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Ren X, Wu Y, Deng R, Li J. Single-Cell Imaging of mRNA by Target RNA-Initiated RCA. Methods Mol Biol 2024; 2822:65-75. [PMID: 38907912 DOI: 10.1007/978-1-0716-3918-4_6] [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: 06/24/2024]
Abstract
We present a powerful method for direct mRNA detection based on ligation-based recognition and in situ amplification, capable of single-cell imaging mRNA at single-nucleotide and single-molecule resolution. Attributed to the use of Splint R ligase that can ligate padlock probe with RNA as target template, this method can efficiently detect mRNA in the absence of reverse transcription. This method enables spatial localization and correlation analysis of gene expression in single cells, which helps us to elucidate gene function and regulatory mechanisms.
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Affiliation(s)
- Xiaojun Ren
- Department of Chemistry, College of Chemistry and Life Science, Beijing University of Technology, Beijing, China
| | - Yifan Wu
- Department of Chemistry, College of Chemistry and Life Science, Beijing University of Technology, Beijing, China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, China
| | - Jinghong Li
- Beijing Life Science Academy, Beijing, China.
- Department of Chemistry, Center for BioAnalytical Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, China.
- New Cornerstone Science Laboratory, Shenzhen, China.
- Center for BioAnalytical Chemistry, Hefei National Laboratory of Physical Science at Microscale, University of Science and Technology of China, Hefei, China.
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2
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Zhang M, Wang H, Han J, Wang H, Jia Y, Hong W, Tang F, Li Z. Specific recognition and sensitive quantification of mRNA splice variants via one-pot ligation-dependent loop-mediated isothermal amplification. Analyst 2023; 148:5605-5611. [PMID: 37818948 DOI: 10.1039/d3an01382k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Specific recognition and sensitive quantification of mRNA alternative splice variants have been a necessity for exploring the regulatory mechanism of RNA splicing and revealing the association between pre-mRNA splicing and transcriptome function, as well as disease diagnosis. However, their wide abundance range and high sequence homology pose enormous challenges for high sensitivity and selectivity quantification of splice variants. Herein, taking advantage of the excellent specificity of ligation and the powerful nucleic acid replication feature of loop-mediated isothermal amplification (LAMP), we developed a one-pot method (termed one-pot ligation-LAMP) for specific recognition and sensitive quantification of mRNA splicing variants based on two splicing junction-specific stem-loop DNA probe ligation and the subsequently initiating LAMP. The one-pot ligation-LAMP can specifically detect as low as 100 aM mRNA splice variants without any nonspecific signals and quantify them with a wide dynamics range spanning at least six orders of magnitude. We have demonstrated that the one-pot ligation-LAMP is a versatile and practical strategy for accurately quantifying different splicing variants in complex biological samples with high sensitivity all in one tube within 90 min, thereby providing an attractive tool for mRNA splice variant-related studies.
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Affiliation(s)
- Mai Zhang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China.
| | - Hui Wang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China.
| | - Jun Han
- National Textile and Leather Product Quality Inspection and Testing Centre, 15 Xili-Balizhuang, Chaoyang District, Beijing 100025, China
| | - Honghong Wang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China.
| | - Yuting Jia
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China.
| | - Weixiang Hong
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China.
| | - Fu Tang
- School of Materials Science and Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Zhengping Li
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China.
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3
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Chen X, Deng R, Su D, Ma X, Han X, Wang S, Xia Y, Yang Z, Gong N, Jia Y, Gao X, Ren X. Visual genetic typing of glioma using proximity-anchored in situ spectral coding amplification. EXPLORATION (BEIJING, CHINA) 2023; 3:20220175. [PMID: 37933281 PMCID: PMC10582607 DOI: 10.1002/exp.20220175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 04/21/2023] [Indexed: 11/08/2023]
Abstract
Gliomas are histologically and genetically heterogeneous tumors. However, classical histopathological typing often ignores the high heterogeneity of tumors and thus cannot meet the requirements of precise pathological diagnosis. Here, proximity-anchored in situ spectral coding amplification (ProxISCA) is proposed for multiplexed imaging of RNA mutations, enabling visual typing of brain gliomas with different pathological grades at the single-cell and tissue levels. The ligation-based padlock probe can discriminate one-nucleotide variations, and the design of proximity primers enables the anchoring of amplicons on target RNA, thus improving localization accuracy. The DNA module-based spectral coding strategy can dramatically improve the multiplexing capacity for imaging RNA mutations through one-time labelling, with low cost and simple operation. One-target-one-amplicon amplification confers ProxISCA the ability to quantify RNA mutation copy number with single-molecule resolution. Based on this approach, it is found that gliomas with higher malignant grades express more genes with high correlation at the cellular and tissue levels and show greater cellular heterogeneity. ProxISCA provides a tool for glioma research and precise diagnosis, which can reveal the relationship between cellular heterogeneity and glioma occurrence or development and assist in pathological prognosis.
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Affiliation(s)
- Xiaolei Chen
- Department of Chemistry and BiologyFaculty of Environment and Life ScienceBeijing University of TechnologyBeijingChina
| | - Ruijie Deng
- College of Biomass Science and EngineeringHealthy Food Evaluation Research CenterSichuan UniversityChengduChina
| | - Dongdong Su
- Department of Chemistry and BiologyFaculty of Environment and Life ScienceBeijing University of TechnologyBeijingChina
| | - Xiaochen Ma
- Department of Chemistry and BiologyFaculty of Environment and Life ScienceBeijing University of TechnologyBeijingChina
| | - Xu Han
- Institute of High Energy PhysicsChinese Academy of SciencesBeijingChina
| | - Shizheng Wang
- Department of Chemistry and BiologyFaculty of Environment and Life ScienceBeijing University of TechnologyBeijingChina
| | - Yuqing Xia
- Department of Chemistry and BiologyFaculty of Environment and Life ScienceBeijing University of TechnologyBeijingChina
| | - Zifu Yang
- Department of Chemistry and BiologyFaculty of Environment and Life ScienceBeijing University of TechnologyBeijingChina
| | - Ningqiang Gong
- Department of BioengineeringUniversity of PennsylvaniaPhiladelphiaUSA
| | - Yanwei Jia
- State‐Key Laboratory of Analog and Mixed‐Signal VLSIInstitute of MicroelectronicsUniversity of MacauMacauChina
| | - Xueyun Gao
- Department of Chemistry and BiologyFaculty of Environment and Life ScienceBeijing University of TechnologyBeijingChina
| | - Xiaojun Ren
- Department of Chemistry and BiologyFaculty of Environment and Life ScienceBeijing University of TechnologyBeijingChina
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Shang J, Yu S, Li R, He Y, Wang Y, Wang F. Bioorthogonal Disassembly of Hierarchical DNAzyme Nanogel for High-Performance Intracellular microRNA Imaging. NANO LETTERS 2023; 23:1386-1394. [PMID: 36719793 DOI: 10.1021/acs.nanolett.2c04658] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Rolling circle amplification (RCA) enables the facile construction of compact and versatile DNA nanoassemblies which are yet rarely explored for intracellular analysis. This is might be ascribed to the uncontrollable and inefficient probe integration/activation. Herein, by encoding with tandem allosteric deoxyribozyme (DNA-cleaving DNAzyme), a multifunctional RCA nanogel was established for realizing the efficient intracellular microRNA imaging via the successive activation of the RCA-disassembly module and signal amplification module. The endogenous microRNA stimulates the precise degradation of DNA nanocarriers, thus leading to the efficient exposure of RCA-entrapped DNAzyme biocatalyst for an amplified readout signal. Our bioorthogonal DNAzyme disassembly strategy achieved the robust analysis of intracellular biomolecules, thus showing more prospects in clinical diagnosis.
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Affiliation(s)
- Jinhua Shang
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430072, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Shanshan Yu
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430072, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Ruomeng Li
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430072, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Yuqiu He
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430072, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Yushi Wang
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430072, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Fuan Wang
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430072, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
- Research Institute of Shenzhen, Wuhan University, Shenzhen 518057, P. R. China
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5
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Miao W, Porter DF, Lopez-Pajares V, Siprashvili Z, Meyers RM, Bai Y, Nguyen DT, Ko LA, Zarnegar BJ, Ferguson ID, Mills MM, Jilly-Rehak CE, Wu CG, Yang YY, Meyers JM, Hong AW, Reynolds DL, Ramanathan M, Tao S, Jiang S, Flynn RA, Wang Y, Nolan GP, Khavari PA. Glucose dissociates DDX21 dimers to regulate mRNA splicing and tissue differentiation. Cell 2023; 186:80-97.e26. [PMID: 36608661 PMCID: PMC10171372 DOI: 10.1016/j.cell.2022.12.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 10/17/2022] [Accepted: 12/02/2022] [Indexed: 01/07/2023]
Abstract
Glucose is a universal bioenergy source; however, its role in controlling protein interactions is unappreciated, as are its actions during differentiation-associated intracellular glucose elevation. Azido-glucose click chemistry identified glucose binding to a variety of RNA binding proteins (RBPs), including the DDX21 RNA helicase, which was found to be essential for epidermal differentiation. Glucose bound the ATP-binding domain of DDX21, altering protein conformation, inhibiting helicase activity, and dissociating DDX21 dimers. Glucose elevation during differentiation was associated with DDX21 re-localization from the nucleolus to the nucleoplasm where DDX21 assembled into larger protein complexes containing RNA splicing factors. DDX21 localized to specific SCUGSDGC motif in mRNA introns in a glucose-dependent manner and promoted the splicing of key pro-differentiation genes, including GRHL3, KLF4, OVOL1, and RBPJ. These findings uncover a biochemical mechanism of action for glucose in modulating the dimerization and function of an RNA helicase essential for tissue differentiation.
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Affiliation(s)
- Weili Miao
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Douglas F Porter
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Vanessa Lopez-Pajares
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Zurab Siprashvili
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Robin M Meyers
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yunhao Bai
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Duy T Nguyen
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lisa A Ko
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Brian J Zarnegar
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ian D Ferguson
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA; Program in Cancer Biology, Stanford University, Stanford, CA, USA
| | - Matthew M Mills
- Department of Earth System Science, Stanford University, Stanford, CA, USA
| | | | - Cheng-Guo Wu
- Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yen-Yu Yang
- Department of Chemistry, University of California, Riverside, CA, USA
| | - Jordan M Meyers
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Audrey W Hong
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - David L Reynolds
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Shiying Tao
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Sizun Jiang
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Ryan A Flynn
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, CA, USA
| | - Garry P Nolan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Paul A Khavari
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA; Program in Cancer Biology, Stanford University, Stanford, CA, USA; Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA.
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Xu L, Su X, Liu Z, Zhou A. Predicted Immune-Related Genes and Subtypes in Systemic Lupus Erythematosus Based on Immune Infiltration Analysis. DISEASE MARKERS 2022; 2022:8911321. [PMID: 35864995 PMCID: PMC9296307 DOI: 10.1155/2022/8911321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 12/07/2022]
Abstract
Objective The present investigation is aimed at identifying key immune-related genes linked with SLE and their roles using integrative analysis of publically available gene expression datasets. Methods Four gene expression datasets pertaining to SLE, 2 from whole blood and 2 experimental PMBC, were sourced from GEO. Shared differentially expressed genes (DEG) were determined as SLE-related genes. Immune cell infiltration analysis was performed using CIBERSORT, and case samples were subjected to k-means cluster analysis using high-abundance immune cells. Key immune-related SLE genes were identified using correlation analysis with high-abundance immune cells and subjected to functional enrichment analysis for enriched Gene Ontology Biological Processes and KEGG pathways. A PPI network of genes interacting with the key immune-related SLE genes was constructed. LASSO regression analysis was performed to identify the most significant key immune-related SLE genes, and correlation with clinicopathological features was examined. Results 309 SLE-related genes were identified and found functionally enriched in several pathways related to regulation of viral defenses and T cell functions. k-means cluster analysis identified 2 sample clusters which significantly differed in monocytes, dendritic cell resting, and neutrophil abundance. 65 immune-related SLE genes were identified, functionally enriched in immune response-related signaling, antigen receptor-mediated signaling, and T cell receptor signaling, along with Th17, Th1, and Th2 cell differentiation, IL-17, NF-kappa B, and VEGF signaling pathways. LASSO regression identified 9 key immune-related genes: DUSP7, DYSF, KCNA3, P2RY10, S100A12, SLC38A1, TLR2, TSR2, and TXN. Imputed neutrophil percentage was consistent with their expression pattern, whereas anti-Ro showed the inverse pattern as gene expression. Conclusions Comprehensive bioinformatics analyses revealed 9 key immune-related genes and their associated functions highly pertinent to SLE pathogenesis, subtypes, and identified valuable candidates for experimental research.
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Affiliation(s)
- Lin Xu
- Department of Nephrology, The Affiliated Taian City Centeral Hospital of Qingdao University, Tai'an 271000, Shandong Province, China
| | - Xiaoyan Su
- Intensive Care Unit, The Affiliated Taian City Centeral Hospital of Qingdao University, Tai'an, Shandong Province, China
| | - Zhongcheng Liu
- Department of Neurosurgery, The First People's Hospital of Taian, Tai'an city, Shandong Province, China
| | - Aihong Zhou
- Department of Rheumatology Immunology, The Second Affiliated Hospital of Shandong First Medical University, Shandong Province, China
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Fernandez-Castillo E, Barbosa-Santillán LI, Falcon-Morales L, Sánchez-Escobar JJ. Deep Splicer: A CNN Model for Splice Site Prediction in Genetic Sequences. Genes (Basel) 2022; 13:907. [PMID: 35627292 PMCID: PMC9141016 DOI: 10.3390/genes13050907] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 02/05/2023] Open
Abstract
Many living organisms have DNA in their cells that is responsible for their biological features. DNA is an organic molecule of two complementary strands of four different nucleotides wound up in a double helix. These nucleotides are adenine (A), thymine (T), guanine (G), and cytosine (C). Genes are DNA sequences containing the information to synthesize proteins. The genes of higher eukaryotic organisms contain coding sequences, known as exons and non-coding sequences, known as introns, which are removed on splice sites after the DNA is transcribed into RNA. Genome annotation is the process of identifying the location of coding regions and determining their function. This process is fundamental for understanding gene structure; however, it is time-consuming and expensive when done by biochemical methods. With technological advances, splice site detection can be done computationally. Although various software tools have been developed to predict splice sites, they need to improve accuracy and reduce false-positive rates. The main goal of this research was to generate Deep Splicer, a deep learning model to identify splice sites in the genomes of humans and other species. This model has good performance metrics and a lower false-positive rate than the currently existing tools. Deep Splicer achieved an accuracy between 93.55% and 99.66% on the genetic sequences of different organisms, while Splice2Deep, another splice site detection tool, had an accuracy between 90.52% and 98.08%. Splice2Deep surpassed Deep Splicer on the accuracy obtained after evaluating C. elegans genomic sequences (97.88% vs. 93.62%) and A. thaliana (95.40% vs. 94.93%); however, Deep Splicer's accuracy was better for H. sapiens (98.94% vs. 97.15%) and D. melanogaster (97.14% vs. 92.30%). The rate of false positives was 0.11% for human genetic sequences and 0.25% for other species' genetic sequences. Another splice prediction tool, Splice Finder, had between 1% and 3% of false positives for human sequences, while other species' sequences had around 4% and 10%.
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Affiliation(s)
- Elisa Fernandez-Castillo
- School of Engineering and Sciences, Monterrey Institute of Technology and Higher Education, Guadalajara 45201, Mexico; (L.I.B.-S.); (L.F.-M.)
| | - Liliana Ibeth Barbosa-Santillán
- School of Engineering and Sciences, Monterrey Institute of Technology and Higher Education, Guadalajara 45201, Mexico; (L.I.B.-S.); (L.F.-M.)
| | - Luis Falcon-Morales
- School of Engineering and Sciences, Monterrey Institute of Technology and Higher Education, Guadalajara 45201, Mexico; (L.I.B.-S.); (L.F.-M.)
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8
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Teng X, Dai Y, Li J. Module Assembly Strategy for Single‐Cell Nucleic Acid Imaging at the Sub‐Molecule Level. Chemistry 2022; 28:e202104628. [DOI: 10.1002/chem.202104628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Indexed: 11/11/2022]
Affiliation(s)
- Xucong Teng
- Department of Chemistry Center for BioAnalytical Chemistry Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology Tsinghua University 100084 Beijing P. R. China
| | - Yicong Dai
- Department of Chemistry Center for BioAnalytical Chemistry Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology Tsinghua University 100084 Beijing P. R. China
| | - Jinghong Li
- Department of Chemistry Center for BioAnalytical Chemistry Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology Tsinghua University 100084 Beijing P. R. China
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9
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Du W, Zhang L, Li X, Ling G, Zhang P. Nuclear targeting Subcellular-delivery nanosystems for precise cancer treatment. Int J Pharm 2022; 619:121735. [DOI: 10.1016/j.ijpharm.2022.121735] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 03/27/2022] [Accepted: 04/06/2022] [Indexed: 12/20/2022]
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10
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Chemiluminescent screening of specific hybridoma cells via a proximity-rolling circle activated enzymatic switch. Commun Biol 2022; 5:308. [PMID: 35379898 PMCID: PMC8979942 DOI: 10.1038/s42003-022-03283-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 03/16/2022] [Indexed: 11/12/2022] Open
Abstract
The mass-production capability of hybridoma technology is bottlenecked by the routine screening procedure which is time-consuming and laborious as the requirement of clonal expansion. Here, we describe a 1-day chemiluminescent screening protocol for specific hybridoma cells on conventional 96-well plate via a proximity-rolling circle activated enzymatic switch (P-RCAES) strategy. The P-RCAES uses a pair of antigen-DNA probes to recognize secreted specific antibody and proximity-induce rolling circle amplification for mass-production of pyrophosphate to activate Cu(II) inhibited horseradish peroxidase and generate a strong chemiluminescent signal. The P-RCAES based homogeneous chemiluminescent assay can detect antibody down to 18 fM, and enables the screening of specific hybridoma cells secreting PCSK9 antibody at single-cell level without tedious cloning process. The proposed fast screening protocol has good expansibility without need of sophisticated instruments, and provides a screening method for greatly improving the efficiency of hybridoma technology. In order to realize fast screening of specific hybridoma cells in hybridoma technology, a 1-day chemiluminescent screening method is reported on common 96-well plate via a proximity-rolling circle activated enzymatic switch strategy.
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11
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Wang S, Ma X, Yang Z, Zhang X, Chen X, Xia Y, Gao X, Ren X. Dual-Functional Nanocluster Probe-Based Single-Cell Analysis of RNA Splice Variants. Anal Chem 2022; 94:5014-5022. [PMID: 35298123 DOI: 10.1021/acs.analchem.1c04918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Differential expression of RNA splice variants among individual cells accounts for cell heterogeneity of gene expression, which plays a key role in the regulation of the immune system. However, currently available techniques face difficulties in achieving single-cell analysis of RNA splice variants with high base resolution, high spatial resolution and accurate quantification. Herein, we constructed DNA-templated dual-functional nanocluster probes to achieve in situ imaging and accurate quantification of RNA splice variants at the single-cell level. By designing ultrasmall nanocluster labeled probes to directly target the splicing junction sequence of RNA splice variants, the base recognition resolution is significantly improved. Benefit from the controllable fluorescence of nanoclusters, in situ imaging and genotyping of RNA splice variants are achieved. Due to the atom-precise nanocluster, RNA splice variants can be accurately quantified by laser ablation inductively coupled plasma mass spectrometry at the single-cell level. We further applied the probes to explore the function of MyD88 splice variants in mononuclear macrophages under immune activation. This strategy provides a novel single-cell analysis tool for studying the functional diversity of the immune system and splicing-related immune diseases.
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Affiliation(s)
- Shizheng Wang
- Department of Chemistry and Biology, Faculty of Environment and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Xiaochen Ma
- Department of Chemistry and Biology, Faculty of Environment and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Zifu Yang
- Department of Chemistry and Biology, Faculty of Environment and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Xiangchun Zhang
- Department of Chemistry and Biology, Faculty of Environment and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Xiaolei Chen
- Department of Chemistry and Biology, Faculty of Environment and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Yuqing Xia
- Department of Chemistry and Biology, Faculty of Environment and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Xueyun Gao
- Department of Chemistry and Biology, Faculty of Environment and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Xiaojun Ren
- Department of Chemistry and Biology, Faculty of Environment and Life Science, Beijing University of Technology, Beijing 100124, China
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12
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Ren X, Li J. In Situ Imaging of mRNA Splicing Variants by SpliceRCA. Methods Mol Biol 2022; 2537:197-209. [PMID: 35895266 DOI: 10.1007/978-1-0716-2521-7_12] [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: 06/15/2023]
Abstract
We present a method for multiplexed in situ imaging of individual RNA splicing variants. This method enables quantifying RNA splicing variants with single-molecule resolution, discriminating splicing isoforms with single-base precision as well as analyzing the subcellular localization of transcripts. With this technology, it is possible to study cell heterogeneity of gene expression, potentially helping to decipher rich diversity in posttranscriptional function and assist clinical monitoring.
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Affiliation(s)
- Xiaojun Ren
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, China
- Department of Chemistry and Biology, Faculty of Environment and Life Science, Beijing University of Technology, Beijing, China
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, China.
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13
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Wu X, Che C, Wang X, Du Q, Liang H, Gao P, Xia F. Ionic Signal Enhancement by the Space Charge Effect through the DNA Rolling Circle Amplification on the Outer Surface of Nanochannels. Anal Chem 2021; 93:16043-16050. [PMID: 34807570 DOI: 10.1021/acs.analchem.1c03631] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA species are recognized as a powerful probe for nanochannel analyses to address the issues of specific target recognition and highly efficient signal conversion due to their programmable and predictable Watson-Crick bases. However, in the conventional view, abundant sophisticated DNA structures synthesized by DNA amplification strategies are unsuitable for use in nanochannel analyses owing to their low probability to enter a nanochannel restricted by the smaller opening of the nanochannel, as well as the faint ion signal produced by the steric effect. Here, we present an integrated strategy of nanochannel analyses that combines the target recognitions by encoded rolling circle amplification (RCA) in solution and the ionic signal enhancement by the space charge effect through the immobilization of highly negative-charged RCA amplicons on the outer surface of the nanochannels. Owing to the highly negative-charged RCA amplicons with 100 nm sizes, a sharp increase of ionic current up to 7454% has been achieved. The RCA amplicon triggered by mRNA-21 on the outer surface of the poly(ethylene terephthalate) membrane with a single nanochannel realized the single-base mismatch detection of mRNA-21 with a sensitivity of 6 fM. The DNA amplicon endows the nanochannel with high sensitivity and selectivity that could extend to other applications, such as DNA sequencing, desalination, sieving, and water-energy nexus.
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Affiliation(s)
- Xiaoqing Wu
- State Key Laboratory of Biogeology and Envi-ronmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, P. R. China
| | - Cheng Che
- State Key Laboratory of Biogeology and Envi-ronmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, P. R. China
| | - Xinmeng Wang
- State Key Laboratory of Biogeology and Envi-ronmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, P. R. China
| | - Qiujiao Du
- School of Mathematics and Physics, China University of Geosciences, Wuhan 430074, P. R. China
| | - Huageng Liang
- Department of Urology, Union Hospital, Tongji Medical College, School of Materials Science and Engineering, Huazhong University of Since and Technology, Wuhan 430022, P. R. China
| | - Pengcheng Gao
- State Key Laboratory of Biogeology and Envi-ronmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, P. R. China
| | - Fan Xia
- State Key Laboratory of Biogeology and Envi-ronmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, P. R. China
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14
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Zhen W, An S, Wang S, Hu W, Li Y, Jiang X, Li J. Precise Subcellular Organelle Targeting for Boosting Endogenous-Stimuli-Mediated Tumor Therapy. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2101572. [PMID: 34611949 DOI: 10.1002/adma.202101572] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/15/2021] [Indexed: 06/13/2023]
Abstract
Though numerous external-stimuli-triggered tumor therapies, including phototherapy, radiotherapy, and sonodynamic therapy have made great progress in cancer therapy, the low penetration depth of the laser, safety concerns of radiation, the therapeutic resistance, and the spatio-temporal constraints of the specific equipment restrict their convenient clinical applications. What is more, the inherent physiological barriers of the tumor microenvironment (TME), including hypoxia, heterogeneity, and high expression of antioxidant molecules also restrict the efficiency of tumor therapy. As a result, the development of nanoplatforms responsive to endogenous stimuli (such as glucose, acidic pH, cellular redox events, and etc.) has attracted great attention for starvation therapy, ion therapy, prodrug-mediated chemotherapy, or enzyme-catalyzed therapy. In addition, nanomedicines can be modified by some targeted units for precisely locating in subcellular organelles and boosting the destroying of tumor tissue, decreasing the dosage of nanoagents, reducing side effects, and enhancing the therapeutic efficiency. Herein, the properties of the TME, the advantages of endogenous stimuli, and the principles of subcellular-organelle-targeted strategies will be emphasized. Some necessary considerations for the exploitation of precision medicine and clinical translation of multifunctional nanomedicines in the future are also pointed out.
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Affiliation(s)
- Wenyao Zhen
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Shangjie An
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Shuqi Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Wenxue Hu
- Shenyang University of Chemical Technology, Shenyang, Liaoning, 110142, China
| | - Yujie Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Xiue Jiang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, 100084, China
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15
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Yang Q, Yang F, Dai W, Meng X, Wei W, Cheng Y, Dong J, Lu H, Dong H. DNA Logic Circuits for Multiple Tumor Cells Identification Using Intracellular MicroRNA Molecular Bispecific Recognition. Adv Healthc Mater 2021; 10:e2101130. [PMID: 34486246 DOI: 10.1002/adhm.202101130] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 08/11/2021] [Indexed: 12/19/2022]
Abstract
The aberrant expression level of intracellular microRNAs (miRNAs) holds great promise for differentiating cell types at the molecular level. However, cell subtype discrimination based on a single miRNA molecular level is not sufficient and reliable. Herein, multiple identifiable and reporting modules are integrated into a single DNA circuit for multiple cancer cell subtypes identification based on miRNAs bispecific recognition. The DNA three-dimensional (3D) logic gate nano-hexahedron framework extends three recognition modules and three reporting modules to form three "AND" logic gates. Each Boolean operator "AND" returns an "ON" signal in the presence of bispecific miRNAs, simultaneously enabling three types of cell subtype identification. It not only enables the discrimination of cancer cells A549 and MCF-7 from normal cells NHDF but also successfully distinguishes different types of cancer cells. The bispecific intracellular miRNA controllable DNA circuit, with low signal-to-noise ratio, easily extends to various cell type discrimination by adjusting the miRNA species, provides huge opportunities for accurately differentiating multiple cell types at the molecular level.
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Affiliation(s)
- Qiqi Yang
- Beijing Key Laboratory for Bioengineering and Sensing Technology Department of Chemistry & Biological Engineering University of Science and Technology Beijing Beijing 100083 P. R. China
| | - Fan Yang
- Beijing Key Laboratory for Bioengineering and Sensing Technology Department of Chemistry & Biological Engineering University of Science and Technology Beijing Beijing 100083 P. R. China
| | - Wenhao Dai
- Beijing Key Laboratory for Bioengineering and Sensing Technology Department of Chemistry & Biological Engineering University of Science and Technology Beijing Beijing 100083 P. R. China
| | - Xiangdan Meng
- Beijing Key Laboratory for Bioengineering and Sensing Technology Department of Chemistry & Biological Engineering University of Science and Technology Beijing Beijing 100083 P. R. China
| | - Wei Wei
- Beijing Key Laboratory for Bioengineering and Sensing Technology Department of Chemistry & Biological Engineering University of Science and Technology Beijing Beijing 100083 P. R. China
| | - Yaru Cheng
- Beijing Key Laboratory for Bioengineering and Sensing Technology Department of Chemistry & Biological Engineering University of Science and Technology Beijing Beijing 100083 P. R. China
| | - Jinhong Dong
- Beijing Key Laboratory for Bioengineering and Sensing Technology Department of Chemistry & Biological Engineering University of Science and Technology Beijing Beijing 100083 P. R. China
| | - Huiting Lu
- Department of Chemistry School of Chemistry and Bioengineering University of Science and Technology Beijing Beijing 100083 P. R. China
| | - Haifeng Dong
- Beijing Key Laboratory for Bioengineering and Sensing Technology Department of Chemistry & Biological Engineering University of Science and Technology Beijing Beijing 100083 P. R. China
- Department of Chemistry School of Chemistry and Bioengineering University of Science and Technology Beijing Beijing 100083 P. R. China
- Marshall Laboratory of Biomedical Engineering School of Biomedical Engineering Health Science Centre Shenzhen University Shenzhen 518071 P. R. China
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16
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Ren X, Deng R, Zhang K, Sun Y, Li Y, Li J. Single‐Cell Imaging of m
6
A Modified RNA Using m
6
A‐Specific In Situ Hybridization Mediated Proximity Ligation Assay (m
6
AISH‐PLA). Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202109118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Xiaojun Ren
- Department of Chemistry Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology Tsinghua University Beijing 100084 China
- Department of Chemistry and Biology Faculty of Environment and Life Science Beijing University of Technology Beijing 100124 China
| | - Ruijie Deng
- Department of Chemistry Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology Tsinghua University Beijing 100084 China
| | - Kaixiang Zhang
- Department of Chemistry Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology Tsinghua University Beijing 100084 China
| | - Yupeng Sun
- Department of Chemistry Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology Tsinghua University Beijing 100084 China
| | - Yue Li
- Department of Chemistry Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology Tsinghua University Beijing 100084 China
| | - Jinghong Li
- Department of Chemistry Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology Tsinghua University Beijing 100084 China
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17
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Bai M, Cao X, Chen F, Xue J, Zhao Y, Zhao Y. Bioorthogonal Chemical Signature Enabling Amplified Visualization of Cellular Oxidative Thymines. Anal Chem 2021; 93:10495-10501. [PMID: 34293865 DOI: 10.1021/acs.analchem.1c01285] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Cellular oxidative thymines, 5-hydroxymethyluracil (5hmU) and 5-formyluracil (5fU), are found in the genomes of a diverse range of organisms, the distribution of which profoundly influence biological processes and living systems. However, the distribution of cellular oxidative thymines has not been explored because of lacking both specific bioorthogonal labeling and sensitivity methods for single-cell analysis. Herein, we report a bioorthogonal chemical signature enabling amplified visualization of cellular oxidative thymines in single cells. The synthesized ATP-γ-alkyne, an ATP analogue with bioorthogonal tag modified on γ-phosphate can be specifically linked to cellular 5hmU by chemoenzymatic labeling. DNA with 5-alkynephosphomethyluracil were then clicked with azide (N3)-modified 5hmU-primer. Identification of 5fU is based on selective reduction from 5fU to 5hmU, subsequent chemoenzymatic labeling of the newly generated 5hmU, and cross-linking with N3-modified 5fU-primer via click chemistry. Then, all of the 5hmU and 5fU sites are encoded with respective circularized barcodes. These barcodes are simultaneously amplified for multiplexed single-molecule imaging. The above two kinds of barcodes can be simultaneously amplified for differentiated visualization of 5hmU and 5fU in single cells. We find these two kinds of cellular oxidative thymines are spatially organized in a cell-type-dependent style with cell-to-cell heterogeneity. We also investigate their multilevel subcellular information and explore their dynamic changes during cell cycles. Further, using DNA sequencing instead of fluorescence imaging, our proposed bioorthogonal chemical signature holds great potential to offer the sequence information of these oxidative thymines in cells and may provide a reliable chemical biology approach for studying the whole-genome oxidative thymines profiles and insights into their functional role and dynamics in biology.
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Affiliation(s)
- Min Bai
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xianning West Road, Xi'an 710049, Shaanxi, P. R. China
| | - Xiaowen Cao
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xianning West Road, Xi'an 710049, Shaanxi, P. R. China
| | - Feng Chen
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xianning West Road, Xi'an 710049, Shaanxi, P. R. China
| | - Jing Xue
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xianning West Road, Xi'an 710049, Shaanxi, P. R. China
| | - Yue Zhao
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xianning West Road, Xi'an 710049, Shaanxi, P. R. China
| | - Yongxi Zhao
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xianning West Road, Xi'an 710049, Shaanxi, P. R. China
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18
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Ren X, Deng R, Zhang K, Sun Y, Li Y, Li J. Single-Cell Imaging of m 6 A Modified RNA Using m 6 A-Specific In Situ Hybridization Mediated Proximity Ligation Assay (m 6 AISH-PLA). Angew Chem Int Ed Engl 2021; 60:22646-22651. [PMID: 34291539 DOI: 10.1002/anie.202109118] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Indexed: 12/31/2022]
Abstract
N6 -methyladenosine (m6 A) modification-the most prevalent mammalian RNA internal modification-plays key regulatory roles in mRNA metabolism. Current approaches for m6 A modified RNA analysis limit at bulk-population level, resulting in a loss of spatiotemporal and cell-to-cell variability information. Here we proposed a m6 A-specific in situ hybridization mediated proximity ligation assay (m6 AISH-PLA) for cellular imaging of m6 A RNA, allowing to identify m6 A modification at specific location in RNAs and image m6 A RNA with single-cell and single-molecule resolution. Using m6 AISH-PLA, we investigated the m6 A level and subcellular location of HSP70 RNA103-m6 A in response to heat shock stress, and found an increased m6 A modified ratio and an increased distribution ratio in cytoplasm under heat shock. m6 AISH-PLA can serve in the study of m6 A RNA in single cells for deciphering epitranscriptomic mechanisms and assisting clinical diagnosis.
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Affiliation(s)
- Xiaojun Ren
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
- Department of Chemistry and Biology, Faculty of Environment and Life Science, Beijing University of Technology, Beijing, 100124, China
| | - Ruijie Deng
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Kaixiang Zhang
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Yupeng Sun
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Yue Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
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19
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Gong X, Wang H, Li R, Tan K, Wei J, Wang J, Hong C, Shang J, Liu X, Liu J, Wang F. A smart multiantenna gene theranostic system based on the programmed assembly of hypoxia-related siRNAs. Nat Commun 2021; 12:3953. [PMID: 34172725 PMCID: PMC8233311 DOI: 10.1038/s41467-021-24191-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 06/08/2021] [Indexed: 02/06/2023] Open
Abstract
The systemic therapeutic utilisation of RNA interference (RNAi) is limited by the non-specific off-target effects, which can have severe adverse impacts in clinical applications. The accurate use of RNAi requires tumour-specific on-demand conditional activation to eliminate the off-target effects of RNAi, for which conventional RNAi systems cannot be used. Herein, a tumourous biomarker-activated RNAi platform is achieved through the careful design of RNAi prodrugs in extracellular vesicles (EVs) with cancer-specific recognition/activation features. These RNAi prodrugs are assembled by splitting and reconstituting the principal siRNAs into a hybridisation chain reaction (HCR) amplification machine. EVs facilitate the specific and efficient internalisation of RNAi prodrugs into target tumour cells, where endogenous microRNAs (miRNAs) promote immediate and autonomous HCR-amplified RNAi activation to simultaneously silence multiantenna hypoxia-related genes. With multiple guaranteed cancer recognition and synergistic therapy features, the miRNA-initiated HCR-promoted RNAi cascade holds great promise for personalised theranostics that enable reliable diagnosis and programmable on-demand therapy.
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Affiliation(s)
- Xue Gong
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, P. R. China
| | - Haizhou Wang
- Department of Gastroenterology, Zhongnan Hospital, Wuhan University, Wuhan, P. R. China
| | - Ruomeng Li
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, P. R. China
| | - Kaiyue Tan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, P. R. China
| | - Jie Wei
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, P. R. China
| | - Jing Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, P. R. China
| | - Chen Hong
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, P. R. China
| | - Jinhua Shang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, P. R. China
| | - Xiaoqing Liu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, P. R. China.
| | - Jing Liu
- Department of Gastroenterology, Zhongnan Hospital, Wuhan University, Wuhan, P. R. China
| | - Fuan Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, P. R. China.
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20
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Zhao Z, Yang H, Zhao W, Deng S, Zhang K, Deng R, He Q, Gao H, Li J. Graphene-nucleic acid biointerface-engineered biosensors with tunable dynamic range. J Mater Chem B 2021; 8:3623-3630. [PMID: 31934712 DOI: 10.1039/c9tb02388g] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Programmed biosensors with tunable quantification range and sensitivity would greatly broaden their application in medical diagnosis, food safety and environmental analysis. Herein, we proposed a graphene-nucleic acid biointerface-engineered biosensor, allowing target molecules to be detected with adjustable dynamic ranges and sensitivities. The biosensors were programmed by simply tuning the poly A tail of aptamer probes. The tuning of the poly A tail would allow the interaction between aptamer probes and graphene oxide (GO) to be modulated, in turn programing the competitive binding processes of aptamer probes to target molecules and GO. The biosensors, termed affinity-tunable aptasensors (atAptasensors) could be easily tuned with different dynamic ranges by using aptamer probes with different tail lengths, and the dynamic range could be extended to be over 3 orders by a combined use of multiple aptamer probes. Remarkably, the specificity of aptamer probes could be increased by increasing the interaction between aptamer probes and GO. Reliability of atAptasensor for ATP detection was tested in serum and milk samples, and we also applied atAptasensor for culture-independent analysis of microorganism pollution.
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Affiliation(s)
- Zhifeng Zhao
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China.
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21
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Lysosomal escaped protein nanocarriers for nuclear-targeted siRNA delivery. Anal Bioanal Chem 2021; 413:3493-3499. [PMID: 33770206 DOI: 10.1007/s00216-021-03297-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/27/2021] [Accepted: 03/16/2021] [Indexed: 01/25/2023]
Abstract
In the process of drug carrier design, lysosome degradation in cells is often neglected, which makes a considerable number of drugs not play a role. Here, we have constructed a tumor treatment platform (Apn/siRNA/NLS/HA/Apt) with unique lysosomal escape function and excellent cancer treatment effect. Apoferritin (Apn) has attracted more and more attention because of its high uniformity, modifiability, and controllability. Meanwhile, its endogenous nature can avoid the risk of immune response being eliminated. We used aptamer modified iron deficient protein nanocages (Apn) to tightly encapsulate the combination of siRNA and NLS (siRNA/NLS) with influenza virus hemagglutinin (HA peptide). After Apn/siRNA/NLS/HA/Apt was targeted into cells, the acidic environment of lysosome led to the cleavage of Apn nanocages, and the release of siRNA/NLS and HA peptide. HA peptide can destroy lysosome membrane, make siRNA/NLS escape lysosome, and enter the nucleus under the action of NLS, resulting in efficient gene silencing effect. This kind of cancer treatment strategy based on Apn nanocage shows high biocompatibility and unique lysosome escape property, which significantly improves the drug delivery and treatment efficiency. Lysosomal escape protein nanocarriers for nuclear-targeted siRNA delivery.
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22
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Jia Y, Shen X, Sun F, Na N, Ouyang J. Metal-DNA coordination based bioinspired hybrid nanospheres for in situ amplification and sensing of microRNA. J Mater Chem B 2020; 8:11074-11081. [PMID: 33201165 DOI: 10.1039/d0tb02315a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Sufficient delivery of biomolecules into cells with high loading efficiency and easy cleavability would be significant for the visualization of biomolecules in living cells. Herein, a facile approach based on nano-wire balls (NWs) for efficient loading, intracellular delivery of nucleic acids and in situ targeted miRNA bioimaging is proposed, by feeding of Zn ions for generating DNA-inorganic hybrid structures with large surface areas and good stability. Given that the versatile and robust hybridization chain reaction (HCR) amplification strategy combines DNA assembly with intracellular assay, the resulting NWs without any complicated modification are capable of enhanced signals for the targeted imaging of cancer cells. This method realized a linear detection range of 100 fM to 10 nM, with a low detection limit of 83.6 fM in vitro, and could be used to effectively differentiate the expression levels of miRNA-21 in living cells. Due to its high loading efficiency, excellent biocompatibility and low toxicity, this system can be used to construct a coordination-based delivery nanoplatform for in situ enzyme-free amplified imaging of miRNAs, expanding the application of DNA-based nanomaterials for cellular delivery and intracellular molecule analysis.
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Affiliation(s)
- Yijing Jia
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.
| | - Xiaotong Shen
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Feifei Sun
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.
| | - Na Na
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.
| | - Jin Ouyang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.
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23
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Zhang K, Deng R, Gao H, Teng X, Li J. Lighting up single-nucleotide variation in situ in single cells and tissues. Chem Soc Rev 2020; 49:1932-1954. [PMID: 32108196 DOI: 10.1039/c9cs00438f] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The ability to 'see' genetic information directly in single cells can provide invaluable insights into complex biological systems. In this review, we discuss recent advances of in situ imaging technologies for visualizing the subtlest sequence alteration, single-nucleotide variation (SNV), at single-cell level. The mechanism of recently developed methods for SNV discrimination are summarized in detail. With recent developments, single-cell SNV imaging methods have opened a new door for studying the heterogenous and stochastic genetic information in individual cells. Furthermore, SNV imaging can be used on morphologically preserved tissue, which can provide information on histological context for gene expression profiling in basic research and genetic diagnosis. Moreover, the ability to visualize SNVs in situ can be further developed into in situ sequencing technology. We expect this review to inspire more research work into in situ SNV imaging technologies for investigating cellular phenotypes and gene regulation at single-nucleotide resolution, and developing new clinical and biomedical applications.
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Affiliation(s)
- Kaixiang Zhang
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China. and School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Ruijie Deng
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China.
| | - Hua Gao
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China. and Department of Pathogeny Biology, Medical College, Zhengzhou University, Zhengzhou 450001, China
| | - Xucong Teng
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China.
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China.
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24
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Affiliation(s)
- Peng Gao
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China
| | - Yuanyuan Chen
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China
| | - Wei Pan
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China
| | - Na Li
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China
| | - Bo Tang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China
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25
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Hu Y, Chu X, Chen TT, Pan Q, Liu C, Yi J, Chu X. Improving resolving ability of expansion microscopy by varying crosslinker concentration. Chem Commun (Camb) 2020; 56:4176-4179. [PMID: 32167109 DOI: 10.1039/d0cc00052c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here, we systematically investigated the performance of expansion microscopy (ExM) with different crosslinker concentrations. We modified ExM with 0.06% N,N'-methylenebisacrylamide (MBAA) (termed 0.06%-MBAA ExM), increased the expansion factor to 5.7 and achieved a lateral resolution of ∼50 nm with a common confocal microscope.
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Affiliation(s)
- Yanlei Hu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China.
| | - Ximing Chu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China.
| | - Ting-Ting Chen
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China.
| | - Qingshan Pan
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China.
| | - Chang Liu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China.
| | - Jintao Yi
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China.
| | - Xia Chu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China.
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26
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Wang G, Tian W, Liu X, Ren W, Liu C. New CRISPR-Derived microRNA Sensing Mechanism Based on Cas12a Self-Powered and Rolling Circle Transcription-Unleashed Real-Time crRNA Recruiting. Anal Chem 2020; 92:6702-6708. [DOI: 10.1021/acs.analchem.0c00680] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Gaoting Wang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi’an 710119, Shaanxi Province, P. R. China
| | - Weimin Tian
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi’an 710119, Shaanxi Province, P. R. China
| | - Xiaoling Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi’an 710119, Shaanxi Province, P. R. China
| | - Wei Ren
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi’an 710119, Shaanxi Province, P. R. China
| | - Chenghui Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi’an 710119, Shaanxi Province, P. R. China
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27
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Wei J, Zhao Z, Gao J, Wang Y, Ma L, Meng X, Wang Z. Polyacrylamide/Phytic Acid/Polydopamine Hydrogel as an Efficient Substrate for Electrochemical Enrichment of Circulating Cell-Free DNA from Blood Plasma. ACS OMEGA 2020; 5:5365-5371. [PMID: 32201826 PMCID: PMC7081438 DOI: 10.1021/acsomega.9b04397] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 02/20/2020] [Indexed: 05/26/2023]
Abstract
A facile method has been developed for the rapid and efficient enrichment of DNAs from different media including synthetic single-strand DNAs (ssDNAs) from buffer solutions and cell-free DNAs (cfDNAs) from blood plasma through electric field-driven adsorption and desorption of DNAs by a polyacrylamide/phytic acid/polydopamine (PAAM/PA/PDA) hydrogel. The as-prepared PAAM/PA/PDA hydrogel possesses regular porosity with a large surface area, strong electric field responsiveness/good conductivity, and a rich aromatic structure, which can be used as an ideal adsorbent for DNA enrichment under a positive electric field. The enriched DNAs can be released efficiently when the positive electric field is converted to a negative electric field. The PAAM/PA/PDA hydrogel-based electrochemical method enables the completion of the process of DNA adsorption and release within 5 min and exhibits reasonable enrichment efficiencies and recovery rates of various DNAs. For instance, the high enrichment sensitivity (0.1 pmol L-1) together with the excellent recovery (>75%) of an ssDNA with 78 nucleotides is obtained. Combined with the PCR amplification technique, the practicability of the as-proposed method is demonstrated by the screening of circulating tumor DNAs (ctDNAs) with a BRAFV600E mutation in cfDNAs from the blood plasma samples of patients with papillary thyroid cancer or thyroid nodule and random patients from a clinical laboratory.
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Affiliation(s)
- Jia Wei
- Department
of Thyroid Surgery, The First Hospital of
Jilin University, Changchun, Jilin 130021, P. R. China
| | - Zhen Zhao
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
| | - Jiaxue Gao
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
| | - Yaoqi Wang
- Department
of Thyroid Surgery, The First Hospital of
Jilin University, Changchun, Jilin 130021, P. R. China
| | - Lina Ma
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
| | - Xianying Meng
- Department
of Thyroid Surgery, The First Hospital of
Jilin University, Changchun, Jilin 130021, P. R. China
| | - Zhenxin Wang
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
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28
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Wei J, Wang H, Wu Q, Gong X, Ma K, Liu X, Wang F. A Smart, Autocatalytic, DNAzyme Biocircuit for in Vivo, Amplified, MicroRNA Imaging. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201911712] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Jie Wei
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)College of Chemistry and Molecular SciencesWuhan University 430072 Wuhan P. R. China
| | - Huimin Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)College of Chemistry and Molecular SciencesWuhan University 430072 Wuhan P. R. China
| | - Qiong Wu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)College of Chemistry and Molecular SciencesWuhan University 430072 Wuhan P. R. China
| | - Xue Gong
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)College of Chemistry and Molecular SciencesWuhan University 430072 Wuhan P. R. China
| | - Kang Ma
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)College of Chemistry and Molecular SciencesWuhan University 430072 Wuhan P. R. China
| | - Xiaoqing Liu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)College of Chemistry and Molecular SciencesWuhan University 430072 Wuhan P. R. China
| | - Fuan Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)College of Chemistry and Molecular SciencesWuhan University 430072 Wuhan P. R. China
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29
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Wei J, Wang H, Wu Q, Gong X, Ma K, Liu X, Wang F. A Smart, Autocatalytic, DNAzyme Biocircuit for in Vivo, Amplified, MicroRNA Imaging. Angew Chem Int Ed Engl 2020; 59:5965-5971. [PMID: 31961985 DOI: 10.1002/anie.201911712] [Citation(s) in RCA: 126] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 11/30/2019] [Indexed: 01/07/2023]
Abstract
DNAzymes have been recognized as promising transducing agents for visualizing endogenous biomarkers, but their inefficient intracellular delivery and limited amplification capacity (including insufficient cofactor supply) preclude their extensive biological application. Herein, an autocatalytic DNAzyme (ACD) biocircuit is constructed for amplified microRNA imaging in vivo based on a hybridization chain reaction (HCR) and DNAzyme biocatalysis, sustained by a honeycomb MnO2 nanosponge (hMNS). The hMNS not only delivers DNA probes, but also supplies Mn2+ as a DNAzyme cofactor and magnetic resonance imaging (MRI) agent. Through the subsequent cross-activation of HCR and DNAzyme amplicons, the ACD amplifies the limited signal resulting from miRNA recognition. The hMNS/ACD system was used to image microRNA in vivo, thus demonstrating its great promise in cancer diagnosis.
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Affiliation(s)
- Jie Wei
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Huimin Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Qiong Wu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Xue Gong
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Kang Ma
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Xiaoqing Liu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Fuan Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, P. R. China
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30
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Ge J, Qi Z, Zhang L, Shen X, Shen Y, Wang W, Li Z. Label-free and enzyme-free detection of microRNA based on a hybridization chain reaction with hemin/G-quadruplex enzymatic catalysis-induced MoS 2 quantum dots via the inner filter effect. NANOSCALE 2020; 12:808-814. [PMID: 31830179 DOI: 10.1039/c9nr08154b] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A new simple, sensitive and specific strategy for microRNA analysis has been described based on a hybridization chain reaction with hemin/G-quadruplex enzymatic catalysis-induced MoS2 quantum dots via the inner filter effect. The target microRNA triggers the hybridization chain reaction between two DNA probes to generate long dsDNA with many hemin/G-quadruplex DNAzymes in the presence of hemin. With the assistance of H2O2, the produced hemin/G-quadruplex DNAzyme could oxidize o-phenylenediamine (OPD) to 2,3-diaminophenazine (DAP) directly, resulting in the fluorescence quenching of MoS2 quantum dots via the inner filter effect. As an example, the fluorescence response of MoS2 quantum dots is linearly related with the logarithm of the microRNA let-7a concentration with a detection limit of 42 fM. The proposed label-free assay has promising potential to be applied in practical diagnosis.
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Affiliation(s)
- Jia Ge
- College of Chemistry, Green Catalysis Center, Zhengzhou University, Zhengzhou 450001, P. R. China.
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31
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Gao H, Zhang K, Teng X, Li J. Rolling circle amplification for single cell analysis and in situ sequencing. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.115700] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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32
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Zhang M, Ye J, He JS, Zhang F, Ping J, Qian C, Wu J. Visual detection for nucleic acid-based techniques as potential on-site detection methods. A review. Anal Chim Acta 2019; 1099:1-15. [PMID: 31986265 DOI: 10.1016/j.aca.2019.11.056] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 11/21/2019] [Accepted: 11/22/2019] [Indexed: 12/15/2022]
Abstract
Nucleic acid-based techniques could achieve highly sensitive detection by amplifying template molecules to millions of folds. It has been one of the most valued analytical methods and is applied in many detection fields, such as diagnosis of infectious diseases, food safety assurance and so on. Nucleic acid-based techniques consist of three steps: nucleic acid extraction, amplification, and product detection. Among them, the detection step plays a vital role because it shows the results directly. As the trend of detection is simple, rapid and instrument-free, it is of necessity to carry out visual detection, where the result read-out could be visible and distinguished by the naked eye. In this critical review, advanced visual detection methods are summarized and discussed in detail, aiming to promote the potential application in on-site detection.
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Affiliation(s)
- Mengyao Zhang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Jing Ye
- Zhijiangnan Think Tank, Zhejiang Institute of Science and Technology Information, Hangzhou, 310006, China
| | - Jin-Song He
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201, China.
| | - Fang Zhang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, 350108, China
| | - Jianfeng Ping
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Cheng Qian
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Jian Wu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China; Key Laboratory of on Site Processing Equipment for Agricultural Products, Ministry of Agriculture, Hangzhou, 310058, China.
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33
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Song F, Deng R, Liu H, Wang A, Ma C, Wei Y, Cui X, Wan Y, Li J. Trypsin-Amplified Aerolysin Nanopore Amplified Sandwich Assay for Attomolar Nucleic Acid and Single Bacteria Detection. Anal Chem 2019; 91:14043-14048. [PMID: 31577421 DOI: 10.1021/acs.analchem.9b03717] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Nanopore technology is promising for the next-generation of nucleic acid-based diagnosis. However, sequence reservation could still be hardly achieved in low-concentration. Herein, we propose a trypsin-activated catalysis reaction for amplified detection, which substantially improves the sensitivity of nanopore technique. The proposed trypsin-amplified nanopore amplified sandwich assay (tNASA) could contribute to a sensitivity approximately 100 000 times higher based on nucleic acid probe design. Remarkably, tNASA is capable of attomolar nucleic acid and single cell detection by using a miniaturized current amplifier without alignment algorithm. Also it allows 10 pathogenic species in serum to be accurately and robustly profiled, thus be utilized for the diagnosis of infectious diseases. tNASA may evolve the construction of nanopore techniques for nucleic acid detection and would facilitate its translation for pocket diagnosis and precision medicine.
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Affiliation(s)
- Fengge Song
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Marine College, State Key Laboratory of Marine Resource Utilization in South China Sea , Hainan University , Haikou 570228 , China
| | - Ruijie Deng
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology , Tsinghua University , Beijing 100084 , China.,College of Light Industry, Textile and Food Engineering and Healthy Food Evaluation Research Centre , Sichuan University , Chengdu 610065 , China
| | - Hong Liu
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Marine College, State Key Laboratory of Marine Resource Utilization in South China Sea , Hainan University , Haikou 570228 , China
| | - Aimin Wang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Marine College, State Key Laboratory of Marine Resource Utilization in South China Sea , Hainan University , Haikou 570228 , China
| | - Chunxin Ma
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Marine College, State Key Laboratory of Marine Resource Utilization in South China Sea , Hainan University , Haikou 570228 , China
| | - Yangdao Wei
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Marine College, State Key Laboratory of Marine Resource Utilization in South China Sea , Hainan University , Haikou 570228 , China
| | - Xiaojian Cui
- National Marine Data & Information Service , Tianjin 300170 , China
| | - Yi Wan
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Marine College, State Key Laboratory of Marine Resource Utilization in South China Sea , Hainan University , Haikou 570228 , China.,Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology , Tsinghua University , Beijing 100084 , China
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology , Tsinghua University , Beijing 100084 , China
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34
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Yang H, Zhao W, Deng S, Zhang K, Zhao Z, Deng R, He Q, Li J. Intrinsic Conformation-Induced Fluorescence Resonance Energy Transfer Aptasensor. ACS APPLIED BIO MATERIALS 2019; 3:2553-2559. [DOI: 10.1021/acsabm.9b00738] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Hao Yang
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Wenyue Zhao
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Sha Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Kaixiang Zhang
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Zhifeng Zhao
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Qiang He
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
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35
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Wang H, Wang H, Wu Q, Liang M, Liu X, Wang F. A DNAzyme-amplified DNA circuit for highly accurate microRNA detection and intracellular imaging. Chem Sci 2019; 10:9597-9604. [PMID: 32055333 PMCID: PMC7006504 DOI: 10.1039/c9sc03552d] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 08/25/2019] [Indexed: 12/27/2022] Open
Abstract
A rationally and modularly engineered CHA-HCR-DNAzyme circuit was constructed for amplified biosensing and bioimaging with high performance.
Biomolecular self-assembly circuits have been well developed for high-performance biosensing and bioengineering applications. Here we designed an isothermal concatenated nucleic acid amplification system which is composed of a lead-in catalyzed hairpin assembly (CHA), intermediate hybridization chain reaction (HCR) and ultimate DNAzyme amplifier units. The analyte initiates the self-assembly of hairpin reactants into dsDNA products in CHA, which generates numerous trigger sequences for activating the subsequent HCR-assembled long tandem DNAzyme nanowires. The as-acquired DNAzyme catalyzed the successive cleavage of its substrates, leading to an amplified fluorescence readout. The sophisticated design of our CHA-HCR-DNAzyme scheme was systematically investigated in vitro and showed dramatically enhanced detection performance. As a general sensing strategy, this CHA-HCR-DNAzyme method enables the amplified analysis of miRNA and its accurate intracellular imaging in living cells, originating from their synergistic signal amplifications. This method shows great potential for analyzing trace amounts of biomarkers in various clinical research studies.
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Affiliation(s)
- Hong Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , P. R. China .
| | - Huimin Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , P. R. China .
| | - Qiong Wu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , P. R. China .
| | - Meijuan Liang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , P. R. China .
| | - Xiaoqing Liu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , P. R. China .
| | - Fuan Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , P. R. China .
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36
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Qian C, Wang R, Wu H, Zhang F, Wu J, Wang L. Uracil-Mediated New Photospacer-Adjacent Motif of Cas12a To Realize Visualized DNA Detection at the Single-Copy Level Free from Contamination. Anal Chem 2019; 91:11362-11366. [DOI: 10.1021/acs.analchem.9b02554] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Cheng Qian
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Rui Wang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Hui Wu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Fang Zhang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China
| | - Jian Wu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Liu Wang
- Institute of Quality and Standards for Agro-products, Zhejiang Academy of Agricultural Sciences, State Key Laboratory of Quality and Safety of Agro-products, Hangzhou 310021, China
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