1
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Xue G, Cheng Y, Xu H, Xue C. Target-Induced Stepwise Disintegration of Starlike Branched and Multiplex Embedded Systems for Amplified Detection of Serum MicroRNA. Anal Chem 2023; 95:13140-13148. [PMID: 37602702 DOI: 10.1021/acs.analchem.3c01863] [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: 08/22/2023]
Abstract
DNA nanotechnology has shown great promise for biosensing and molecular recognition. However, the practical application of conventional DNA biosensors is constrained by inadequate target stimuli, intricate design schemes, multicomponent systems, and susceptibility to nuclease degradation. To overcome these limitations, we present a class of starlike branched and multiplex embedded system (SBES) with an integrated functional design and cascade exponential amplification for serum microRNA (miRNA) detection. The DNA arms can be integrated into an all-in-one system by surrounding a branch point, with each arm endowed with specific functionalities by embedding different DNA fragments. These fragments include a segment complementary to the target miRNA for the recognition element, palindromic tails for self-primed polymerization, and a region with the same sequences as the target serving as the target analogue. Upon exposure to a target miRNA, the DNA arms unwind in a stepwise manner through palindrome-mediated dimerization and polymerization. This enables target recycling for subsequent reactions while releasing the target analogue to generate a secondary response in a feedback manner. A comparative analysis illustrates that the signal-to-noise ratio (SNR) of a full SBES with a feedback strategy is approximately 250% higher than the system without a feedback design. We demonstrate that the four-arm 4pSBES has the benefits of multifunctional integration, enhanced sensitivity, and low false-positive signals, which makes this approach ideally suited for clinical diagnosis. Moreover, an upgraded SBES with additional DNA arms (e.g., 6pSBES) can be constructed to allow multifunctional extension, offering unprecedented opportunities to build versatile DNA nanostructures for biosensing.
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Affiliation(s)
- Guohui Xue
- Department of Clinical Laboratory, Jiujiang No.1 People's Hospital, Jiujiang, Jiangxi 332000, P. R. China
| | - Yinghao Cheng
- Wenzhou Key Laboratory of Cancer Pathogenesis and Translation, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325000, P. R. China
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou, Fujian 350108, China
| | - Huo Xu
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou, Fujian 350108, China
| | - Chang Xue
- Wenzhou Key Laboratory of Cancer Pathogenesis and Translation, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325000, P. R. China
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2
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Zeng H, Huang S, Chen Y, Chen M, He K, Fu C, Wang Q, Zhang F, Wang L, Xu X. Label-Free Sequence-Specific Visualization of LAMP Amplified Salmonella via DNA Machine Produces G-Quadruplex DNAzyme. BIOSENSORS 2023; 13:bios13050503. [PMID: 37232864 DOI: 10.3390/bios13050503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/20/2023] [Accepted: 04/25/2023] [Indexed: 05/27/2023]
Abstract
Salmonella is one of four key global causes of diarrhea, and in humans, it is generally contracted through the consumption of contaminated food. It is necessary to develop an accurate, simple, and rapid method to monitor Salmonella in the early phase. Herein, we developed a sequence-specific visualization method based on loop-mediated isothermal amplification (LAMP) for the detection of Salmonella in milk. With restriction endonuclease and nicking endonuclease, amplicons were produced into single-stranded triggers, which further promoted the generation of a G-quadruplex by a DNA machine. The G-quadruplex DNAzyme possesses peroxidase-like activity and catalyzes the color development of 2,2'-azino-di-(3-ethylbenzthiazoline sulfonic acid) (ABTS) as the readouts. The feasibility for real samples analysis was also confirmed with Salmonella spiked milk, and the sensitivity was 800 CFU/mL when observed with the naked eye. Using this method, the detection of Salmonella in milk can be completed within 1.5 h. Without the involvement of any sophisticated instrument, this specific colorimetric method can be a useful tool in resource-limited areas.
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Affiliation(s)
- Huan Zeng
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China
| | - Shuqin Huang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China
| | - Yunong Chen
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China
- Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Minshi Chen
- Technology Center of Fuzhou Customs District, Fuzhou 350015, China
| | - Kaiyu He
- Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Caili Fu
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China
| | - Qiang Wang
- Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Fang Zhang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China
| | - Liu Wang
- Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Hangzhou 310021, China
| | - Xiahong Xu
- Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
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3
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Wang B, Wang M, Peng F, Fu X, Wen M, Shi Y, Chen M, Ke G, Zhang XB. Construction and Application of DNAzyme-based Nanodevices. Chem Res Chin Univ 2023; 39:42-60. [PMID: 36687211 PMCID: PMC9841151 DOI: 10.1007/s40242-023-2334-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 01/02/2023] [Indexed: 01/19/2023]
Abstract
The development of stimuli-responsive nanodevices with high efficiency and specificity is very important in biosensing, drug delivery, and so on. DNAzymes are a class of DNA molecules with the specific catalytic activity. Owing to their unique catalytic activity and easy design and synthesis, the construction and application of DNAzymes-based nanodevices have attracted much attention in recent years. In this review, the classification and properties of DNAzyme are first introduced. The construction of several common kinds of DNAzyme-based nanodevices, such as DNA motors, signal amplifiers, and logic gates, is then systematically summarized. We also introduce the application of DNAzyme-based nanodevices in sensing and therapeutic fields. In addition, current limitations and future directions are discussed.
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Affiliation(s)
- Bo Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Menghui Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Fangqi Peng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Xiaoyi Fu
- Institute of Basic Medicine and Cancer(IBMC), Chinese Academy of Sciences, Hangzhou, 310022 P. R. China
| | - Mei Wen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Yuyan Shi
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Mei Chen
- College of Materials Science and Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Guoliang Ke
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Xiao-Bing Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
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4
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Wang J, Sun J, Zhang J, Shen C, Zhang X, Xu J. Engineered G-Quadruplex-Embedded Self-Quenching Probes Regulate Single Probe-Based Multiplex Isothermal Amplification to Light Road Lamp Probes for Sensitized Determination of microRNAs. Anal Chem 2022; 94:4437-4445. [PMID: 35234452 DOI: 10.1021/acs.analchem.1c05402] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Design of oligonucleotide probe-based isothermal amplification with the ability to identify miRNA biomarkers is crucial for molecular diagnostics. In this work, we engineered a miRNA-21-responsive G-quadruplex-embedded self-quenching probe (GE-SQP) that can regulate single probe-based multiplex amplifications. The free GE-SQP is tightly locked in a quenching state with no active G-quadruplexes. Introduction of target miRNA to hybridize with GE-SQP would induce a multiplex isothermal amplification to significantly build a lot of one-bulb-contained road lamp probe (OC-RLP) and two-bulb-contained road lamp probe (TC-RLP) using G-quadruplex as the lamp bulb. When lightened by thioflavin T (ThT), beams of fluorescence were emitted to show the presented miRNA-21. Specially, the whole amplification is only a one probe-involved one-step reaction without any wasted species. The mix-to-detection and all-in amplification behavior allows the sensing system a maximally maintained operation simplicity and high assay performance. In such a way, the detection range of miRNA-21 is from 1 fM to 1 nM with a limit of detection of 0.86 fM. The practicability was demonstrated by determining miRNA-21 from serum samples with acceptable results. We expect that this method can open a new avenue for exploring advanced biosensors with improved analytical performances.
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Affiliation(s)
- Jie Wang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, Institute for Liver Diseases of Anhui Medical University, School of Pharmacy, Anhui Medical University, Hefei 230032, P.R. China
| | - Jiayin Sun
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, Institute for Liver Diseases of Anhui Medical University, School of Pharmacy, Anhui Medical University, Hefei 230032, P.R. China
| | - Jing Zhang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, Institute for Liver Diseases of Anhui Medical University, School of Pharmacy, Anhui Medical University, Hefei 230032, P.R. China
| | - Chenlin Shen
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, Institute for Liver Diseases of Anhui Medical University, School of Pharmacy, Anhui Medical University, Hefei 230032, P.R. China
| | - Xinlei Zhang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Jianguo Xu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
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5
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Liu Y, Sun X, Yuan H, Liu B, Zhou B, Chen X, Li X, Xue Q. Sensitive detection of p53 DNA based on spatially confined fluorescence resonance energy transfer and multivalent assembly of branched DNA. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:4314-4319. [PMID: 34476425 DOI: 10.1039/d1ay01110c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
A key challenge for the discrete distribution-based Förster resonance energy transfer system (D-FRET) is the reduced intensity and stability of signal probes in complex biological matrices. Here, we present a spatially confined FRET (SC-FRET) probe with a stable structure and strong signal output. It consists of multivalent FRET pairs labeled with FAM or TAMRA. In this assay, p53 DNA was chosen as a model hairpin probe (HP), and two kinds of branched DNA probes (ssDNA-FAM, ssDNA-TAMRA) were involved. Under the action of p53 DNA, the unfolded HP acts as a primer to initiate polymerization extension of KFP polymerase and cleavage of Nb.BbvCI endonuclease, which produces plenty of ssDNA (primer-DNA). The branched DNA is designed to have the same binding core and different sticky ends, the core part of which can self-assemble to form X-shaped branched DNA (X-FAM or X-TAMRA), and the sticky ends of which are complementary to the primer-DNA. Therefore, the primer-DNAs released during the polymerization cleavage process will combine a large number of X-FAM and X-TAMRA in a limited space through complementary base pairing. Fluorescence was transferred from FAM to TAMRA, and a strong FRET response was generated by the locational effects. The proposed SC-FRET system based on the multivalent assembly of branched DNA exhibited a strong FRET response with an LOD of 0.01394 pM. Importantly, it also showed a high-contrast and stable FRET response in HeLa cells. Its superior biological stability is attributed to the large steric hindrance of the compact and rigid frame of the SC-FRET probe, which helps prevent intracellular degradation and provides a powerful tool for biomedical research.
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Affiliation(s)
- Yeling Liu
- Department of Chemistry, Liaocheng University, Liaocheng 252059, China.
| | - Xia Sun
- Department of Chemistry, Liaocheng University, Liaocheng 252059, China.
| | - Hui Yuan
- Department of Chemistry, Liaocheng University, Liaocheng 252059, China.
| | - Bingxin Liu
- Department of Chemistry, Liaocheng University, Liaocheng 252059, China.
| | - Bingqian Zhou
- Department of Chemistry, Liaocheng University, Liaocheng 252059, China.
| | - Xuening Chen
- College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, China
| | - Xia Li
- Department of Chemistry, Liaocheng University, Liaocheng 252059, China.
| | - Qingwang Xue
- Department of Chemistry, Liaocheng University, Liaocheng 252059, China.
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6
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Hairpin DNA-Mediated isothermal amplification (HDMIA) techniques for nucleic acid testing. Talanta 2021; 226:122146. [PMID: 33676697 DOI: 10.1016/j.talanta.2021.122146] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 01/21/2021] [Accepted: 01/24/2021] [Indexed: 01/19/2023]
Abstract
Nucleic acid detection is of great importance in a variety of areas, from life science and clinical diagnosis to environmental monitoring and food safety. Unfortunately, nucleic acid targets are always found in trace amounts and their response signals are difficult to be detected. Amplification mechanisms are then practically needed to either duplicate nucleic acid targets or enhance the detection signals. Polymerase chain reaction (PCR) is one of the most popular and powerful techniques for nucleic acid analysis. But the requirement of costly devices for precise thermo-cycling procedures in PCR has severely hampered the wide applications of PCR. Fortunately, isothermal molecular reactions have emerged as promising alternatives. The past decade has witnessed significant progress in the research of isothermal molecular reactions utilizing hairpin DNA probes (HDPs). Based on the nucleic acid strand interaction mechanisms, the hairpin DNA-mediated isothermal amplification (HDMIA) techniques can be mainly divided into three categories: strand assembly reactions, strand decomposition reactions, and strand creation reactions. In this review, we introduce the basics of HDMIA methods, including the sensing principles, the basic and advanced designs, and their wide applications, especially those benefiting from the utilization of G-quadruplexes and nanomaterials during the past decade. We also discuss the current challenges encountered, highlight the potential solutions, and point out the possible future directions in this prosperous research area.
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7
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Zhang T, Zhou W, Lin X, Khan MR, Deng S, Zhou M, He G, Wu C, Deng R, He Q. Light-up RNA aptamer signaling-CRISPR-Cas13a-based mix-and-read assays for profiling viable pathogenic bacteria. Biosens Bioelectron 2020; 176:112906. [PMID: 33342694 DOI: 10.1016/j.bios.2020.112906] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 12/10/2020] [Accepted: 12/12/2020] [Indexed: 02/08/2023]
Abstract
Viable pathogenic bacteria cause serious human diseases via systemic infections and food poisoning. Herein, we constructed a light-up RNA aptamer signaling-CRISPR-Cas13a assay enabling mix-and-read detection of viable pathogenic bacteria. Directly targeting pathogen RNAs via CRISPR-Cas13a allows precisely discriminating viable bacteria from dead bacteria. We introduced a light-up RNA aptamer, Broccoli, serving as the substate of activated CRISPR-Cas13a to monitor the presence of pathogen RNAs, eliminating the need to use chemically labeled RNA substrate. Sequentially, the assay allows a reverse transcription-free, nucleic acid amplification-free, and label-free quantification of RNA targets and viable pathogenic bacteria. It could detect as low as 10 CFU of Bacillus cereus and precisely quantify viable bacteria with a content ranging from 0% to 100% in 105 CFU total bacteria. The quantification of viable bacteria allows more accurately estimating the ability of B. cereus to spoil food. The RNA assay promises its use in point-of-use detection of viable pathogens and biosafety control.
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Affiliation(s)
- Ting Zhang
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China
| | - Wenhu Zhou
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan, China
| | - Xiaoya Lin
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China
| | - Mohammad Rizwan Khan
- Department of Chemistry, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Sha Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China
| | - Mi Zhou
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China
| | - Guiping He
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China
| | - Chengyong Wu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, 610041, PR China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China.
| | - Qiang He
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China
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8
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Kim DM, Yoo SM. DNA-modifying enzyme reaction-based biosensors for disease diagnostics: recent biotechnological advances and future perspectives. Crit Rev Biotechnol 2020; 40:787-803. [DOI: 10.1080/07388551.2020.1764485] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Dong Min Kim
- Center for Applied Life Science, Hanbat National University, Daejeon, Republic of Korea
| | - Seung Min Yoo
- School of Integrative Engineering, Chung-Ang University, Seoul, Republic of Korea
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9
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Wang J, Li S, Xu J, Lu Y, Lin M, Wang C, Zhang C, Lin G, Jia L. A functionalized dumbbell probe-based cascading exponential amplification DNA machine enables amplified probing of microRNAs. Chem Commun (Camb) 2020; 56:1681-1684. [PMID: 31939961 DOI: 10.1039/c9cc08289a] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A functionalized dumbbell probe (FDP) based amplification method, termed as a cascading exponential amplification DNA machine (CEA-DNA machine), has been developed to autonomously accumulate single G-quadruplexes (SGQs) and twin-G-quadruplexes (TGQs) for robust fluorescence signal-on probing of miRNA-21.
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Affiliation(s)
- Jie Wang
- Cancer Metastasis Alert and Prevention Center, and Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention, College of Chemistry, Fuzhou University, Fuzhou 350002, China
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10
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Fu X, Peng F, Lee J, Yang Q, Zhang F, Xiong M, Kong G, Meng HM, Ke G, Zhang XB. Aptamer-Functionalized DNA Nanostructures for Biological Applications. Top Curr Chem (Cham) 2020; 378:21. [PMID: 32030541 DOI: 10.1007/s41061-020-0283-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/17/2020] [Indexed: 12/31/2022]
Abstract
DNA nanostructures hold great promise for various applications due to their remarkable properties, including programmable assembly, nanometric positional precision, and dynamic structural control. The past few decades have seen the development of various kinds of DNA nanostructures that can be employed as useful tools in fields such as chemistry, materials, biology, and medicine. Aptamers are short single-stranded nucleic acids that bind to specific targets with excellent selectivity and high affinity and play critical roles in molecular recognition. Recently, many attempts have been made to integrate aptamers with DNA nanostructures for a range of biological applications. This review starts with an introduction to the features of aptamer-functionalized DNA nanostructures. The discussion then focuses on recent progress (particularly during the last five years) in the applications of these nanostructures in areas such as biosensing, bioimaging, cancer therapy, and biophysics. Finally, challenges involved in the practical application of aptamer-functionalized DNA nanostructures are discussed, and perspectives on future directions for research into and applications of aptamer-functionalized DNA nanostructures are provided.
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Affiliation(s)
- Xiaoyi Fu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Fangqi Peng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Jungyeon Lee
- Department of Chemistry, Rutgers University, 73 Warren Street, Newark, NJ, 07102, USA
| | - Qi Yang
- Department of Chemistry, Rutgers University, 73 Warren Street, Newark, NJ, 07102, USA
| | - Fei Zhang
- Department of Chemistry, Rutgers University, 73 Warren Street, Newark, NJ, 07102, USA
| | - Mengyi Xiong
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Gezhi Kong
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Hong-Min Meng
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China
| | - Guoliang Ke
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China.
| | - Xiao-Bing Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
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11
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Pirzada M, Altintas Z. Nanomaterials for Healthcare Biosensing Applications. SENSORS (BASEL, SWITZERLAND) 2019; 19:E5311. [PMID: 31810313 PMCID: PMC6928990 DOI: 10.3390/s19235311] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 11/22/2019] [Accepted: 11/27/2019] [Indexed: 12/12/2022]
Abstract
In recent years, an increasing number of nanomaterials have been explored for their applications in biomedical diagnostics, making their applications in healthcare biosensing a rapidly evolving field. Nanomaterials introduce versatility to the sensing platforms and may even allow mobility between different detection mechanisms. The prospect of a combination of different nanomaterials allows an exploitation of their synergistic additive and novel properties for sensor development. This paper covers more than 290 research works since 2015, elaborating the diverse roles played by various nanomaterials in the biosensing field. Hence, we provide a comprehensive review of the healthcare sensing applications of nanomaterials, covering carbon allotrope-based, inorganic, and organic nanomaterials. These sensing systems are able to detect a wide variety of clinically relevant molecules, like nucleic acids, viruses, bacteria, cancer antigens, pharmaceuticals and narcotic drugs, toxins, contaminants, as well as entire cells in various sensing media, ranging from buffers to more complex environments such as urine, blood or sputum. Thus, the latest advancements reviewed in this paper hold tremendous potential for the application of nanomaterials in the early screening of diseases and point-of-care testing.
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Affiliation(s)
| | - Zeynep Altintas
- Technical University of Berlin, Straße des 17. Juni 124, 10623 Berlin, Germany;
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12
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Kosman J, Juskowiak B. Bioanalytical Application of Peroxidase-Mimicking DNAzymes: Status and Challenges. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2019; 170:59-84. [PMID: 28474157 DOI: 10.1007/10_2017_7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
DNAzymes with peroxidase-mimicking activity are a new class of catalytically active DNA molecules. This system is formed as a complex of hemin and a G-quadruplex structure created by oligonucleotides rich in guanine. Considering catalytic activity, this DNAzyme mimics horseradish peroxidase, the enzyme most commonly used for signal generation in bioassays. Because DNAzymes exhibit many advantages over protein enzymes (thermal stability, easy and cheap synthesis and purification) they can successfully replace HRP in bioanalytical applications. HRP-like DNAzymes have been applied in the detection of several DNA sequences. Many amplification techniques have been conjugated with DNAzyme systems, resulting in ultrasensitive bioassays. On the other hand, the combination of aptamers and DNAzymes has led to the development of aptazymes for specific targets. An up-to-date summary of the most interesting DNAzyme-based assays is presented here. The elaborated systems can be used in medical diagnosis or chemical and biological studies.
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Affiliation(s)
- J Kosman
- Laboratory of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Poznan, Poland.
| | - B Juskowiak
- Laboratory of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Poznan, Poland
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13
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Ultrasensitive assay based on a combined cascade amplification by nicking-mediated rolling circle amplification and symmetric strand-displacement amplification. Anal Chim Acta 2019; 1047:172-178. [DOI: 10.1016/j.aca.2018.10.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 08/31/2018] [Accepted: 10/03/2018] [Indexed: 01/05/2023]
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14
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Yan Q, Duan Q, Huang Y, Guo J, Zhong L, Wang H, Yi G. Symmetric exponential amplification reaction-based DNA nanomachine for the fluorescent detection of nucleic acids. RSC Adv 2019; 9:41305-41310. [PMID: 35540087 PMCID: PMC9076420 DOI: 10.1039/c9ra08854g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 11/28/2019] [Indexed: 11/21/2022] Open
Abstract
By introducing palindromic sequences into the classical exponential amplification reaction (EXPAR), we constructed a new palindromic fragment-incorporated multifunctional hairpin probe (P-HP)-mediated symmetric exponential amplification reaction (S-EXPAR), to significantly reduce the background signal caused by inherent nonspecific amplification. A G-triplex/ThT complex was used as the signal reporter for the proposed label-free DNA nanomachine. The P-HP consists of five functional regions: a C-rich region (C), a target DNA recognition region (T′), two nicking sites (X′) and a palindromic fragment (P). When target DNA (T) hybridizes with P-HP, the palindromic fragment at the 3′ end of P-HP is fully exposed. Then, the P-HP/T duplexes hybridize with each other through the exposed P, and EXPAR occurs automatically and continuously on both sides of P under the synergistic effect of polymerase and nicking endonuclease. This is called the S-EXPAR assay. In this system, one T converts to a large number of G-triplex fragments, which can combine with ThT within a short time. The G-triplex/ThT complexes formed act as the signal reporter in a label-free and environmentally friendly format. In this way, the limit of detection of this method is as low as 10 pM with a dynamic response range of 10 pM to 300 nM. In addition, this method can detect other nucleic acids by simply changing the T′ region of the P-HP. Thus, the proposed DNA nanomachine is a potential alternative method for nucleic acid detection. This label-free and ultra-low background signal DNA nanomachine was based on P-HP mediated S-EXPAR and the G-triplex/ThT complex.![]()
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Affiliation(s)
- Qi Yan
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education of China)
- Department of Laboratory Medicine
- Chongqing Medical University
- Chongqing
- P. R. China
| | - Qiuyue Duan
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education of China)
- Department of Laboratory Medicine
- Chongqing Medical University
- Chongqing
- P. R. China
| | - Yuqi Huang
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education of China)
- Department of Laboratory Medicine
- Chongqing Medical University
- Chongqing
- P. R. China
| | - Jing Guo
- Department of Clinical Laboratory
- Qingdao Municipal Hospital
- Qingdao
- P. R. China
| | - Liang Zhong
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education of China)
- Department of Laboratory Medicine
- Chongqing Medical University
- Chongqing
- P. R. China
| | - Hong Wang
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education of China)
- Department of Laboratory Medicine
- Chongqing Medical University
- Chongqing
- P. R. China
| | - Gang Yi
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education of China)
- Department of Laboratory Medicine
- Chongqing Medical University
- Chongqing
- P. R. China
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15
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Xu H, Jiang Y, Liu D, Liu K, Zhang Y, Yu S, Shen Z, Wu ZS. Twin target self-amplification-based DNA machine for highly sensitive detection of cancer-related gene. Anal Chim Acta 2018; 1011:86-93. [DOI: 10.1016/j.aca.2018.01.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 01/05/2018] [Accepted: 01/06/2018] [Indexed: 01/08/2023]
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16
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Zhang H, Liu X, Liu M, Gao T, Huang Y, Liu Y, Zeng W. Gene detection: An essential process to precision medicine. Biosens Bioelectron 2018; 99:625-636. [DOI: 10.1016/j.bios.2017.08.033] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 08/12/2017] [Indexed: 01/08/2023]
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17
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Peroxidyme-Amplified Radical Chain Reaction (PARCR): Visible Detection of a Catalytic Reporter. Angew Chem Int Ed Engl 2017; 56:13411-13415. [DOI: 10.1002/anie.201706163] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 08/14/2017] [Indexed: 12/31/2022]
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18
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Goertz JP, White IM. Peroxidyme-Amplified Radical Chain Reaction (PARCR): Visible Detection of a Catalytic Reporter. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201706163] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- John P. Goertz
- Department of Bioengineering; University of Maryland; College Park MD 20742 USA
| | - Ian M. White
- Department of Bioengineering; University of Maryland; College Park MD 20742 USA
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19
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Zou M, Li D, Yuan R, Xiang Y. Metal-ion dependent DNAzyme recycling amplification for sensitive and homogeneous immuno-proximity binding assay of α-fetoprotein biomarker. Biosens Bioelectron 2017; 92:624-629. [DOI: 10.1016/j.bios.2016.10.044] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 10/04/2016] [Accepted: 10/19/2016] [Indexed: 11/30/2022]
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20
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A New Strategy for Silver Deposition on Au Nanoparticles with the Use of Peroxidase-Mimicking DNAzyme Monitored via a Localized Surface Plasmon Resonance Technique. SENSORS 2017; 17:s17040849. [PMID: 28406432 PMCID: PMC5424726 DOI: 10.3390/s17040849] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 04/06/2017] [Accepted: 04/10/2017] [Indexed: 01/09/2023]
Abstract
Peroxidase-mimicking DNAzyme was applied as a catalyst of silver deposition on gold nanoparticles. This DNAzyme is formed when hemin binds to the G-quadruplex-forming DNA sequence. Such a system is able to catalyze a redox reaction with a one- or two-electron transfer. The process of silver deposition was monitored via a localized surface plasmon resonance technique (LSPR), which allows one to record scattering spectrum of a single nanoparticle. Our study showed that DNAzyme is able to catalyze silver deposition. The AFM experiments proved that DNAzyme induced the deposition of silver shells of approximately 20 nm thickness on Au nanoparticles (AuNPs). Such an effect is not observed when hemin is absent in the system. However, we noticed non-specific binding of hemin to the capture oligonucleotides on a gold NP probe that also induced some silver deposition, even though the capture probe was unable to form G-quadruplex. Analysis of SEM images indicated that the surface morphology of the silver layer deposited by DNAzyme is different from that obtained for hemin alone. The proposed strategy of silver layer synthesis on gold nanoparticles catalyzed by DNAzyme is an innovative approach and can be applied in bioanalysis (LSPR, electrochemistry) as well as in material sciences.
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21
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Xu J, Zheng T, Le J, Jia L. Long-stem shaped multifunctional molecular beacon for highly sensitive nucleic acids determination via intramolecular and intermolecular interactions based strand displacement amplification. Analyst 2017; 142:4438-4445. [DOI: 10.1039/c7an01205e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
LS-MMB based intra-SDA and inter-SDA for amplified gene signaling.
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Affiliation(s)
- Jianguo Xu
- School of Food Science and Engineering
- Hefei University of Technology
- Hefei 230009
- China
- Cancer Metastasis Alert and Prevention Center
| | - Tingting Zheng
- Cancer Metastasis Alert and Prevention Center
- and Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment
- College of Chemistry
- Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy
- Fuzhou University
| | - Jingqing Le
- Cancer Metastasis Alert and Prevention Center
- and Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment
- College of Chemistry
- Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy
- Fuzhou University
| | - Lee Jia
- Cancer Metastasis Alert and Prevention Center
- and Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment
- College of Chemistry
- Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy
- Fuzhou University
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22
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Two-wheel drive-based DNA nanomachine and its sensing potential for highly sensitive analysis of cancer-related gene. Biomaterials 2016; 100:110-7. [PMID: 27254471 DOI: 10.1016/j.biomaterials.2016.05.020] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 04/20/2016] [Accepted: 05/17/2016] [Indexed: 12/16/2022]
Abstract
With the biological significance and important advances of nano-scale DNA devices, scientific activities have been directed toward developing molecular machinery. In this work, we present a novel two-wheel drive-based DNA nanomachine composed of one signaling recognition probe (SRP), one label-free recognition probe (LRP), and one driving primer (DP). Target DNA hybridization can activate LRP-based wheel driving by resorting to DP-mediated polymerization/nicking/displacement cycles. This in turn results in the accumulation of nicked strand 1 (NS1) that can initiate extended SRP-based wheel driving. As a result, the hairpin structure of SRP is stretched and pre-quenched fluorescence is restored. Meanwhile, lots of nicked strand 2 (NS2) are produced, which could hybridize perfectly with SRP and lead to further fluorescence amplification. It is worth noting that, because the nanomachine operation relies strongly on inputted target trigger, the unwanted background is completely eliminated. The detection limit of 1 pM and an excellent capability to recognize the single-base mutation were achieved. Significantly, the interrogating of target trigger extracted from cancer cells is already available, reflecting the potential for practical applications. As a proof-of-concept building, the unique analytical properties would significantly benefit the DNA nanomachines and reveal great promise in biochemical and biomedical studies.
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23
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Yang C, Dou B, Yang J, Yuan R, Xiang Y. Cross-triggered and cascaded recycling amplification for ultrasensitive electrochemical sensing of the mutant human p53 gene. Chem Commun (Camb) 2016; 52:8707-10. [DOI: 10.1039/c6cc04587a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cross-triggered and cascaded recycling amplification enables the highly sensitive electrochemical detection of the mutant p53 gene in human serum.
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Affiliation(s)
- Cuiyun Yang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Baoting Dou
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Jianmei Yang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Yun Xiang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
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