1
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Hu Y, Cui Y, Zhang Z, Zhang X, Ma X, Qiao Z, Zheng F, Feng F, Liu W, Han L. A Dual-Recognition Fluorescence Enzyme-Linked Immunosorbent Assay for Specific Detection of Intact Lipid Nanoparticles via a Localized Scaffolding Autocatalytic DNA Circuit Amplifier. Anal Chem 2024; 96:11205-11215. [PMID: 38967035 DOI: 10.1021/acs.analchem.4c00455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2024]
Abstract
Lipid nanoparticles (LNPs) are emerging as one of the most promising drug delivery systems. The long-circulating effect of intact LNPs (i-LNPs) is the key to efficacy and toxicity in vivo. However, the significant challenge is specific and sensitive detection of i-LNPs. Herein, a dual-recognition fluorescence enzyme-linked immunosorbent assay (DR-FELISA) was developed to directly isolate and detect i-LNPs by combining dual-recognition separation with a one-step signal amplification strategy. The microplates captured and enriched i-LNPs through antibody-antigen reaction. Dual-chol probes were spontaneously introduced into the lipid bilayer of captured i-LNPs, converting the detection of i-LNPs into the detection of double-cholesterol probes. Finally, the end of the dual-chol probes initiated the localized scaffolding autocatalytic DNA circuits (SADC) system for further signal amplification. The SADC system provides a sensitive and efficient amplifier through localized network structures and self-assembled triggers. Simultaneous recognition of i-LNPs surface PEG-lipid and lipid bilayer structures significantly eliminates interference from biological samples. i-LNPs were detected with high selectivity, ranging from 0.2 to 1.25 mg/mL with a limit of detection of 0.1 mg/mL. Moreover, this method allows the isolation and quantitative analysis of different formulations of i-LNPs in serum samples with a satisfactory recovery rate ranging from 94.8 to 116.3%. Thus, the DR-FELISA method provides an advanced platform for the exclusive and sensitive detection of i-LNPs, providing new insights for the study of the quality and intracorporal process of complex formulations.
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Affiliation(s)
- Yexin Hu
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 211198, China
| | - Yuqing Cui
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 211198, China
| | - Zhemeng Zhang
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 211198, China
| | - Xinyi Zhang
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 211198, China
| | - Xiao Ma
- Gansu Institute for Drug Control, Gansu 730000, China
| | - Zhou Qiao
- China Pharmaceutical University Center for Analysis and Testing, China Pharmaceutical University, Nanjing 211198, China
| | - Feng Zheng
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 211198, China
| | - Feng Feng
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Wenyuan Liu
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 211198, China
- Zhejiang Center for Safety Study of Drug Substances (Industrial Technology Innovation Platform), Hangzhou 310018, China
| | - Lingfei Han
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 211198, China
- Zhejiang Center for Safety Study of Drug Substances (Industrial Technology Innovation Platform), Hangzhou 310018, China
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2
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Lin N, Ouyang Y, Qin Y, Karmi O, Sohn YS, Liu S, Nechushtai R, Zhang Y, Willner I, Zhou Z. Spatially Localized Entropy-Driven Evolution of Nucleic Acid-Based Constitutional Dynamic Networks for Intracellular Imaging and Spatiotemporal Programmable Gene Therapy. J Am Chem Soc 2024. [PMID: 39012486 DOI: 10.1021/jacs.4c03651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
The primer-guided entropy-driven high-throughput evolution of the DNA-based constitutional dynamic network, CDN, is introduced. The entropy gain associated with the process provides a catalytic principle for the amplified emergence of the CDN. The concept is applied to develop a programmable, spatially localized DNA circuit for effective in vitro and in vivo theranostic, gene-regulated treatment of cancer cells. The localized circuit consists of a DNA tetrahedron core modified at its corners with four tethers that include encoded base sequences exhibiting the capacity to emerge and assemble into a [2 × 2] CDN. Two of the tethers are caged by a pair of siRNA subunits, blocking the circuit into a mute, dynamically inactive configuration. In the presence of miRNA-21 as primer, the siRNA subunits are displaced, resulting in amplified release of the siRNAs silencing the HIF-1α mRNA and fast dynamic reconfiguration of the tethers into a CDN. The resulting CDN is, however, engineered to be dynamically reconfigured by miRNA-155 into an equilibrated mixture enriched with a DNAzyme component, catalyzing the cleavage of EGR-1 mRNA. The DNA tetrahedron nanostructure stimulates enhanced permeation into cancer cells. The miRNA-triggered entropy-driven reconfiguration of the spatially localized circuit leads to the programmable, cooperative bis-gene-silencing of HIF-1α and EGR-1 mRNAs, resulting in the effective and selective apoptosis of breast cancer cells and effective inhibition of tumors in tumor bearing mice.
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Affiliation(s)
- Nina Lin
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Yu Ouyang
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Yunlong Qin
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Ola Karmi
- Institute of Life Science, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Yang Sung Sohn
- Institute of Life Science, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Songqin Liu
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Rachel Nechushtai
- Institute of Life Science, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Yuanjian Zhang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Itamar Willner
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Zhixin Zhou
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
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3
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Jiang M, Zhou J, Chai Y, Yuan R. Ultrahigh-Speed 3D DNA Walker with Dual Self-Protected DNAzymes for Ultrasensitive Fluorescence Detection and Intracellular Imaging of microRNA. Anal Chem 2024; 96:9866-9875. [PMID: 38835317 DOI: 10.1021/acs.analchem.4c00462] [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: 06/06/2024]
Abstract
Herein, a dual self-protected DNAzyme-based 3D DNA walker (dSPD walker), composed of activated dual self-protected walking particles (ac-dSPWPs) and track particles (TPs), was constructed for ultrasensitive and ultrahigh-speed fluorescence detection and imaging of microRNAs (miRNAs) in living cells. Impressively, compared with the defect that "one" target miRNA only initiates "one" walking arm of the conventional single self-protected DNAzyme walker, the dSPD walker benefits from the secondary amplification and spatial confinement effect and could guide "one" target miRNA to generate "n" secondary targets, thereby initiating "n" nearby walking strands immediately, realizing the initial rate over one-magnitude-order faster than that of the conventional one. Moreover, in the process of relative motion between ac-dSPWPs and TPs, the ac-dSPWPs could cleave multiple substrate strands simultaneously to speed up movement and reduce the derailment rate, as well as combine with successive TPs to facilitate a large amount of continuous signal accumulation, achieving an ultrafast detection of miRNA-221 within 10 min in vitro and high sensitivity with a low detection limit of 0.84 pM. In addition, the DNA nanospheres obtained by the rolling circle amplification reaction can capture the Cy5 fluorescence dispersed in liquids, which achieves the high-contrast imaging of miRNA-221, resulting in further ultrasensitive imaging of miRNA-221 in cancer cells. The proposed strategy has made a bold innovation in the rapid and sensitive detection as well as intracellular imaging of low-abundance biomarkers, offering promising application in early diagnosis and relevant research of cancer and tumors.
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Affiliation(s)
- Mengshi Jiang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Jie Zhou
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Yaqin Chai
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
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4
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Zhu Y, Li R, Wang Y, Zhang Q, He Y, Shang J, Liu X, Wang F. A Methylation-Gated DNAzyme Circuit for Spatially Controlled Imaging of MicroRNA in Cells and Animals. Anal Chem 2024; 96:9666-9675. [PMID: 38815126 DOI: 10.1021/acs.analchem.4c01556] [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: 06/01/2024]
Abstract
Epigenetic modification plays an indispensable role in regulating routine molecular signaling pathways, yet it is rarely used to modulate molecular self-assembly networks. Herein, we constructed a bioorthogonal demethylase-stimulated DNA circuitry (DSC) system for high-fidelity imaging of microRNA (miRNA) in live cells and mice by eliminating undesired off-site signal leakage. The simple and robust DSC system is composed of a primary cell-specific circuitry regulation (CR) module and an ultimate signal-transducing amplifier (SA) module. After the modularly designed DSC system was delivered into target live cells, the DNAzyme of the CR module was site-specifically activated by endogenous demethylase to produce fuel strands for the subsequent miRNA-targeting SA module. Through the on-site and multiply guaranteed molecular recognitions, the lucid yet efficient DSC system realized the reliably amplified in vivo miRNA sensing and enabled the in-depth exploration of the demethylase-involved signal pathway with miRNA in live cells. Our bioorthogonally on-site-activated DSC system represents a universal and versatile biomolecular sensing platform via various demethylase regulations and shows more prospects for more different personalized theragnostics.
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Affiliation(s)
- Yuxuan Zhu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
- Research Institute of Shenzhen, Wuhan University, Shenzhen 518057, P. R. China
| | - Ruomeng Li
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
- Research Institute of Shenzhen, Wuhan University, Shenzhen 518057, P. R. China
| | - Yifei Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
- Research Institute of Shenzhen, Wuhan University, Shenzhen 518057, P. R. China
| | - Qingqing Zhang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
- Research Institute of Shenzhen, Wuhan University, Shenzhen 518057, P. R. China
| | - Yuqiu He
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
- Research Institute of Shenzhen, Wuhan University, Shenzhen 518057, P. R. China
| | - Jinhua Shang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
- Research Institute of Shenzhen, Wuhan University, Shenzhen 518057, P. R. China
| | - Xiaoqing Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
- Research Institute of Shenzhen, Wuhan University, Shenzhen 518057, P. R. China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
- Department of Gastroenterology, Zhongnan Hospital of 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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Tan K, Chen L, Cao D, Xiao W, Lv Q, Zou L. Two-layer cascaded catalytic hairpin assemblies based on locked nucleic acids for one-step and highly sensitive ctDNA detection. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:3515-3521. [PMID: 38774994 DOI: 10.1039/d4ay00611a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
Enzyme-free signal amplification of catalytic hairpin assembly (CHA) has enabled sensitive detection of circulating tumor DNA (ctDNA) in early clinical diagnosis. Conventional CHA strategies are restrained by the limited amplification efficiency of the single-stage system, and signal leakage from "breathing" influence and nuclease degradation. Here, we introduced two-layer cascaded locked nucleic acid (LNA)-assisted CHA circuits with the intelligent incorporation of LNA in the hairpins and reporter for the highly sensitive one-step detection of scarce ctDNA. The target-triggered upstream CHA reaction continuously generates hybrid products to catalyze the downstream CHA reaction for transducing the primary sensing event, and the released target and the produced hybrid product trigger the next catalytic reaction round at the same time and finally cascade to amplify the target ctDNA fluorescence output signal. Meanwhile, the stronger binding affinity of the LNA-DNA duplex endows the two-layer LNA-assisted CHA system with thermodynamic stability and nuclease resistance, and thus our designed system exhibits an excellent detection performance for target ctDNA in the range from 2 pM to 5 nM with a low detection limit of 0.6 pM. Significantly, the two-layer LNA-assisted CHA circuits have been successfully implemented for the feasible analysis of clinical samples. This two-layer cascaded LNA-assisted CHA strategy provides a promising high sensitivity tool for one-step detection of scarce ctDNA from complex clinical samples and would facilitate the reconfiguration of DNA circuit-based DNA nanotechnology for the precise analysis of other biomarkers in clinical research fields.
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Affiliation(s)
- Kaiyue Tan
- National Engineering Research Center for Healthcare Devices, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou 510316, China.
- Guangdong Engineering Technology Research Center for Diagnosis and Rehabilitation of Dementia, Guangzhou 510316, China
- Guangdong Provincial Key Laboratory of Medical Electronic Instruments and Polymer Material Products, Guangzhou 510316, China
| | - Longsheng Chen
- National Engineering Research Center for Healthcare Devices, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou 510316, China.
- Guangdong Engineering Technology Research Center for Diagnosis and Rehabilitation of Dementia, Guangzhou 510316, China
- Guangdong Provincial Key Laboratory of Medical Electronic Instruments and Polymer Material Products, Guangzhou 510316, China
| | - Donglin Cao
- Department of Laboratory Medicine, Guangdong Provincial Key Laboratory of Point-of-Care Testing (POCT), Guangdong Second Provincial General Hospital, Guangzhou, 510500, China
| | - Wei Xiao
- Department of Laboratory Medicine, Guangdong Provincial Key Laboratory of Point-of-Care Testing (POCT), Guangdong Second Provincial General Hospital, Guangzhou, 510500, China
| | - Qian Lv
- National Engineering Research Center for Healthcare Devices, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou 510316, China.
- Guangdong Engineering Technology Research Center for Diagnosis and Rehabilitation of Dementia, Guangzhou 510316, China
- Guangdong Provincial Key Laboratory of Medical Electronic Instruments and Polymer Material Products, Guangzhou 510316, China
| | - Lili Zou
- National Engineering Research Center for Healthcare Devices, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou 510316, China.
- Guangdong Engineering Technology Research Center for Diagnosis and Rehabilitation of Dementia, Guangzhou 510316, China
- Guangdong Provincial Key Laboratory of Medical Electronic Instruments and Polymer Material Products, Guangzhou 510316, China
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6
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Sun M, Zhou Q, Peng J, Liu S, Luo J, Bai L, Duan WJ, Chen JX, Dai Z, Chen J. Toehold Strand Displacement-Mediated Exponential HCR for Highly Sensitive and Specific Analysis of miRNA in Living Cells. Anal Chem 2024; 96:9078-9087. [PMID: 38770734 DOI: 10.1021/acs.analchem.4c00594] [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: 05/22/2024]
Abstract
As an important disease biomarker, the development of sensitive detection strategies for miRNA, especially intracellular miRNA imaging strategies, is helpful for early diagnosis of diseases, pathological research, and drug development. Hybridization chain reaction (HCR) is widely used for miRNA imaging analysis because of its high specificity and lack of biological enzymes. However, the classic HCR reaction exhibits linear amplification with low efficiency, limiting its use for the rapid analysis of trace miRNA in living cells. To address this problem, we proposed a toehold-mediated exponential HCR (TEHCR) to achieve highly sensitive and efficient imaging of miRNA in living cells using β-FeOOH nanoparticles as transfection vectors. The detection limit of TEHCR was as low as 92.7 fM, which was 8.8 × 103 times lower compared to traditional HCR, and it can effectively distinguish single-base mismatch with high specificity. The TEHCR can also effectively distinguish the different expression levels of miRNA in cancer cells and normal cells. Furthermore, TEHCR can be used to construct OR logic gates for dual miRNA analysis without the need for additional probes, demonstrating high flexibility. This method is expected to play an important role in clinical miRNA-related disease diagnosis and drug development as well as to promote the development of logic gates.
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Affiliation(s)
- Mengxu Sun
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Qianying Zhou
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jing Peng
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Simin Liu
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jiaxin Luo
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Lingling Bai
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Wen-Jun Duan
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jin-Xiang Chen
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Zong Dai
- Key Laboratory of Sensing Technology and Biomedical Instrument of Guangdong Province, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen 518107, China
| | - Jun Chen
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
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7
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Wang Z, Shang Y, Zhu Y, He Y, Chen Y, Liu X, Wang F. Multiply Guaranteed Catalytic DNA Circuit for Cancer-Cell-Selective Imaging of miRNA and Robust Evaluation of Drug Resistance. Anal Chem 2024; 96:5560-5569. [PMID: 38529650 DOI: 10.1021/acs.analchem.4c00018] [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: 03/27/2024]
Abstract
Catalytic DNA circuits are desirable for sensitive bioimaging in living cells; yet, it remains a challenge to monitor these intricate signal communications because of the uncontrolled circuitry leakage and insufficient cell selectivity. Herein, a simple yet powerful DNA-repairing enzyme (APE1) activation strategy is introduced to achieve the site-specific exposure of a catalytic DNA circuit for realizing the selectively amplified imaging of intracellular microRNA and robust evaluation of the APE1-involved drug resistance. Specifically, the circuitry reactants are firmly blocked by the enzyme recognition/cleavage site to prevent undesirable off-site circuitry leakage. The caged DNA circuit has no target-sensing activity until its circuitry components are activated via the enzyme-mediated structural reconstitution and finally transduces the amplified fluorescence signal within the miRNA stimulation. The designed DNA circuit demonstrates an enhanced signal-to-background ratio of miRNA assay as compared with the conventional DNA circuit and enables the cancer-cell-selective imaging of miRNA. In addition, it shows robust sensing performance in visualizing the APE1-mediated chemoresistance in living cells, which is anticipated to achieve in-depth clinical diagnosis and chemotherapy research.
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Affiliation(s)
- Zeyue Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Yu Shang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Yuxuan Zhu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Yuqiu He
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Yingying Chen
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Xiaoqing Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Fuan Wang
- 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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8
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Wang LJ, Liu WJ, Wang LY, Ho YP, Han Y, Li DL, Zhang CY. Construction of an Enzymatically Controlled DNA Nanomachine for One-Step Imaging of Telomerase in Living Cells. Anal Chem 2024; 96:4647-4656. [PMID: 38441540 DOI: 10.1021/acs.analchem.3c05795] [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: 03/20/2024]
Abstract
Telomerase is a basic reverse transcriptase that maintains the telomere length in cells, and accurate and specific sensing of telomerase in living cells is critical for medical diagnostics and disease therapeutics. Herein, we demonstrate for the first time the construction of an enzymatically controlled DNA nanomachine with endogenous apurinic/apyrimidinic endonuclease 1 (APE1) as a driving force for one-step imaging of telomerase in living cells. The DNA nanomachine is designed by rational engineering of substrate probes and reporter probes embedded with an enzyme-activatable site (i.e., AP site) and their subsequent assembly on a gold nanoparticle (AuNP). Upon recognition and cleavage of the AP site in the substrate probe by APE1, the loop of the substrate probe unfolds, exposing telomeric primer (TP) with the 3'-OH end. Subsequently, the TP is elongated by telomerase at the 3'-OH end to generate a long telomeric product. The resultant telomeric product acts as a swing arm that can hybridize with a reporter probe to initiate the APE1-powered walking reaction, ultimately generating a significantly enhanced fluorescence signal. Notably, endogenous APE1 is used as the driving force of the DNA nanomachine, avoiding the introduction of exogenous auxiliary cofactors into the cellular microenvironment. Owing to the high kinetics and high amplification efficiency of the APE1-powered DNA nanomachine, this strategy enables one-step sensitive sensing of telomerase in vitro and in vivo. It can successfully discriminate telomerase activity between cancer cells and normal cells, screen telomerase inhibitors, and monitor the variations of telomerase activity in living cells, offering a prospective platform for molecular diagnostics and drug discovery.
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Affiliation(s)
- Li-Juan Wang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Wen-Jing Liu
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Lu-Yao Wang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Yi-Ping Ho
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China
| | - Yun Han
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Dong-Ling Li
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Chun-Yang Zhang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
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9
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Li Y, Zhou P, Wang Z, Ren Y, Zhu X, Wang J, Yan H, Hua L, Gao F. Sea Anemone-like Nanomachine Based on DNA Strand Displacement Composed of Three Boolean Logic Gates: Diversified Input for Intracellular Multitarget Detection. Anal Chem 2024; 96:4120-4128. [PMID: 38412037 DOI: 10.1021/acs.analchem.3c05059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Efficient and accurate acquisition of cellular biomolecular information is crucial for exploring cell fate, achieving early diagnosis, and the effective treatment of various diseases. However, current DNA biosensors are mostly limited to single-target detection, with few complex logic circuits for comprehensive analysis of three or more targets. Herein, we designed a sea anemone-like DNA nanomachine based on DNA strand displacement composed of three logic gates (YES-AND-YES) and delivered into the cells using gold nano bipyramid carriers. The AND gate activation depends on the trigger chain released by upstream DNA strand displacement reactions, while the output signal relies on the downstream DNAzyme structure. Under the influence of diverse inputs (including enzymes, miRNA, and metal ions), the interconnected logic gates simultaneously perform logical analysis on multiple targets, generating a unique output signal in the YES/NO format. This sensor can successfully distinguish healthy cells from tumor cells and can be further used for the diagnosis of different tumor cells, providing a promising platform for accurate cell-type identification.
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Affiliation(s)
- Yuting Li
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou 221004, China
| | - Peng Zhou
- Department of Orthopedics, The Affiliated Huai'an Hospital of Xuzhou Medical University, The Second People's Hospital of Huai'an, Huai'an 223002, China
| | - Zhenxin Wang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou 221004, China
| | - Yiping Ren
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou 221004, China
| | - Xu Zhu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou 221004, China
| | - Jin Wang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou 221004, China
| | - Hanrong Yan
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou 221004, China
| | - Lei Hua
- Department of Neurosurgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou 221002, China
| | - Fenglei Gao
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou 221004, China
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10
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Yang H, Chen D, Zhang Y, Yuan P, Xie N, Dai Z. MiRNA and mRNA-Controlled Double-Cascaded Amplifying Circuit Nanosensor for Accurate Discrimination of Breast Cancers in Living Cells, Animals, and Organoids. Anal Chem 2024; 96:4154-4162. [PMID: 38426698 DOI: 10.1021/acs.analchem.3c05085] [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: 03/02/2024]
Abstract
Metastasis is the leading cause of death in patients with breast cancer. Detecting high-risk breast cancer, including micrometastasis, at an early stage is vital for customizing the right and efficient therapies. In this study, we propose an enzyme-free isothermal cascade amplification-based DNA logic circuit in situ biomineralization nanosensor, HDNAzyme@ZIF-8, for simultaneous imaging of multidimensional biomarkers in live cells. Taking miR-21 and Ki-67 mRNA as the dual detection targets achieved sensitive logic operations and molecular recognition through the cascade hybridization chain reaction and DNAzyme. The HDNAzyme@ZIF-8 nanosensor has the ability to accurately differentiate breast cancer cells and their subtypes by comparing their relative fluorescence intensities. Of note, our nanosensor can also achieve visualization within breast cancer organoids, faithfully recapitulating the functional characteristics of parental tumor. Overall, the combination of these techniques offers a universal strategy for detecting cancers with high sensitivity and holds vast potential in clinical cancer diagnosis.
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Affiliation(s)
- Huihui Yang
- Biobank, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen 518035, China
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen 518060, China
| | - Dong Chen
- Department of Thyroid and Breast Surgery, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Yanfei Zhang
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen 518107, China
| | - Peixiu Yuan
- College of Materials and Energy, South China Agricultural University, Guangzhou 510642, China
| | - Ni Xie
- Biobank, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen 518035, China
| | - Zong Dai
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen 518107, China
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11
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Deng F, Li Y, Yang B, Sang R, Deng W, Kansara M, Lin F, Thavaneswaran S, Thomas DM, Goldys EM. Topological barrier to Cas12a activation by circular DNA nanostructures facilitates autocatalysis and transforms DNA/RNA sensing. Nat Commun 2024; 15:1818. [PMID: 38443394 PMCID: PMC10914725 DOI: 10.1038/s41467-024-46001-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 02/09/2024] [Indexed: 03/07/2024] Open
Abstract
Control of CRISPR/Cas12a trans-cleavage is crucial for biosensor development. Here, we show that small circular DNA nanostructures which partially match guide RNA sequences only minimally activate Cas12a ribonucleoproteins. However, linearizing these structures restores activation. Building on this finding, an Autocatalytic Cas12a Circular DNA Amplification Reaction (AutoCAR) system is established which allows a single nucleic acid target to activate multiple ribonucleoproteins, and greatly increases the achievable reporter cleavage rates per target. A rate-equation-based model explains the observed near-exponential rate trends. Autocatalysis is also sustained with DNA nanostructures modified with fluorophore-quencher pairs achieving 1 aM level (<1 copy/μL) DNA detection (106 times improvement), without additional amplification, within 15 min, at room temperature. The detection range is tuneable, spanning 3 to 11 orders of magnitude. We demonstrate 1 aM level detection of SNP mutations in circulating tumor DNA from blood plasma, genomic DNA (H. Pylori) and RNA (SARS-CoV-2) without reverse transcription as well as colorimetric lateral flow tests of cancer mutations with ~100 aM sensitivity.
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Affiliation(s)
- Fei Deng
- Graduate School of Biomedical Engineering, Faculty of Engineering, University of New South Wales, Sydney, NSW, 2052, Australia
- ARC Centre of Excellence for Nanoscale Biophotonics, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Yi Li
- Graduate School of Biomedical Engineering, Faculty of Engineering, University of New South Wales, Sydney, NSW, 2052, Australia.
- ARC Centre of Excellence for Nanoscale Biophotonics, University of New South Wales, Sydney, NSW, 2052, Australia.
| | - Biyao Yang
- Graduate School of Biomedical Engineering, Faculty of Engineering, University of New South Wales, Sydney, NSW, 2052, Australia
- ARC Centre of Excellence for Nanoscale Biophotonics, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Rui Sang
- Graduate School of Biomedical Engineering, Faculty of Engineering, University of New South Wales, Sydney, NSW, 2052, Australia
- ARC Centre of Excellence for Nanoscale Biophotonics, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Wei Deng
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Maya Kansara
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, 2011, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, NSW, 2011, Australia
- Omico, Australian Genomic Cancer Medicine Centre, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Frank Lin
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, 2011, Australia
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, NSW, Australia
| | - Subotheni Thavaneswaran
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, 2011, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, NSW, 2011, Australia
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, NSW, Australia
| | - David M Thomas
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, 2011, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, NSW, 2011, Australia
- Omico, Australian Genomic Cancer Medicine Centre, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Ewa M Goldys
- Graduate School of Biomedical Engineering, Faculty of Engineering, University of New South Wales, Sydney, NSW, 2052, Australia
- ARC Centre of Excellence for Nanoscale Biophotonics, University of New South Wales, Sydney, NSW, 2052, Australia
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12
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Zhang M, Yang T, Hu R, Li M, Liu Y, He W, Zhao L, Xu Y, Guo M, Ding S, Chen J, Cheng W. Zipper-Confined DNA Nanoframe for High-Efficient and High-Contrast Imaging of Heterogeneous Tumor Cell. Anal Chem 2024; 96:2253-2263. [PMID: 38277203 DOI: 10.1021/acs.analchem.3c05619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
Current study in the heterogeneity and physiological behavior of tumor cells is limited by the fluorescence in situ hybridization technology in terms of probe assembly efficiency, background suppression capability, and target compatibility. In a typically well-designed assay, hybridization probes are constructed in a confined nanostructure to achieve a rapid assembly for efficient signal response, while the excessively high local concentration between different probes inevitably leads to nonspecific background leakage. Inspired by the fabric zipper, we propose a novel confinement reaction pattern in a zipper-confined DNA nanoframe (ZCDN), where two kinds of hairpin probes are independently anchored respective tracks. The metastable states of the dual tracks can well avoid signal leakage caused by the nonspecific probe configuration change. Biomarker-mediated proximity ligation reduces the local distance of dual tracks, kinetically triggering an efficient allosteric chain reaction between the hairpin probes. This method circumvents nonspecific background leakage while maintaining a high efficiency in responding to targets. ZCDN is employed to track different cancer biomarkers located in both the cytoplasm and cytomembrane, of which the expression level and oligomerization behavior can provide crucial information regarding intratumoral heterogeneity. ZCDN exhibits high target response efficiency and strong background suppression capabilities and is compatible with various types of biological targets, thus providing a desirable tool for advanced molecular diagnostics.
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Affiliation(s)
- Mengxuan Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P. R. China
| | - Tiantian Yang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P. R. China
- Biobank Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P. R. China
| | - Ruiwei Hu
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Menghan Li
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Yuanjie Liu
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Wen He
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Lina Zhao
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Yuan Xu
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Minghui Guo
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Junman Chen
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Wei Cheng
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P. R. China
- Biobank Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P. R. China
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13
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Liu Z, Duan X, Yun Y, Li S, Feng Z, Zhan J, Liu R, Li Y, Zhang J. Photoactivatable Aptamer-CRISPR Nanodevice Enables Precise Profiling of Interferon-Gamma Release in Humanized Mice. ACS NANO 2024; 18:3826-3838. [PMID: 38241471 DOI: 10.1021/acsnano.3c12499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2024]
Abstract
Real-time dynamic imaging of immunoactivation-related cytokines is crucial for evaluating the efficacy of immune checkpoint blockade therapy and optimizing the treatment regimen. We introduce herein a spatiotemporally controlled nanodevice that allows in situ photoactivated imaging of interferon-gamma (IFN-γ) secretion from T cells in vitro and in vivo. The nanodevice is constructed by rational engineering of an aptamer-embedded, UV-cleavable PC-DNA probe and further integration with upconversion nanoparticles- and CRISPR-Cas12a-enhanced fluorescence systems. Using human peripheral blood mononuclear cells (PBMC)-engrafted mouse models, this nanodevice allows for the quantitative imaging of endogenous IFN-γ and its intratumoral dynamics responding to antiprogrammed cell death receptor 1 (anti-PD-1) therapy. This study thus provides a toolbox for boosting the sensitivity and precision of cytokine imaging during immune checkpoint blockade therapy, enlightening research toward imaging-guided tumor therapy.
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Affiliation(s)
- Zheng Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Xiang Duan
- State Key Laboratory of Pharmaceutical Biotechnology, National Resource Center for Mutant Mice, MOE Key Laboratory of Model Animals for Disease Study, MOE Engineering Research Center of Protein and Peptide Medicine, Chemistry and Biomedicine Innovation Center, Jiangsu Key Laboratory of Molecular Medicine, Model Animal Research Center, Medical School of Nanjing University, Nanjing 210061, China
| | - Yangfang Yun
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Siqi Li
- State Key Laboratory of Pharmaceutical Biotechnology, National Resource Center for Mutant Mice, MOE Key Laboratory of Model Animals for Disease Study, MOE Engineering Research Center of Protein and Peptide Medicine, Chemistry and Biomedicine Innovation Center, Jiangsu Key Laboratory of Molecular Medicine, Model Animal Research Center, Medical School of Nanjing University, Nanjing 210061, China
| | - Zhiyuan Feng
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Jiayin Zhan
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Ran Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Yan Li
- State Key Laboratory of Pharmaceutical Biotechnology, National Resource Center for Mutant Mice, MOE Key Laboratory of Model Animals for Disease Study, MOE Engineering Research Center of Protein and Peptide Medicine, Chemistry and Biomedicine Innovation Center, Jiangsu Key Laboratory of Molecular Medicine, Model Animal Research Center, Medical School of Nanjing University, Nanjing 210061, China
| | - Jingjing Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
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14
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Cao H, Mao K, Zhang H, Wu Q, Ju H, Feng X. Thermal stability and micrdose-based coupling CRISPR/Cas12a biosensor for amplification-free detection of hgcA gene in paddy soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 909:168536. [PMID: 37977400 DOI: 10.1016/j.scitotenv.2023.168536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/21/2023] [Accepted: 11/10/2023] [Indexed: 11/19/2023]
Abstract
The lack of point-of-use (POU) methods hinders the utilization of the hgcA gene to rapidly evaluate methylmercury risks. CRISPR/Cas12a is a promising technology, but shortcomings such as low sensitivity, a strict reaction temperature and high background signal limit its further utilization. Here, a thermally stable microsystem-based CRISPR/Cas12a biosensor was constructed to achieve POU analysis for hgcA. First, three target gRNAs were designed to recognize hgcA. Then, a microsystem was developed to eliminate the background signal. Next, the effect of temperature on the activity of the Cas12a-gRNA complex was explored and its thermal stability was discovered. After that, coupling gRNA assay was introduced to improve sensitivity, exhibiting a limit of detection as low as 0.49 pM with a linear range of 0.98-125 pM, and a recovery rate between 90 and 110 % for hgcA. The biosensor was finally utilized to assess hgcA abundance in paddy soil, and high abundance of hgcA was found in these paddy soil samples. This study not only systematically explored the influence of temperature and microsystem on CRISPR/Cas12a, providing vital references for other novel CRISPR-based detection methods, but also applied the CRISPR-based analytical method to the field of environmental geochemistry for the first time, demonstrating enormous potential for POU detection in this field.
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Affiliation(s)
- Haorui Cao
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kang Mao
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China.
| | - Hua Zhang
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China.
| | - Qingqing Wu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xinbin Feng
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
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15
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Zhang Q, Yu S, Shang J, He S, Liu X, Wang F. Spatiotemporally Programmed Disassembly of Multifunctional Integrated DNAzyme Nanoplatfrom for Amplified Intracellular MicroRNA Imaging. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2305672. [PMID: 37670211 DOI: 10.1002/smll.202305672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/12/2023] [Indexed: 09/07/2023]
Abstract
The sensing performance of DNAzymes in live cells is tremendously hampered by the inefficient and inhomogeneous delivery of DNAzyme probes and their incontrollable off-site activation, originating from their susceptibility to nuclease digestion. This requires the development of a more compact and robust DNAzyme-delivering system with site-specific DNAzyme activation property. Herein, a highly compact and robust Zn@DDz nanoplatform is constructed by integrating the unimolecular microRNA-responsive DNA-cleaving DNAzyme (DDz) probe with the requisite DNAzyme Zn2+ -ion cofactors, and the amplified intracellular imaging of microRNA via the spatiotemporally programmed disassembly of Zn@DDz nanoparticles is achieved. The multifunctional Zn@DDz nanoplatform is simply composed of a structurally blocked self-hydrolysis DDz probe and the inorganic Zn2+ -ion bridge, with high loading capacity, and can effectively deliver the initially catalytic inert DDz probe and Zn2+ into living cells with enhanced stabilities. Upon their entry into the acidic microenvironment of living cells, the self-sufficient Zn@DDz nanoparticle is disassembled to release DDz probe and simultaneously supply Zn2+ -ion cofactors. Then, endogenous microRNA-21 catalyzes the reconfiguration and activation of DDz for generating the amplified readout signal with multiply guaranteed imaging performance. Thus, this work paves an effective way for promoting DNAzyme-based biosensing systems in living cells, and shows great promise in clinical diagnosis.
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Affiliation(s)
- Qingqing Zhang
- Department of Gastroenterology, 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
| | - Shanshan Yu
- Department of Gastroenterology, 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
| | - Jinhua Shang
- Department of Gastroenterology, 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
| | - Shizhen He
- Department of Gastroenterology, 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
| | - Xiaoqing Liu
- Department of Gastroenterology, 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
| | - Fuan Wang
- Department of Gastroenterology, 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
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, 430072, China
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16
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Gong X, Zhang J, Zhang P, Jiang Y, Hu L, Jiang Z, Wang F, Wang Y. Engineering of a Self-Regulatory Bidirectional DNA Assembly Circuit for Amplified MicroRNA Imaging. Anal Chem 2023; 95:18731-18738. [PMID: 38096424 DOI: 10.1021/acs.analchem.3c02822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
The engineering of catalytic hybridization DNA circuits represents versatile ways to orchestrate a complex flux of molecular information at the nanoscale, with potential applications in DNA-encoded biosensing, drug discovery, and therapeutics. However, the diffusive escape of intermediates and unintentional binding interactions remain an unsolved challenge. Herein, we developed a compact, yet efficient, self-regulatory assembly circuit (SAC) for achieving robust microRNA (miRNA) imaging in live cells through DNA-templated guaranteed catalytic hybridization. By integrating the toehold strand with a preblocked palindromic fragment in the stem domain, the proposed miniature SAC system allows the reactant-to-template-controlled proximal hybridization, thus facilitating the bidirectional-sustained assembly and the localization-intensified signal amplification without undesired crosstalk. With condensed components and low reactant complexity, the SAC amplifier realized high-contrast intracellular miRNA imaging. We anticipate that this simple and template-controlled design can enrich the clinical diagnosis and prognosis toolbox.
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Affiliation(s)
- Xue Gong
- Engineering Research Center for Biotechnology of Active Substances (Ministry of Education), Chongqing Key Laboratory of Green Synthesis and Applications, College of Chemistry, Chongqing Normal University, Chongqing 401331, P. R. China
| | - Jiajia Zhang
- Engineering Research Center for Biotechnology of Active Substances (Ministry of Education), Chongqing Key Laboratory of Green Synthesis and Applications, College of Chemistry, Chongqing Normal University, Chongqing 401331, P. R. China
| | - Pu Zhang
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, P. R. China
| | - Yuqian Jiang
- Research Institute of Shenzhen, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Lianzhe Hu
- Engineering Research Center for Biotechnology of Active Substances (Ministry of Education), Chongqing Key Laboratory of Green Synthesis and Applications, College of Chemistry, Chongqing Normal University, Chongqing 401331, P. R. China
| | - Zhongwei Jiang
- Engineering Research Center for Biotechnology of Active Substances (Ministry of Education), Chongqing Key Laboratory of Green Synthesis and Applications, College of Chemistry, Chongqing Normal University, Chongqing 401331, P. R. China
| | - Fuan Wang
- Research Institute of Shenzhen, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Yi Wang
- Engineering Research Center for Biotechnology of Active Substances (Ministry of Education), Chongqing Key Laboratory of Green Synthesis and Applications, College of Chemistry, Chongqing Normal University, Chongqing 401331, P. R. China
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17
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Wang C, Xie Y, Song X, Chao Z, Wu K, Fang Y, Zhao H, Ju H, Liu Y. A NIR Programmable In Vivo miRNA Magnifier for NIR-II Imaging of Early Stage Cancer. Angew Chem Int Ed Engl 2023; 62:e202312665. [PMID: 37903741 DOI: 10.1002/anie.202312665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/28/2023] [Accepted: 10/30/2023] [Indexed: 11/01/2023]
Abstract
Aberrant expressions of biomolecules occur much earlier than tumor visualized size and morphology change, but their common measurement strategies such as biopsy suffer from invasive sampling process. In vivo imaging of slight biomolecule expression difference is urgently needed for early cancer detection. Fluorescence of rare earth nanoparticles (RENPs) in second near-infrared (NIR-II) region makes them appropriate tool for in vivo imaging. However, the incapacity to couple with signal amplification strategies, especially programmable signal amplification strategies, limited their application in lowly expressed biomarkers imaging. Here we develop a 980/808 nm NIR programmed in vivo microRNAs (miRNAs) magnifier by conjugating activatable DNAzyme walker set to RENPs, which achieves more effective NIR-II imaging of early stage tumor than size monitoring imaging technique. Dye FD1080 (FD1080) modified substrate DNA quenches NIR-II downconversion emission of RENPs under 808 nm excitation. The miRNA recognition region in DNAzyme walker is sealed by a photo-cleavable strand to avoid "false positive" signal in systemic circulation. Upconversion emission of RENPs under 980 nm irradiation activates DNAzyme walker for miRNA recognition and amplifies NIR-II fluorescence recovery of RENPs via DNAzyme catalytic reaction to achieve in vivo miRNA imaging. This strategy demonstrates good application potential in the field of early cancer detection.
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Affiliation(s)
- Caixia Wang
- State Key Laboratory of Analytical Chemistry for Life Science Department, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Yuxin Xie
- State Key Laboratory of Analytical Chemistry for Life Science Department, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Xuefang Song
- State Key Laboratory of Analytical Chemistry for Life Science Department, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Zhicong Chao
- State Key Laboratory of Analytical Chemistry for Life Science Department, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Kun Wu
- State Key Laboratory of Analytical Chemistry for Life Science Department, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Yanyun Fang
- State Key Laboratory of Analytical Chemistry for Life Science Department, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Hongxia Zhao
- State Key Laboratory of Analytical Chemistry for Life Science Department, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science Department, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Ying Liu
- State Key Laboratory of Analytical Chemistry for Life Science Department, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, 210023, China
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18
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Wang S, Shang J, Zhao B, Wang H, Yang C, Liu X, Wang F. Integration of Isothermal Enzyme-Free Nucleic Acid Circuits for High-Performance Biosensing Applications. Chempluschem 2023; 88:e202300432. [PMID: 37706615 DOI: 10.1002/cplu.202300432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 09/10/2023] [Accepted: 09/11/2023] [Indexed: 09/15/2023]
Abstract
The isothermal enzyme-free nucleic acid amplification method plays an indispensable role in biosensing by virtue of its simple, robust, and highly efficient properties without the assistance of temperature cycling or/and enzymatic biocatalysis. Up to now, enzyme-free nucleic acid amplification has been extensively utilized for biological assays and has achieved the highly sensitive detection of various biological targets, including DNAs, RNAs, small molecules, proteins, and even cells. In this Review, the mechanisms of entropy-driven reaction, hybridization chain reaction, catalytic hairpin assembly and DNAzyme are concisely described and their recent application as biosensors is comprehensively summarized. Furthermore, the current problems and the developments of these DNA circuits are also discussed.
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Affiliation(s)
- Siyuan Wang
- College of Biological and Pharmaceutical Sciences, China Three Gorges University, 443002, Yichang, Hubei, P. R. China
| | - Jinhua Shang
- Research Institute of Shenzhen, Wuhan University, 518057, Shenzhen, Guangdong, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, Hubei, P. R. China
| | - Bingyue Zhao
- College of Biological and Pharmaceutical Sciences, China Three Gorges University, 443002, Yichang, Hubei, P. R. China
| | - Huimin Wang
- College of Biological and Pharmaceutical Sciences, China Three Gorges University, 443002, Yichang, Hubei, P. R. China
| | - Changying Yang
- College of Biological and Pharmaceutical Sciences, China Three Gorges University, 443002, Yichang, Hubei, P. R. China
| | - Xiaoqing Liu
- Research Institute of Shenzhen, Wuhan University, 518057, Shenzhen, Guangdong, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, Hubei, P. R. China
| | - Fuan Wang
- Research Institute of Shenzhen, Wuhan University, 518057, Shenzhen, Guangdong, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, Hubei, P. R. China
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19
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He Y, Wang Q, Hong C, Li R, Shang J, Yu S, Liu X, Wang F. A Smart Deoxyribozyme-Programmable Catalytic DNA Circuit for High-Contrast MicroRNA Imaging. Angew Chem Int Ed Engl 2023; 62:e202307418. [PMID: 37379042 DOI: 10.1002/anie.202307418] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 06/29/2023]
Abstract
Synthetic catalytic DNA circuits have been recognized as a promising signal amplification toolbox for sensitive intracellular imaging, yet their selectivity and efficiency are always constrained by uncontrolled off-site signal leakage and inefficient on-site circuitry activation. Thus, the endogenously controllable on-site exposure/activation of DNA circuits is highly desirable for achieving the selective imaging of live cells. Herein, an endogenously activated DNAzyme strategy was facilely integrated with a catalytic DNA circuit for guiding the selective and efficient microRNA imaging in vivo. To prevent the off-site activation, the circuitry constitute was initially caged without sensing functions, which could be selectively liberated by DNAzyme amplifier to guarantee the high-contrast microRNA imaging in target cells. This intelligent on-site modulation strategy can tremendously expand these molecularly engineered circuits in biological systems.
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Affiliation(s)
- Yuqiu He
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Qing Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Chen Hong
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Ruomeng Li
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Jinhua Shang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Shanshan Yu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Xiaoqing Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Fuan Wang
- 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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20
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Yang C, Shi Y, Zhang Y, He J, Li M, Huang W, Yuan R, Xu W. Modular DNA Tetrahedron Nanomachine-Guided Dual-Responsive Hybridization Chain Reactions for Discernible Bivariate Assay and Cell Imaging. Anal Chem 2023. [PMID: 37365899 DOI: 10.1021/acs.analchem.3c01091] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Engineering of multivariate biosensing and imaging platforms involved in disease plays a vital role in effectively discerning cancer cells from normal cells and facilitating reliable targeted therapy. Multiple biomarkers such as mucin 1 (MUC1) and nucleolin are typically overexpressed in breast cancer cells compared to normal human breast epithelium cells. Motivated by this knowledge, a dual-responsive DNA tetrahedron nanomachine (drDT-NM) is constructed through immobilizing two recognition modules, MUC1 aptamer (MA) and a hairpin H1* encoding nucleolin-specific G-rich AS1411 aptamer, in two separate vertexes of a functional DT architecture tethering two localized pendants (PM and PN). When drDT-NM identifiably binds bivariate MUC1 and nucleolin, two independent hybridization chain reactions (HCRM and HCRN) as amplification modules are initiated with two sets of four functional hairpin reactants. Among them, one hairpin for HCRM is dually ended by fluorescein and quencher BHQ1 to sense MUC1. The responsiveness of nucleolin is executed by operating HCRN utilizing another two hairpins programmed with two pairs of AS1411 splits. In the shared HCRN duplex products, the parent AS1411 aptamers are cooperatively merged and folded into G-quadruplex concatemers to embed Zn-protoporphyrin IX (ZnPPIX/G4) for fluorescence signaling readout, thereby achieving a highly sensitive intracellular assay and discernible cell imaging. The tandem ZnPPIX/G4 unities also act as imaging agents and therapeutic cargos for efficient photodynamic therapy of cancer cells. Based on drDT-NM to guide bispecific HCR amplifiers for adaptive bivariate detection, we present a paradigm of exquisitely integrating modular DNA nanostructures with nonenzymatic nucleic acid amplification, thus creating a versatile biosensing platform as a promising candidate for accurate assay, discernible cell imaging, and targeted therapy.
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Affiliation(s)
- Chunli Yang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Yanan Shi
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Yuqing Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Jiayang He
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Mengdie Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Weixiang Huang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Wenju Xu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
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21
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Chai Q, Chen J, Zeng S, Zhu T, Chen J, Qi C, Mao G, Liu Y. Closed Cyclic DNA Machine for Sensitive Logic Operation and APE1 Detection. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2207736. [PMID: 36916696 DOI: 10.1002/smll.202207736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 02/16/2023] [Indexed: 06/08/2023]
Abstract
DNA self-assembly has been developed as a kind of robust signal amplification strategy, but most of reported assembly pathways are programmed to amplify signal in one direction. Herein, based on mutual-activated cascade cycle of hybridization chain reaction (HCR) and catalytic hairpin assembly (CHA), a closed cycle circuit (CCC) based DNA machine is developed for sensitive logic operation and molecular recognition. Benefiting from the synergistically accelerated signal amplification, the closed cyclic DNA machine enabled the logic computing with strong and significant output signals even at weak input signals. The typical logic operations such as OR, YES, AND, INHIBIT, NOR, and NAND gate, are conveniently and clearly executed with this DNA machine through rational design of the input and computing elements. Moreover, by integrating the target recognition module with the CCC module, the proposed DNA machine is further employed in the homogeneous detection of apurinic/apyrimidinic endonuclease 1 (APE1). The precise recognition and exponential signal amplification facilitated the highly selective and sensitive detection of APE1 with limit of detection (LOD) of 7.8 × 10-5 U mL-1 . Besides, the normal cells and tumor cells are distinguished unambiguously by this method according to the detected concentration difference of cellular APE1, which indicates the robustness and practicability of this method.
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Affiliation(s)
- Qingli Chai
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi, Hubei, 435002, China
| | - Jinyang Chen
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi, Hubei, 435002, China
| | - Shasha Zeng
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi, Hubei, 435002, China
| | - Ting Zhu
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi, Hubei, 435002, China
| | - Jintao Chen
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi, Hubei, 435002, China
| | - Chunjiao Qi
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi, Hubei, 435002, China
| | - Guobin Mao
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, 518055, China
| | - Yucheng Liu
- Core Facility of Wuhan University, Wuhan, Hubei, 430072, China
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22
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Wei J, Yu M, Tan K, Shang J, He S, Xie C, Liu X, Wang F. Tailoring a Minimal Self-Replicate DNA Circuit for Highly Efficient Intracellular Imaging of microRNA. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2207961. [PMID: 36717281 DOI: 10.1002/smll.202207961] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/09/2023] [Indexed: 06/18/2023]
Abstract
Trace analyte detection in complex intracellular environment requires the development of simple yet robust self-sufficient molecular circuits with high signal-gain and anti-interference features. Herein, a minimal non-enzymatic self-replicate DNA circuitry (SDC) system is proposed with high-signal-gain for highly efficient biosensing in living cells. It is facilely engineered through the self-stacking of only one elementary cascade hybridization reaction (CHR), thus is encoding with more economic yet effective amplification pathways and reactants. Trigger (T) stimulates the activation of CHR for producing numerous T replica that reversely motivate new CHR reaction cycles, thus achieving the successive self-replication of CHR system with an exponentially magnified readout signal. The intrinsic self-replicate circuity design and the self-accelerated reaction format of SDC system is experimentally demonstrated and theoretically simulated. With simple circuitry configuration and low reactant complexity, the SDC amplifier enables the high-contrast and accurate visualization of microRNA (miRNA), ascribing to its robust molecular recognition and self-sufficient signal amplification, thus offering a promising strategy for monitoring these clinically significant analytes.
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Affiliation(s)
- Jie Wei
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, P. R. China
| | - Mengdi Yu
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Kaiyue Tan
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Jinhua Shang
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Shizhen He
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Chenxia Xie
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Xiaoqing Liu
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, 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, 430071, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
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23
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Liu L, Xiong M, Rong Q, Zhang M, Zhang X. Nucleic acid sensors in vivo: challenges and opportunities. VIEW 2023. [DOI: 10.1002/viw.20220064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023] Open
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24
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Wang J, Fu X, Liu S, Liu R, Li J, Wang K, Huang J. Catalyst-Accelerated Circular Cascaded DNA Circuits: Simpler Design, Faster Speed, Higher Gain. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2205903. [PMID: 36638250 DOI: 10.1002/smll.202205903] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/28/2022] [Indexed: 06/17/2023]
Abstract
DNA cascaded circuits have great potential in detecting low abundance molecules in complex biological environment due to their powerful signal amplification capability and nonenzymatic feature. However, the problem of the cascaded circuits is that the design is relatively complex and the kinetics is slow. Herein, a new design paradigm called catalyst-accelerated circular cascaded circuits is proposed, where the catalyst inlet is implanted and the reaction speed can be adjusted by the catalyst concentration. This new design is very simple and only requires three hairpin probes. Meanwhile, the results of a series of studies demonstrate that the reaction speed can be accelerated and the sensitivity can be also improved. Moreover, endogenous mRNA can also be used as a catalyst to drive the circuits to amplify the detection of target miRNA in live cells and in mice. These catalyst-accelerated circular cascaded circuits can substantially expand the toolbox for intracellular low abundance molecular detection.
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Affiliation(s)
- Jiaoli Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, P. R. China
| | - Xiaoxiao Fu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, P. R. China
| | - Shiyuan Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, P. R. China
| | - Ruiting Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, P. R. China
| | - Jing Li
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, 225012, P. R. China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, P. R. China
| | - Jin Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, P. R. China
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25
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Li Y, Si Q, Liu C, Huang Z, Chen Q, Jiao T, Chen X, Chen Q, Wei J. Construction of a self-sufficient DNA circuit for amplified detection of kanamycin. Food Chem 2023; 418:136048. [PMID: 36996659 DOI: 10.1016/j.foodchem.2023.136048] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 03/21/2023] [Accepted: 03/25/2023] [Indexed: 03/29/2023]
Abstract
Improper use of kanamycin can lead to trace kanamycin residues in animal-derived foods, which can pose a potential threat to public health. Isothermal enzyme-free DNA circuits have provided a versatile toolbox for detecting kanamycin residues in complicated food samples, yet they are always limited by low amplification efficiency and intricate design. Herein, we present a simple-yet-robust nonenzymatic self-driven hybridization chain reaction (SHCR) amplifier for kanamycin determination with 5800-fold sensitivity over that of the conventional HCR circuit. The analyte kanamycin-activated SHCR circuitry can generate numerous new initiators to promote the reaction and improve the amplification efficiency, thus achieving an exponential signal gain. With precise target recognition and multilayer amplification capability, our self-sustainable SHCR aptasensor facilitated the highly sensitive and reliable analysis of kanamycin in buffer, milk, and honey samples, thus holding great potential for the amplified detection of trace contaminants in liquid food matrices.
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26
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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: 18] [Impact Index Per Article: 18.0] [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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27
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Li R, Li F, Zhang Y, He Y, Wang Y, Wang F. Miniature Hierarchical DNA Hybridization Circuit for Amplified Multiplexed MicroRNA Imaging. Anal Chem 2023; 95:3848-3855. [PMID: 36745869 DOI: 10.1021/acs.analchem.2c05373] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Accurate diagnosis requires the development of multiple-guaranteed DNA circuits. Nevertheless, for reliable multiplexed molecular imaging, existing DNA circuits are limited by poor cell-delivering homogeneity due to their cumbersome and dispersive reactants. Herein, we developed a compact-yet-efficient hierarchical DNA hybridization (HDH) circuit for in situ simultaneous analysis of multiple miRNAs, which could be further exploited for specifically discriminating cancer cells from normal ones. By integrating the traditional hybridization chain reaction and catalytic hairpin assembly reactants into two highly organized hairpins, the HDH circuit is fitted with condensed components and multiple response domains, thus permitting the programmable multiple microRNA-guaranteed sequential activations and the localized cascaded signal amplification. The synergistic multi-recognition and amplification features of the HDH circuit facilitate the magnified detection of multiplex endogenous miRNAs in living cells. The in vitro and cellular imaging experimental results revealed that the HDH circuit displayed a reliable sensing performance with high selective cell-identification capacity. We anticipate that this compact design can provide a powerful toolkit for accurate diagnostics and pathological evolution.
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Affiliation(s)
- Ruomeng Li
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P.R. China
| | - Fengzhe Li
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P.R. China
| | - Yanping Zhang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P.R. China
| | - Yuqiu He
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P.R. China
| | - Yushi Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P.R. China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P.R. China.,Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan 430072, P.R. China
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28
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Li R, Zhu Y, Gong X, Zhang Y, Hong C, Wan Y, Liu X, Wang F. Self-Stacking Autocatalytic Molecular Circuit with Minimal Catalytic DNA Assembly. J Am Chem Soc 2023; 145:2999-3007. [PMID: 36700894 DOI: 10.1021/jacs.2c11504] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Isothermal autocatalytic DNA circuits have been proven to be versatile and powerful biocomputing platforms by virtue of their self-sustainable and self-accelerating reaction profiles, yet they are currently constrained by their complicated designs, severe signal leakages, and unclear reaction mechanisms. Herein, we developed a simpler-yet-efficient autocatalytic assembly circuit (AAC) for highly robust bioimaging in live cells and mice. The scalable and sustainable AAC system was composed of a mere catalytic DNA assembly reaction with minimal strand complexity and, upon specific stimulation, could reproduce numerous new triggers to expedite the whole reaction. Through in-depth theoretical simulations and systematic experimental demonstrations, the catalytic efficiency of these reproduced triggers was found to play a vital role in the autocatalytic profile and thus could be facilely improved to achieve more efficient and characteristic autocatalytic signal amplification. Due to its exponentially high signal amplification and minimal reaction components, our self-stacking AAC facilitated the efficient detection of trace biomolecules with low signal leakage, thus providing great clinical diagnosis and therapeutic assessment potential.
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Affiliation(s)
- Ruomeng Li
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Yuxuan Zhu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Xue Gong
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Yanping Zhang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Chen Hong
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Yeqing Wan
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Xiaoqing Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China.,Research Institute of Shenzhen, Wuhan University, Shenzhen 518057, P. R. China
| | - Fuan Wang
- 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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29
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Zhang Q, Yuan ZZ, Zhang X, Zhang Y, Zou X, Ma F, Zhang CY. Entropy-Driven Self-Assembly of Single Quantum Dot Sensor for Catalytic Imaging of Telomerase in Living Cells. Anal Chem 2022; 94:18092-18098. [PMID: 36519804 DOI: 10.1021/acs.analchem.2c04747] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Telomerase is a highly valuable cancer diagnosis biomarker and a promising cancer therapy target. So far, most telomerase assays are limited by the involvement of tedious procedures, multiple enzymes, and complicated reaction schemes. Sensitive monitoring of low-abundant telomerase in living cells remains a challenge. Herein, we demonstrate an entropy-driven catalytic assembly of quantum dot (QD) sensors for accurate detection and imaging of telomerase activity in living cells. In this sensor, target telomerase specifically catalyzes extension of telomerase primer, and the extended primer subsequently acts as a catalyst to continuously initiate entropy-driven catalytic reaction, generating a large number of fluorophore- and biotin-labeled DNAs that can be self-assembled on the QD surface to induce an efficient Föster resonance energy transfer signal. The proposed sensor requires a single step for both recognition and amplification of the telomerase signal, eliminating the use of either protein enzymes or laborious procedures. Taking advantage of the inherent superiority of single-molecule fluorescence detection and high amplification efficiency of the entropy-driven reaction, this sensor demonstrates single-cell sensitivity for the in vitro assay. Moreover, it is capable of screening the telomerase inhibitor, discriminating different tumor cells from normal ones, and even real-time imaging telomerase in living cells, providing a novel platform for telomerase-associated cancer diagnosis and drug screening.
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Affiliation(s)
- Qian Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan250014, China
| | - Zhen-Zhen Yuan
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan250014, China
| | - Xinyi Zhang
- School of Chemistry and Chemical Engineering, Guangdong Pharmaceutical University, Zhongshan528458, China
| | - Yan Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan250014, China
| | - Xiaoran Zou
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan250014, China
| | - Fei Ma
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing211189, China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan250014, China
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30
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Yang C, Yuan Y, Shen M, Wang K, Xu H, Wang Y, Chen M, Bao J, Gao M. Modularized Enzymatic Tandem Reaction for tsRNA Detection. Anal Chem 2022; 94:15887-15895. [DOI: 10.1021/acs.analchem.2c04010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Cheng Yang
- Department of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), No. 30 Gaotanyan Road, Chongqing 400038, P. R. China
| | - Yi Yuan
- College of Pharmacy and Laboratory Medicine, Third Military Medical University (Army Medical University), No. 29 Gaotanyan Road, Chongqing 400038, China
| | - Man Shen
- Department of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), No. 30 Gaotanyan Road, Chongqing 400038, P. R. China
| | - Ke Wang
- Department of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), No. 30 Gaotanyan Road, Chongqing 400038, P. R. China
| | - Hanqing Xu
- Department of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), No. 30 Gaotanyan Road, Chongqing 400038, P. R. China
| | - Yingran Wang
- Department of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), No. 30 Gaotanyan Road, Chongqing 400038, P. R. China
| | - Ming Chen
- Department of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), No. 30 Gaotanyan Road, Chongqing 400038, P. R. China
- College of Pharmacy and Laboratory Medicine, Third Military Medical University (Army Medical University), No. 29 Gaotanyan Road, Chongqing 400038, China
- State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, No. 30 Gaotanyan Road, Chongqing 400038, P. R. China
| | - Jing Bao
- Department of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), No. 30 Gaotanyan Road, Chongqing 400038, P. R. China
| | - Mingxuan Gao
- Department of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), No. 30 Gaotanyan Road, Chongqing 400038, P. R. China
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31
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Li H, Lu H, Tang Y, Wang H, Xiao Y, Li B. A Rebuilding‐Free Nucleic Acid Detection Strategy Enables Ultrasensitive Genotyping, N‐in‐1 Logic Screening and Accurate Multiplex Assay of Dangerous Pathogens. Angew Chem Int Ed Engl 2022; 61:e202209496. [DOI: 10.1002/anie.202209496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Huan Li
- State Key Lab 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
| | - Huiying Lu
- School of Life Sciences Northeast Normal University Changchun Jilin, 130024 China
| | - Yidan Tang
- State Key Lab of Electroanalytical Chemistry Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun Jilin, 130022 China
| | - Huaning Wang
- State Key Lab 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
| | - Yao Xiao
- State Key Lab 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
| | - Bingling Li
- State Key Lab 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
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32
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Zhang Q, Zhao R, Li CC, Zhang Y, Tang C, Luo X, Ma F, Zhang CY. Construction of an Entropy-Driven Dumbbell-Type DNAzyme Assembly Circuit for Lighting Up Uracil-DNA Glycosylase in Living Cells. Anal Chem 2022; 94:13978-13986. [PMID: 36179339 DOI: 10.1021/acs.analchem.2c03223] [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
Sensitive monitoring of intracellular uracil-DNA glycosylase (UDG) in living cells is essential to understanding the DNA repair pathways and discovery of anticancer drugs. Herein, we demonstrate the construction of an entropy-driven dumbbell-type DNAzyme assembly circuit for lighting up UDG in living cells via the integration of entropy-driven DNA catalysis (EDC) with the DNAzyme biocatalyst. Target UDG excises the damaged uracil base, causing the breakage of detection probe and the release of trigger. The released trigger can initiate the downstream EDC reaction to form two catalytically active DNAzyme units. The resultant dual Mg2+-DNAzyme units serve as the signal transducers to cyclically cleave the fluorophore/quenched-modified reporters, generating an enhanced fluorescence signal. In contrast to the single-layered EDC method with a linear amplification, the proposed doublet EDC-DNAzyme strategy exhibits high signal gain and achieves a detection limit of 8.71 × 10-6 U/mL. Notably, this assay can be performed in one-step manner at room temperature without the requirement of strict temperature control and complicated reaction procedures, and it can further screen the UDG inhibitors, measure kinetic parameters, and discriminate cancer cells from normal cells. Moreover, this strategy can monitor intracellular UDG activity with improved signal gain, and it may be exploited for sensing and imaging of other types of DNA modifying enzymes with the integration of the corresponding detection substrate, providing a facile and robust approach for biological research studies and clinical diagnosis.
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Affiliation(s)
- Qian Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Ran Zhao
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Chen-Chen Li
- College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Yan Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Chunying Tang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Xiliang Luo
- College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Fei Ma
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
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Zhang Y, Li R, Yu S, Shang J, He Y, Wang Y, Liu X, Wang F. Sensitive Autocatalytic Hybridization Circuit for Reliable In Situ Intracellular Polynucleotide Kinase Imaging. Anal Chem 2022; 94:13951-13957. [PMID: 36170650 DOI: 10.1021/acs.analchem.2c03169] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Exploring the characteristic functions of polynucleotide kinase (PNK) could substantially promote the elucidation of PNK-related mechanistic pathways. Yet, the sensitive and reliable detection of intracellular PNK still presents a challenging goal. Herein, we propose a simple autocatalytic hybridization circuit (AHC) for in situ intracellular imaging of PNK with high reliability. The AHC amplifier consists of two mutually activated hybridization chain reaction (HCR) modules for magnified signal transduction. The PNK is transduced into initiator I by phosphorylation and cleavage of mediator Hp. Initiator I activates the initial HCR-1 module, leading to the formation of long dsDNA nanowires that carry numerous initiator T. Then, T-initiated feedback HCR-2 module generates branched products that contain plentiful initiator I, thus realizing an autocatalytic HCR amplification reaction. Simultaneously, the HCR-2 module is also assembled as a versatile signal transduction unit for generating the amplified readout. Based on the mutually sustained accumulation of two initiators for the reciprocal activation of two reaction modules, continuous signal amplification and assembly of high-molecular-weight copolymers endow the AHC system with high sensitivity and robustness for the PNK assay. Moreover, the PNK-sensing AHC system achieves reliable imaging of intracellular PNK, thus showing great potential to decipher the correlation between PNK and related diseases.
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Affiliation(s)
- Yanping Zhang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Ruomeng Li
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Shanshan Yu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Jinhua Shang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Yuqiu He
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Yushi Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Xiaoqing Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China.,Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan 430072, P. R. China
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34
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He S, Yu S, Li R, Chen Y, Wang Q, He Y, Liu X, Wang F. On‐Site Non‐enzymatic Orthogonal Activation of a Catalytic DNA Circuit for Self‐Reinforced In Vivo MicroRNA Imaging. Angew Chem Int Ed Engl 2022; 61:e202206529. [DOI: 10.1002/anie.202206529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Shizhen He
- College of Chemistry and Molecular Sciences Wuhan University Wuhan P. R. China
| | - Shanshan Yu
- College of Chemistry and Molecular Sciences Wuhan University Wuhan P. R. China
| | - Ruomeng Li
- College of Chemistry and Molecular Sciences Wuhan University Wuhan P. R. China
| | - Yingying Chen
- College of Chemistry and Molecular Sciences Wuhan University Wuhan P. R. China
| | - Qing Wang
- College of Chemistry and Molecular Sciences Wuhan University Wuhan P. R. China
| | - Yuqiu He
- College of Chemistry and Molecular Sciences Wuhan University Wuhan P. R. China
| | - Xiaoqing Liu
- College of Chemistry and Molecular Sciences Wuhan University Wuhan P. R. China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences Wuhan University Wuhan P. R. China
- Department of Gastrointestinal Surgery Zhongnan Hospital of Wuhan University Wuhan P. R. China
- Research Centre for Infectious Diseases and Cancer Chinese Academy of Medical Sciences Wuhan P. R. China
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35
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Li H, Lu H, Tang Y, Wang H, Xiao Y, Li B. A Rebuilding‐Free Nucleic Acid Detection Strategy Enables Ultrasensitive Genotyping, N‐in‐1 Logic Screening and Accurate Multiplex Assay of Dangerous Pathogens. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202209496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Huan Li
- Changchun Institute of Applied Chemistry Chinese Academy of Sciences: Chang Chun Institute of Applied Chemistry Chinese Academy of Sciences State Key Lab of Electroanalytical Chemistry Changchun Institute of Applied Chemistry 130022 Changchun CHINA
| | - Huiying Lu
- Northeast Normal University School of Life Sciences CHINA
| | - Yidan Tang
- Changchun Institute of Applied Chemistry Chinese Academy of Sciences: Chang Chun Institute of Applied Chemistry Chinese Academy of Sciences State Key Lab of Electroanalytical Chemistry 5625 Remin StreetChangchun 130022 Changchun CHINA
| | - Huaning Wang
- Changchun Institute of Applied Chemistry Chinese Academy of Sciences: Chang Chun Institute of Applied Chemistry Chinese Academy of Sciences State Key Lab of Electroanalytical Chemistry CHINA
| | - Yao Xiao
- Changchun Institute of Applied Chemistry Chinese Academy of Sciences: Chang Chun Institute of Applied Chemistry Chinese Academy of Sciences State Key Lab of Electroanalytical Chemistry CHINA
| | - Bingling Li
- Changchun Institute of Applied Chemistry, Chinese Academy of Science State Key Lab of Electroanalytical Chemistry 5625 Renmin Street 130022 Changchun CHINA
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36
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Yu S, Shang J, He S, Wang Q, Li R, Chen Y, Liu X, Wang F. Multiply Guaranteed and Successively Amplified Activation of a Catalytic DNA Machine for Highly Efficient Intracellular Imaging of MicroRNA. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2203341. [PMID: 35843889 DOI: 10.1002/smll.202203341] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/24/2022] [Indexed: 06/15/2023]
Abstract
DNA amplification machines show great promise for intracellular imaging, yet are always constrained by off-site machinery activation or signal leakage, originating from the inherent thermodynamically driven hybridization between machinery substrates. Herein, an entropy-driven catalytic DNA amplification machine is integrated with the on-site amplified substrate exposure procedure to realize the high-contrast in vivo imaging of microRNA (miRNA). The key machinery substrate (fuel strands) is initially split into substrate subunits that are respectively grafted into an auxiliary DNA polymerization amplification accessory for eliminating the undesired signal leakage. Meanwhile, in target cells, the auxiliary polymerization accessory can be motivated by cell-specific mRNA for successively restoring their intact machine-propelling functions for guaranteeing the on-site amplified imaging of miRNA with high specificity. This intelligent on-site multiply guaranteed machinery can improve the specificity of catalytic DNA machines for discriminating different cell types and, thus, can provide a remarkable prospect in biomedical diagnosis.
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Affiliation(s)
- Shanshan Yu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Jinhua Shang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Shizhen He
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Qing Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Ruomeng Li
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Yingying Chen
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Xiaoqing Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, 430072, China
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37
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He S, Yu S, Li R, Chen Y, Wang Q, He Y, Liu X, Wang F. On‐Site Nonenzymatic Orthogonal Activation of a Catalytic DNA Circuit for Self‐Reinforced In Vivo MicroRNA Imaging. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202206529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
| | | | | | | | | | - Yuqiu He
- Wuhan University Chemistry CHINA
| | | | - Fuan Wang
- Wuhan University College of Chemistry and Molecular Sciences Bayi Road 299 430072 Wuhan CHINA
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