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Qi F, Li H, Wang Y, Ding C. Responsive DNA hydrogels: design strategies and prospects for biosensing. Chem Commun (Camb) 2024. [PMID: 39171719 DOI: 10.1039/d4cc03829k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
Hydrogels, water-filled networks that can adapt to external stimuli by altering their volume, are known for their high flexibility and biocompatibility. DNA, a critical biomolecule renowned for its exceptional characteristics including information transmission, molecular recognition, and editability, has found widespread applications in the biosensing field as well. The integration of these two biomaterials offers promising opportunities for the development of novel biosensors with enhanced sensitivity, specificity, and adaptability. Therefore, by virtue of the collective features, researchers have recently focused on the construction of responsive DNA hydrogel systems. This feature article describes recent developments in fabricating DNA hydrogels and their applications in the biosensing area. Initially, it focuses on the design strategies employed in preparing DNA hydrogels, encompassing both pure DNA hydrogels and hybridized DNA hydrogels. Subsequently, it summarizes the use of DNA hydrogels in biosensing applications, highlighting their applications in visual detection, electrochemical sensing, and optical biosensing analyses. Furthermore, the underlying responsive mechanisms within these biosensing systems are also described. Lastly, this article presents a comprehensive discussion on the existing challenges and prospects of responsive DNA hydrogels, offering insights into their potential to revolutionize the field of biosensing.
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Affiliation(s)
- Fenglian Qi
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, Shandong, 266042, P. R. China.
| | - Hanwen Li
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, Shandong, 266042, P. R. China.
| | - Yonghao Wang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, Shandong, 266042, P. R. China.
| | - Caifeng Ding
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, Shandong, 266042, P. R. China.
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2
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Zhang Y, Hu C, Yin Y, Ren K, He Y, Gao Y, Han H, Zhu C, Wang W. CRISPR/Cas12a-Responsive Smart DNA Hydrogel for Sensitive Electrochemiluminescence Detection of the Huanglongbing Outer Membrane Protein Gene. Anal Chem 2024; 96:11611-11618. [PMID: 38943567 DOI: 10.1021/acs.analchem.4c02489] [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: 07/01/2024]
Abstract
Citrus Huanglongbing (HLB) is known as the cancer of citrus, where Candidatus Liberibacter asiaticus (CLas) is the most prevalent strain causing HLB. In this study, we report a novel electrochemiluminescence (ECL) biosensor for the highly sensitive detection of the CLas outer membrane protein (Omp) gene by coupling rolling circle amplification (RCA) with a CRISPR/Cas12a-responsive smart DNA hydrogel. In the presence of the target, a large number of amplicons are generated through RCA. The amplicons activate the trans-cleavage activity of CRISPR/Cas12a through hybridizing with crRNA, triggering the response of smart DNA hydrogel to release the encapsulated AuAg nanoclusters (AuAg NCs) on the electrode and therefore leading to a decreased ECL signal. The ECL intensity change (I0 - I) is positively correlated with the concentration of the target in the range 50 fM to 5 nM, with a limit of detection of 40 fM. The performance of the sensor has also been evaluated with 10 samples of live citrus leaves (five HLB negative and five HLB positive), and the result is in excellent agreement with the gold standard qPCR result. The sensing strategy has expanded the ECL versatility for detecting varying levels of dsDNA or ssDNA in plants with high sensitivity.
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Affiliation(s)
- Yutian Zhang
- National Key Laboratory of Agricultural Microbiology, College of Chemistry, Huazhong Agricultural University, Wuhan 430070, China
| | - Can Hu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yashi Yin
- National Key Laboratory of Agricultural Microbiology, College of Chemistry, Huazhong Agricultural University, Wuhan 430070, China
| | - Kejing Ren
- National Key Laboratory of Agricultural Microbiology, College of Chemistry, Huazhong Agricultural University, Wuhan 430070, China
| | - Yingsi He
- National Key Laboratory of Agricultural Microbiology, College of Chemistry, Huazhong Agricultural University, Wuhan 430070, China
| | - Yanru Gao
- National Key Laboratory of Agricultural Microbiology, College of Chemistry, Huazhong Agricultural University, Wuhan 430070, China
| | - Heyou Han
- National Key Laboratory of Agricultural Microbiology, College of Chemistry, Huazhong Agricultural University, Wuhan 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Chengzhou Zhu
- State Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Wenjing Wang
- National Key Laboratory of Agricultural Microbiology, College of Chemistry, Huazhong Agricultural University, Wuhan 430070, China
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Li Z, Duan S, Liu B. Freezing Functional Nucleic Acids: From Molecular Reactions to Surface Immobilization. Chembiochem 2024:e202400416. [PMID: 38979890 DOI: 10.1002/cbic.202400416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 07/08/2024] [Accepted: 07/08/2024] [Indexed: 07/10/2024]
Abstract
Biochemical reactions are typically slowed down by decreasing temperature. However, accelerated reaction kinetics have been observed for a long time. More recent examples have highlighted the unique role of freezing in fabricating supermaterials, degrading environmental contaminants, and accelerating bioreactions. Functional nucleic acids are DNA or RNA oligonucleotides with versatile properties, including target recognition, catalysis, and molecular co4mputing. In this review, we discuss the current observations and understanding of freezing-facilitated reactions involving functional nucleic acids. Molecular reactions such as ligation/conjugation, cleavage, and hybridization are discussed. Moreover, freezing-induced DNA-nanoparticle conjugations are introduced. Then, we describe our effect in immobilizing DNA on bulk surfaces. Finally, we address some critical questions and research opportunities in the field.
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Affiliation(s)
- Zhenglian Li
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
| | - Siyi Duan
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
| | - Biwu Liu
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
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Yao C, Liu X, Lu X, Wang L, Jia J, Li Z. Smartphone-Based Fluorescent Profiling of Quaternary MicroRNAs in Urine for Rapid Diagnosis of Urological Cancers Using a Multiplexed Isothermal Exponential Amplification Reaction. Anal Chem 2024; 96:419-426. [PMID: 38152877 DOI: 10.1021/acs.analchem.3c04461] [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: 12/29/2023]
Abstract
Urological cancers such as bladder or prostate cancer represent one of the most malignant tumors that accounts for an extremely high mortality. However, conventionally standard diagnostics for urological cancers are hardly available in low-resource settings. We developed herein a hand-held fluorescent imaging platform by integrating a multiplexed isothermal exponential amplification reaction (EXPAR) with a microgel-enriched methodology for sensitive profiling of quaternary microRNAs (miRNAs) in urine and quick diagnosis of urological cancers at the early stage. The target miRNA mixtures in the urine underwent four parallel EXPARs without cross-reactivity, followed by surface concentration and hybridization by the encoded polyacrylamide microgels. This mix-and-read strategy allowed for one-pot analysis of several key miRNAs simultaneously and provided 5-fold enhancement in fluorescent detection sensitivities compared to the individual EXPAR-based assays. Four urinary miRNAs (let-7a, miRNA-155, -223, and -143) could be quantitatively determined in a wide linear range from 50 fM to 30 nM, with the limits of detection at femtomolar levels. Using a smartphone-based imaging microreader, healthy and cancerous cohorts with prostate, bladder, and renal cell cancers could be discriminated in 30 min with the accuracy >83% using linear discriminant analysis. The developed detection platform has proven to be a portable, noninvasive, and useful complement to the toolbox for miRNA-based liquid biopsies, which holds immense potential and advantage for regular and large-scale applications in early cancer diagnosis.
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Affiliation(s)
- Chanyu Yao
- Institute for Advanced Study, Shenzhen University, 3688 Nanhai Road, Shenzhen, Guangdong 518060, P. R. China
| | - Xueliang Liu
- School of Basic Medical Sciences, Xinxiang Medical University, 601 Jinsui Road, Xinxiang, Henan 453003, P. R. China
| | - Xiaohui Lu
- Institute for Advanced Study, Shenzhen University, 3688 Nanhai Road, Shenzhen, Guangdong 518060, P. R. China
| | - Lei Wang
- Department of Urology, Xinxiang Central Hospital, Xinxiang Medical College, 56 Jinsui Road, Xinxiang, Henan 453003, P. R. China
| | - Jia Jia
- Department of Anesthesiology and Perioperative Medicine, Zhengzhou University People's Hospital, Zhengzhou, Henan 450003, P. R. China
| | - Zheng Li
- Institute for Advanced Study, Shenzhen University, 3688 Nanhai Road, Shenzhen, Guangdong 518060, P. R. China
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Yu M, Ye R, Zeng T, Tan L, Zhao Z, Gao W, Chen X, Lian Z, Ma Y, Li A, Hu J. Constructing an Ultra-Rapid Nanoconfinement-Enhanced Fluorescence Clinical Detection Platform by Using Machine Learning and Tunable DNA Xerogel "Probe". Anal Chem 2023; 95:15690-15699. [PMID: 37830461 DOI: 10.1021/acs.analchem.3c02955] [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: 10/14/2023]
Abstract
Low mass transfer efficiency and unavoidable matrix effects seriously limit the development of rapid and accurate determination of biosensing systems. Herein, we have successfully constructed an ultra-rapid nanoconfinement-enhanced fluorescence clinical detection platform based on machine learning (ML) and DNA xerogel "probe", which was performed by detecting neutrophil gelatinase-associated lipocalin (NGAL, protein biomarker of acute kidney injury). By regulating pore sizes of the xerogels, the transfer of NGAL in xerogels can approximate that in homogeneous solution. Due to electrostatic attraction of the pore entrances, NGAL rapidly enriches on the surface and inside the xerogels. The reaction rate of NGAL and aptamer cross-linked in xerogels is also accelerated because of the nanoconfinement effect-induced increasing reactant concentration and the enhanced affinity constant KD between reactants, which can be promoted by ∼667-fold than that in bulk solution, thus achieving ultra-rapid detection (ca. 5 min) of human urine. The platform could realize one-step detection without sample pretreatments due to the antiligand exchange effect on the surface of N-doped carbon quantum dots (N-CQDs) in xerogels, in which ligand exchange between -COOH and underlying interfering ions in urine will be inhibited due to higher adsorption energy of -COOH on the N-CQD surface relative to the interfering ions. Based on the ML-extended program, the real-time analysis of the urine fluorescence spectra can be completed within 2 s. Interestingly, by changing DNA, aptamer sequences, or xerogel fluorescence intensities, the detection platform can be customized for targeted diseases.
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Affiliation(s)
- Meng Yu
- School of Chemistry and Chemical Engineering, Key Lab of Fuel Cell Technology of Guangdong Province, South China University of Technology, Guangzhou 510641, China
- Division of Nephrology, Nanfang Hospital, National Clinical Research Center for Kidney Disease, State Key Laboratory of Organ Failure Research, Guangdong Provincial Institute of Nephrology, Guangdong Provincial Key Laboratory of Renal Failure Research, Southern Medical University, Guangzhou 510515, China
| | - Rongkai Ye
- School of Chemistry and Chemical Engineering, Key Lab of Fuel Cell Technology of Guangdong Province, South China University of Technology, Guangzhou 510641, China
| | - Tao Zeng
- Division of Nephrology, Nanfang Hospital, National Clinical Research Center for Kidney Disease, State Key Laboratory of Organ Failure Research, Guangdong Provincial Institute of Nephrology, Guangdong Provincial Key Laboratory of Renal Failure Research, Southern Medical University, Guangzhou 510515, China
| | - Li Tan
- School of Chemistry and Chemical Engineering, Key Lab of Fuel Cell Technology of Guangdong Province, South China University of Technology, Guangzhou 510641, China
| | - Ziyu Zhao
- School of Chemistry and Chemical Engineering, Key Lab of Fuel Cell Technology of Guangdong Province, South China University of Technology, Guangzhou 510641, China
| | - Wenjing Gao
- School of Chemistry and Chemical Engineering, Key Lab of Fuel Cell Technology of Guangdong Province, South China University of Technology, Guangzhou 510641, China
| | - Xin Chen
- School of Chemistry and Chemical Engineering, Key Lab of Fuel Cell Technology of Guangdong Province, South China University of Technology, Guangzhou 510641, China
| | - Ziqi Lian
- School of Chemistry and Chemical Engineering, Key Lab of Fuel Cell Technology of Guangdong Province, South China University of Technology, Guangzhou 510641, China
| | - Ying Ma
- School of Chemistry and Chemical Engineering, Key Lab of Fuel Cell Technology of Guangdong Province, South China University of Technology, Guangzhou 510641, China
| | - Aiqing Li
- Division of Nephrology, Nanfang Hospital, National Clinical Research Center for Kidney Disease, State Key Laboratory of Organ Failure Research, Guangdong Provincial Institute of Nephrology, Guangdong Provincial Key Laboratory of Renal Failure Research, Southern Medical University, Guangzhou 510515, China
| | - Jianqiang Hu
- School of Chemistry and Chemical Engineering, Key Lab of Fuel Cell Technology of Guangdong Province, South China University of Technology, Guangzhou 510641, China
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Li M, Shi Q, Song N, Xiao Y, Wang L, Chen Z, James TD. Current trends in the detection and removal of heavy metal ions using functional materials. Chem Soc Rev 2023; 52:5827-5860. [PMID: 37531220 DOI: 10.1039/d2cs00683a] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2023]
Abstract
The shortage of freshwater resources caused by heavy metal pollution is an acute global issue, which has a great impact on environmental protection and human health. Therefore, the exploitation of new strategies for designing and synthesizing green, efficient, and economical materials for the detection and removal of heavy metal ions is crucial. Among the various methods for the detection and removal of heavy ions, advanced functional systems including nanomaterials, polymers, porous materials, and biomaterials have attracted considerable attention over the past several years due to their capabilities of real-time detection, excellent removal efficiency, anti-interference, quick response, high selectivity, and low limit of detection. In this tutorial review, we review the general design principles underlying the aforementioned functional materials, and in particular highlight the fundamental mechanisms and specific examples of detecting and removing heavy metal ions. Additionally, the methods which enhance water purification quality using these functional materials have been reviewed, also current challenges and opportunities in this exciting field have been highlighted, including the fabrication, subsequent treatment, and potential future applications of such functional materials. We envision that this tutorial review will provide invaluable guidance for the design of functional materials tailored towards the detection and removal of heavy metals, thereby expediting the development of high-performance materials and fostering the development of more efficient approaches to water pollution remediation.
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Affiliation(s)
- Meng Li
- Hebei Key Lab of Power Plant Flue Gas Multi-Pollutants Control, Department of Environmental Science and Engineering, North China Electric Power University, Baoding, 071003, P. R. China.
| | - Quanyu Shi
- Hebei Key Lab of Power Plant Flue Gas Multi-Pollutants Control, Department of Environmental Science and Engineering, North China Electric Power University, Baoding, 071003, P. R. China.
| | - Ningxin Song
- Hebei Key Lab of Power Plant Flue Gas Multi-Pollutants Control, Department of Environmental Science and Engineering, North China Electric Power University, Baoding, 071003, P. R. China.
| | - Yumeng Xiao
- Hebei Key Lab of Power Plant Flue Gas Multi-Pollutants Control, Department of Environmental Science and Engineering, North China Electric Power University, Baoding, 071003, P. R. China.
| | - Lidong Wang
- Hebei Key Lab of Power Plant Flue Gas Multi-Pollutants Control, Department of Environmental Science and Engineering, North China Electric Power University, Baoding, 071003, P. R. China.
| | - Zhijun Chen
- Key Laboratory of Bio-based Material Science and Technology of Ministry of Education, Material Science and Engineering College, Northeast Forestry University, Hexing Road 26, Harbin 150040, P. R. China.
| | - Tony D James
- Department of Chemistry, University of Bath, Bath, BA2 7AY, UK.
- School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, P. R. China
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Zandieh M, Hogan ÚE, Smith RDL, Liu J. Spherical DNA for Probing Wettability of Microplastics. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:4959-4966. [PMID: 36988268 DOI: 10.1021/acs.langmuir.2c03417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Wettability of microplastics may change due to chemical or physical transformations at their surface. In this work, we studied the adsorption of spherical nucleic acids (SNAs) with a gold nanoparticle core and linear DNA of the same sequence to probe the wettability of microplastics. Soaking microplastics in water at room temperature for 3 months resulted in the enhancement of SNA adsorption capacity and affinity, whereas linear DNA adsorption was the same on the fresh and soaked microplastics. Drying of the soaked microplastics followed by rehydration decreased the adsorption of the SNA, suggesting that the effect of soaking was reversible and related to physical changes instead of chemical changes of the microplastics. Raman spectroscopy data also revealed no chemical transformations of the soaked microplastics. Heating of microplastics over a short period induced a similar effect to long-term soaking. We propose that soaking or heating removes air entrapped in the nanosized pores at the water-plastic interface, increasing the contact surface area of the SNA to afford stronger adsorption. However, such wetted porosity would not change the adsorption of linear DNA because of its much smaller size.
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Affiliation(s)
- Mohamad Zandieh
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo N2L 3G1, Ontario, Canada
| | - Úna E Hogan
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo N2L 3G1, Ontario, Canada
| | - Rodney D L Smith
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo N2L 3G1, Ontario, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo N2L 3G1, Ontario, Canada
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Zhou Y, Liu J. Graphene Oxide-Assisted Aptamer-Based Fluorescent Detection of Tetracycline Antibiotics. CHEMISTRY 2023. [DOI: 10.3390/chemistry5020056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023] Open
Abstract
Tetracyclines are a group of common antibiotics, but owing to their toxicity, most of them are only used in animal husbandry and veterinary medicine. A DNA aptamer for tetracyclines has recently been reported. Upon aptamer binding, the fluorescence of tetracyclines was enhanced. This unique fluorescence enhancement was used to selectively detect the tetracyclines. The purpose of this study was to use graphene oxide (GO) to suppress the background fluorescence for enhanced detection. First, the adsorption of doxycycline on GO was studied. At pH 8.0, 82.7% of doxycycline was adsorbed by GO, and adding 2 µM aptamer desorbed 55.4% of doxycycline. With GO, the signal increase was comparable from pH 6 to 8, whereas without GO, the increase was significantly lower at pH 8. Under optimized condition, a detection limit of 1.6 nM doxycycline was achieved at pH 8.0 in the presence of GO, whereas without GO, the detection limit was 18.9 nM. This is an interesting example of the use of nanomaterials to enhance the performance of aptamer-based biosensors.
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Affiliation(s)
- Yang Zhou
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
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Zhu Y, Wu J, Zhou Q. Functional DNA sensors integrated with nucleic acid signal amplification strategies for non-nucleic acid targets detection. Biosens Bioelectron 2023; 230:115282. [PMID: 37028002 DOI: 10.1016/j.bios.2023.115282] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 03/27/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023]
Abstract
In addition to carrying and transmitting genetic material, some DNA molecules have specific binding ability or catalytic function. DNA with this special function is collectively referred to as functional DNA (fDNA), such as aptamer, DNAzyme and so on. fDNA has the advantages of simple synthetic process, low cost and low toxicity. It also has high chemical stability, recognition specificity and biocompatibility. In recent years, fDNA biosensors have been widely investigated as signal recognition elements and signal transduction elements for the detection of non-nucleic acid targets. However, the main problem of fDNA sensors is their limited sensitivity to trace targets, especially when the affinity of fDNA to the targets is low. To further improve the sensitivity, various nucleic acid signal amplification strategies (NASAS) are explored to improve the limit of detection of fDNA. In this review, we will introduce four NASAS (hybridization chain reaction, entropy-driven catalysis, rolling circle amplification, CRISPR/Cas system) and the corresponding design principles. The principle and application of these fDNA sensors integrated with signal amplification strategies for detection of non-nucleic acid targets are summarized. Finally, the main challenges and application prospects of NASAS integrated fDNA biosensing system are discussed.
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10
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Stimulus-responsive hydrogels: A potent tool for biosensing in food safety. Trends Food Sci Technol 2023. [DOI: 10.1016/j.tifs.2022.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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11
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Wang Z, Chen R, Yang S, Li S, Gao Z. Design and application of stimuli-responsive DNA hydrogels: A review. Mater Today Bio 2022; 16:100430. [PMID: 36157049 PMCID: PMC9493390 DOI: 10.1016/j.mtbio.2022.100430] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/11/2022] [Accepted: 09/13/2022] [Indexed: 11/25/2022] Open
Abstract
Deoxyribonucleic acid (DNA) hydrogels combine the properties of DNAs and hydrogels, and adding functionalized DNAs is key to the wide application of DNA hydrogels. In stimuli-responsive DNA hydrogels, the DNA transcends its application in genetics and bridges the gap between different fields. Specifically, the DNA acts as both an information carrier and a bridge in constructing DNA hydrogels. The programmability and biocompatibility of DNA hydrogel make it change macroscopically in response to a variety of stimuli. In order to meet the needs of different scenarios, DNA hydrogels were also designed into microcapsules, beads, membranes, microneedle patches, and other forms. In this study, the stimuli were classified into single biological and non-biological stimuli and composite stimuli. Stimuli-responsive DNA hydrogels from the past five years were summarized, including but not limited to their design and application, in particular logic gate pathways and signal amplification mechanisms. Stimuli-responsive DNA hydrogels have been applied to fields such as sensing, nanorobots, information carriers, controlled drug release, and disease treatment. Different potential applications and the developmental pro-spects of stimuli-responsive DNA hydrogels were discussed.
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Affiliation(s)
- Zhiguang Wang
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Institute of Environmental and Operational Medicine, Tianjin, 300050, China
- College of Chemistry and Materials Science, Shanghai Normal University, Shanghai, 200234, China
| | - Ruipeng Chen
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Shiping Yang
- College of Chemistry and Materials Science, Shanghai Normal University, Shanghai, 200234, China
| | - Shuang Li
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Zhixian Gao
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Institute of Environmental and Operational Medicine, Tianjin, 300050, China
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12
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Zhang P, Qin K, Lopez A, Li Z, Liu J. General Label-Free Fluorescent Aptamer Binding Assay Using Cationic Conjugated Polymers. Anal Chem 2022; 94:15456-15463. [DOI: 10.1021/acs.analchem.2c03564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Pengbo Zhang
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Ke Qin
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Anand Lopez
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Zhengping Li
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
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13
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Zhao Y, Gao B, Sun P, Liu J, Liu J. Metal and pH-Dependent Aptamer Binding of Tetracyclines Enabling Highly Sensitive Fluorescence Sensing. BIOSENSORS 2022; 12:bios12090717. [PMID: 36140102 PMCID: PMC9496453 DOI: 10.3390/bios12090717] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/28/2022] [Accepted: 08/30/2022] [Indexed: 11/16/2022]
Abstract
Tetracyclines are a widely used group of antibiotics, many of which are currently only used in veterinary medicine and animal husbandry due to their adverse side effects. For the detection of tetracyclines, we previously reported a DNA aptamer named OTC5 that binds to tetracycline, oxytetracycline, and doxycycline with similar KD’s of ~100 nM. Tetracyclines have an intrinsic fluorescence that is enhanced upon binding to OTC5, which can be used as a label-free and dye-free sensor. In this work, the effect of pH and metal ions on the sensor was studied. Mg2+ ions are required for the binding of OTC5 to its target with an optimal concentration of 2 mM. Other metal ions including Ca2+ and Zn2+ can also support aptamer binding. Although Mn2+ barely supported binding, the binding can be rescued by Mg2+. ITC studies confirmed that OTC5 had a KD of 0.2 μM at a pH of 6.0 and 0.03 μM at a pH of 8.3. Lower pH (pH 6) showed better fluorescence enhancement than higher pH (pH 8.3), although a pH of 6.0 had slightly higher KD values. Under optimized sensing conditions, sensors with limit of detections (LODs) of 0.1–0.7 nM were achieved for tetracycline, oxytetracycline, and doxycycline, which are up to 50-fold lower than previously reported. Milk samples were also tested yielding an LOD of 16 nM oxytetracycline at a pH of 6.0.
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14
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Cao D, Xie Y, Song J. DNA Hydrogels in the Perspective of Mechanical Properties. Macromol Rapid Commun 2022; 43:e2200281. [PMID: 35575627 DOI: 10.1002/marc.202200281] [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: 04/25/2022] [Indexed: 11/10/2022]
Abstract
Tailoring the mechanical properties has always been a key to the field of hydrogels in terms of different applications. Particularly, deoxyribonucleic acid (DNA) hydrogels offer an unambiguous way to precisely tune the mechanical properties, largely on account of their programmable sequences, abundant responding toolbox, and various ligation approaches. In this review, DNA hydrogels from the perspective of mechanical properties, from synthetic standpoint to different applications are introduced. The relationship between the structure and their mechanical properties in DNA hydrogels and the methods of regulating the mechanical properties of DNA hydrogels are specifically summarized. Furthermore, several recent applications of DNA hydrogels in relation to their mechanical properties are discussed. Benefiting from the tunability and flexibility, rational design of mechanical properties in DNA hydrogels provided unheralded interest from fundamental science to extensive applications. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Dengjie Cao
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yujie Xie
- School of Medicine, Shanghai University, Shanghai, 200444, China
| | - Jie Song
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.,Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, The Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, P. R. China
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Zhang Y, Wang Y, Chen L, Zheng J, Fan X, Xu X, Zhou G, Ullah N, Feng X. An injectable antibacterial chitosan-based cryogel with high absorbency and rapid shape recovery for noncompressible hemorrhage and wound healing. Biomaterials 2022; 285:121546. [DOI: 10.1016/j.biomaterials.2022.121546] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 04/10/2022] [Accepted: 04/22/2022] [Indexed: 12/12/2022]
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Xiong H, Liu L, Wang Y, Jiang H, Wang X. Engineered Aptamer-Organic Amphiphile Self-Assemblies for Biomedical Applications: Progress and Challenges. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2104341. [PMID: 34622570 DOI: 10.1002/smll.202104341] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/21/2021] [Indexed: 06/13/2023]
Abstract
Currently, nucleic acid aptamers are exploited as robust targeting ligands in the biomedical field, due to their specific molecular recognition, little immunogenicity, low cost, ect. Thanks to the facile chemical modification and high hydrophilicity, aptamers can be site-specifically linked with hydrophobic moieties to prepare aptamer-organic amphiphiles (AOAs), which spontaneously assemble into aptamer-organic amphiphile self-assemblies (AOASs). These polyvalent self-assemblies feature with enhanced target-binding ability, increased resistance to nuclease, and efficient cargo-loading, making them powerful platforms for bioapplications, including targeted drug delivery, cell-based cancer therapy, biosensing, and bioimaging. Besides, the morphology of AOASs can be elaborately manipulated for smarter biomedical functions, by regulating the hydrophilicity/hydrophobicity ratio of AOAs. Benefiting from the boom in DNA synthesis technology and nanotechnology, various types of AOASs, including aptamer-polymer amphiphile self-assemblies, aptamer-lipid amphiphile self-assemblies, aptamer-cell self-assemblies, ect, have been constructed with great biomedical potential. Particularly, stimuli-responsive AOASs with transformable structure can realize site-specific drug release, enhanced tumor penetration, and specific target molecule detection. Herein, the general synthesis methods of oligonucleotide-organic amphiphiles are firstly summarized. Then recent progress in different types of AOASs for bioapplications and strategies for morphology control are systematically reviewed. The present challenges and future perspectives of this field are also discussed.
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Affiliation(s)
- Hongjie Xiong
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Liu Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Yihan Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Hui Jiang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Xuemei Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
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