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Chen K, Zhu L, Li J, Zhang Y, Yu Y, Wang X, Wei W, Huang K, Xu W. High-content tailoring strategy to improve the multifunctionality of functional nucleic acids. Biosens Bioelectron 2024; 261:116494. [PMID: 38901394 DOI: 10.1016/j.bios.2024.116494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 05/30/2024] [Accepted: 06/11/2024] [Indexed: 06/22/2024]
Abstract
Functional nucleic acids (FNAs) have attracted increasing attention in recent years due to their diverse physiological functions. The understanding of their conformational recognition mechanisms has advanced through nucleic acid tailoring strategies and sequence optimization. With the development of the FNA tailoring techniques, they have become a methodological guide for nucleic acid repurposing. Therefore, it is necessary to systematize the relationship between FNA tailoring strategies and the development of nucleic acid multifunctionality. This review systematically categorizes eight types of FNA multifunctionality, and introduces the traditional FNA tailoring strategy from five aspects, including deletion, substitution, splitting, fusion and elongation. Based on the current state of FNA modification, a new generation of FNA tailoring strategy, called the high-content tailoring strategy, was unprecedentedly proposed to improve FNA multifunctionality. In addition, the multiple applications of rational tailoring-driven FNA performance enhancement in various fields were comprehensively summarized. The limitations and potential of FNA tailoring and repurposing in the future are also explored in this review. In summary, this review introduces a novel tailoring theory, systematically summarizes eight FNA performance enhancements, and provides a systematic overview of tailoring applications across all categories of FNAs. The high-content tailoring strategy is expected to expand the application scenarios of FNAs in biosensing, biomedicine and materials science, thus promoting the synergistic development of various fields.
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Affiliation(s)
- Keren Chen
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Longjiao Zhu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Jie Li
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Yangzi Zhang
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Yongxia Yu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Xiaofu Wang
- Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Wei Wei
- Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Kunlun Huang
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Wentao Xu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China; Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China.
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2
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Fan Y, Li J, Jiang M, Zhao J, He L, Wang Y, Shao F. Self-assembly of DNA G-quadruplex nanowires: a study of the mechanism towards micrometer length. NANOSCALE 2024. [PMID: 39235476 DOI: 10.1039/d4nr02696a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/06/2024]
Abstract
The G-quadruplex (GQ) formed by guanine-rich DNA strands exhibits superior thermal stability and electric properties, which have generated substantial interest in applying GQ DNA to bioelectric interfaces. However, single G-wires formed by GQs have not yet surpassed the μm length due to the lack of an optimal assembly protocol and understanding of assembly mechanisms that limit application. Herein, we optimized a self-assembly protocol for a short 4-nt oligonucleotide (dG4) to achieve micrometer lengths of G-wires, including the buffer composition, incubation process and surface assembly. Furthermore, both theoretical modeling and chemical modifications were applied to unveil the atomic-level detail of GQ monomer interfaces and indicated that the assembly process follows a stepwise mechanism from nucleation to grow into oligomers and nanowires.
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Affiliation(s)
- Yiqi Fan
- National Key Laboratory of Biobased Transportation Fuel Technology, Zhejiang University-University of Illinois, Urbana-Champaign Institute, Zhejiang University, Haining, 314400, P.R. China
- Department of Chemistry, Zhejiang University, Hangzhou, 310000, P.R. China
| | - Jiachen Li
- College of Life Sciences, Zhejiang University, Hangzhou, 310000, P.R. China
| | - Min Jiang
- National Key Laboratory of Biobased Transportation Fuel Technology, Zhejiang University-University of Illinois, Urbana-Champaign Institute, Zhejiang University, Haining, 314400, P.R. China
| | - Jing Zhao
- National Key Laboratory of Biobased Transportation Fuel Technology, Zhejiang University-University of Illinois, Urbana-Champaign Institute, Zhejiang University, Haining, 314400, P.R. China
- Department of Chemistry, Zhejiang University, Hangzhou, 310000, P.R. China
| | - Lei He
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing, 100029, P.R. China
| | - Yong Wang
- College of Life Sciences, Zhejiang University, Hangzhou, 310000, P.R. China
| | - Fangwei Shao
- National Key Laboratory of Biobased Transportation Fuel Technology, Zhejiang University-University of Illinois, Urbana-Champaign Institute, Zhejiang University, Haining, 314400, P.R. China
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3
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Yu F, Li X, Sheng C, Li L. DNA Nanotechnology Targeting Mitochondria: From Subcellular Molecular Imaging to Tailor-Made Therapeutics. Angew Chem Int Ed Engl 2024; 63:e202409351. [PMID: 38872505 DOI: 10.1002/anie.202409351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 06/07/2024] [Accepted: 06/14/2024] [Indexed: 06/15/2024]
Abstract
Mitochondria, one of the most important organelles, represent a crucial subcellular target for fundamental research and biomedical applications. Despite significant advances in the design of DNA nanotechnologies for a variety of bio-applications, the dearth of strategies that enable mitochondria targeting for subcellular molecular imaging and therapy remains an outstanding challenge in this field. In this Minireview, we summarize the recent progresses on the emerging design and application of DNA nanotechnology for mitochondria-targeted molecular imaging and tumor treatment. We first highlight the engineering of mitochondria-localized DNA nanosensors for in situ detection and imaging of diverse key molecules that are essential to maintain mitochondrial functions, including mitochondrial DNA and microRNA, enzymes, small molecules, and metal ions. Then, we compile the developments of DNA nanotechnologies for mitochondria-targeted anti-tumor therapy, including modularly designed DNA nanodevices for subcellular delivery of therapeutic agents, and programmed DNA assembly for mitochondrial interference. We will place an emphasis on clarification of the chemical principles of how DNA nanobiotechnology can be designed to target mitochondria for various biomedical applications. Finally, the remaining challenges and future directions in this emerging field will be discussed, hoping to inspire further development of advanced DNA toolkits for both academic and clinical research regarding mitochondria.
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Affiliation(s)
- Fangzhi Yu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, China, College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiangfei Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, China, College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chuangui Sheng
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, China, College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lele Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, China, College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
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4
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Dong W, Yan W, Xu Y, Shang X, Wang W, Qiu J, Wang B, Wang H, Zhang Z, Zhao T. Multiplex Profiling of miR-122 for Preclinical and Clinical Evaluation of Drug-Induced Liver Injury by a Full-Scale Platform. ACS NANO 2024. [PMID: 39195723 DOI: 10.1021/acsnano.4c05081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/29/2024]
Abstract
Diagnostic and monitoring for drug-induced liver injury (DILI) predominantly rely on serum aminotransferases. However, owing to their widespread expression across multiple organs, a significant challenge emerges from the absence of reliable biomarkers for DILI diagnosis. Herein, we introduce a concept for DILI detection, circumventing the nonspecific elevation and delayed release of aminotransferases and then straightforwardly focusing on the core feature of DILI, abnormal gene expression caused by drug overdose. The developed full-scale platform integrates the properties of spherical nucleic acids with elaborately designed fluorescence in situ hybridization sequences, enabling the sensitive and specific profiling of drug-overdosed miR-122 expression alterations across molecular, cellular, organismal, and clinical scales and effectively bypassing the phenotypic features of disease. Furthermore, the diagnostic efficacies of serum and total RNA extracted from both mouse and human blood samples for DILI diagnosis were analyzed using the receiver operating characteristic curve and principal component analysis. We anticipate that this universal platform holds potential in facilitating DILI diagnosis, therapeutic evaluation, and prognosis.
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Affiliation(s)
- Wuqi Dong
- School of Basic Medical Sciences, Biopharmaceutical Research Institute, Anhui Provincial Institute of Translational Medicine, Anhui Medical University, Hefei, Anhui 230032, China
| | - Weizhen Yan
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yuechen Xu
- The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230032, China
| | - Xiaofei Shang
- School of Basic Medical Sciences, Biopharmaceutical Research Institute, Anhui Provincial Institute of Translational Medicine, Anhui Medical University, Hefei, Anhui 230032, China
| | - Wanrong Wang
- The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230032, China
| | - Jie Qiu
- School of Basic Medical Sciences, Biopharmaceutical Research Institute, Anhui Provincial Institute of Translational Medicine, Anhui Medical University, Hefei, Anhui 230032, China
| | - Baoxin Wang
- School of Basic Medical Sciences, Biopharmaceutical Research Institute, Anhui Provincial Institute of Translational Medicine, Anhui Medical University, Hefei, Anhui 230032, China
| | - Hua Wang
- The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230032, China
| | - Zhongping Zhang
- School of Chemistry and Chemical Engineering, Anhui University, Hefei, Anhui 230601, China
| | - Tingting Zhao
- School of Basic Medical Sciences, Biopharmaceutical Research Institute, Anhui Provincial Institute of Translational Medicine, Anhui Medical University, Hefei, Anhui 230032, China
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Dong Z, Su R, Fu Y, Wang Y, Chang L. Recent Progress in DNA Biosensors for Detecting Biomarkers in Living Cells. ACS Biomater Sci Eng 2024. [PMID: 39143919 DOI: 10.1021/acsbiomaterials.4c01339] [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: 08/16/2024]
Abstract
Analysis of biomarkers in living cells is crucial for deciphering the dynamics of cells as well as for precise diagnosis of diseases. DNA biosensors employ DNA sequences as probes to offer insights into living cells, and drive progress in disease diagnosis and drug development. In this review, we present recent advances in DNA biosensors for detecting biomarkers in living cells. The basic structural components of DNA biosensors and the signal output method are presented. The strategies of DNA biosensors crossing the cell membrane are also described, including coincubation, nanocarriers, and nanoelectroporation techniques. Based on biomarker categorization, we detail recent applications of DNA biosensors for detecting small molecules, RNAs, proteins, and integrated targets in living cells. Furthermore, the future development directions of DNA biosensors are summarized to encourage further research in this growing field.
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Affiliation(s)
- Zaizai Dong
- School of Engineering Medicine, Beihang University, Beijing 100191, China
| | - Rongtai Su
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Yao Fu
- School of Engineering Medicine, Beihang University, Beijing 100191, China
| | - Yupei Wang
- Gansu Provincial Maternity and Child-Care Hospital (Gansu Provincial Central Hospital), Lanzhou 730050, China
| | - Lingqian Chang
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
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Wang W, Wang W, Chen Y, Lin M, Chen YR, Zeng R, He T, Shen Z, Wu ZS. Superlarge, Rigidified DNA Tetrahedron with a Y-Shaped Backbone for Organizing Biomolecules Spatially and Maintaining Their Full Bioactivity. ACS NANO 2024; 18:18257-18281. [PMID: 38973121 DOI: 10.1021/acsnano.3c13189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
A major impediment to the clinical translation of DNA tiling nanostructures is a technical bottleneck for the programmable assembly of DNA architectures with well-defined local geometry due to the inability to achieve both sufficient structural rigidity and a large framework. In this work, a Y-backbone was inserted into each face to construct a superlarge, sufficiently rigidified tetrahedral DNA nanostructure (called RDT) with extremely high efficiency. In RDT, the spatial size increased by 6.86-fold, and the structural rigidity was enhanced at least 4-fold, contributing to an ∼350-fold improvement in the resistance to nucleolytic degradation even without a protective coating. RDT can be mounted onto an artificial lipid-bilayer membrane with molecular-level precision and well-defined spatial orientation that can be validated using the fluorescence resonance energy transfer (FRET) assay. The spatial orientation of Y-shaped backbone-rigidified RDT is unachievable for conventional DNA polyhedrons and ensures a high level of precision in the geometric positioning of diverse biomolecules with an approximately homogeneous environment. In tests of RDT, surface-confined horseradish peroxidase (HRP) exhibited nearly 100% catalytic activity and targeting aptamer-immobilized gold nanoparticles showed 5.3-fold enhanced cellular internalization. Significantly, RDT exhibited a 27.5-fold enhanced structural stability in a bodily environment and did not induce detectable systemic toxicity.
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Affiliation(s)
- Weijun Wang
- Key Laboratory of Laboratory Medicine of the Ministry of Education, Zhejiang Provincial Key Laboratory of Medicine Genetics, School of Laboratory Medicine and Life Sciences, Institute of Functional Nucleic Acids and Personalized Cancer Theranostics, Wenzhou Medical University, Wenzhou 325035, China
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
- College of Chemistry and Food Science, Nanchang Normal University, Nanchang 330032, China
| | - Wenqing Wang
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Yaxin Chen
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Mengling Lin
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Yan-Ru Chen
- Key Laboratory of Laboratory Medicine of the Ministry of Education, Zhejiang Provincial Key Laboratory of Medicine Genetics, School of Laboratory Medicine and Life Sciences, Institute of Functional Nucleic Acids and Personalized Cancer Theranostics, Wenzhou Medical University, Wenzhou 325035, China
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Ruijin Zeng
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Tenghang He
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Zhifa Shen
- Key Laboratory of Laboratory Medicine of the Ministry of Education, Zhejiang Provincial Key Laboratory of Medicine Genetics, School of Laboratory Medicine and Life Sciences, Institute of Functional Nucleic Acids and Personalized Cancer Theranostics, Wenzhou Medical University, Wenzhou 325035, China
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Zai-Sheng Wu
- Key Laboratory of Laboratory Medicine of the Ministry of Education, Zhejiang Provincial Key Laboratory of Medicine Genetics, School of Laboratory Medicine and Life Sciences, Institute of Functional Nucleic Acids and Personalized Cancer Theranostics, Wenzhou Medical University, Wenzhou 325035, China
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
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Liu Y, Fan Z, Xiang XW, Tao X, Xia X, Shi Q, Lu Y, Lu J, Gu H, Liu YJ, Liu B. Engineering of Multivalent Membrane-Anchored DNA Frameworks for Precise Profiling of Variable Membrane Permeability During Reversible Electroporation. SMALL METHODS 2024; 8:e2301198. [PMID: 38152955 DOI: 10.1002/smtd.202301198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/08/2023] [Indexed: 12/29/2023]
Abstract
Electroporation techniques have emerged as attractive tools for intracellular delivery, rendering promising prospects towards clinical therapies. Transient disruption of membrane permeability is the critical process for efficient electroporation-based cargo delivery. However, smart nanotools for precise characterization of transient membrane changes induced by strong electric pulses are extremely limited. Herein, multivalent membrane-anchored fluorescent nanoprobes (MMFNPs) that take advantages of flexible functionalization and spatial arrangement of DNA frameworks are developed for in situ evaluation of electric field-induced membrane permeability during reversible electroporation . Single-molecule fluorescence imaging techniques are adopted to precisely verify the excellent analytical performance of the engineered MMFNPs. Benefited from tight membrane anchoring and sensitive adenosine triphosphate (ATP) profiling, varying degrees of membrane disturbances are visually exhibited under different intensities of the microsecond pulse electric field (µsPEF). Significantly, the dynamic process of membrane repair during reversible electroporation is well demonstrated via ATP fluctuations monitored by the designed MMFNPs. Furthermore, molecular dynamics (MD) simulations are performed for accurate verification of electroporation-driven dynamic cargo entry via membrane nanopores. This work provides an avenue for effectively capturing transient fluctuations of membrane permeability under external stimuli, offering valuable guidance for developing efficient and safe electroporation-driven delivery strategies for clinical diagnosis and therapeutics.
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Affiliation(s)
- Yixin Liu
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Lab of Molecular Engineering of Polymers, Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Zihui Fan
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Lab of Molecular Engineering of Polymers, Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Xiao-Wei Xiang
- Westlake Laboratory of Life Sciences and Biomedicine, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310030, China
| | - Xiaonan Tao
- School of Information Science and Technology, Fudan University, Shanghai, 200032, China
| | - Xinwei Xia
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Lab of Molecular Engineering of Polymers, Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Qian Shi
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Lab of Molecular Engineering of Polymers, Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Yanwei Lu
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Lab of Molecular Engineering of Polymers, Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Jiayin Lu
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Lab of Molecular Engineering of Polymers, Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Hongzhou Gu
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Lab of Molecular Engineering of Polymers, Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Yan-Jun Liu
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Lab of Molecular Engineering of Polymers, Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Baohong Liu
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Lab of Molecular Engineering of Polymers, Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
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Qi C, Li W, Luo Y, Ni S, Ji M, Wang Z, Zhang T, Bai X, Tang J, Yuan B, Liu K. Selective inhibition of c-Met signaling pathways with a bispecific DNA nanoconnector for the targeted therapy of cancer. Int J Biol Macromol 2024; 273:133134. [PMID: 38876234 DOI: 10.1016/j.ijbiomac.2024.133134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 06/11/2024] [Accepted: 06/11/2024] [Indexed: 06/16/2024]
Abstract
Hepatocyte growth factor receptor (c-Met) is a suitable molecular target for the targeted therapy of cancer. Novel c-Met-targeting drugs need to be developed because conventional small-molecule inhibitors and antibodies of c-Met have some limitations. To synthesize such drugs, we developed a bispecific DNA nanoconnector (STPA) to inhibit c-Met function. STPA was constructed by using DNA triangular prism as a scaffold and aptamers as binding molecules. After c-Met-specific SL1 and nucleolin-specific AS1411 aptamers were integrated with STPA, STPA could bind to c-Met and nucleolin on the cell membrane. This led to the formation of the c-Met/STPA/nucleolin complex, which in turn blocked c-Met activation. In vitro experiments showed that STPA could not only inhibit the c-Met signaling pathways but also facilitate c-Met degradation through lysosomes. STPA also inhibited c-Met-promoted cell migration, invasion, and proliferation. The results of in vivo experiments showed that STPA could specifically target to tumor site in xenograft mouse model, and inhibit tumor growth with low toxicity by downregulating c-Met pathways. This study provided a novel and simple strategy to develop c-Met-targeting drugs for the targeted therapy of cancer.
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Affiliation(s)
- Cuihua Qi
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Wei Li
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Yanchao Luo
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Shanshan Ni
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Mengmeng Ji
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Zhaoting Wang
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Tianlu Zhang
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Xue Bai
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Jinlu Tang
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou 450001, Henan, China.
| | - Baoyin Yuan
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China; Henan Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou 450000, Henan, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou 450001, Henan, China.
| | - Kangdong Liu
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China; Henan Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou 450000, Henan, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou 450001, Henan, China; China-US (Henan) Hormel Cancer Institute, Zhengzhou 450003, Henan, China; Cancer Chemoprevention International Collaboration Laboratory, Zhengzhou 450000, Henan, China
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9
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Reiber T, Hübner O, Dose C, Yushchenko DA, Resch-Genger U. Fluorophore multimerization on a PEG backbone as a concept for signal amplification and lifetime modulation. Sci Rep 2024; 14:11882. [PMID: 38789582 PMCID: PMC11126734 DOI: 10.1038/s41598-024-62548-4] [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: 03/22/2024] [Accepted: 05/17/2024] [Indexed: 05/26/2024] Open
Abstract
Fluorescent labels have strongly contributed to many advancements in bioanalysis, molecular biology, molecular imaging, and medical diagnostics. Despite a large toolbox of molecular and nanoscale fluorophores to choose from, there is still a need for brighter labels, e.g., for flow cytometry and fluorescence microscopy, that are preferably of molecular nature. This requires versatile concepts for fluorophore multimerization, which involves the shielding of dyes from other chromophores and possible quenchers in their neighborhood. In addition, to increase the number of readout parameters for fluorescence microscopy and eventually also flow cytometry, control and tuning of the labels' fluorescence lifetimes is desired. Searching for bright multi-chromophoric or multimeric labels, we developed PEGylated dyes bearing functional groups for their bioconjugation and explored their spectroscopic properties and photostability in comparison to those of the respective monomeric dyes for two exemplarily chosen fluorophores excitable at 488 nm. Subsequently, these dyes were conjugated with anti-CD4 and anti-CD8 immunoglobulins to obtain fluorescent conjugates suitable for the labeling of cells and beads. Finally, the suitability of these novel labels for fluorescence lifetime imaging and target discrimination based upon lifetime measurements was assessed. Based upon the results of our spectroscopic studies including measurements of fluorescence quantum yields (QY) and fluorescence decay kinetics we could demonstrate the absence of significant dye-dye interactions and self-quenching in these multimeric labels. Moreover, in a first fluorescence lifetime imaging (FLIM) study, we could show the future potential of this multimerization concept for lifetime discrimination and multiplexing.
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Affiliation(s)
- Thorge Reiber
- Department of Chemical Biology, Miltenyi Biotec B.V. & Co. KG, Friedrich-Ebert-Straße 68, 51429, Bergisch Gladbach, Germany
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany
| | - Oskar Hübner
- Division Biophotonics, Federal Institute for Materials Research and Testing (BAM), Richard‑Willstaetter‑Str. 11, 12489, Berlin, Germany
| | - Christian Dose
- Department of Chemical Biology, Miltenyi Biotec B.V. & Co. KG, Friedrich-Ebert-Straße 68, 51429, Bergisch Gladbach, Germany
| | - Dmytro A Yushchenko
- Department of Chemical Biology, Miltenyi Biotec B.V. & Co. KG, Friedrich-Ebert-Straße 68, 51429, Bergisch Gladbach, Germany.
| | - Ute Resch-Genger
- Division Biophotonics, Federal Institute for Materials Research and Testing (BAM), Richard‑Willstaetter‑Str. 11, 12489, Berlin, Germany.
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10
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Quan K, Li X, Deng J, Chen W, Zou Z, Chen K, Wu L, Liu J, Qing Z. Pt-Decorated Gold Nanoflares for High-Fidelity Phototheranostics: Reducing Side-Effects and Enhancing Cytotoxicity toward Target Cells. Angew Chem Int Ed Engl 2024; 63:e202402881. [PMID: 38433093 DOI: 10.1002/anie.202402881] [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: 02/08/2024] [Revised: 03/01/2024] [Accepted: 03/01/2024] [Indexed: 03/05/2024]
Abstract
Functionalized with the Au-S bond, gold nanoflares have emerged as promising candidates for theranostics. However, the presence of intracellular abundantly biothiols compromises the conventional Au-S bond, leading to the unintended release of cargoes and associated side-effects on non-target cells. Additionally, the hypoxic microenvironment in diseased regions limits treatment efficacy, especially in photodynamic therapy. To address these challenges, high-fidelity photodynamic nanoflares constructed on Pt-coated gold nanoparticles (Au@Pt PDNF) were communicated to avoid false-positive therapeutic signals and side-effects caused by biothiol perturbation. Compared with conventional photodynamic gold nanoflares (AuNP PDNF), the Au@Pt PDNF were selectively activated by cancer biomarkers and exhibited high-fidelity phototheranostics while reducing side-effects. Furthermore, the ultrathin Pt-shell catalysis was confirmed to generate oxygen which alleviated hypoxia-related photodynamic resistance and enhanced the antitumor effect. This design might open a new venue to advance theranostics performance and is adaptable to other theranostic nanomaterials by simply adding a Pt shell.
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Affiliation(s)
- Ke Quan
- Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Chemical Engineering, and School of Food and Bioengineering, Changsha University of Science and Technology, Changsha, 410114, China
| | - Xiaoyuan Li
- Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Chemical Engineering, and School of Food and Bioengineering, Changsha University of Science and Technology, Changsha, 410114, China
| | - Jiaqi Deng
- Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Chemical Engineering, and School of Food and Bioengineering, Changsha University of Science and Technology, Changsha, 410114, China
| | - Weiju Chen
- Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, 410081, China
| | - Zhen Zou
- Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, 410081, China
| | - Kun Chen
- Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Chemical Engineering, and School of Food and Bioengineering, Changsha University of Science and Technology, Changsha, 410114, China
| | - Linlin Wu
- Department of Oncology, Tengzhou Central People's Hospital Affiliated Xuzhou Medical University, Zaozhuang, Tengzhou, 277500, China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - Zhihe Qing
- Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Chemical Engineering, and School of Food and Bioengineering, Changsha University of Science and Technology, Changsha, 410114, China
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11
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Xi Q, Wang SY, Deng XB, Zhang CH. Catalytic Hairpin Assembly-Based Self-Ratiometric Gel Electrophoresis Detection Platform for Reliable Nucleic Acid Analysis. BIOSENSORS 2024; 14:232. [PMID: 38785706 PMCID: PMC11118829 DOI: 10.3390/bios14050232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 04/30/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024]
Abstract
The development of gel electrophoresis-based biodetection assays for point-of-care analysis are highly demanding. In this work, we proposed a ratiometric gel electrophoresis-based biosensing platform by employing catalytic hairpin assembly (CHA) process functions as both the signal output and the signal amplification module. Two types of nucleic acids, DNA and miRNA, are chosen for demonstration. The proposed strategy indeed provides a new paradigm for the design of a portable detection platform and may hold great potential for sensitive diagnoses.
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Affiliation(s)
- Qiang Xi
- Hunan Prevention and Treatment Institute for Occupational Diseases, Affiliated Prevention and Treatment Institute for Occupational Diseases of University of South China, Changsha 410007, China; (Q.X.); (S.-Y.W.)
| | - Si-Yi Wang
- Hunan Prevention and Treatment Institute for Occupational Diseases, Affiliated Prevention and Treatment Institute for Occupational Diseases of University of South China, Changsha 410007, China; (Q.X.); (S.-Y.W.)
| | - Xiao-Bing Deng
- Hunan Prevention and Treatment Institute for Occupational Diseases, Affiliated Prevention and Treatment Institute for Occupational Diseases of University of South China, Changsha 410007, China; (Q.X.); (S.-Y.W.)
| | - Chong-Hua Zhang
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China
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12
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Deng J, Liu C, Sun J. DNA-Based Nanomaterials for Analysis of Extracellular Vesicles. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2303092. [PMID: 38016069 DOI: 10.1002/adma.202303092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/21/2023] [Indexed: 11/30/2023]
Abstract
Extracellular vesicles (EVs) are cell-derived nanovesicles comprising a myriad of molecular cargo such as proteins and nucleic acids, playing essential roles in intercellular communication and physiological and pathological processes. EVs have received substantial attention as noninvasive biomarkers for disease diagnosis and prognosis. Owing to their ability to recognize protein and nucleic acid targets, DNA-based nanomaterials with excellent programmability and modifiability provide a promising tool for the sensitive and accurate detection of molecular cargo carried by EVs. In this perspective, recent advancements in EV analysis using a variety of DNA-based nanomaterials are summarized, which can be broadly classified into three categories: linear DNA probes, DNA nanostructures, and hybrid DNA nanomaterials. The design, construction, advantages, and disadvantages of different types of DNA nanomaterials, as well as their performance for detecting EVs are reviewed. The challenges and opportunities in the field of EV analysis by DNA nanomaterials are also discussed.
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Affiliation(s)
- Jinqi Deng
- Beijing Engineering Research Center for BioNanotechnology, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, National Center for Nanoscience and Technology, Beijing, 100190, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chao Liu
- Beijing Engineering Research Center for BioNanotechnology, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, National Center for Nanoscience and Technology, Beijing, 100190, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiashu Sun
- Beijing Engineering Research Center for BioNanotechnology, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, National Center for Nanoscience and Technology, Beijing, 100190, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
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13
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Xue X, Persson H, Ye L. Polydopamine functionalized dendritic fibrous silica nanoparticles as a generic platform for nucleic acid-based biosensing. Mikrochim Acta 2024; 191:180. [PMID: 38443718 PMCID: PMC10914921 DOI: 10.1007/s00604-024-06234-2] [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: 11/06/2023] [Accepted: 02/13/2024] [Indexed: 03/07/2024]
Abstract
Accurate and rapid detection of nucleic acid sequences is of utmost importance in various fields, including disease monitoring, clinical treatment, gene analysis and drug discovery. In this study, we developed a "turn-on" fluorescence biosensor that enables simple and highly efficient detection of nucleic acid biomarkers. Our approach involves the utilization of 6-carboxyfluorescein modified single-stranded DNA (FAM-ssDNA) as molecular recognition element, along with polydopamine-functionalized dendritic fibrous nanosilica (DFNS). FAM-ssDNA serves as both specific molecular recognition element for the target analyte and reporter capable of transducing a detectable signal through Watson-Crick base pairing. The polydopamine-functionalized DFNS (DFNS@DA) exhibits strong binding to FAM-ssDNA via polyvalent metal mediated coordination leading to effective quenching by fluorescence resonance energy transfer. In the presence of a complementary target sequence, FAM-ssDNA forms hybridized structure and detaches from DFNS@DA, which causes an increased fluorescence emission. The analytical system based on FAM-ssDNA and DFNS@DA demonstrates exceptional sensitivity, selectivity, and rapid response for the detection of nucleic acid sequences, leveraging the high adsorption and quenching properties of DFNS@DA. For the first proof of concept, we demonstrated the successful detection of microRNA (miR-21) in cancer cells using the FAM-ssDNA/DFNS@DA system. Our results highlight the promising capabilities of DFNS@DA and nucleic acid-based biosensors, offering a generic and cost-effective solution for the detection of nucleic acid-related biomarkers.
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Affiliation(s)
- Xiaoting Xue
- Division of Pure and Applied Biochemistry, Department of Chemistry, Lund University, 22100, Lund, Sweden
| | - Helena Persson
- Division of Oncology, Department of Clinical Sciences, Lund University Cancer Center, 22381, Lund, Sweden
| | - Lei Ye
- Division of Pure and Applied Biochemistry, Department of Chemistry, Lund University, 22100, Lund, Sweden.
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14
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Zhang F, Yang N, Zhou F, Qiao R, Wan Y, Liu R, Yang S, Gu M, Xu H, Dong X, Wang G. Orthogonally Sequential Activation of Self-Powered DNAzymes Cascade for Reliable Monitoring of mRNA in Living Cells. Adv Healthc Mater 2024; 13:e2303074. [PMID: 38197479 DOI: 10.1002/adhm.202303074] [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: 09/13/2023] [Revised: 12/06/2023] [Indexed: 01/11/2024]
Abstract
Ratiometric imaging of tumor-related mRNA is significant, yet spatiotemporally resolved regulation on the ratiometric signals to avoid non-specific activation in the living cells remains challenging. Herein, orthogonally sequential activation of concatenated DNAzyme circuits is, first, developed for Spatio Temporally regulated Amplified and Ratiometric (STAR) imaging of TK1 mRNA inside living cells with enhanced reliability and accuracy. By virtue of the synthesized CuO/MnO2 nanosheets, orthogonally regulated self-powered DNAzyme circuits are operated precisely in living cells, sequentially activating two-layered DNAzyme cleavage reactions to achieve the two ratiometric signal readouts successively for reliable monitoring of low-abundance mRNA in living cells. It is found that the ratiometric signals can only be derived from mRNA over-expressed tumor cells, also irrespective of probes' delivery concentration. The presented approach could provide new insight into orthogonally regulated ratiometric systems for reliable imaging of specific biomarkers in living cells, benefiting disease precision diagnostics.
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Affiliation(s)
- Fuqiang Zhang
- Anhui Province Key Laboratory of Biomedical Materials and Chemical Measurement, Anhui Province Key Laboratory of Chem-Biosensing, Ministry of Education Key Laboratory of Functional Molecular Solids, College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241002, China
| | - Nan Yang
- Key Laboratory of Flexible Electronics (KLOFE) and Institute of Advanced Materials (IAM), Nanjing Tech University (NanjingTech), Nanjing, 211816, China
| | - Fu Zhou
- Anhui Province Key Laboratory of Biomedical Materials and Chemical Measurement, Anhui Province Key Laboratory of Chem-Biosensing, Ministry of Education Key Laboratory of Functional Molecular Solids, College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241002, China
| | - Ruonan Qiao
- Anhui Province Key Laboratory of Biomedical Materials and Chemical Measurement, Anhui Province Key Laboratory of Chem-Biosensing, Ministry of Education Key Laboratory of Functional Molecular Solids, College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241002, China
| | - Yifei Wan
- Anhui Province Key Laboratory of Biomedical Materials and Chemical Measurement, Anhui Province Key Laboratory of Chem-Biosensing, Ministry of Education Key Laboratory of Functional Molecular Solids, College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241002, China
| | - Rong Liu
- Anhui Province Key Laboratory of Biomedical Materials and Chemical Measurement, Anhui Province Key Laboratory of Chem-Biosensing, Ministry of Education Key Laboratory of Functional Molecular Solids, College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241002, China
| | - Suwan Yang
- Anhui Province Key Laboratory of Biomedical Materials and Chemical Measurement, Anhui Province Key Laboratory of Chem-Biosensing, Ministry of Education Key Laboratory of Functional Molecular Solids, College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241002, China
| | - Mingzheng Gu
- Anhui Province Key Laboratory of Biomedical Materials and Chemical Measurement, Anhui Province Key Laboratory of Chem-Biosensing, Ministry of Education Key Laboratory of Functional Molecular Solids, College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241002, China
| | - Huae Xu
- Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Nanjing, 210009, China
| | - Xiaochen Dong
- Key Laboratory of Flexible Electronics (KLOFE) and Institute of Advanced Materials (IAM), Nanjing Tech University (NanjingTech), Nanjing, 211816, China
- School of Chemistry & Materials Science, Jiangsu Normal University, Xuzhou, 221116, China
| | - Guangfeng Wang
- Anhui Province Key Laboratory of Biomedical Materials and Chemical Measurement, Anhui Province Key Laboratory of Chem-Biosensing, Ministry of Education Key Laboratory of Functional Molecular Solids, College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241002, China
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15
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Li T, Sun M, Xia S, Huang T, Li RT, Li C, Dai Z, Chen JX, Chen J, Jia N. A binary system based DNA tetrahedron and fluorogenic RNA aptamers for highly specific and label-free mRNA imaging in living cells. Talanta 2024; 269:125465. [PMID: 38008022 DOI: 10.1016/j.talanta.2023.125465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/08/2023] [Accepted: 11/21/2023] [Indexed: 11/28/2023]
Abstract
Developing simple, rapid and specific mRNA imaging strategy plays an important role in the early diagnosis of cancer and the new drugs development. Herein, we have established a novel binary system based DNA tetrahedron and fluorogenic RNA aptamers for highly specific and label-free mRNA imaging in living cells. This developed system consisted of tetrahedron probe A (TPA) and tetrahedron probe B (TPB). TK1 mRNA was chosen as the study model. After TPA and TPB enter into the live cells, the TK1 mRNA induces TPA and TPB to approach and activate the fluorescent aptamer, resulting in enhanced fluorescent signal in the presence of small molecules of DFHBI-1T. By this design, the high specificity label-free detection of nucleic acids was achieved with a detection limit of 1.34 nM. Confocal fluorescence imaging experiments had proved that this strategy could effectively distinguish the TK1 mRNA expression level between normal cell and cancer cell. The developed method is expected to provide a new tool for early diagnosis of diseases and new drug development.
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Affiliation(s)
- Tong Li
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, PR China
| | - Mengxu Sun
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, PR China
| | - Suping Xia
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, PR China
| | - Ting Huang
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, PR China
| | - Rong-Tian Li
- Southern University of Science and Technology Hospital, Shenzhen, 518055, PR China
| | - Chunrong Li
- Qiannan Medical College for Nationalities, Duyun, 558000, PR China
| | - Zong Dai
- Key Laboratory of Sensing Technology and Biomedical Instrument of Guangdong Province, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen, 518107, PR China
| | - Jin-Xiang Chen
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, PR China.
| | - Jun Chen
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, PR China; Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Qingdao University of Science and Technology, Qingdao, 266042, PR China.
| | - Nuan Jia
- Southern University of Science and Technology Hospital, Shenzhen, 518055, PR China.
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16
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Chen W, Lai J, Dong S, Chen L, Yang H. Engineering Logic DNA Nanoprobes on Live Cell Membranes for Simultaneously Monitoring Extracellular pH and Precise Drug Delivery. Anal Chem 2024; 96:3462-3469. [PMID: 38358853 DOI: 10.1021/acs.analchem.3c05064] [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: 02/17/2024]
Abstract
It remains a challenge to use a single probe to simultaneously detect extracellular pH fluctuations and specifically recognize cancer cells for precise drug delivery. Here, we engineered a tetrahedral framework nucleic acid-based logic nanoprobe (isgc8-tFNA) on live cell membranes for simultaneously monitoring extracellular pH and targeted drug delivery. Isgc8-tFNA was anchored stably on the cell surface through three cholesterol molecules inserting into the bilayer of the cell membrane. Once responding to the acidic tumor microenvironment, isgc8-tFNA formed an i-motif structure, leading to turn-on FRET signals for monitoring changes of extracellular pH. The nanoprobe exhibited a narrow pH-response window and excellent reversibility. Moreover, the nanoprobe could execute logic identification on the cell surface for precise drug delivery. Only if both in the acidic microenvironment and aptamer-targeting marker are present on the cell surface, the sgc8-ASO-chimera strand, carrying an antisense oligonucleotide drug, was released from the nanoprobe and entered into targeted cancer cells for gene silence. Additionally, the in situ drug release facilitated the uptake of drugs mediated by the interaction between sgc8 aptamer and membrane proteins, resulting in enhanced inhibition of cancer cell migration and proliferation. This logic nanoprobe will provide inspiration for designing smart devices for diagnosis of pH-related diseases and targeted drug delivery.
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Affiliation(s)
- Wanzhen Chen
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou 350108, PR China
| | - Jingjing Lai
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou 350108, PR China
| | - Siqi Dong
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou 350108, PR China
| | - Lanlan Chen
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou 350108, PR China
| | - Huanghao Yang
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou 350108, PR China
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17
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Anil A, Chaskar J, Pawar AB, Tiwari A, Chaskar AC. Recent advances in DNA-based probes for photoacoustic imaging. J Biotechnol 2024; 382:8-20. [PMID: 38211667 DOI: 10.1016/j.jbiotec.2023.12.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 11/29/2023] [Accepted: 12/30/2023] [Indexed: 01/13/2024]
Abstract
Photoacoustic imaging(PAI) is a widely developing imaging modality that has seen tremendous evolvement in the last decade. PAI has gained the upper hand in the imaging field as it takes advantage of optical absorption and ultrasound detection that imparts higher resolution, rich contrast and elevated penetration depth. Unlike other imaging techniques, PAI does not use ionising radiation and is a better, cost-effective and healthier alternative to other imaging techniques. It offers greater specificity than conventional ultrasound imaging with the ability to detect haemoglobin, lipids, water and other light-absorbing chromophores. These properties of PAI have led to its extended applications in the biomedical field in the treatment of diseases such as cancer. This paper reviews how DNA probes have been used in PAI, the various techniques by which it has been modified, and their role in the process. We also focus on different nanocomposites containing DNA having PAI and photothermal therapy(PTT) properties for detection, diagnosis and therapy, its constituents and the role of DNA in it.
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Affiliation(s)
- Anusri Anil
- National Centre for Nanosciences and Nanotechnology, University of Mumbai, Kalina, Mumbai 400098, India
| | - Jyotsna Chaskar
- National Centre for Nanosciences and Nanotechnology, University of Mumbai, Kalina, Mumbai 400098, India
| | - Avinash B Pawar
- Department of Chemistry, Bharati Vidyapeeth (Deemed to be University), Yashwantrao Mohite College of Arts, Science & Commerce, Pune 411038, India
| | - Abhishekh Tiwari
- National Centre for Nanosciences and Nanotechnology, University of Mumbai, Kalina, Mumbai 400098, India.
| | - Atul Changdev Chaskar
- National Centre for Nanosciences and Nanotechnology, University of Mumbai, Kalina, Mumbai 400098, India; Department of Chemistry, Institute of Chemical Technology, Mumbai.
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18
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Sun Z, Ren Y, Zhu W, Xiao Y, Wu H. DNA nanotechnology-based nucleic acid delivery systems for bioimaging and disease treatment. Analyst 2024; 149:599-613. [PMID: 38221846 DOI: 10.1039/d3an01871g] [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: 01/16/2024]
Abstract
Nucleic acids, including DNA and RNA, have been considered as powerful and functional biomaterials owing to their programmable structure, good biocompatibility, and ease of synthesis. However, traditional nucleic acid-based probes have always suffered from inherent limitations, including restricted cell internalization efficiency and structural instability. In recent years, DNA nanotechnology has shown great promise for the applications of bioimaging and drug delivery. The attractive superiorities of DNA nanostructures, such as precise geometries, spatial addressability, and improved biostability, have enabled them to be a novel category of nucleic acid delivery systems for biomedical applications. In this review, we introduce the development of DNA nanotechnology, and highlight recent advances of DNA nanostructure-based delivery systems for cellular imaging and therapeutic applications. Finally, we propose the challenges as well as opportunities for the future development of DNA nanotechnology in biomedical research.
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Affiliation(s)
- Zhaorong Sun
- Department of Pharmacy, The Second Affiliated Hospital of Shandong First Medical University, Tai'an, Shandong, 271000, China
| | - Yingjie Ren
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
| | - Wenjun Zhu
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
| | - Yuliang Xiao
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
- Institute of Brain Science and Brain-inspired Research, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
| | - Han Wu
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
- Institute of Brain Science and Brain-inspired Research, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
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19
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Feng Y, Liu S, Yao Y, Chen M, Liu Q, Chen X. Endogenous mRNA-Powered and Spatial Confinement-Derived DNA Nanomachines for Ultrarapid and Sensitive Imaging of Let-7a. Anal Chem 2024; 96:564-571. [PMID: 38112715 DOI: 10.1021/acs.analchem.3c04837] [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: 12/21/2023]
Abstract
DNA nanostructure-based signal amplifiers offer new tools for imaging intracellular miRNA. However, the inadequate kinetics and susceptibility to enzymatic hydrolysis of these amplifiers, combined with a deficient cofactor concentration within the intracellular environment, significantly undermine their operational efficiency. In this study, we address these challenges by encapsulating a localized target strand displacement assembly (L-SD) and a toehold-exchange endogenous-powered component (R-mRNA) within a framework nucleic acid (FNA) structure─20 bp cubic DNA nanocage (termed RL-cube). This design enables the construction of an endogenous-powered and spatial-confinement DNA nanomachine for ratiometric fluorescence imaging of intracellular miRNA Let-7a. The R-mRNA is designed to be specifically triggered by glyceraldehyde 3-phosphate dehydrogenase (GAPDH), an abundant cellular enzyme, and concurrently releases a component that can recycle the target Let-7a. Meanwhile, L-SD reacts with Let-7a to release a stem-loop beacon, generating a FRET signal. The spatial confinement provided by the framework, combined with the ample intracellular supply of GAPDH, imparts remarkable sensitivity (7.57 pM), selectivity, stability, biocompatibility, and attractive dynamic performance (2240-fold local concentration, approximately four times reaction rate, and a response time of approximately 7 min) to the nanomachine-based biosensor. Consequently, this study introduces a potent sensing approach for detecting nucleic acid biomarkers with significant potential for application in clinical diagnostics and therapeutics.
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Affiliation(s)
- Yinghui Feng
- College of Chemistry and Chemical Engineering, the Hunan Provincial Key Laboratory of Water Environment and Agriculture Product Safety, Central South University, Changsha 410083, Hunan, China
| | - Shenghong Liu
- College of Chemistry and Chemical Engineering, the Hunan Provincial Key Laboratory of Water Environment and Agriculture Product Safety, Central South University, Changsha 410083, Hunan, China
| | - Yao Yao
- College of Chemistry and Chemical Engineering, the Hunan Provincial Key Laboratory of Water Environment and Agriculture Product Safety, Central South University, Changsha 410083, Hunan, China
| | - Miao Chen
- College of Life Science, Central South University, Changsha 410083, Hunan, China
| | - Qi Liu
- College of Chemistry and Chemical Engineering, the Hunan Provincial Key Laboratory of Water Environment and Agriculture Product Safety, Central South University, Changsha 410083, Hunan, China
| | - Xiaoqing Chen
- College of Chemistry and Chemical Engineering, the Hunan Provincial Key Laboratory of Water Environment and Agriculture Product Safety, Central South University, Changsha 410083, Hunan, China
- Xiangjiang Laboratory, Changsha 410205, Hunan, China
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20
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Yang GQ, Cai W, Zhang Z, Wang Y. Progress in Programmable DNA-Aided Self-Assembly of the Master Frame of a Drug Delivery System. ACS APPLIED BIO MATERIALS 2023; 6:5125-5144. [PMID: 38011318 DOI: 10.1021/acsabm.3c00636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Every year cancer causes approximately 10 million deaths globally. Researchers have developed numerous targeted drug delivery systems (DDSs) with nanoparticles, polymers, and liposomes, but these synthetic materials have poor degradability and low biocompatibility. Because DNA nanostructures have good degradability and high biocompatibility, extensive studies have been performed to construct DDSs with DNA nanostructures as the molecular-layer master frame (MF) assembled via programmable DNA-aided self-assembly for targeted drug release. To learn the progressing trend of self-assembly techniques and keep pace with their recent rapid advancements, it is crucial to provide an overview of their past and recent progress. In this review article, we first present the techniques to assemble the MF of a DDS with solely DNA strands; to assemble MFs with one or more additional type of construction materials, e.g., polymers (including RNA and protein), inorganic nanoparticle, or metal ions, in addition to DNA strands; and to assemble the more complex DNA nanocomplexes. It is observed that both the techniques used and the MFs constructed have become increasingly complex and that the DDS constructed has an increasing number of advanced functions. From our focused review, we anticipate that DDSs with the MF of multiple building materials and DNA nanocomplexes will attract an increasing number of researchers' interests. On the basis of knowledge about materials and functional components (e.g., targeting aptamers/peptides/antibodies and stimuli for drug release) obtained from previously performed studies, researchers can combine more materials with DNA strands to assemble more powerful MFs and incorporate more components to endow DDSs with improved or additional properties/functions, thereby subsequently contributing to cancer prevention.
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Affiliation(s)
- Gary Q Yang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P. R. China
| | - Weibin Cai
- School of Chemical and Environmental Engineering, China University of Mining and Technology, Beijing 100083, P. R. China
| | - Zhiwen Zhang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P. R. China
| | - Yujun Wang
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, P. R. China
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21
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Nie W, He K, Zhao Z, Luo X, Liu J. Luminescent Gold Nanoparticles with Discrete DNA Valences for Precisely Controlled Transport at the Subcellular Level. Angew Chem Int Ed Engl 2023; 62:e202314896. [PMID: 37929305 DOI: 10.1002/anie.202314896] [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: 10/04/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/07/2023]
Abstract
Ultrasmall luminescent gold nanoparticles (AuNPs) with excellent capabilities to cross biological barriers offer great promise in designing intelligent model nanomedicines for investigating structure-property relationships at the subcellular level. However, the strict surface controllability of ultrasmall AuNPs is challenging because of their small size. Herein, we report a facile in situ method for precisely controlling DNA aptamer valences on the surface of luminescent AuNPs with emission in the second near-infrared window using a phosphorothioate-modified DNA aptamer, AS1411, as a template. The discrete DNA aptamer number of AS1411-functionalized AuNPs (AS1411-AuNPs, ≈1.8 nm) with emission at 1030 nm was controlled in one aptamer (V1), two aptamers (V2), and four aptamers (V4). It was then discovered that not only the tumor-targeting efficiencies but also the subcellular transport of AS1411-AuNPs were precisely dependent on valences. A slight increase in valence from V1 to V2 increased tumor-targeting efficiencies and resulted in higher nucleus accumulation, whereas a further increase in valence (e.g., V4) significantly increased tumor-targeting efficiencies and led to higher cytomembrane accumulation. These results provide a basis for the strict surface control of nanomedicines in the precise regulation of in vivo transport at the subcellular level and their translation into clinical practice in the future.
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Affiliation(s)
- Wenyan Nie
- Key Laboratory of Functional Molecular Engineering of Guangdong Province, School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, 510640, China
| | - Kui He
- Key Laboratory of Functional Molecular Engineering of Guangdong Province, School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, 510640, China
| | - Zhipeng Zhao
- Key Laboratory of Functional Molecular Engineering of Guangdong Province, School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, 510640, China
| | - Xiaoxi Luo
- Key Laboratory of Functional Molecular Engineering of Guangdong Province, School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, 510640, China
| | - Jinbin Liu
- Key Laboratory of Functional Molecular Engineering of Guangdong Province, School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, 510640, China
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22
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Shang Z, Deng Z, Yi X, Yang M, Nong X, Lin M, Xia F. Construction and bioanalytical applications of poly-adenine-mediated gold nanoparticle-based spherical nucleic acids. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:5564-5576. [PMID: 37861233 DOI: 10.1039/d3ay01618h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Owing to the versatile photophysical and chemical properties, spherical nucleic acids (SNAs) have been widely used in biosensing. However, traditional SNAs are formed by self-assembly of thiolated DNA on the surface of a gold nanoparticle (AuNP), where it is challenging to precisely control the orientation and surface density of DNA. As a new SNA, a polyadenine (polyA)-mediated SNA using the high binding affinity of consecutive adenines to AuNPs shows controllable surface density and configuration of DNA, which can be used to improve the performance of a biosensor. Herein, we first introduce the properties of polyA-mediated SNAs and fundamental principles regarding the polyA-AuNP interaction. Then, we provide an overview of current representative synthesis methods of polyA-mediated SNAs and their advantages and disadvantages. After that, we summarize the application of polyA-mediated SNAs in biosensing based on fluorescence and colorimetric methods, followed by discussion and an outlook of future challenges in this field.
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Affiliation(s)
- Zhiwei Shang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China.
| | - Zixuan Deng
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China.
| | - Xiaoqing Yi
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou 341000, China
| | - Mengyu Yang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China.
| | - Xianliang Nong
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China.
| | - Meihua Lin
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China.
| | - Fan Xia
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China.
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23
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Liu S, Yu CY, Wei H. Spherical nucleic acids-based nanoplatforms for tumor precision medicine and immunotherapy. Mater Today Bio 2023; 22:100750. [PMID: 37545568 PMCID: PMC10400933 DOI: 10.1016/j.mtbio.2023.100750] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/23/2023] [Accepted: 07/26/2023] [Indexed: 08/08/2023] Open
Abstract
Precise diagnosis and treatment of tumors currently still face considerable challenges due to the development of highly degreed heterogeneity in the dynamic evolution of tumors. With the rapid development of genomics, personalized diagnosis and treatment using specific genes may be a robust strategy to break through the bottleneck of traditional tumor treatment. Nevertheless, efficient in vivo gene delivery has been frequently hampered by the inherent defects of vectors and various biological barriers. Encouragingly, spherical nucleic acids (SNAs) with good modularity and programmability are excellent candidates capable of addressing traditional gene transfer-associated issues, which enables SNAs a precision nanoplatform with great potential for diverse biomedical applications. In this regard, there have been detailed reviews of SNA in drug delivery, gene regulation, and dermatology treatment. Still, to the best of our knowledge, there is no published systematic review summarizing the use of SNAs in oncology precision medicine and immunotherapy, which are considered new guidelines for oncology treatment. To this end, we summarized the notable advances in SNAs-based precision therapy and immunotherapy for tumors following a classification standard of different types of precise spatiotemporal control on active species by SNAs. Specifically, we focus on the structural diversity and programmability of SNAs. Finally, the challenges and possible solutions were discussed in the concluding remarks. This review will promote the rational design and development of SNAs for tumor-precise medicine and immunotherapy.
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24
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Zhang Y, Tang H, Zhou J, Zhang L, Wang R. Designing Multimodal ON-OFF Nanoswitches of DNA-Functionalized Nanoparticles by Stimuli-Responsive Polymers. J Phys Chem B 2023; 127:8049-8056. [PMID: 37699428 DOI: 10.1021/acs.jpcb.3c04409] [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: 09/14/2023]
Abstract
It is a challenging task to realize highly reversible ON-OFF nanoswitches over a wide range of temperatures, which emerge as a versatile toolbox for use in nanobiotechnology. Herein, nanoparticles (NPs) bifunctionalized by DNA strands and stimuli-responsive polymers are proposed to construct multimodal ON-OFF nanoswitches by the coarse-grained model. The successful achievement of multimodal ON-OFF nanoswitches for bifunctionalized NPs at lower temperatures is attributed to the synergistic effects of the contraction and expansion configurations of stimuli-responsive polymers, combined with the hybridization-dehybridization event of DNA strands. Importantly, our simulations isolate the conditions of programmable self-assembly of bifunctionalized NPs to realize the multimodal ON-OFF nanoswitches by the changes of temperature and chain rigidity. In addition, it is found that the bifunctionalized NPs in the ON state display anisotropic and patchy features due to an introduction of stimuli-responsive polymers. Our simulation results provide fundamental insights on qualitative predictions of ON/OFF states of DNA-based NPs, which can aid in realizing a set of ON-OFF nanoswitches by the rational design of functionalization molecules.
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Affiliation(s)
- Yixin Zhang
- Department of Polymer Science and Engineering, State Key Laboratory of Coordination Chemistry, Key Laboratory of High Performance Polymer Materials and Technology of Ministry of Education, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Hao Tang
- Department of Polymer Science and Engineering, State Key Laboratory of Coordination Chemistry, Key Laboratory of High Performance Polymer Materials and Technology of Ministry of Education, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Junwei Zhou
- Department of Polymer Science and Engineering, State Key Laboratory of Coordination Chemistry, Key Laboratory of High Performance Polymer Materials and Technology of Ministry of Education, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Liangshun Zhang
- Shanghai Key Laboratory of Advanced Polymeric Materials, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Rong Wang
- Department of Polymer Science and Engineering, State Key Laboratory of Coordination Chemistry, Key Laboratory of High Performance Polymer Materials and Technology of Ministry of Education, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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25
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Nixon SR, Phukan IK, Armijo BJ, Ebrahimi SB, Samanta D. Proximity-Driven DNA Nanosensors. ECS SENSORS PLUS 2023; 2:030601. [PMID: 37424706 PMCID: PMC10323711 DOI: 10.1149/2754-2726/ace068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/12/2023] [Indexed: 07/11/2023]
Abstract
In proximity-driven sensing, interactions between a probe and an analyte produce a detectable signal by causing a change in distance of two probe components or signaling moieties. By interfacing such systems with DNA-based nanostructures, platforms that are highly sensitive, specific, and programmable can be designed. In this Perspective, we delineate the advantages of using DNA building blocks in proximity-driven nanosensors and provide an overview of recent progress in the field, from sensors that rapidly detect pesticides in food to probes that identify rare cancer cells in blood. We also discuss current challenges and identify key areas that need further development.
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Affiliation(s)
- Sara R. Nixon
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, United States of America
| | - Imon Kanta Phukan
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, United States of America
| | - Brian J. Armijo
- Department of Chemistry, Southwestern University, Georgetown, TX 78626, United States of America
| | - Sasha B. Ebrahimi
- Drug Product Development—Steriles, GlaxoSmithKline, Collegeville, PA 19426, United States of America
| | - Devleena Samanta
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, United States of America
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26
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Zhao X, Xu Y, Mi X. Fluorescence intensity coded DNA frameworks based on the FRET effect enable multiplexed miRNA imaging in living cells. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:3051-3056. [PMID: 37313594 DOI: 10.1039/d3ay00578j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
miRNA analysis has played an important role in precise diagnosis, treatment and prognosis of cancer, especially multiplexed miRNA imaging. In this work, a novel fluorescence emission intensity (FEI) encoding strategy was developed based on a tetrahedron DNA framework (TDF) carrier and the FRET effect between Cy3 and Cy5. Six FEI-encoded TDF (FEI-TDF) samples were constructed by tuning the labeling number of Cy3 and Cy5 at the vertexes of the TDF. For fluorescence characterization in vitro, distinct FEIs in the spectra and different colors under ultraviolet (UV) irradiation of FEI-TDF samples were observed. By dividing the ranges of FEIs of samples, the stability of FEIs was highly improved. Based on the ranges of FEIs in each sample, five codes with good discrimination were finally developed. Before the application of intracellular imaging, the excellent biocompatibility of the TDF carrier was proved by CCK-8 assay. The barcode probes based on samples 12, 21 and 11 were designed as example models to realize multiplexed imaging of miRNA-16, miRNA-21 and miRNA-10b in MCF-7 cells with obviously different fluorescence merged colors. FEI-TDFs provide a new research perspective for the development of fluorescence multiplexing strategies in the future.
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Affiliation(s)
- Xiaoshuang Zhao
- Key Laboratory of Functional Materials for Informatics, Shanghai Institute of Microsystems and Information Technology, Chinese Academy of Science, Shanghai 200050, China.
- University of Chinese Academy of Science, Beijing 100049, China
| | - Yi Xu
- Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai 201210, China.
| | - Xianqiang Mi
- Key Laboratory of Functional Materials for Informatics, Shanghai Institute of Microsystems and Information Technology, Chinese Academy of Science, Shanghai 200050, China.
- Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai 201210, China.
- University of Chinese Academy of Science, Beijing 100049, China
- Research Center for Sensing Materials and Devices Zhejiang Lab, Hangzhou, Zhejiang, 311121, China
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27
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Li W, Zhang P, Liu C, Xu Y, Gan Z, Kang L, Hou Y. Oncogene-targeting nanoprobes for early imaging detection of tumor. J Nanobiotechnology 2023; 21:197. [PMID: 37340418 DOI: 10.1186/s12951-023-01943-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/29/2023] [Indexed: 06/22/2023] Open
Abstract
Malignant tumors have been one of the major reasons for deaths worldwide. Timely and accurate diagnosis as well as effective intervention of tumors play an essential role in the survival of patients. Genomic instability is the important foundation and feature of cancer, hence, in vivo oncogene imaging based on novel probes provides a valuable tool for the diagnosis of cancer at early-stage. However, the in vivo oncogene imaging is confronted with great challenge, due to the extremely low copies of oncogene in tumor cells. By combining with various novel activatable probes, the molecular imaging technologies provide a feasible approach to visualize oncogene in situ, and realize accurate treatment of tumor. This review aims to declare the design of nanoprobes responded to tumor associated DNA or RNA, and summarize their applications in detection and bioimaging for tumors. The significant challenges and prospective of oncogene-targeting nanoprobes towards tumors diagnosis are revealed as well.
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Affiliation(s)
- Wenyue Li
- College of Materials Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 10029, China
| | - Peisen Zhang
- College of Materials Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 10029, China.
| | - Chuang Liu
- College of Materials Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 10029, China
| | - Yuping Xu
- College of Materials Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 10029, China
| | - Zhihua Gan
- College of Materials Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 10029, China
| | - Lei Kang
- Department of Nuclear Medicine, Peking University First Hospital, Beijing, 100034, China.
| | - Yi Hou
- College of Materials Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 10029, China.
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28
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Li M, Li L. Enzyme-Triggered DNA Sensor Technology for Spatially-Controlled, Cell-Selective Molecular Imaging. Acc Chem Res 2023. [PMID: 37262339 DOI: 10.1021/acs.accounts.3c00085] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
ConspectusWith unparalleled programmability, DNA has evolved as a powerful scaffold for engineering intricate and dynamic systems that can perform diverse tasks. By allowing serial detection of molecular targets in complex cellular milieus, increasingly sophisticated DNA sensors have not only promoted significant advances in unveiling the fundamental mechanisms of various pathophysiological processes but also provided a useful toolkit for disease diagnostics based on molecular signatures. Despite much progress, an inherent limitation of DNA-based sensors is that they often lack spatial control and cell-type selectivity for the sensing activity because of their "always active" design mechanism. Since most molecular targets of interests are not exclusive to disease cells, they are also shared by normal cells, the application of such biosensors for disease-specific imaging is limited by inadequate signal-to-background ratios due to indistinguishable signal response in both disease and normal cells. Therefore, imparting biosensors with spatial controllability remains a key issue to achieve molecular imaging with high sensitivity and cell specificity.As a biocatalyst, enzyme has been found to be closely related with the pathological conditions of numerous diseases. For example, many nucleases, protease, and kinases have been identified overexpressed in disease cells and considered as important biomarkers of cancer, inflammation, and neurological diseases. Recently, we have envisioned that such pathophysiology-associated enzymes could be leveraged as endogenous triggers to achieve spatial control over the molecular imaging activity of the DNA-based sensors with improved cell-specificity. In this Account, we outline the research efforts from our group on the development of endogenous enzyme-triggered, DNA-based sensor technology that enables spatially controlled, cell-type selective molecular imaging. With programmable DNA design and further engineering of enzymatically cleavable sites, a series of DNAzyme- and aptamer-based sensors have been developed for enzyme-controlled imaging of various molecular targets (e.g., metal ions and small molecules) in a cancer cell-selective manner. In particular, by introduction of PNA as bridge molecules to engineer DNA-based sensors with functional peptides, the conceptual design of protease-activated DNA biosensors has been established for spatioselective molecular imaging in cancer cells and extracellular tumor microenvironments. Furthermore, enzyme-triggered signal amplification approaches, such as enzymatically activated molecular beacon and catalytic hairpin assembly, have been developed for spatially selective RNA imaging in specific disease cells (e.g., inflammatory cells and cancer cells), which enables enhanced disease-site specificity and thus improved signal-to-background ratio. The signal amplification strategy is further expanded to cell-selective amplified imaging of non-RNA species through the combination with functional DNA design. Finally, the challenges and potential future directions in this burgeoning field are discussed. We hope this Account offers insights into rational design of enzymatically controlled, DNA-based sensor platforms for opening new frontiers in spatially resolved, cell-selective molecular imaging. We believe that the continuing advances in DNA-based molecular sensing technology together with the discoveries of diverse disease-associated enzymes will promise to usher a new era of diagnosis.
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Affiliation(s)
- Mengyuan Li
- School of Chemistry and Biological Engineering, Beijing Key Laboratory for Bioengineering and Sensing Technology, University of Science and Technology Beijing, Beijing 100083, China
| | - Lele Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, China
- College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing 100049, China
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29
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Wei W, Zhang Y, Yang F, Zhou L, Zhang Y, Wang Y, Yang S, Li J, Dong H. Orthometric multicolor encoded hybridization chain reaction amplifiers for multiplexed microRNA profiling in living cells. Chem Sci 2023; 14:5503-5509. [PMID: 37234881 PMCID: PMC10208064 DOI: 10.1039/d3sc00563a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/19/2023] [Indexed: 05/28/2023] Open
Abstract
Multiplexed microRNA (miRNA) profiling of more than four types in living cells is challenging due to fluorescent spectral overlap, representing a significant limitation in studying the complex interactions related to the occurrence and development of diseases. Herein, we report a multiplexed fluorescent imaging strategy based on an orthometric multicolor encoded hybridization chain reaction amplifier named multi-HCR. The targeting miRNA can trigger this multi-HCR strategy due to the specific sequence recognition, and then its self-assembly to amplify the programmability signals. We take the four-colored chain amplifiers, showing that the multi-HCR can form 15 combinations simultaneously. In a living process of hypoxia-induced apoptosis and autophagy under complicated mitochondria and endoplasmic reticulum stress, the multi-HCR demonstrates excellent performance in detecting eight different miRNA changes. The multi-HCR provides a robust strategy for simultaneously profiling multiplexed miRNA biomarkers in studying complicated cellular processes.
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Affiliation(s)
- Wei Wei
- Marshall Laboratory of Biomedical Engineering, Shenzhen Key Laboratory for Nano-Biosensing Technology, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University 518060 Guangdong China
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Bioengineering, University of Science and Technology Beijing 30 Xueyuan Road 100083 Beijing China
- Beijing Yaogen Biotechnology Co. Ltd 26 Yongwangxi Road 102609 Beijing China
| | - Yiyi Zhang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Bioengineering, University of Science and Technology Beijing 30 Xueyuan Road 100083 Beijing China
| | - Fan Yang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Bioengineering, University of Science and Technology Beijing 30 Xueyuan Road 100083 Beijing China
| | - Liping Zhou
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Bioengineering, University of Science and Technology Beijing 30 Xueyuan Road 100083 Beijing China
| | - Yufan Zhang
- Marshall Laboratory of Biomedical Engineering, Shenzhen Key Laboratory for Nano-Biosensing Technology, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University 518060 Guangdong China
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Bioengineering, University of Science and Technology Beijing 30 Xueyuan Road 100083 Beijing China
| | - Yeyu Wang
- Marshall Laboratory of Biomedical Engineering, Shenzhen Key Laboratory for Nano-Biosensing Technology, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University 518060 Guangdong China
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Bioengineering, University of Science and Technology Beijing 30 Xueyuan Road 100083 Beijing China
- Beijing Yaogen Biotechnology Co. Ltd 26 Yongwangxi Road 102609 Beijing China
| | - Shuangshuang Yang
- Marshall Laboratory of Biomedical Engineering, Shenzhen Key Laboratory for Nano-Biosensing Technology, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University 518060 Guangdong China
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Bioengineering, University of Science and Technology Beijing 30 Xueyuan Road 100083 Beijing China
| | - Jinze Li
- Marshall Laboratory of Biomedical Engineering, Shenzhen Key Laboratory for Nano-Biosensing Technology, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University 518060 Guangdong China
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Bioengineering, University of Science and Technology Beijing 30 Xueyuan Road 100083 Beijing China
| | - Haifeng Dong
- Marshall Laboratory of Biomedical Engineering, Shenzhen Key Laboratory for Nano-Biosensing Technology, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University 518060 Guangdong China
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Bioengineering, University of Science and Technology Beijing 30 Xueyuan Road 100083 Beijing China
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30
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Huang L, Mao X, Li J, Li Q, Shen J, Liu M, Fan C, Tian Y. Nanoparticle Spikes Enhance Cellular Uptake via Regulating Myosin IIA Recruitment. ACS NANO 2023; 17:9155-9166. [PMID: 37171255 DOI: 10.1021/acsnano.2c12660] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Spike-like nanostructures are omnipresent in natural and artificial systems. Although biorecognition of nanostructures to cellular receptors has been indicated as the primary factor for virus infection pathways, how the spiky morphology of DNA-modified nanoparticles affects their cellular uptake and intracellular fate remains to be explored. Here, we design dually emissive gold nanoparticles with varied spikiness (from 0 to 2) to probe the interactions of spiky nanoparticles with cells. We discovered that nanospikes at the nanoparticle regulated myosin IIA recruitment at the cell membrane during cellular uptake, thereby enhancing cellular uptake efficiency, as revealed by dual-modality (plasmonic and fluorescence) imaging. Furthermore, the spiky nanoparticles also exhibited facilitated endocytosis dynamics, as revealed by real-time dark-field microscopy (DFM) imaging and colorimetry-based classification algorithms. These findings highlight the crucial role of the spiky morphology in regulating the intracellular fate of nanoparticles, which may shed light on engineering theranostic nanocarriers.
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Affiliation(s)
- Lulu Huang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| | - Xiuhai Mao
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Jie Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jianlei Shen
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mengmeng Liu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| | - Chunhai Fan
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yang Tian
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
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31
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Ding D, Zhao H, Wei D, Yang Q, Yang C, Wang R, Chen Y, Li L, An S, Xia Q, Huang G, Liu J, Xiao Z, Tan W. The First-in-Human Whole-Body Dynamic Pharmacokinetics Study of Aptamer. RESEARCH (WASHINGTON, D.C.) 2023; 6:0126. [PMID: 37223462 PMCID: PMC10202413 DOI: 10.34133/research.0126] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 03/30/2023] [Indexed: 05/25/2023]
Abstract
Serving as targeting ligands, aptamers have shown promise in precision medicine. However, the lack of knowledge of the biosafety and metabolism patterns in the human body largely impeded aptamers' clinical translation. To bridge this gap, here we report the first-in-human pharmacokinetics study of protein tyrosine kinase 7 targeted SGC8 aptamer via in vivo PET tracking of gallium-68 (68Ga) radiolabeled aptamers. The specificity and binding affinity of a radiolabeled aptamer, named 68Ga[Ga]-NOTA-SGC8, were maintained as proven in vitro. Further preclinical biosafety and biodistribution evaluation confirmed that aptamers have no biotoxicity, potential mutation risks, or genotoxicity at high dosage (40 mg/kg). Based on this result, a first-in-human clinical trial was approved and carried out to evaluate the circulation and metabolism profiles, as well as biosafety, of the radiolabeled SGC8 aptamer in the human body. Taking advantage of the cutting-edge total-body PET, the aptamers' distribution pattern in the human body was acquired in a dynamic fashion. This study revealed that radiolabeled aptamers are harmless to normal organs and most of them are accumulated in the kidney and cleared from the bladder via urine, which agrees with preclinical studies. Meanwhile, a physiologically based pharmacokinetic model of aptamer was developed, which could potentially predict therapeutic responses and plan personalized treatment strategies. This research studied the biosafety and dynamic pharmacokinetics of aptamers in the human body for the first time, as well as demonstrated the capability of novel molecular imaging fashion in drug development.
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Affiliation(s)
- Ding Ding
- Institute of Molecular Medicine (IMM), Renji Hospital, State Key Laboratory of Oncogenes and Related Genes,
Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Haitao Zhao
- Department of Nuclear Medicine, Renji Hospital, School of Medicine,
Shanghai Jiao Tong University, Shanghai 200127, China
| | - Dali Wei
- Institute of Molecular Medicine (IMM), Renji Hospital, State Key Laboratory of Oncogenes and Related Genes,
Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qinglai Yang
- Institute of Molecular Medicine (IMM), Renji Hospital, State Key Laboratory of Oncogenes and Related Genes,
Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- Center for Molecular Imaging Probes, Cancer Research Institute,
University of South China, Hengyang, Hunan 421001, China
| | - Cai Yang
- Institute of Molecular Medicine (IMM), Renji Hospital, State Key Laboratory of Oncogenes and Related Genes,
Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital,Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering,
Hunan University, Changsha, Hunan 410082, China
| | - Ruowen Wang
- Institute of Molecular Medicine (IMM), Renji Hospital, State Key Laboratory of Oncogenes and Related Genes,
Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yumei Chen
- Department of Nuclear Medicine, Renji Hospital, School of Medicine,
Shanghai Jiao Tong University, Shanghai 200127, China
| | - Lianghua Li
- Department of Nuclear Medicine, Renji Hospital, School of Medicine,
Shanghai Jiao Tong University, Shanghai 200127, China
| | - Shuxian An
- Department of Nuclear Medicine, Renji Hospital, School of Medicine,
Shanghai Jiao Tong University, Shanghai 200127, China
| | - Qian Xia
- Institute of Molecular Medicine (IMM), Renji Hospital, State Key Laboratory of Oncogenes and Related Genes,
Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- Department of Nuclear Medicine, Renji Hospital, School of Medicine,
Shanghai Jiao Tong University, Shanghai 200127, China
| | - Gang Huang
- Department of Nuclear Medicine, Renji Hospital, School of Medicine,
Shanghai Jiao Tong University, Shanghai 200127, China
- Shanghai Key Laboratory of Molecular Imaging,
Shanghai University of Medicine and Health Sciences, Shanghai 201318, China
| | - Jianjun Liu
- Department of Nuclear Medicine, Renji Hospital, School of Medicine,
Shanghai Jiao Tong University, Shanghai 200127, China
| | - Zeyu Xiao
- Institute of Molecular Medicine (IMM), Renji Hospital, State Key Laboratory of Oncogenes and Related Genes,
Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- Department of Pharmacology and Chemical Biology,
Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Weihong Tan
- Institute of Molecular Medicine (IMM), Renji Hospital, State Key Laboratory of Oncogenes and Related Genes,
Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital,Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering,
Hunan University, Changsha, Hunan 410082, China
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32
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Ebrahimi SB, Samanta D. Engineering protein-based therapeutics through structural and chemical design. Nat Commun 2023; 14:2411. [PMID: 37105998 PMCID: PMC10132957 DOI: 10.1038/s41467-023-38039-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
Protein-based therapeutics have led to new paradigms in disease treatment. Projected to be half of the top ten selling drugs in 2023, proteins have emerged as rivaling and, in some cases, superior alternatives to historically used small molecule-based medicines. This review chronicles both well-established and emerging design strategies that have enabled this paradigm shift by transforming protein-based structures that are often prone to denaturation, degradation, and aggregation in vitro and in vivo into highly effective therapeutics. In particular, we discuss strategies for creating structures with increased affinity and targetability, enhanced in vivo stability and pharmacokinetics, improved cell permeability, and reduced amounts of undesired immunogenicity.
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Affiliation(s)
- Sasha B Ebrahimi
- Drug Product Development-Steriles, GlaxoSmithKline, Collegeville, PA, 19426, USA.
| | - Devleena Samanta
- Department of Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA.
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33
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Sardaru MC, Marangoci NL, Palumbo R, Roviello GN, Rotaru A. Nucleic Acid Probes in Bio-Imaging and Diagnostics: Recent Advances in ODN-Based Fluorescent and Surface-Enhanced Raman Scattering Nanoparticle and Nanostructured Systems. Molecules 2023; 28:molecules28083561. [PMID: 37110795 PMCID: PMC10141977 DOI: 10.3390/molecules28083561] [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: 03/06/2023] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Raman nanoparticle probes are a potent class of optical labels for the interrogation of pathological and physiological processes in cells, bioassays, and tissues. Herein, we review the recent advancements in fluorescent and Raman imaging using oligodeoxyribonucleotide (ODN)-based nanoparticles and nanostructures, which show promise as effective tools for live-cell analysis. These nanodevices can be used to investigate a vast number of biological processes occurring at various levels, starting from those involving organelles, cells, tissues, and whole living organisms. ODN-based fluorescent and Raman probes have contributed to the achievement of significant advancements in the comprehension of the role played by specific analytes in pathological processes and have inaugurated new possibilities for diagnosing health conditions. The technological implications that have emerged from the studies herein described could open new avenues for innovative diagnostics aimed at identifying socially relevant diseases like cancer through the utilization of intracellular markers and/or guide surgical procedures based on fluorescent or Raman imaging. Particularly complex probe structures have been developed within the past five years, creating a versatile toolbox for live-cell analysis, with each tool possessing its own strengths and limitations for specific studies. Analyzing the literature reports in the field, we predict that the development of ODN-based fluorescent and Raman probes will continue in the near future, disclosing novel ideas on their application in therapeutic and diagnostic strategies.
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Affiliation(s)
- Monica-Cornelia Sardaru
- "Petru Poni" Institute of Macromolecular Chemistry, Romanian Academy, Centre of Advanced Research in Bionanoconjugates and Biopolymers, Grigore Ghica Voda Alley 41 A, 700487 Iasi, Romania
- The Research Institute of the University of Bucharest (ICUB), 90 Sos. Panduri, 050663 Bucharest, Romania
| | - Narcisa-Laura Marangoci
- "Petru Poni" Institute of Macromolecular Chemistry, Romanian Academy, Centre of Advanced Research in Bionanoconjugates and Biopolymers, Grigore Ghica Voda Alley 41 A, 700487 Iasi, Romania
| | - Rosanna Palumbo
- Institute of Biostructures and Bioimaging, Italian National Council for Research (IBB-CNR), Area di Ricerca Site and Headquarters, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Giovanni N Roviello
- Institute of Biostructures and Bioimaging, Italian National Council for Research (IBB-CNR), Area di Ricerca Site and Headquarters, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Alexandru Rotaru
- "Petru Poni" Institute of Macromolecular Chemistry, Romanian Academy, Centre of Advanced Research in Bionanoconjugates and Biopolymers, Grigore Ghica Voda Alley 41 A, 700487 Iasi, Romania
- Institute for Research, Innovation and Technology Transfer, UPS "Ion Creanga", Ion Creanga Str. 1, MD2069 Chisinau, Moldova
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34
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Chen K, Zhu L, Du Z, Lan X, Huang K, Zhang W, Xu W. Docking-aided rational tailoring of a fluorescence- and affinity-enhancing aptamer for a label-free ratiometric malachite green point-of-care aptasensor. JOURNAL OF HAZARDOUS MATERIALS 2023; 447:130798. [PMID: 36669418 DOI: 10.1016/j.jhazmat.2023.130798] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 06/17/2023]
Abstract
Although nucleic acid aptasensors are increasingly applied in the detection of environmentally hazardous biomolecules, several formidable challenges remain with this technique because of their vulnerability, high cost and suboptimal sensitivity. Here, a docking-aided rational tailoring (DART) strategy was established at three levels and in two dimensions for the refinement of malachite green (MG) DNA aptamers. Guided by in silico molecular docking, coarse and fine tailoring were conducted at three levels each, to significantly enhance fluorescence activation intensity and binding affinity in two dimensions. Empowered by the results of the rational tailoring, a mechanistic view of the MG DNA aptamer-target interaction was thoroughly analyzed via four types of interactions. To meet the demand for point-of-care testing (POCT), a label-free and ratiometric fluorescent aptasensor was developed leveraging the tailored MG aptamer, based on the binding site competition-equilibrium effect via the introduction of a reference dye. This sensitive, specific, low-cost and rapid aptasensor subsequently demonstrated outstanding detection performance, achieving an ideal signal response range of 5 nmol·L-1 - 6 μmol·L-1 and a low limit of detection (LOD) of 1.49 nmol·L-1. The DART strategy and systematic exploration of the MG DNA luminescent aptamers herein will provide a valuable reference in the field of aptamer tailoring, biosensing and bioimaging. The proposed label-free ratiometric aptasensor also provides a highly generalizable strategy for hazardous biomolecular detection.
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Affiliation(s)
- Keren Chen
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China; Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Longjiao Zhu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China
| | - Zaihui Du
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China; Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Xinyue Lan
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China; Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Kunlun Huang
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Wenqiang Zhang
- Department of Mechanical Design and Manufacturing, College of Engineering, China Agricultural University, Beijing 100083, China
| | - Wentao Xu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China; Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
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35
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Langlois NI, Ma KY, Clark HA. Nucleic acid nanostructures for in vivo applications: The influence of morphology on biological fate. APPLIED PHYSICS REVIEWS 2023; 10:011304. [PMID: 36874908 PMCID: PMC9869343 DOI: 10.1063/5.0121820] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 12/12/2022] [Indexed: 05/23/2023]
Abstract
The development of programmable biomaterials for use in nanofabrication represents a major advance for the future of biomedicine and diagnostics. Recent advances in structural nanotechnology using nucleic acids have resulted in dramatic progress in our understanding of nucleic acid-based nanostructures (NANs) for use in biological applications. As the NANs become more architecturally and functionally diverse to accommodate introduction into living systems, there is a need to understand how critical design features can be controlled to impart desired performance in vivo. In this review, we survey the range of nucleic acid materials utilized as structural building blocks (DNA, RNA, and xenonucleic acids), the diversity of geometries for nanofabrication, and the strategies to functionalize these complexes. We include an assessment of the available and emerging characterization tools used to evaluate the physical, mechanical, physiochemical, and biological properties of NANs in vitro. Finally, the current understanding of the obstacles encountered along the in vivo journey is contextualized to demonstrate how morphological features of NANs influence their biological fates. We envision that this summary will aid researchers in the designing novel NAN morphologies, guide characterization efforts, and design of experiments and spark interdisciplinary collaborations to fuel advancements in programmable platforms for biological applications.
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Affiliation(s)
- Nicole I. Langlois
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, USA
| | - Kristine Y. Ma
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, USA
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36
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Wang J, Wang K, Peng H, Zhang Z, Yang Z, Song M, Jiang G. Entropy-Driven Three-Dimensional DNA Nanofireworks for Simultaneous Real-Time Imaging of Telomerase and MicroRNA in Living Cells. Anal Chem 2023; 95:4138-4146. [PMID: 36790864 DOI: 10.1021/acs.analchem.2c05200] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Real-time monitoring of different types of intracellular tumor-related biomarkers is of key importance for the identification of tumor cells. However, it is hampered by the low abundance of biomarkers, inefficient free diffusion of reactants, and complex cytoplasmic milieu. Herein, we present a stable and general method for in situ imaging of microRNA-21 and telomerase utilizing simple highly integrated dual tetrahedral DNA nanostructures (TDNs) that can naturally enter cells, which could initiate to form the three-dimensional (3D) higher-order DNA superstructures (DNA nanofireworks, DNFs) through a reliable target-triggered entropy-driven strand displacement reaction in living cells for remarkable signal amplification. Importantly, the excellent biostability, biocompatibility, and sensitivity of this approach benefited from (i) the precise multidirectional arrangement of probes with a pure DNA structure and (ii) the local target concentration enhanced by the spatially confined microdomain inside the DNFs. This strategy provides a pivotal molecular toolbox for broad applications such as biomedical imaging and early precise cancer diagnosis.
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Affiliation(s)
- Jin Wang
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Kaixuan Wang
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China.,School of Water, Energy, and Environment, Cranfield University, Cranfield, Milton Keynes MK43 0AL, U.K
| | - Hanyong Peng
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco- Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Zhen Zhang
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Zhugen Yang
- School of Water, Energy, and Environment, Cranfield University, Cranfield, Milton Keynes MK43 0AL, U.K
| | - Maoyong Song
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco- Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Guibin Jiang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco- Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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37
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Zheng Y, Guo M, Wu S, Wang W, Jin M, Wang Q, Wang K. Construction of a DNA Nanoassembly Based on Spatially Ordered Recognition Elements for Inhibiting β-Amyloid Aggregation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:2192-2203. [PMID: 36735839 DOI: 10.1021/acs.langmuir.2c02675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
A β-amyloid (Aβ) aggregation process is a spontaneous process where the original random coil or helical structure changes into a regularly arranged β-sheet structure. The development of inhibitors with the features of low cost, high efficiency, and biosafety by targeting Aβ self-aggregation is significant for Alzheimer's disease treatment. However, the issues of low inhibition efficiency under low concentrations of inhibitors and biological toxicity are currently to be addressed. To resolve the above problems, a DNA nanoassembly (HCR-Apt) based on spatially ordered recognition elements was constructed by targeted disruption of Aβ ordered arrangement. It was discovered that HCR-Apt could inhibit effectively the fibrillation of Aβ40 monomers and oligomers at substoichiometric ratios. This may be due to orderly arrangement of aptamers in rigid nanoskeletons for enhancing the recognition interaction between aptamers and Aβ40. The strong interaction between HCR-Apt and Aβ40 limited the flexible conformational conversion of Aβ40 molecules, thereby inhibiting their self-assembly. Computational simulations and experimental analysis revealed the interactions of Apt42 with Aβ40, which explained different inhibition effects on the fibrillation of Aβ40 monomers and oligomers. Furthermore, the analysis of tyrosine intrinsic fluorescence spectra and surface plasmon resonance imaging showed that the interaction of HCR-Apt and Aβ40 was stronger than that of Apt42 and Aβ40. These findings contributed to establishing a promising method of boosting the recognition interaction by orderly arrangement of recognition elements. Taken together, this work is expected to provide a simple and efficient strategy for inhibiting Aβ aggregation, expanding aptamer's application potential in neurodegenerative diseases.
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Affiliation(s)
- Yan Zheng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, P. R. China
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Institute of Engineering Medicine, Beijing Institute of Technology, Beijing 100081, P. R. China
| | - Mingmei Guo
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Institute of Engineering Medicine, Beijing Institute of Technology, Beijing 100081, P. R. China
| | - Shang Wu
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Institute of Engineering Medicine, Beijing Institute of Technology, Beijing 100081, P. R. China
| | - Weizhi Wang
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Institute of Engineering Medicine, Beijing Institute of Technology, Beijing 100081, P. R. China
| | - Meimei Jin
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, P. R. China
| | - Qing Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, P. R. China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, P. R. China
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38
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Zheng Z, Yuan L, Hu JJ, Xia F, Lou X. Modular Peptide Probe for Protein Analysis. Chemistry 2023; 29:e202203225. [PMID: 36333271 DOI: 10.1002/chem.202203225] [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: 10/15/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 11/07/2022]
Abstract
The analysis and regulation of proteins are of great significance for the development of disease diagnosis and treatment. However, complicated analytical environment and complex protein structure severely limit the accuracy of their analysis results. Nowadays, ascribing to the editability and bioactivity of peptides, peptide-based probes could meet the requirements of good selectivity and high affinity to overcome the challenges. In this review, we summarize the advances in the use of modular peptide probes for proteins analysis. It focuses on how to design and optimize the structure of probes, as well as their performance. Then, the strategies and application to improve the analysis result of modular peptide probes are introduced. Finally, we also discuss current challenge and provide some ideas for the future direction for modular peptide probes, hoping to accelerate their clinical transformation.
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Affiliation(s)
- Zhi Zheng
- State Key Laboratory of Biogeology and Environmental Geology Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
| | - Lizhen Yuan
- State Key Laboratory of Biogeology and Environmental Geology Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
| | - Jing-Jing Hu
- State Key Laboratory of Biogeology and Environmental Geology Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
| | - Fan Xia
- State Key Laboratory of Biogeology and Environmental Geology Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
| | - Xiaoding Lou
- State Key Laboratory of Biogeology and Environmental Geology Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
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39
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Bencurova E, Akash A, Dobson RC, Dandekar T. DNA storage-from natural biology to synthetic biology. Comput Struct Biotechnol J 2023; 21:1227-1235. [PMID: 36817961 PMCID: PMC9932295 DOI: 10.1016/j.csbj.2023.01.045] [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: 11/19/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/04/2023] Open
Abstract
Natural DNA storage allows cellular differentiation, evolution, the growth of our children and controls all our ecosystems. Here, we discuss the fundamental aspects of DNA storage and recent advances in this field, with special emphasis on natural processes and solutions that can be exploited. We point out new ways of efficient DNA and nucleotide storage that are inspired by nature. Within a few years DNA-based information storage may become an attractive and natural complementation to current electronic data storage systems. We discuss rapid and directed access (e.g. DNA elements such as promotors, enhancers), regulatory signals and modulation (e.g. lncRNA) as well as integrated high-density storage and processing modules (e.g. chromosomal territories). There is pragmatic DNA storage for use in biotechnology and human genetics. We examine DNA storage as an approach for synthetic biology (e.g. light-controlled nucleotide processing enzymes). The natural polymers of DNA and RNA offer much for direct storage operations (read-in, read-out, access control). The inbuilt parallelism (many molecules at many places working at the same time) is important for fast processing of information. Using biology concepts from chromosomal storage, nucleic acid processing as well as polymer material sciences such as electronical effects in enzymes, graphene, nanocellulose up to DNA macramé , DNA wires and DNA-based aptamer field effect transistors will open up new applications gradually replacing classical information storage methods in ever more areas over time (decades).
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Affiliation(s)
- Elena Bencurova
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany
| | - Aman Akash
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany
| | - Renwick C.J. Dobson
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand,Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, Australia
| | - Thomas Dandekar
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany,Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany,Corresponding author at: Department of Bioinformatics, University of Würzburg, Würzburg, Germany.
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40
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He H, Zhou Y, Chen B, Zhang Y, Zhong X, Xu L, Guo B, Yin C, Zhou X, Li Q, Huang Z, Luo G, Guo X. Nucleic acid amplification with specific signal filtration and magnification for ultrasensitive colorimetric detection. Talanta 2023; 253:123978. [PMID: 36209643 DOI: 10.1016/j.talanta.2022.123978] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/20/2022] [Accepted: 09/27/2022] [Indexed: 11/23/2022]
Abstract
Recently, sensitive, fast and low cost nucleic acid isothermal amplification technologies (such as loop-mediated isothermal amplification, LAMP) have attracted great attention in the urgent needs of point-of-care testing (POCT) and regular epidemic prevention and control. However, unlike PCR which usually employs TaqMan probe to report specific signals, specific-signal-output strategies in isothermal amplification are immature and visual detection even rare, which limits their popularity in POCT. We hypothesize to address this issue by designing a visual-signal-report system to both filtrate and magnify the target information in isothermal amplification. In this work, we developed a specific signal filtration and magnification colorimetric isothermal sensing platform (SFMC for short) for ultrasensitive detection of DNA and RNA. SFMC consists of two processes: an isothermal amplification with specific signal filtration and a self-replication catalyzed hairpin assembly (SRCHA) for rapid target-specific signal magnification and outputting. With these unique properties, this biosensing platform could detect target DNA as low as 5 copies per reaction and target RNA as low as 10 copies per reaction by naked eyes. Benefited from the excellent colorimetric detection performance, this biosensing platform has been successfully used for African swine fever virus (ASFV) and SARS-CoV-2 detection.
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Affiliation(s)
- Hongfei He
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Yan Zhou
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China; School of Pharmacy & School of Preclinical Medicine, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Bin Chen
- Sichuan Provincial Center for Animal Disease Control and Prevention, Chengdu, 610041, PR China
| | - Yi Zhang
- Sichuan Provincial Center for Animal Disease Control and Prevention, Chengdu, 610041, PR China
| | - Xiaowu Zhong
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Lei Xu
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Bin Guo
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Chong Yin
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Xi Zhou
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Qingrong Li
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Zhen Huang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, PR China.
| | - Guangcheng Luo
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China.
| | - Xiaolan Guo
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China.
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41
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Wang L, Wang K, Wang X, Niu R, Chen X, Zhu Y, Sun Z, Yang J, Liu G, Luo Y. Intelligent Dual-Lock Deoxyribonucleic Acid Automatons Boosting Precise Tumor Imaging. ACS APPLIED MATERIALS & INTERFACES 2023; 15:3826-3838. [PMID: 36625537 DOI: 10.1021/acsami.2c20024] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
An early and accurate cancer diagnosis holds the potential to improve treatment and prognosis. Nevertheless, the complexity of the biological system limits the selectivity of existing approaches and makes tumor imaging in vivo particularly challenging. In this study, tumor-specific fluorescence imaging was achieved by building intelligent dual-lock deoxyribonucleic acid automatons (IDEAs) that employed a DNA walking system standing on ZrMOF@MnO2 multifunctional nanocomposites for controllable molecular recognition. The IDEAs exhibited significantly enhanced fluorescence signals only in the coexistence of both miRNA and GSH of tumor cells, enabling accurate distinguishing of tumor cells from healthy ones. Furthermore, the feasibility and specificity of IDEAs were also validated in vivo with tumor bearing mice successfully. This work highlights the potential of the proposed IDEA strategy for tumor-specific imaging, paving the way for successful precision diagnosis and treatment.
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Affiliation(s)
- Liu Wang
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing400044, P. R. China
| | - Kang Wang
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing400044, P. R. China
- College of Bioengineering, Chongqing University, Chongqing400044, P. R. China
| | - Xiaohui Wang
- Department of Oncology, Jiangjin Hospital, Chongqing University, Chongqing402260, P. R. China
| | - Ruyan Niu
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing400044, P. R. China
- College of Bioengineering, Chongqing University, Chongqing400044, P. R. China
| | - Xiaohui Chen
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing400044, P. R. China
- College of Bioengineering, Chongqing University, Chongqing400044, P. R. China
| | - Ying Zhu
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing400044, P. R. China
| | - Zixin Sun
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing400044, P. R. China
| | - Jichun Yang
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing400044, P. R. China
| | - Guoxiang Liu
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing400044, P. R. China
| | - Yang Luo
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing400044, P. R. China
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Ding Y, Huang PJJ, Zandieh M, Wang J, Liu J. Gold Nanoparticles Synthesized Using Various Reducing Agents and the Effect of Aging for DNA Sensing. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:256-264. [PMID: 36577094 DOI: 10.1021/acs.langmuir.2c02458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Gold nanoparticles (AuNPs) are one of the most commonly used reagents in colloidal science and biosensor technology. In this work, we first compared AuNPs prepared using four different reducing agents including citrate, glucose, ascorbate, and 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES). At the same absorbance at the surface plasmon peak of 520-530 nm, citrate-AuNPs and glucose-AuNPs adsorbed more DNA and achieved higher affinity to the adsorbed DNA. In addition, citrate-AuNPs had better sensitivity than glucose-AuNPs for label-free DNA detection. Then, using citrate-AuNPs, the effect of aging was studied by incubation of the AuNPs at 22 °C (room temperature) and at 4 °C for up to 6 months. During aging, the colloidal stability and DNA adsorption efficiency gradually decreased. In addition, the DNA sensing sensitivity using a label-free method also dropped around 4-fold after 6 months. Heating at boiling temperature of the aged citrate-AuNPs could not rejuvenate the sensing performance. This study shows that while citrate-AuNPs are initially better than the other three AuNPs in their colloid properties and sensing properties, this edge in performance might gradually decrease due to constantly changing surface properties caused from the aging effect.
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Affiliation(s)
- Yuzhe Ding
- Department of Chemistry, Waterloo Institute for Nanotechnology, Waterloo, Ontario N2L 3G1, Canada
| | - Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, Waterloo, Ontario N2L 3G1, Canada
| | - Mohamad Zandieh
- Department of Chemistry, Waterloo Institute for Nanotechnology, Waterloo, Ontario N2L 3G1, Canada
| | - Jinghan Wang
- Department of Chemistry, Waterloo Institute for Nanotechnology, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, Waterloo, Ontario N2L 3G1, Canada
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43
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Akiyama Y, Kimura K, Komatsu S, Takarada T, Maeda M, Kikuchi A. A Simple Colorimetric Assay of Bleomycin-Mediated DNA Cleavage Utilizing Double-Stranded DNA-Modified Gold Nanoparticles. Chembiochem 2023; 24:e202200451. [PMID: 36156837 PMCID: PMC10092608 DOI: 10.1002/cbic.202200451] [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: 08/04/2022] [Revised: 09/23/2022] [Indexed: 01/05/2023]
Abstract
A colorimetric assay of DNA cleavage by bleomycin (BLM) derivatives was developed utilizing high colloidal stability on double-stranded (ds) DNA-modified gold nanoparticles (dsDNA-AuNPs) possessing a cleavage site. The assay was performed using dsDNA-AuNPs treated with inactive BLM or activated BLM (Fe(II)⋅BLM). A 10-min exposure in dsDNA-AuNPs with inactive BLM treatment resulted in a rapid color change from red to purple because of salt-induced non-crosslinking aggregation of dsDNA-AuNPs. In contrast, the addition of active Fe(II)⋅BLM retained the red color, probably because of the formation of protruding structures at the outermost phase of dsDNA-AuNPs caused by BLM-mediated DNA cleavage. Furthermore, the results of our model experiments indicate that oxidative base release and DNA-cleavage pathways could be visually distinguished with color change. The present methodology was also applicable to model screening assays using several drugs with different mechanisms related to antitumor activity. These results strongly suggest that this assay with a rapid color change could lead to simple and efficient screening of potent antitumor agents.
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Affiliation(s)
- Yoshitsugu Akiyama
- Katsushika Division, Institute of Arts and Sciences, Tokyo University of Science, 6-3-1 Niijuku, 125-8585, Katsushika, Tokyo, Japan.,Department of Materials Science and Technology, Graduate School of Advanced Engineering, Tokyo University of Science, 6-3-1 Niijuku, 125-8585, Katsushika, Tokyo, Japan
| | - Kazunori Kimura
- Department of Materials Science and Technology, Graduate School of Advanced Engineering, Tokyo University of Science, 6-3-1 Niijuku, 125-8585, Katsushika, Tokyo, Japan
| | - Syuuhei Komatsu
- Department of Materials Science and Technology, Graduate School of Advanced Engineering, Tokyo University of Science, 6-3-1 Niijuku, 125-8585, Katsushika, Tokyo, Japan
| | - Tohru Takarada
- Surface and Interface Science Laboratory, RIKEN, 2-1 Hirosawa, 351-0198, Wako, Saitama, Japan
| | - Mizuo Maeda
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, 351-0198, Wako, Saitama, Japan
| | - Akihiko Kikuchi
- Department of Materials Science and Technology, Graduate School of Advanced Engineering, Tokyo University of Science, 6-3-1 Niijuku, 125-8585, Katsushika, Tokyo, Japan
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44
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Li H, Xie Y, Chen F, Bai H, Xiu L, Zhou X, Guo X, Hu Q, Yin K. Amplification-free CRISPR/Cas detection technology: challenges, strategies, and perspectives. Chem Soc Rev 2023; 52:361-382. [PMID: 36533412 DOI: 10.1039/d2cs00594h] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Rapid and accurate molecular diagnosis is a prerequisite for precision medicine, food safety, and environmental monitoring. The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas)-based detection, as a cutting-edged technique, has become an immensely effective tool for molecular diagnosis because of its outstanding advantages including attomolar level sensitivity, sequence-targeted single-base specificity, and rapid turnover time. However, the CRISPR/Cas-based detection methods typically require a pre-amplification step to elevate the concentration of the analyte, which may produce non-specific amplicons, prolong the detection time, and raise the risk of carryover contamination. Hence, various strategies for target amplification-free CRISPR/Cas-based detection have been developed, aiming to minimize the sensitivity loss due to lack of pre-amplification, enable detection for non-nucleic acid targets, and facilitate integration in portable devices. In this review, the current status and challenges of target amplification-free CRISPR/Cas-based detection are first summarized, followed by highlighting the four main strategies to promote the performance of target amplification-free CRISPR/Cas-based technology. Furthermore, we discuss future perspectives that will contribute to developing more efficient amplification-free CRISPR/Cas detection systems.
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Affiliation(s)
- Huimin Li
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China. .,One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, People's Republic of China
| | - Yi Xie
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China. .,One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, People's Republic of China
| | - Fumin Chen
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China. .,One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, People's Republic of China
| | - Huiwen Bai
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, 220 South 33rd St., Philadelphia, Pennsylvania, USA
| | - Leshan Xiu
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China. .,One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, People's Republic of China
| | - Xiaonong Zhou
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China. .,One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, People's Republic of China
| | - Xiaokui Guo
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China. .,One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, People's Republic of China
| | - Qinqin Hu
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China. .,One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, People's Republic of China
| | - Kun Yin
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China. .,One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, People's Republic of China
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45
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Tang J, Li Q, Yao C, Yang D. DNA Nanomaterial-Based Optical Probes for Exosomal miRNA Detection. Chempluschem 2023; 88:e202200345. [PMID: 36650721 DOI: 10.1002/cplu.202200345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 12/19/2022] [Indexed: 12/24/2022]
Abstract
Micro ribonucleic acids (miRNAs) in exosomes have been proven as reliable biomarkers to detect disease progression. In recent years, deoxyribonucleic acid (DNA)-based nanomaterials show great potential in the field of diagnosis due to the programmable sequence, various molecule recognition and predictable assembly/disassembly of DNA. In this review, we focus on the molecular design and detection mechanism of DNA nanomaterials, and the developed DNA nanomaterial-based optical probes for exosomal miRNA detection are summarized and discussed. The rationally-designed DNA sequences endows these probes with low background signal and high sensitivity in exosomal miRNA detection, and the detection mechanisms based on different DNA nanomaterials are detailly introduced. At the end, the challenges and future opportunities of DNA nanomaterial-based optical probes in exosomal miRNA detection are discussed. We envision that DNA nanomaterial-based optical probes will be promising in precise biomedicine.
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Affiliation(s)
- Jianpu Tang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P. R. China
| | - Qian Li
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P. R. China
| | - Chi Yao
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P. R. China
| | - Dayong Yang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P. R. China
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46
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Matthews EZ, Lanham S, White K, Kyriazi ME, Alexaki K, El-Sagheer AH, Brown T, Kanaras AG, J West J, MacArthur BD, Stumpf PS, Oreffo ROC. Single-cell RNA-sequence analysis of human bone marrow reveals new targets for isolation of skeletal stem cells using spherical nucleic acids. J Tissue Eng 2023; 14:20417314231169375. [PMID: 37216034 PMCID: PMC10192814 DOI: 10.1177/20417314231169375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/24/2023] [Indexed: 05/24/2023] Open
Abstract
There is a wealth of data indicating human bone marrow contains skeletal stem cells (SSC) with the capacity for osteogenic, chondrogenic and adipogenic differentiation. However, current methods to isolate SSCs are restricted by the lack of a defined marker, limiting understanding of SSC fate, immunophenotype, function and clinical application. The current study applied single-cell RNA-sequencing to profile human adult bone marrow populations from 11 donors and identified novel targets for SSC enrichment. Spherical nucleic acids were used to detect these mRNA targets in SSCs. This methodology was able to rapidly isolate potential SSCs found at a frequency of <1 in 1,000,000 in human bone marrow, with the capacity for tri-lineage differentiation in vitro and ectopic bone formation in vivo. The current studies detail the development of a platform to advance SSC enrichment from human bone marrow, offering an invaluable resource for further SSC characterisation, with significant therapeutic impact therein.
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Affiliation(s)
- Elloise Z Matthews
- Faculty of Medicine, Centre for Human
Development, Stem Cells and Regeneration, Human Development and Health, Institute of
Developmental Sciences, University of Southampton, Southampton, UK
| | - Stuart Lanham
- Faculty of Medicine, Centre for Human
Development, Stem Cells and Regeneration, Human Development and Health, Institute of
Developmental Sciences, University of Southampton, Southampton, UK
- Cancer Sciences, Faculty of Medicine,
University of Southampton, Southampton, UK
| | - Kate White
- Faculty of Medicine, Centre for Human
Development, Stem Cells and Regeneration, Human Development and Health, Institute of
Developmental Sciences, University of Southampton, Southampton, UK
| | - Maria-Eleni Kyriazi
- College of Engineering and Technology,
American University of the Middle East, Kuwait
| | - Konstantina Alexaki
- Physics and Astronomy, Faculty of
Physical Sciences and Engineering, University of Southampton, Southampton, UK
| | - Afaf H El-Sagheer
- Department of Chemistry, Chemistry
Research Laboratory, University of Oxford, Oxford, UK
- Chemistry Branch, Department of Science
and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez,
Egypt
| | - Tom Brown
- Department of Chemistry, Chemistry
Research Laboratory, University of Oxford, Oxford, UK
| | - Antonios G Kanaras
- Physics and Astronomy, Faculty of
Physical Sciences and Engineering, University of Southampton, Southampton, UK
- Institute for Life Sciences, University
of Southampton, Southampton, UK
| | - Jonathan J West
- Cancer Sciences, Faculty of Medicine,
University of Southampton, Southampton, UK
- Physics and Astronomy, Faculty of
Physical Sciences and Engineering, University of Southampton, Southampton, UK
| | - Ben D MacArthur
- Faculty of Medicine, Centre for Human
Development, Stem Cells and Regeneration, Human Development and Health, Institute of
Developmental Sciences, University of Southampton, Southampton, UK
- Institute for Life Sciences, University
of Southampton, Southampton, UK
- Mathematical Sciences, University of
Southampton, Southampton, UK
| | - Patrick S Stumpf
- Faculty of Medicine, Centre for Human
Development, Stem Cells and Regeneration, Human Development and Health, Institute of
Developmental Sciences, University of Southampton, Southampton, UK
- Joint Research Center for Computational
Biomedicine, RWTH Aachen University, Aachen, Germany
| | - Richard OC Oreffo
- Faculty of Medicine, Centre for Human
Development, Stem Cells and Regeneration, Human Development and Health, Institute of
Developmental Sciences, University of Southampton, Southampton, UK
- Institute for Life Sciences, University
of Southampton, Southampton, UK
- College of Biomedical Engineering,
China Medical University, Taichung, Taiwan
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47
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Zhang J, Wang D, Chen H, Yuan X, Jiang X, Ai L, He J, Chen F, Xie S, Cui C, Tan W. A pH-Responsive Covalent Nanoscale Device Enhancing Temporal and Force Stability for Specific Tumor Imaging. NANO LETTERS 2022; 22:9441-9449. [PMID: 36442508 DOI: 10.1021/acs.nanolett.2c03487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Approaches to DNA probe-mediated precision medicine have been extensively explored for the diagnosis and treatment of diverse types of cancer. Despite this, simple nanoscale devices with the required recognition specificity and sensitivity for clinical application have remained elusive until now. Here, we report a pH-driven covalent nanoscale device that integrates pH-responsive, switchable structure and proximity-driven covalent cross-linking. A tumor acidic, pH-driven mechanism eliminates "on-target, off-tumor" nonspecific recognition. By manipulating covalent binding to target molecule on the cell surface, this nanodevice avoids binding-then-shedding to improve the sensitivity of tumor recognition. We envision that this pH-driven covalent nanoscale device will inspire more clinical applications toward specific, long-term tumor imaging in the cancer microenvironment.
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Affiliation(s)
- Jing Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan410082, China
| | - Dan Wang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan410082, China
| | - Hong Chen
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan410082, China
| | - Xi Yuan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan410082, China
| | - Xinyi Jiang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan410082, China
| | - Lili Ai
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan410082, China
| | - Jiaxuan He
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang310022, China
| | - Fengming Chen
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan410082, China
| | - Sitao Xie
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang310022, China
| | - Cheng Cui
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan410082, China
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang310022, China
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai200240, China
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48
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Dong F, Yan W, Dong W, Shang X, Xu Y, Liu W, Wu Y, Wei W, Zhao T. DNA-enabled fluorescent-based nanosensors monitoring tumor-related RNA toward advanced cancer diagnosis: A review. Front Bioeng Biotechnol 2022; 10:1059845. [DOI: 10.3389/fbioe.2022.1059845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 11/18/2022] [Indexed: 12/02/2022] Open
Abstract
As a burgeoning non-invasive indicator for reproducible cancer diagnosis, tumor-related biomarkers have a wide range of applications in early cancer screening, efficacy monitoring, and prognosis predicting. Accurate and efficient biomarker determination, therefore, is of great importance to prevent cancer progression at an early stage, thus reducing the disease burden on the entire population, and facilitating advanced therapies for cancer. During the last few years, various DNA structure-based fluorescent probes have established a versatile platform for biological measurements, due to their inherent biocompatibility, excellent capacity to recognize nucleic and non-nucleic acid targets, obvious accessibility to synthesis as well as chemical modification, and the ease of interfacing with signal amplification protocols. After decades of research, DNA fluorescent probe technology for detecting tumor-related mRNAs has gradually grown to maturity, especially the advent of fluorescent nanoprobes has taken the process to a new level. Here, a systematic introduction to recent trends and advances focusing on various nanomaterials-related DNA fluorescent probes and the physicochemical properties of various involved nanomaterials (such as AuNP, GO, MnO2, SiO2, AuNR, etc.) are also presented in detail. Further, the strengths and weaknesses of existing probes were described and their progress in the detection of tumor-related mRNAs was illustrated. Also, the salient challenges were discussed later, with a few potential solutions.
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49
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Liu J, Li M, Zuo X. DNA Nanotechnology-Empowered Live Cell Measurements. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2204711. [PMID: 36124715 DOI: 10.1002/smll.202204711] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/30/2022] [Indexed: 06/15/2023]
Abstract
The systematic analysis and precise manipulation of a variety of biomolecules should lead to unprecedented findings in fundamental biology. However, conventional technology cannot meet the current requirements. Despite this, there has been progress as DNA nanotechnology has evolved to generate DNA nanostructures and circuits over the past four decades. Many potential applications of DNA nanotechnology for live cell measurements have begun to emerge owing to the biocompatibility, nanometer addressability, and stimulus responsiveness of DNA. In this review, the DNA nanotechnology-empowered live cell measurements which are currently available are summarized. The stability of the DNA nanostructures, in a cellular microenvironment, which is crucial for accomplishing precise live cell measurements, is first summarized. Thereafter, measurements in the extracellular and intracellular microenvironment, in live cells, are introduced. Finally, the challenges that are innate to, and the further developments that are possible in this nascent field are discussed.
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Affiliation(s)
- Jiangbo Liu
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Min Li
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
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50
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Spherical nucleic acids-based biosensors for cancer biomarkers detection. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116807] [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]
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