificity are insufficient, which greatly restrains its application range. Here, we discovered a new targeting substrate for LbaCas12a (Lachnospiraceae bacterium Cas12a), namely double-stranded DNA (dsDNA) with a sticky-end region (PAM-SE+ dsDNA). We discovered that CRISPR-Cas12a had special enzymatic properties for this substrate DNA, including the ability to recognize and cleave it without needing a protospacer adjacent motif (PAM) sequence and a high sensitivity to single-base mismatches in that substrate. Further mechanism studies revealed that guide RNA (gRNA) formed a triple-stranded flap structure with the substrate dsDNA. We also discovered the property of low-temperature activation of CRISPR-Cas12a and, by coupling with the unique DNA hybridization kinetics at low temperature, we constructed a complete workflow for low-abundance point mutation detection in real samples, which was fast, convenient and free of single-stranded DNA (ssDNA) transformation. The detection limits were 0.005-0.01% for synthesized strands and 0.01-0.05% for plasmid genomic DNA, and the mutation abundances provided by our system for 28 clinical samples were in accordance with next-generation sequencing results. We believe that our work not only reveals novel information about the target recognition mechanism of the CRISPR-Cas12a system, but also greatly broadens its application scenarios.
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Affiliation(s)
| | | | - Kejun Dong
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Lei Zhang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Bei Yan
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Hao Hu
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yangwei Liao
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Rong Zhao
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Wan Shu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Zhengxin Ye
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yaping Lu
- Sinopharm Genomics Technology Co., Ltd, Wuhan 430000, China
| | - Chong Wan
- Precision Medicine Center, Yangtze Delta Region Institute of Tsinghua University, Jiaxing 314006, China
| | - Qiangqiang Sun
- Life Health Care Clinical Laboratories, Beijing 100000, China
| | - Longjie Li
- Correspondence may also be addressed to Longjie Li.
| | - Hongbo Wang
- Correspondence may also be addressed to Hongbo Wang.
| | - Xianjin Xiao
- To whom correspondence should be addressed. Tel: +86 027 8369 2651; Fax: +86 027 8369 2651;
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Song T, Wang X, Yao D, Liang H, Lu Y. Identifying and Differentiating Topological G-Quadruplex Structures with DNA-Encoded Plasmonic Gold Nanoparticles. Angew Chem Int Ed Engl 2022; 61:e202204201. [PMID: 35894268 PMCID: PMC9489634 DOI: 10.1002/anie.202204201] [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: 03/21/2022] [Indexed: 11/10/2022]
Abstract
DNA G-quadruplexes (G4s) have been identified as critical elements in modulating genomic functions and many other biological processes. Their functions are highly dependent on the primary nucleotides and secondary folding structures. Therefore, to understand their functions, methods to identify and differentiate structures of G4 with speed and accuracy are required but limited. In this report, we have applied a synthetic G4 DNA-encoded nanoparticle approach to identify and differentiate G4 DNA molecules with different topologies and nucleotide residues. We found that the resulting plasmonic properties of the gold nanoparticles, monitored by UV/Vis spectroscopy, are quite sensitive to different G4 structures, including stacking layers, loop sequences, capping bases on G4s, and topological structures. Through these systematic investigations, we demonstrate that this G4-encoded gold nanoparticle approach can be used to profile the G4 structures and distinguish G4s from human telomeres. Such a method may have wide applications in G4 research.
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Affiliation(s)
- Tingjie Song
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Xiaojing Wang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Dongbao Yao
- Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Haojun Liang
- Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
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10
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Safenkova IV, Burkin KM, Bodulev OL, Razo SC, Ivanov AV, Zherdev AV, Dzantiev BB, Sakharov IY. Comparative study of magnetic beads and microplates as supports in heterogeneous amplified assay of miRNA-141 by using mismatched catalytic hairpin assembly reaction. Talanta 2022; 247:123535. [DOI: 10.1016/j.talanta.2022.123535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 04/08/2022] [Accepted: 05/06/2022] [Indexed: 11/16/2022]
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11
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Li Y, Li W, Xu W, Huang J, Sun Z, Liao T, Kovaleva EG, Xu C, Cheng J, Li H. Specific extraction of nucleic acids employing pillar[6]arene-functionalized nanochannel platforms. Chem Commun (Camb) 2022; 58:9278-9281. [PMID: 35904069 DOI: 10.1039/d2cc02693g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The rapid extraction of high-purity nucleic acids from complex biological samples using conventional methods is complicated. Therefore, in this study, glycine-pillar[6]arene (Gly-P6)-functionalized tapered nanochannels were constructed using 32-mer single-stranded E. coli DNA (ssDNA) as a model sequence, which can selectively transport ssDNA by multiple noncovalent forces (transport flux of 2.65 nM cm-2 h-1) under the interference of amino acids and other substances. In view of these prospective results, the selective transport of nucleic acids with nanochannels could be applied in the design of nucleic acid enrichment and separation systems in the future.
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Affiliation(s)
- Yu Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, China.,Key Laboratory of Pesticide and Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Wenjie Li
- Key Laboratory of Pesticide and Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Weiwei Xu
- Key Laboratory of Pesticide and Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Jinmei Huang
- Key Laboratory of Pesticide and Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Zhongyue Sun
- School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan 430065, P. R. China
| | - Tangbin Liao
- School of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, P. R. China
| | - Elena G Kovaleva
- Department of Technology for Organic Synthesis, Ural Federal University, Mira Street, 28, 620002 Yekaterinburg, Russia
| | - Chuanlai Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, China
| | - Jing Cheng
- State Key Laboratory of Food Science and Technology, Jiangnan University, China.,Key Laboratory of Pesticide and Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Haibing Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, China.,Key Laboratory of Pesticide and Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
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12
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Song T, Wang X, Yao D, Liang H, Lu Y. Identifying and Differentiating Topological G‐Quadruplex Structures with DNA‐encoded Plasmonic Gold Nanoparticles. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202204201] [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)
- Tingjie Song
- University of Illinois at Urbana-Champaign Chemistry A429 CLSL,600 South Mathews Avenue 61801 Urbana UNITED STATES
| | - Xiaojing Wang
- University of Illinois at Urbana-Champaign Chemistry 600 South Mathews Avenue 61801 Urbana UNITED STATES
| | - Dongbao Yao
- University of Science and Technology of China Polymer Science and Engineering jinzhai Road, NO.96 230026 hefei CHINA
| | - Haojun Liang
- University of Science and Technology of China Polymer Science and Engineering jinzhai Road, NO.96 230026 hefei CHINA
| | - Yi Lu
- University of Illinois Chemistry 600 South Mathews Ave. 61801 Urbana UNITED STATES
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13
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A Turn Off Fluorescence Probe Based on Carbon Dots for Highly Sensitive Detection of BRCA1 Gene in Real Samples and Cellular Imaging. J Fluoresc 2022; 32:1733-1741. [DOI: 10.1007/s10895-022-02954-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 04/11/2022] [Indexed: 10/18/2022]
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14
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Hu P, Dong Y, Yao C, Yang D. Construction of branched DNA-based nanostructures for diagnosis, therapeutics and protein engineering. Chem Asian J 2022; 17:e202200310. [PMID: 35468254 DOI: 10.1002/asia.202200310] [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: 03/26/2022] [Revised: 04/23/2022] [Indexed: 11/08/2022]
Abstract
Branched DNA with multibranch-like anisotropic topology serves as a promising and powerful building block in constructing multifunctional-integrated nanomaterials in a programmable and controllable manner. Recently, a series of branched DNA-based functional nanomaterials were developed by elaborate molecular design. In this review, we focused on the construction of branched DNA-based nanostructures for biological and biomedical applications. First, the molecular design and synthesis method of branched DNA monomer were briefly described. Then, the construction strategies of branched DNA-based nanostructures were categorially discussed, including target-triggered polymerization, enzymatic extension and hybrid assembly. Finally, the biological and biomedical applications including diagnosis, therapeutics and protein engineering were summarized. We envision that the review will contribute to the further development of branched DNA-based nanomaterials with great application potential in the field of biomedicine, thus building a new bridge between material chemistry and biomedicine.
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Affiliation(s)
- Pin Hu
- Tianjin University, School of Chemical Engineering and Technology, CHINA
| | - Yuhang Dong
- Tianjin University, School of Chemical Engineering and Technology, CHINA
| | - Chi Yao
- Tianjin University, School of Chemical Engineering and Technology, CHINA
| | - Dayong Yang
- Tianjin University, Chemistry Department, Room 328, Building 54, 300350, Tianjin, CHINA
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15
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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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16
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Zhan S, Jiang J, Zeng Z, Wang Y, Cui H. DNA-templated coinage metal nanostructures and their applications in bioanalysis and biomedicine. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214381] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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17
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Mahshid SS, Higazi AM, Ogier JM, Dabdoub A. Extracellular Biomarkers of Inner Ear Disease and Their Potential for Point-of-Care Diagnostics. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2104033. [PMID: 34957708 PMCID: PMC8948604 DOI: 10.1002/advs.202104033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 11/09/2021] [Indexed: 06/14/2023]
Abstract
Rapid diagnostic testing has become a mainstay of patient care, using easily obtained samples such as blood or urine to facilitate sample analysis at the point-of-care. These tests rely on the detection of disease or organ-specific biomarkers that have been well characterized for a particular disorder. Currently, there is no rapid diagnostic test for hearing loss, which is one of the most prevalent sensory disorders in the world. In this review, potential biomarkers for inner ear-related disorders, their detection, and quantification in bodily fluids are described. The authors discuss lesion-specific changes in cell-free deoxyribonucleic acids (DNAs), micro-ribonucleic acids (microRNAs), proteins, and metabolites, in addition to recent biosensor advances that may facilitate rapid and precise detection of these molecules. Ultimately, these biomarkers may be used to provide accurate diagnostics regarding the site of damage in the inner ear, providing practical information for individualized therapy and assessment of treatment efficacy in the future.
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Affiliation(s)
- Sahar Sadat Mahshid
- Biological SciencesSunnybrook Research InstituteSunnybrook Health Sciences CentreTorontoONM4N 3M5Canada
| | - Aliaa Monir Higazi
- Biological SciencesSunnybrook Research InstituteSunnybrook Health Sciences CentreTorontoONM4N 3M5Canada
- Department of Clinical and Chemical PathologyMinia UniversityMinia61519Egypt
| | - Jacqueline Michelle Ogier
- Biological SciencesSunnybrook Research InstituteSunnybrook Health Sciences CentreTorontoONM4N 3M5Canada
| | - Alain Dabdoub
- Biological SciencesSunnybrook Research InstituteSunnybrook Health Sciences CentreTorontoONM4N 3M5Canada
- Department of Otolaryngology–Head & Neck SurgeryUniversity of TorontoTorontoONM5G 2C4Canada
- Department of Laboratory Medicine and PathobiologyUniversity of TorontoTorontoONM5S 1A8Canada
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18
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Wu H, Ma X, Chu Y, Qi X, Zou B, Liu Y, Zhou G. Digital Nucleic Acid Signal Amplification Platform for Highly Sensitive DNA Mutation Analysis. Anal Chem 2022; 94:3858-3864. [PMID: 35212518 DOI: 10.1021/acs.analchem.1c04765] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Digital nucleic acid analysis technology has shown great application potential due to its excellent performance. However, most current digital nucleic acid detection methods are based on PCR or other template amplification strategies. Here, we present an alternative analysis platform based on digital nucleic acid signal amplification in droplets termed dNASA. Using a bead-based controllable extension bridged cascade signal amplification reaction, we achieved an ultralow background, high efficiency, and highly specific nucleic acid signal amplification analysis. As a "proof of concept", we demonstrated the feasibility of the proposed dNASA platform in single-base DNA mutation analysis using artificially synthesized samples. This platform provides innovative ideas for the field of digital nucleic acid analysis.
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Affiliation(s)
- Haiping Wu
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing 210002, China.,School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Xueping Ma
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing 210002, China
| | - Yanan Chu
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing 210002, China
| | - Xiemin Qi
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing 210002, China
| | - Bingjie Zou
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing 210002, China.,Key Laboratory of Drug Quality Control and Pharmacovigilance of Ministry of Education, China Pharmaceutical University, Nanjing 210009, China.,School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Yunlong Liu
- State Key Laboratory of Natural Medicines, Department of Biomedical Engineering, School of Engineering, China Pharmaceutical University, Nanjing 210009, China
| | - Guohua Zhou
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing 210002, China.,School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, Guangdong, China
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19
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Recombinase polymerase amplification integrated with microfluidics for nucleic acid testing at point of care. Talanta 2022; 240:123209. [PMID: 35026642 DOI: 10.1016/j.talanta.2022.123209] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 12/30/2021] [Accepted: 01/03/2022] [Indexed: 12/12/2022]
Abstract
Nucleic acid testing (NAT) implemented on a portable, miniaturized, and integrated device with rapid and sensitive results readout is highly demanded for pathogen detection or genetic screening at resource-limited settings, especially after the outbreak of coronavirus disease 2019 (COVID-19). The integration of recombinase polymerase amplification (RPA) with emerging microfluidics, classified by paper-based microfluidics and chip-based microfluidics, shows great potential to perform laboratory independent NAT assays at point of care with minimal labor, time and energy consumption. This review summarizes the state-of-the-art of RPA integrated with paper-based microfluidics and chip-based microfluidics, and discusses their pros and cons. Finally, existing challenges and possible ways for optimization of microfluidics-based RPA are proposed.
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20
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Numan A, Singh S, Zhan Y, Li L, Khalid M, Rilla K, Ranjan S, Cinti S. Advanced nanoengineered-customized point-of-care tools for prostate-specific antigen. Mikrochim Acta 2021; 189:27. [PMID: 34905090 DOI: 10.1007/s00604-021-05127-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/02/2021] [Indexed: 01/06/2023]
Abstract
Change in the level of human prostate-specific antigen (PSA) is a major element in the development and progression of prostate cancer (PCa). Most of the methodologies are currently restricted to their application in routine clinical screening due to the scarcity of adequate screening tools, false reading, long assay time, and cost. Innovative techniques and the integration of knowledge from a variety of domains, such as materials science and engineering, are needed to provide sustainable solutions. The convergence of precision point-of-care (POC) diagnostic techniques, which allow patients to respond in real time to changes in PSA levels, provides promising possibilities for quantitative and quantitative detection of PSA. This solution could be interesting and relevant for use in PCa diagnosis at the POC. The approaches enable low-cost real-time detection and are simple to integrate into user-friendly sensor devices. This review focuses on the investigations, prospects, and challenges associated with integrating engineering sciences with cancer biology to develop nanotechnology-based tools for PCa diagnosis. This article intends to encourage the development of new nanomaterials to construct high-performance POC devices for PCa detection. Finally, the review concludes with closing remarks and a perspective forecast.
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Affiliation(s)
- Arshid Numan
- Graphene & Advanced 2D Materials Research Group (GAMRG), School of Engineering and Technology, Sunway University, No. 5, Jalan Universiti, Bandar Sunway, 47500, Petaling Jaya, Selangor, Malaysia
| | - Sima Singh
- IES Institute of Pharmacy, IES University Campus, Kalkheda, Ratibad Main Road, Bhopal, 462044, Madhya Pradesh, India.,Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131, Naples, Italy
| | - Yiqiang Zhan
- State Key Laboratory of ASIC and System, SIST, Fudan University, Shanghai, 200433, China
| | - Lijie Li
- College of Engineering, Swansea University, Swansea, SA1 8EN, UK
| | - Mohammad Khalid
- Graphene & Advanced 2D Materials Research Group (GAMRG), School of Engineering and Technology, Sunway University, No. 5, Jalan Universiti, Bandar Sunway, 47500, Petaling Jaya, Selangor, Malaysia
| | - Kirsi Rilla
- Institute of Biomedicine, University of Eastern Finland, P.O.Box 1627, 70211, Kuopio, Finland
| | - Sanjeev Ranjan
- Institute of Biomedicine, University of Eastern Finland, P.O.Box 1627, 70211, Kuopio, Finland
| | - Stefano Cinti
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131, Naples, Italy. .,BAT Center - Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology, University of Napoli Federico II, 80055, Naples, Italy.
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21
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Hu M, Zhu D, Zhou X. M-CDC: Magnetic pull-down-assisted colorimetric method based on the CRISPR/Cas12a system. Methods 2021; 203:259-267. [PMID: 34813932 DOI: 10.1016/j.ymeth.2021.11.009] [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: 08/30/2021] [Revised: 10/28/2021] [Accepted: 11/15/2021] [Indexed: 11/30/2022] Open
Abstract
The construction of a rapid, simple, and specific nucleic acid detection platform is of great significance to the control of the large-scale spread of infectious diseases. We have recently established a magnetic pull-down-assisted colorimetric method based on the CRISPR/Cas12a system (termed M-CDC), which effectively integrates the advantages of CRISPR/Cas12a, magnetic beads-based separation, and AuNP bioprobe to provide a simple and specific biosensing platform for nucleic acid assay. The M-CDC method is compatible with point-of-care testing and enables the detection of nucleic acid samples in less than an hour without relying on expensive and complex instruments. In this paper, step-by-step instructions for M-CDC assay, including recombinase polymerase amplification (RPA)/reverse transcription-polymerase chain reaction (RT-RPA) of DNA or RNA, Cas12a-mediated target recognition and cleavage, and subsequent magnetic beads-mediated colorimetric readouts are provided. In addition, the protocol for the expression and purification of Lachnospiraceae bacterium-Cas12a (LbCas12a) protein, the design and synthesis of high-efficient crRNA, and the preparation of AuNP bioprobe are also offered.
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Affiliation(s)
- Menglu Hu
- School of Life Sciences, South China Normal University, Guangzhou 510631, PR China
| | - Debin Zhu
- Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, School of Chemistry, South China Normal University, Guangzhou 510006, PR China.
| | - Xiaoming Zhou
- School of Life Sciences, South China Normal University, Guangzhou 510631, PR China.
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22
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Sklavounos AA, Nemr CR, Kelley SO, Wheeler AR. Bacterial classification and antibiotic susceptibility testing on an integrated microfluidic platform. LAB ON A CHIP 2021; 21:4208-4222. [PMID: 34549763 DOI: 10.1039/d1lc00609f] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
With the prevalence of bacterial infections and increasing levels of antibiotic resistance comes the need for rapid and accurate methods for bacterial classification (BC) and antibiotic susceptibility testing (AST). Here we demonstrate the use of the fluid handling technique digital microfluidics (DMF) for automated and simultaneous BC and AST using growth metabolic markers. Custom instrumentation was developed for this application including an integrated heating module and a machine-learning-enabled low-cost colour camera for real-time absorbance and fluorescent sample monitoring on multipurpose devices. Antibiotic dilutions along with sample handling, mixing and incubation at 37 °C were all pre-programmed and processed automatically. By monitoring the metabolism of resazurin, resorufin beta-D-glucuronide and resorufin beta-D-galactopyranoside to resorufin, BC and AST were achieved in under 18 h. AST was validated in two uropathogenic E. coli strains with antibiotics ciprofloxacin and nitrofurantoin. BC was performed independently and simultaneously with ciprofloxacin AST for E. coli, K. pneumoniae, P. mirabilis and S. aureus. Finally, a proof-of-concept multiplexed system for breakpoint testing of two antibiotics, as well as E. coli and coliform classification was investigated with a multidrug-resistant E. coli strain. All bacteria were correctly identified, while AST and breakpoint test results were in essential and category agreement with reference methods. These results show the versatility and accuracy of this all-in-one microfluidic system for analysis of bacterial growth and phenotype.
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Affiliation(s)
- Alexandros A Sklavounos
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Canada.
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3G9, Canada
| | - Carine R Nemr
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Canada.
| | - Shana O Kelley
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Canada.
- Department of Pharmaceutical Science, University of Toronto, 144 College Street, Toronto, Ontario, M5S 3E5, Canada
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario, M5S 3G9, Canada
| | - Aaron R Wheeler
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Canada.
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3G9, Canada
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario, M5S 3G9, Canada
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23
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Yim Y, Shin H, Ahn SM, Min DH. Graphene oxide-based fluorescent biosensors and their biomedical applications in diagnosis and drug discovery. Chem Commun (Camb) 2021; 57:9820-9833. [PMID: 34494621 DOI: 10.1039/d1cc02157e] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Graphene oxide (GO), an oxidized derivative of graphene, has received much attention for developing novel fluorescent bioanalytic platforms due to its remarkable optical properties and biocompatibility. The reliable performance and robustness of GO-based biosensors have enabled various applications in the biomedical field including diagnosis and drug discovery. Here, recent advances in the development of GO-based fluorescent biosensors are overviewed, particularly nucleic acid detection and enzyme activity assay. In addition, practical applications in biomarker detection and high-throughput screening are also examined. Lastly, basic design principles and remaining challenges of these types of biosensors are discussed for further progress.
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Affiliation(s)
- Yeajee Yim
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea.
| | - Hojeong Shin
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea.
| | - Seong Min Ahn
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea.
| | - Dal-Hee Min
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea. .,Department of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea.,Institute of Biotherapeutics Convergence Technology, Lemonex Inc., Seoul 06683, Republic of Korea
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24
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Prostate Cancer Biomarkers: From diagnosis to prognosis and precision-guided therapeutics. Pharmacol Ther 2021; 228:107932. [PMID: 34174272 DOI: 10.1016/j.pharmthera.2021.107932] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/10/2021] [Accepted: 05/12/2021] [Indexed: 12/23/2022]
Abstract
Prostate cancer (PCa) is one of the most commonly diagnosed malignancies and among the leading causes of cancer-related death worldwide. It is a highly heterogeneous disease, ranging from remarkably slow progression or inertia to highly aggressive and fatal disease. As therapeutic decision-making, clinical trial design and outcome highly depend on the appropriate stratification of patients to risk groups, it is imperative to differentiate between benign versus more aggressive states. The incorporation of clinically valuable prognostic and predictive biomarkers is also potentially amenable in this process, in the timely prevention of metastatic disease and in the decision for therapy selection. This review summarizes the progress that has so far been made in the identification of the genomic events that can be used for the classification, prediction and prognostication of PCa, and as major targets for clinical intervention. We include an extensive list of emerging biomarkers for which there is enough preclinical evidence to suggest that they may constitute crucial targets for achieving significant advances in the management of the disease. Finally, we highlight the main challenges that are associated with the identification of clinically significant PCa biomarkers and recommend possible ways to overcome such limitations.
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25
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Wickhorst PJ, Ihmels H. Selective, pH-Dependent Colorimetric and Fluorimetric Detection of Quadruplex DNA with 4-Dimethylamino(phenyl)-Substituted Berberine Derivatives. Chemistry 2021; 27:8580-8589. [PMID: 33855748 PMCID: PMC8252107 DOI: 10.1002/chem.202100297] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Indexed: 12/20/2022]
Abstract
The 9- and 12-dimethylaminophenyl-substituted berberine derivatives 3 a and 3 b were readily synthesized by Suzuki-Miyaura reactions and shown to be useful fluorescent probes for the optical detection of quadruplex DNA (G4-DNA). Their association with the nucleic acids was investigated by spectrometric titrations, CD and LD spectroscopy, and with DNA-melting analysis. Both ligands bind to duplex DNA by intercalation and to G4-DNA by terminal π stacking. At neutral conditions, they bind with higher affinity (Kb =105 -106 M-1 ) to representative quadruplex forming oligonucleotides 22AG, c-myc, c-kit, and a2, than to duplex calf thymus (ct) DNA (Kb =5-7×104 M-1 ). At pH 5, however, the affinity of 3 a towards G4-DNA 22AG is higher (Kb =1.2×106 M-1 ), whereas the binding constant towards ct DNA is lower (Kb =3.9×103 M-1 ) than under neutral conditions. Notably, the association of the ligand with DNA results in characteristic changes of the absorption and emission properties under specific conditions, which may be used for optical DNA detection. Other than the parent berberine, the ligands do not show a noticeable increase of their very low intrinsic emission intensity upon association with DNA at neutral conditions. In contrast, a fluorescence light-up effect was observed upon association to duplex (Φfl =0.01) and quadruplex DNA (Φfl =0.04) at pH 5. This fluorimetric response to G4-DNA association in combination with the distinct, red-shifted absorption under these conditions provides a simple and conclusive optical detection of G4-DNA at lower pH.
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Affiliation(s)
- Peter Jonas Wickhorst
- Department of Chemistry – BiologyUniversity of Siegen, andCenter of Micro- and Nanochemistry and Engineering (Cμ)Adolf-Reichwein-Str. 257068SiegenGermany
| | - Heiko Ihmels
- Department of Chemistry – BiologyUniversity of Siegen, andCenter of Micro- and Nanochemistry and Engineering (Cμ)Adolf-Reichwein-Str. 257068SiegenGermany
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26
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Zhang W, Sun X, Zhou A, Li M. When Fluorescent Sensing Meets Electrochemical Amplifying: A Powerful Platform for Gene Detection with High Sensitivity and Specificity. Anal Chem 2021; 93:7781-7786. [PMID: 34019763 DOI: 10.1021/acs.analchem.1c01404] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Ultrasensitive and ultraselective detection of the gene requires emergency development to meet the medical demands and infectious disease control. Herein we report a versatile and scalable method based on electrochemical-chemical-cyclic amplification (EC-CA) and fluorescence detection for ultrasensitive gene sensing. The EC-CA is achieved by an electro-Fenton reaction (EFR). The hydroxyl radicals generated at EFR are trapped by terephthalic acid to form highly fluorescent 2-hydroxyterephthalic acid, which can be sensitively detected by a fluorescence spectrophotometer. The method is the first to be able to amplify the signal and reduce the noise simultaneously by using the conventional analytical methods directly. This described method can be used for reliable Fe3+ quantification in the range from 0.1 nM to 0.08 mM. The calculated limit of detection (LOD) is 0.02 nM. Then, hepatitis B virus (HBV) and p53 gene were detected by this proposed method through introducing the Fe3O4 nanoparticles into the gene hybridization system. The LODs for HBV and p53 gene even topped out at 2.6 pM and 1.7 fM, respectively. We demonstrated that the finally recorded signal was triply amplified through the EC cycle, Fe3O4 nanoparticles, and sensitive fluorescence detection. At the same time, the background signal arisen from matrix effects and readout noise was effectively suppressed. This method shows it is simple, convenient, and operational through the detection of Fe3+, HBV, and the p53 gene in blood samples, respectively. We believe our method will make a significant, near-term impact on the development of high-sensitivity methods that are versatile and scalable.
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Affiliation(s)
- Wenzhi Zhang
- Key Laboratory of Functional Molecular Solids, Ministry of Education, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, China.,Wannan Medical College, Department of Pharmacy, Wuhu 241002, China
| | - Xiuxiu Sun
- Key Laboratory of Functional Molecular Solids, Ministry of Education, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, China
| | - Ani Zhou
- Key Laboratory of Functional Molecular Solids, Ministry of Education, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, China
| | - Maoguo Li
- Key Laboratory of Functional Molecular Solids, Ministry of Education, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, China
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27
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Wickhorst PJ, Ihmels H. Berberrubine Phosphate: A Selective Fluorescent Probe for Quadruplex DNA. Molecules 2021; 26:2566. [PMID: 33924894 PMCID: PMC8124163 DOI: 10.3390/molecules26092566] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/20/2021] [Accepted: 04/22/2021] [Indexed: 12/31/2022] Open
Abstract
A phosphate-substituted, zwitterionic berberine derivative was synthesized and its binding properties with duplex DNA and G4-DNA were studied using photometric, fluorimetric and polarimetric titrations and thermal DNA denaturation experiments. The ligand binds with high affinity toward both DNA forms (Kb = 2-7 × 105 M-1) and induces a slight stabilization of G4-DNA toward thermally induced unfolding, mostly pronounced for the telomeric quadruplex 22AG. The ligand likely binds by aggregation and intercalation with ct DNA and by terminal stacking with G4-DNA. Thus, this compound represents one of the rare examples of phosphate-substituted DNA binders. In an aqueous solution, the title compound has a very weak fluorescence intensity (Φfl < 0.01) that increases significantly upon binding to G4-DNA (Φfl = 0.01). In contrast, the association with duplex DNA was not accompanied by such a strong fluorescence light-up effect (Φfl < 0.01). These different fluorimetric responses upon binding to particular DNA forms are proposed to be caused by the different binding modes and may be used for the selective fluorimetric detection of G4-DNA.
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Affiliation(s)
| | - Heiko Ihmels
- Department of Chemistry-Biology, University of Siegen, Center of Micro- and Nanochemistry and Engineering (Cµ), Adolf-Reichwein-Str. 2, 57068 Siegen, Germany;
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28
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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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29
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Abstract
Selective and sensitive detection of nucleic acid biomarkers is of great significance in early-stage diagnosis and targeted therapy. Therefore, the development of diagnostic methods capable of detecting diseases at the molecular level in biological fluids is vital to the emerging revolution in the early diagnosis of diseases. However, the vast majority of the currently available ultrasensitive detection strategies involve either target/signal amplification or involve complex designs. Here, using a p53 tumor suppressor gene whose mutation has been implicated in more than 50% of human cancers, we show a background-free ultrasensitive detection of this gene on a simple platform. The sensor exhibits a relatively static mid-FRET state in the absence of a target that can be attributed to the time-averaged fluorescence intensity of fast transitions among multiple states, but it undergoes continuous dynamic switching between a low- and a high-FRET state in the presence of a target, allowing a high-confidence detection. In addition to its simple design, the sensor has a detection limit down to low femtomolar (fM) concentration without the need for target amplification. We also show that this sensor is highly effective in discriminating against single-nucleotide polymorphisms (SNPs). Given the generic hybridization-based detection platform, the sensing strategy developed here can be used to detect a wide range of nucleic acid sequences enabling early diagnosis of diseases and screening genetic disorders.
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Affiliation(s)
- Anoja Megalathan
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Kalani M Wijesinghe
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Soma Dhakal
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
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30
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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: 60] [Impact Index Per Article: 20.0] [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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31
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Asefifeyzabadi N, Das PK, Onorimuo AH, Durocher G, Shamsi MH. DNA interfaces with dimensional materials for biomedical applications. RSC Adv 2021; 11:28332-28341. [PMID: 35480758 PMCID: PMC9038036 DOI: 10.1039/d1ra04917h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 08/17/2021] [Indexed: 12/30/2022] Open
Abstract
DNA interfaces with nano, micro, and macro materials have gained widespread attention for various applications. Such interfaces exhibit distinct functions and properties not only due to the unique properties of interfacing materials but also sequence- and conformation-dependent characteristics of the DNA. Therefore, DNA interfaces with diverse dimensional materials have advanced our understanding of the interaction mechanisms and the properties of such interfaces. The unique interfacial properties of such novel materials have applications in nanotechnology, biophysics, cell biology, biosensing, and bioelectronics. The field is growing rapidly with the frequent emergence of new interfaces carrying remarkable interfacial character. In this review article, we have classified the DNA interfaces into 0D, 1D, 2D, and 3D categories based on the types of dimensional materials. We review the key efforts made in the last five years and focus on types of interfaces, interfacing mechanisms, and their state-of-the-art applications. This review will draw a general interest because of the diversity in the DNA materials science but also the unique applications that will play a cutting-edge role in biomedical and biosensing research. DNA interfaces with 0–3 dimensional materials through physisorption and chemisorption mechanisms acquire unique interfacial character for novel biomedical applications.![]()
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Affiliation(s)
- Narges Asefifeyzabadi
- School of Chemical and Biomolecular Sciences, Southern Illinois University, Carbondale, IL, USA
| | - Prabhangshu Kumer Das
- School of Chemical and Biomolecular Sciences, Southern Illinois University, Carbondale, IL, USA
| | | | - Grace Durocher
- School of Chemical and Biomolecular Sciences, Southern Illinois University, Carbondale, IL, USA
| | - Mohtashim Hassan Shamsi
- School of Chemical and Biomolecular Sciences, Southern Illinois University, Carbondale, IL, USA
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32
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Chernikova EY, Berdnikova DV. Cucurbiturils in nucleic acids research. Chem Commun (Camb) 2020; 56:15360-15376. [PMID: 33206072 DOI: 10.1039/d0cc06583h] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
During the past ten years, the importance of cucurbiturils (CB[n]) as macrocyclic hosts in supramolecular assemblies with various types of natural and synthetic nucleic acids (NAs) has increased explosively. As a component of such systems, CB[n] macrocycles can play a wide spectrum of roles from drug and gene delivery vehicles to catalysts/inhibitors of biochemical reactions and even building blocks for NA-based materials. The aim of this highlight article is to describe the development of the CB[n] applications in nucleic acids research and to outline the current situation and perspectives of this fascinating synergistic combination of supramolecular chemistry of CB[n] and NAs.
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Affiliation(s)
- Ekaterina Y Chernikova
- Laboratory of Photoactive Supramolecular Systems, A. N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilova St. 28, Moscow, Russia.
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33
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Saha U, Chatterjee S, Dolai M, Suresh Kumar G. Biophysical and Thermodynamic Investigations on the Differentiation of Fluorescence Response towards Interaction of DNA: A Pyrene-Based Receptor versus Its Fe(III) Complex. ACS APPLIED BIO MATERIALS 2020; 3:7810-7820. [DOI: 10.1021/acsabm.0c00983] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Urmila Saha
- Organic and Medicinal Chemistry Division, CSIR—Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, W.B., India
| | - Sabyasachi Chatterjee
- Organic and Medicinal Chemistry Division, CSIR—Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, W.B., India
| | - Malay Dolai
- Department of Chemistry, Prabhat Kumar College, Purba Medinipur 721404, W.B., India
| | - Gopinatha Suresh Kumar
- Organic and Medicinal Chemistry Division, CSIR—Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, W.B., India
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34
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Cheng Q, Parvin B. Rapid identification of a subset of foodborne bacteria in live-cell assays. Appl Microbiol Biotechnol 2020; 104:10571-10584. [PMID: 33185701 DOI: 10.1007/s00253-020-10970-9] [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: 02/20/2020] [Revised: 09/06/2020] [Accepted: 10/21/2020] [Indexed: 11/28/2022]
Abstract
The detection and identification of microbial pathogens in meat and fresh produce play an essential role in food safety for reducing foodborne illnesses every year. A new approach based on targeting a specific sequence of the 16S rRNA region for each bacterium is proposed and validated. The probe complex consists of a C60, a conjugated RNA detector which targets a specific 16S rRNA sequence, and a complementary fluorescent reporter. The RNA detectors were designed by integrating NIH nucleotide and Vienna RNA Webservice databases, and their specificities were validated by the RDP database. Probe complexes were synthesized for identifying E. coli K12, E. coli O157: H7, S. enterica, Y. enterocolitica, C. perfringens, and L. monocytogenes. First, under controlled conditions of known bacterial mixtures, the efficiency and crosstalk for identifying the foodborne bacteria were quantified to be above 94% and below 5%, respectively. Second, experiments were designed by inoculating meat products by known numbers of bacteria and measuring the limit of detection. In one experiment, 225 g of autoclaved ground chicken was inoculated with 9 E. coli O157:H7, where 6.8 ± 1.2 bacteria with 95% confidence interval were recovered. Third, by positionally printing probe complexes in microwells, specific microorganisms were identified with only one fluorophore. The proposed protocol is a cell-based system, can identify live bacteria in 15 min, requires no amplification, and has the potential to open new surveillance opportunities.Key points• The identification of foodborne bacteria is enabled in live-cell assays.• The limit of detection for 100 g of fresh chicken breast inoculated with 4 bacteria is 2.7 ± 1.4 with 95% confidence interval.• The identification of five bacteria in a coded microwell chip is enabled with only one fluorophore.
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Affiliation(s)
- Qingsu Cheng
- Department of Electrical and Biomedical Engineering, University of Nevada, Reno, 1664 N. Virginia St., NV, 89557, Reno, USA.,Department of Cell and Molecular Biology, University of Nevada, Reno, 1664 N. Virginia St., Reno, NV, 89557, USA
| | - Bahram Parvin
- Department of Electrical and Biomedical Engineering, University of Nevada, Reno, 1664 N. Virginia St., NV, 89557, Reno, USA. .,Department of Cell and Molecular Biology, University of Nevada, Reno, 1664 N. Virginia St., Reno, NV, 89557, USA.
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35
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Ivanov AS, Nikolaev KG, Stekolshchikova AA, Tesfatsion WT, Yurchenko SO, Novoselov KS, Andreeva DV, Rubtsova MY, Vorovitch MF, Ishmukhametov AA, Egorov AM, Skorb EV. Tick-Borne Encephalitis Electrochemical Detection by Multilayer Perceptron on Liquid–Metal Interface. ACS APPLIED BIO MATERIALS 2020; 3:7352-7356. [DOI: 10.1021/acsabm.0c00954] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Artemii S. Ivanov
- Infochemistry Scientific Center, ITMO University, Lomonosova Street 9, Saint Petersburg 191002, Russian Federation
| | - Konstantin G. Nikolaev
- Infochemistry Scientific Center, ITMO University, Lomonosova Street 9, Saint Petersburg 191002, Russian Federation
| | - Anna A. Stekolshchikova
- Infochemistry Scientific Center, ITMO University, Lomonosova Street 9, Saint Petersburg 191002, Russian Federation
| | - Weini T. Tesfatsion
- Infochemistry Scientific Center, ITMO University, Lomonosova Street 9, Saint Petersburg 191002, Russian Federation
| | | | - Kostya S. Novoselov
- Department of Materials Science and Engineering, National University of Singapore, Singapore 117575, Singapore
| | - Daria V. Andreeva
- Department of Materials Science and Engineering, National University of Singapore, Singapore 117575, Singapore
| | - Maya Yu. Rubtsova
- Faculty of Chemistry, M. V. Lomonosov Moscow State University, Moscow 119991, Russian Federation
| | - Mikhail F. Vorovitch
- Federal State Budgetary Scientific Institution “Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences” (FSBSI “Chumakov FSC R&D IBP RAS”), Moscow 108819, Russian Federation
- Sechenov First Moscow State Medical University, 119991 Moscow, Russian Federation
| | - Aydar A. Ishmukhametov
- Federal State Budgetary Scientific Institution “Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences” (FSBSI “Chumakov FSC R&D IBP RAS”), Moscow 108819, Russian Federation
- Sechenov First Moscow State Medical University, 119991 Moscow, Russian Federation
| | - Alex M. Egorov
- Faculty of Chemistry, M. V. Lomonosov Moscow State University, Moscow 119991, Russian Federation
- Federal State Budgetary Scientific Institution “Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences” (FSBSI “Chumakov FSC R&D IBP RAS”), Moscow 108819, Russian Federation
| | - Ekaterina V. Skorb
- Infochemistry Scientific Center, ITMO University, Lomonosova Street 9, Saint Petersburg 191002, Russian Federation
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36
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Peng XX, Guo T, Lu H, Yue L, Li Y, Jin D, Zhang GJ, Yang F. Nanostructuring Synergetic Base-Stacking Effect: An Enhanced Versatile Sandwich Sensor Enables Ultrasensitive Detection of MicroRNAs in Blood. ACS Sens 2020; 5:2514-2522. [PMID: 32664724 DOI: 10.1021/acssensors.0c00772] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
MicroRNA (MiRNA)-based noninvasive diagnostics are hampered by the challenge in the quantification of circulating miRNAs using a general strategy. Here, we present a base-stacking effect-mediated ultrasensitive electrochemical miRNA sensor (BSee-miR) with a universal sandwich configuration. In the BSee-miR, a short DNA probe (10 nucleotides) self-assembled on a gold electrode surface could effectively capture the target miRNA synergizing with another sequence based on coaxial sandwich base-stacking, which rivals the fully complementary strength. Importantly, such a sandwich structure is flexible to incorporate signal amplification strategies (e.g., biotin-avidin) that are usually difficult to achieve in short sequence detection. Using this design, the BSee-miR achieves a broad dynamic range with a detection limit down to 7.5 fM. Furthermore, we found a high-curvature nanostructuring synergetic base-stacking effect that could improve the sensitivity of the BSee-miR by two orders of magnitude (79.3 aM). Our BSee-miR also has a single-base resolution to discriminate the highly homologous miRNAs. More importantly, this approach is universal and has been used to probe target miRNAs varying in sequences and secondary structures. Our ultrasensitive sensor could detect miRNA in cell lysates and human blood and distinguish cancer patients from normal individuals, promising a versatile tool to measure clinically relevant miRNAs for tumor diagnostics.
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Affiliation(s)
- Xin-Xin Peng
- School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Tongtong Guo
- School of Pharmacy, Guangxi Medical University, Nanning 530021, China
| | - Hao Lu
- School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Linlin Yue
- School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - You Li
- School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan 430065, China
- Department of Medical Laboratory, the Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430014, China
| | - Dan Jin
- School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Guo-Jun Zhang
- School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Fan Yang
- School of Pharmacy, Guangxi Medical University, Nanning 530021, China
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37
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DNA/RNA Electrochemical Biosensing Devices a Future Replacement of PCR Methods for a Fast Epidemic Containment. SENSORS 2020; 20:s20164648. [PMID: 32824787 PMCID: PMC7472328 DOI: 10.3390/s20164648] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 08/16/2020] [Accepted: 08/17/2020] [Indexed: 12/28/2022]
Abstract
Pandemics require a fast and immediate response to contain potential infectious carriers. In the recent 2020 Covid-19 worldwide pandemic, authorities all around the world have failed to identify potential carriers and contain it on time. Hence, a rapid and very sensitive testing method is required. Current diagnostic tools, reverse transcription PCR (RT-PCR) and real-time PCR (qPCR), have its pitfalls for quick pandemic containment such as the requirement for specialized professionals and instrumentation. Versatile electrochemical DNA/RNA sensors are a promising technological alternative for PCR based diagnosis. In an electrochemical DNA sensor, a nucleic acid hybridization event is converted into a quantifiable electrochemical signal. A critical challenge of electrochemical DNA sensors is sensitive detection of a low copy number of DNA/RNA in samples such as is the case for early onset of a disease. Signal amplification approaches are an important tool to overcome this sensitivity issue. In this review, the authors discuss the most recent signal amplification strategies employed in the electrochemical DNA/RNA diagnosis of pathogens.
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38
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Zhou C, Huang R, Zhou X, Xing D. Sensitive and specific microRNA detection by RNA dependent DNA ligation and rolling circle optical signal amplification. Talanta 2020; 216:120954. [DOI: 10.1016/j.talanta.2020.120954] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 03/13/2020] [Accepted: 03/18/2020] [Indexed: 12/29/2022]
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39
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Solovjev AM, Kurzeev SA, Sakharov IY. Chemiluminescent microplate-based assay of DNA based on isothermal circular strand-displacement polymerization reaction (ICSDPR). Talanta 2020; 215:120895. [DOI: 10.1016/j.talanta.2020.120895] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/28/2020] [Accepted: 03/03/2020] [Indexed: 12/18/2022]
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40
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Milioni D, Mateos-Gil P, Papadakis G, Tsortos A, Sarlidou O, Gizeli E. Acoustic Methodology for Selecting Highly Dissipative Probes for Ultrasensitive DNA Detection. Anal Chem 2020; 92:8186-8193. [PMID: 32449355 DOI: 10.1021/acs.analchem.0c00366] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The objective of this work is to present a methodology for the selection of nanoparticles such as liposomes to be used as acoustic probes for the detection of very low concentrations of DNA. Liposomes, applied in the past as mass amplifiers and detected through frequency measurement, are employed in the current work as probes for energy-dissipation enhancement. Because the dissipation signal is related to the structure of the sensed nanoentity, a systematic investigation of the geometrical features of the liposome/DNA complex was carried out. We introduce the parameter of dissipation capacity by which several sizes of liposome and DNA structures were compared with respect to their ability to dissipate acoustic energy at the level of a single molecule/particle. Optimized 200 nm liposomes anchored to a dsDNA chain led to an improvement of the limit of detection (LoD) by 3 orders of magnitude when compared to direct DNA detection, with the new LoD being 1.2 fmol (or 26 fg/μL or 2 pM). Dissipation monitoring was also shown to be 8 times more sensitive than the corresponding frequency response. The high versatility of this new methodology is demonstrated in the detection of genetic biomarkers down to 1-2 target copies in real samples such as blood. This study offers new prospects in acoustic detection with potential use in real-world diagnostics.
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Affiliation(s)
- Dimitra Milioni
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
| | - Pablo Mateos-Gil
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
| | - George Papadakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
| | - Achilleas Tsortos
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
| | - Olga Sarlidou
- Department of Biology, University of Crete, Heraklion, Crete 71110, Greece
| | - Electra Gizeli
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece.,Department of Biology, University of Crete, Heraklion, Crete 71110, Greece
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41
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Shen R, Jia Y, Mak PI, Martins RP. Clip-to-release on amplification (CRoA): a novel DNA amplification enhancer on and off microfluidics. LAB ON A CHIP 2020; 20:1928-1938. [PMID: 32352133 DOI: 10.1039/d0lc00318b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Despite its high sensitivity, low cost, and high efficiency as a DNA amplification indicator with a yes/no answer, dsDNA-binding dye encounters incompatibility when used in microfluidic systems, resulting in problems such as false negative amplification results. Besides, its inhibition of amplification at high concentrations hinders its application both on-chip and off-chip. In this study, we propose a novel DNA amplification enhancer to counteract the drawbacks of dsDNA-binding dyes. It acts as a temporary reservoir for the free-floating dyes in solution and releases them on demand during the amplification process. Through this clip-to-release on amplification mechanism, the enhancer lowered the background fluorescence of sample droplets before amplification, enhanced the signal-to-background ratio of positive samples, and eliminated the false negative signal of on-chip PCR. Moreover, the enhancer increased the off-chip polymerase chain reaction (PCR) efficiency, boosted the fluorescence signal up to 10-fold, and made less nonspecific amplification product. All the factors affecting the enhancer's performance are investigated in detail, including its structure and concentration, and the types of dsDNA-binding dye used in the reaction. Finally, we demonstrated the broad application of the proposed amplification enhancer in various DNA amplification systems, for various genes, and on various amplification platforms. It would reignite the utilization of dsDNA dyes for wider applications in DNA analysis both on-chip and off-chip.
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Affiliation(s)
- Ren Shen
- State-Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Macau, China. and Faculty of Science and Technology - ECE, University of Macau, Macau, China
| | - Yanwei Jia
- State-Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Macau, China. and Faculty of Science and Technology - ECE, University of Macau, Macau, China and Faculty of Health Sciences, University of Macau, Macau, China
| | - Pui-In Mak
- State-Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Macau, China. and Faculty of Science and Technology - ECE, University of Macau, Macau, China
| | - Rui P Martins
- State-Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Macau, China. and Faculty of Science and Technology - ECE, University of Macau, Macau, China and On Leave from Instituto Superior Técnico, Universidade de Lisboa, Portugal
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42
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Abstract
The detection of biomarkers is critical for enabling early disease diagnosis, monitoring the progression, and tracking the effectiveness of therapeutic intervention. Plasmonic sensors exhibit a broad range of analytical capabilities, from the rapid generation of colorimetric readouts to single-molecule sensitivity in ultralow sample volumes, which have led to their increased exploration in bioanalysis and point-of-care applications. This perspective presents selected accounts of recent developments on the different types of plasmonic sensing platforms, the pervasive challenges, and outlook on the pathway to translation. We highlight the sensing of upcoming biomarkers, including microRNA, circulating tumor cells, exosomes, and cell-free DNA, and discuss the opportunity of utilizing plasmonic nanomaterials and tools for biomarker detection beyond biofluids, such as in tissues, organs, and disease sites. The integration of plasmonic biosensors with established and upcoming technologies of instrumentation, sample pretreatment, and data analysis will help realize their translation to clinical settings for improving healthcare and enhancing the quality of life.
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Affiliation(s)
- Nicole Cathcart
- Department of Chemistry, York University, 4700 Keele Street Toronto, Ontario, Canada M3J 1P3
| | - Jennifer I L Chen
- Department of Chemistry, York University, 4700 Keele Street Toronto, Ontario, Canada M3J 1P3
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Merging new-age biomarkers and nanodiagnostics for precision prostate cancer management. Nat Rev Urol 2020; 16:302-317. [PMID: 30962568 DOI: 10.1038/s41585-019-0178-2] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The accurate identification and stratified treatment of clinically significant early-stage prostate cancer have been ongoing concerns since the outcomes of large international prostate cancer screening trials were reported. The controversy surrounding clinical and cost benefits of prostate cancer screening has highlighted the lack of strategies for discriminating high-risk disease (that requires early treatment) from low-risk disease (that could be managed using watchful waiting or active surveillance). Advances in molecular subtyping and multiomics nanotechnology-based prostate cancer risk delineation can enable refinement of prostate cancer molecular taxonomy into clinically meaningful and treatable subtypes. Furthermore, the presence of intertumoural and intratumoural heterogeneity in prostate cancer warrants the development of novel nanodiagnostic technologies to identify clinically significant prostate cancer in a rapid, cost-effective and accurate manner. Circulating and urinary next-generation prostate cancer biomarkers for disease molecular subtyping and the newest complementary nanodiagnostic platforms for enhanced biomarker detection are promising tools for precision prostate cancer management. However, challenges in merging both aspects and clinical translation still need to be overcome.
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Bergamasco L, Alberghini M, Fasano M. Nano-metering of Solvated Biomolecules Or Nanoparticles from Water Self-Diffusivity in Bio-inspired Nanopores. NANOSCALE RESEARCH LETTERS 2019; 14:336. [PMID: 31659492 PMCID: PMC6816642 DOI: 10.1186/s11671-019-3178-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 10/04/2019] [Indexed: 06/10/2023]
Abstract
Taking inspiration from the structure of diatom algae frustules and motivated by the need for new detecting strategies for emerging nanopollutants in water, we analyze the potential of nanoporous silica tablets as metering devices for the concentration of biomolecules or nanoparticles in water. The concept relies on the different diffusion behavior that water molecules exhibit in bulk and nanoconfined conditions, e.g., in nanopores. In this latter situation, the self-diffusion coefficient of water reduces according to the geometry and surface properties of the pore and to the concentration of suspended biomolecules or nanoparticles in the pore, as extensively demonstrated in a previous study. Thus, for a given pore-liquid system, the self-diffusivity of water in nanopores filled with biomolecules or nanoparticles provides an indirect measure of their concentration. Using molecular dynamics and previous results from the literature, we demonstrate the correlation between the self-diffusion coefficient of water in silica nanopores and the concentration of proteins or nanoparticles contained therein. Finally, we estimate the time required for the nanoparticles to fill the nanopores, in order to assess the practical feasibility of the overall nano-metering protocol. Results show that the proposed approach may represent an alternative method for assessing the concentration of some classes of nanopollutants or biomolecules in water.
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Affiliation(s)
- Luca Bergamasco
- Department of Energy, Politecnico di Torino, Corso Duca degli Abruzzi 24, Torino, 10129 Italy
| | - Matteo Alberghini
- Department of Energy, Politecnico di Torino, Corso Duca degli Abruzzi 24, Torino, 10129 Italy
- Clean Water Center, Politecnico di Torino, Corso Duca degli Abruzzi 24, Torino, 10129 Italy
| | - Matteo Fasano
- Department of Energy, Politecnico di Torino, Corso Duca degli Abruzzi 24, Torino, 10129 Italy
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Zhang W, Li J, Salena B, Li Y. A DNA Switch for Detecting Single Nucleotide Polymorphism within a Long DNA Sequence Under Denaturing Conditions. Chemistry 2019; 26:592-596. [PMID: 31475757 DOI: 10.1002/chem.201903536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 08/28/2019] [Indexed: 01/24/2023]
Abstract
DNA detection is usually conducted under nondenaturing conditions to favor the formation of Watson-Crick base-paring interactions. However, although such a setting is excellent for distinguishing a single-nucleotide polymorphism (SNP) within short DNA sequences (15-25 nucleotides), it does not offer a good solution to SNP detection within much longer sequences. Here we report on a new detection method capable of detecting SNP in a DNA sequence containing 35-90 nucleotides. This is achieved through incorporating into the recognition DNA sequence a previously discovered DNA molecule that forms a stable G-quadruplex in the presence of 7 molar urea, a known condition for denaturing DNA structures. The systems are configured to produce both colorimetric and fluorescent signals upon target binding.
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Affiliation(s)
- Wenqing Zhang
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - Jiuxing Li
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - Bruno Salena
- Department of Medicine, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - Yingfu Li
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
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46
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Dong Y, Yao C, Wang Z, Luo D, Yang D. Target-Triggered Polymerization of Branched DNA Enables Enzyme-free and Fast Discrimination of Single-Base Changes. iScience 2019; 21:228-240. [PMID: 31675552 PMCID: PMC6838547 DOI: 10.1016/j.isci.2019.10.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/24/2019] [Accepted: 10/14/2019] [Indexed: 01/05/2023] Open
Abstract
Single-base changes lead to important biological and biomedical implications; however, the discrimination of single-base changes from normal DNA always remains a grand challenge. Herein we developed a DNA recognition and amplification system based on artificial branched DNA, namely, target-triggered polymerization (TTP), to realize enzyme-free and fast discrimination of single-base changes. Branched DNA as monomers rapidly polymerized into DNA nanospheres only with the trigger of specific DNA. Our TTP system worked reliably over a wide range of conditions. Remarkably, our TTP system was capable of discriminating base-changing DNA from normal DNA, including distinguishing 1-4 nucleotide changes and positions of single base, which was attributed to the significant amplification of small differences in hybridization thermodynamics and kinetics. We further proposed a theoretical method for calculating the hybridization probability of nucleic acids, which performed highly consistent with experimental results.
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Affiliation(s)
- Yuhang Dong
- Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Chi Yao
- Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Zhi Wang
- Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Dan Luo
- Department of Biological & Environmental Engineering, Cornell University, Ithaca, NY 14853, USA; CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, P. R. China
| | - Dayong Yang
- Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China.
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Xiao M, Lai W, Man T, Chang B, Li L, Chandrasekaran AR, Pei H. Rationally Engineered Nucleic Acid Architectures for Biosensing Applications. Chem Rev 2019; 119:11631-11717. [DOI: 10.1021/acs.chemrev.9b00121] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Wei Lai
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Tiantian Man
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Binbin Chang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
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Das AK, Druzhinin SI, Ihmels H, Müller M, Schönherr H. Colorimetric and Fluorimetric DNA Detection with a Hydroxystyryl-Quinolizinium Photoacid and Its Application for Cell Imaging. Chemistry 2019; 25:12703-12707. [PMID: 31418956 PMCID: PMC6790585 DOI: 10.1002/chem.201903017] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/09/2019] [Indexed: 01/09/2023]
Abstract
The combination of styryl dye properties with the acidity and strong photoacidity of the 2,2'-[(1''-hydroxy-4''-methyl-(E)-2'',6''-phenylene)]-bisquinolizinium enables the detection of DNA by distinct absorption and emission color changes and the fluorimetric detection of DNA in cells with epifluorescence and confocal fluorescence microscopy.
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Affiliation(s)
- Avijit Kumar Das
- Department of Chemistry and Biology, and Center of Micro- and Nanochemistry and Engineering (Cμ)University of SiegenAdolf-Reichwein-Str. 257068SiegenGermany
| | - Sergey I. Druzhinin
- Department of Chemistry and Biology, and Center of Micro- and Nanochemistry and Engineering (Cμ)University of SiegenAdolf-Reichwein-Str. 257068SiegenGermany
| | - Heiko Ihmels
- Department of Chemistry and Biology, and Center of Micro- and Nanochemistry and Engineering (Cμ)University of SiegenAdolf-Reichwein-Str. 257068SiegenGermany
| | - Mareike Müller
- Department of Chemistry and Biology, and Center of Micro- and Nanochemistry and Engineering (Cμ)University of SiegenAdolf-Reichwein-Str. 257068SiegenGermany
| | - Holger Schönherr
- Department of Chemistry and Biology, and Center of Micro- and Nanochemistry and Engineering (Cμ)University of SiegenAdolf-Reichwein-Str. 257068SiegenGermany
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Veselinovic J, Almashtoub S, Seker E. Anomalous Trends in Nucleic Acid-Based Electrochemical Biosensors with Nanoporous Gold Electrodes. Anal Chem 2019; 91:11923-11931. [PMID: 31429540 DOI: 10.1021/acs.analchem.9b02686] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Molecular diagnostics have significantly advanced the early detection of diseases, where electrochemical sensing of biomarkers has shown considerable promise. For a nucleic acid-based electrochemical sensor with signal-off behavior, the performance is evaluated by percent signal suppression (% ss), which indicates the change in current after hybridization. The % ss is generally due to more redox molecules (e.g., methylene blue) associating with the probe DNA bases in the single-strand form than the double-strand form upon hybridization with the target nucleic acid. Nanostructured electrodes generally enhance electrochemical sensor performance via several mechanisms, including increased number of capture probes per electrode volume and unique nanoscale transport phenomena. Here, we employ nanoporous gold (np-Au) as a model electrode material to study the influence of probe immobilization solution concentration on sensor performance and the underlying mechanisms. Unlike planar gold (pl-Au) electrodes, where % ss reaches a steady state with increasing concentration of the grafting solution, the % ss displays peak performance at certain grafting solution concentrations followed by rapid deterioration and reversal of the % ss polarity, suggesting an unexpected case of increased charge transfer upon hybridization. Fluorometric assessments of electrochemically desorbed nucleic acids for different electrode morphologies reveal that a significant amount of DNA molecules (unhybridized and hybridized) remain within the nanopores posthybridization. Analysis of electrochemical signals (e.g., square wave voltammogram shape) suggests that the large unbound nucleic acid concentration may be altering the modes of methylene blue interaction with the nucleic acids and charge transfer to the electrode surfaces.
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Affiliation(s)
- Jovana Veselinovic
- Department of Chemical Engineering , University of California, Davis , Davis , California 95616 , United States
| | - Suzan Almashtoub
- Department of Chemical Engineering , University of California, Davis , Davis , California 95616 , United States
| | - Erkin Seker
- Department of Electrical and Computer Engineering , University of California, Davis , Davis , California 95616 , United States
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Zhou Y, Yang J, Yin X, Zheng J, Lu N, Zhang M. Enhanced synergistic effects from multiple iron oxide nanoparticles encapsulated within nitrogen-doped carbon nanocages for simple and label-free visual detection of blood glucose. NANOTECHNOLOGY 2019; 30:355501. [PMID: 31067520 DOI: 10.1088/1361-6528/ab2026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Hollow-structured carbon materials play a crucial role in research of biosensors, energy storage and nanomedicine as a kind of material with advantages like high surface area, tunable pore volume, excellent mechanical properties, and good biocompatibility. Herein, we developed a simple, facile and controllable method for synthesis of Fe3O4 nanoparticles encapsulated in hollow carbon nanocages (FNHCs) with SiO2 nanospheres as a sacrificial template. Owing to the unique structure of multiple Fe3O4 nanoparticles cores integrated with N-doped carbon nanocages, the as-synthesized FNHCs exhibited greatly enhanced peroxidase mimicking activity with extremely high signal-to-noise ratio of ∼91 fold. Also, it was found that the FNHCs possessed a higher peroxidase-like activity than that of other similar-structured Fe3O4 architectures (e.g. Fe3O4@C NPs). The resulting steady-state kinetic curve demonstrated the enzymatic activity of FNHCs with classic Michaelis-Menton kinetics following a ping-pong mechanism. On the basis of the superior enzymatic activity, the FNHCs performed as a high-efficiency peroxidase mimic, realizing facile, label-free, highly sensitive/selective colorimetric detection of H2O2 and glucose. Furthermore, the colorimetric sensor successfully determined glucose in patients' serum samples with high accuracy and precision, suggesting great potential for real applications.
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Affiliation(s)
- Youquan Zhou
- College of Pharmacy, Jiangxi University of Traditional Chinese Medicine, Nanchang, 330004, People's Republic of China
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