1
|
Yan H, Cao G, Wang J, Zhu X, Dong S, Huang Y, Chao M, Li Y, Gao F, Hua L. An enzymatically activated AND-gate DNA logic circuit for tumor cells recognition via multi-microRNAs detection. Biosens Bioelectron 2024; 256:116278. [PMID: 38608497 DOI: 10.1016/j.bios.2024.116278] [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: 12/29/2023] [Revised: 03/26/2024] [Accepted: 04/06/2024] [Indexed: 04/14/2024]
Abstract
The DNA-based logic circuit, constructed to mimic biochemical reaction networks, is highly significant in detecting biomarkers at the molecular level. The differences in the expression levels of microRNAs (miRNAs) within different types of cells provide hope for distinguishing cell subtypes. However, reliance on a single miRNA often leads to unreliable results. Herein, we constructed an enzyme-triggered cascade logic circuit based on the AND gate, which is capable of generating corresponding fluorescence signals in the presence of target miRNAs. The introduction of apurinic/apyrimidinic (AP) sites effectively reduces the likelihood of false signal generation. Amplification of the fluorescence signal relies on the catalytic hairpin assembly and the repetitive reuse of the multicomponent nucleic acid enzyme (MNAzyme). We demonstrated that the logic circuit can not only distinguish cancer cells from normal cells but also identify different types of cancer cells. The programmability of the logic circuits and the simplicity of the assay system allow us to modify the functional sequences to recognize different types of biomarkers, thus providing a reference for the identification of various cell subtypes.
Collapse
Affiliation(s)
- Hanrong Yan
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, China
| | - Guojun Cao
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, China; Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Jin Wang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, China
| | - Xu Zhu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, China
| | - Shuqing Dong
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, China
| | - Yuqi Huang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, China
| | - Minghao Chao
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, China
| | - Yuting Li
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, China
| | - Fenglei Gao
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, China.
| | - Lei Hua
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, China; Department of Neurosurgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, China.
| |
Collapse
|
2
|
Zhang Y, Yang Q, Zhu L, Lu X, Xin W, Ding J, Wang S, Tang Z, Fan GC, Cen Y, Song ZL, Luo X. Intelligent Cell Profiling and Precision Release: Multimolecular Marker-Activated Transmembrane DNA Computing Nanosystem. Anal Chem 2024; 96:7747-7755. [PMID: 38691774 DOI: 10.1021/acs.analchem.4c01122] [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: 05/03/2024]
Abstract
Accurate classification of tumor cells is of importance for cancer diagnosis and further therapy. In this study, we develop multimolecular marker-activated transmembrane DNA computing systems (MTD). Employing the cell membrane as a native gate, the MTD system enables direct signal output following simple spatial events of "transmembrane" and "in-cell target encounter", bypassing the need of multistep signal conversion. The MTD system comprises two intelligent nanorobots capable of independently sensing three molecular markers (MUC1, EpCAM, and miR-21), resulting in comprehensive analysis. Our AND-AND logic-gated system (MTDAND-AND) demonstrates exceptional specificity, allowing targeted release of drug-DNA specifically in MCF-7 cells. Furthermore, the transformed OR-AND logic-gated system (MTDOR-AND) exhibits broader adaptability, facilitating the release of drug-DNA in three positive cancer cell lines (MCF-7, HeLa, and HepG2). Importantly, MTDAND-AND and MTDOR-AND, while possessing distinct personalized therapeutic potential, share the ability of outputting three imaging signals without any intermediate conversion steps. This feature ensures precise classification cross diverse cells (MCF-7, HeLa, HepG2, and MCF-10A), even in mixed populations. This study provides a straightforward yet effective solution to augment the versatility and precision of DNA computing systems, advancing their potential applications in biomedical diagnostic and therapeutic research.
Collapse
Affiliation(s)
- Yuxi Zhang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Qian Yang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Lina Zhu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Xinyi Lu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Wenjuan Xin
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Jiani Ding
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Shumin Wang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Zijie Tang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Gao-Chao Fan
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Yao Cen
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Zhi-Ling Song
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Xiliang Luo
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| |
Collapse
|
3
|
Bi S, Chen W, Fang Y, Shen J, Zhang Q, Guo H, Ju H, Liu Y. Cancer Cell-Selective PD-L1 Inhibition via a DNA Safety Catch to Enhance Immunotherapy Specificity. Angew Chem Int Ed Engl 2024; 63:e202402522. [PMID: 38421189 DOI: 10.1002/anie.202402522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 02/29/2024] [Accepted: 02/29/2024] [Indexed: 03/02/2024]
Abstract
Immune checkpoint protein blockade (ICB) has emerged as a powerful immunotherapy approach, but suppressing immune-related adverse events (irAEs) for noncancerous cells and normal tissues remains challenging. Activatable ICB has been developed with tumor microenvironment highly-expressed molecules as stimuli, but they still lack precision and efficiency considering the diffusion of stimuli molecules in whole tumor tissue. Here we assemble PD-L1 with a duplex DNA strand, termed as "safety catch", to regulate its accessibility for ICB. The safety catch remains at "on" status for noncancerous cells to prevent ICB binding to PD-L1. Cancer cell membrane protein c-Met acts as a trigger protein to react with safety catch, which selectively exposes its hybridization region for ICB reagent. The ICB reagent is a retractable DNA nanostring with repeating hairpin-structural units, whose contraction drives PD-L1 clustering with endocytosis-guided degradation. The safety catch, even remained at "safety on" status, is removed from the cell membrane via a DNA strand displacement reaction to minimize its influence on noncancerous cells. This strategy demonstrates selective and potent immunotherapeutic capabilities only against cancer cells both in vitro and in vivo, and shows effective suppression of irAEs in normal tissues, therefore would become a promising approach for precise immunotherapy in mice.
Collapse
Affiliation(s)
- Shiyi Bi
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Wei Chen
- Department of Urology, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Institute of Urology, Nanjing University, Nanjing, 210008, China
| | - Yanyun Fang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Jieyu Shen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Qing Zhang
- Department of Urology, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Institute of Urology, Nanjing University, Nanjing, 210008, China
| | - Hongqian Guo
- Department of Urology, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Institute of Urology, Nanjing University, Nanjing, 210008, China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Ying Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, 210023, China
| |
Collapse
|
4
|
Zhang YW, Wang SM, Li XQ, Kang B, Chen HY, Xu JJ. Endogenous AND Logic DNA Nanomachine for Highly Specific Cancer Cell Imaging. Anal Chem 2024; 96:7030-7037. [PMID: 38656919 DOI: 10.1021/acs.analchem.4c00211] [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: 04/26/2024]
Abstract
Intracellular cancer-related biomarker imaging strategy has been used for specific identification of cancer cells, which was of great importance to accurate cancer clinical diagnosis and prognosis studies. Localized DNA circuits with improved sensitivity showed great potential for intracellular biomarkers imaging. However, the ability of localized DNA circuits to specifically image cancer cells is limited by off-site signal leakage associated with a single-biomarker sensing strategy. Herein, we integrated the endogenous enzyme-powered strategy with logic-responsive and localized signal amplifying capability to construct a self-assembled endogenously AND logic DNA nanomachine (EDN) for highly specific cancer cell imaging. When the EDN encountered a cancer cell, the overexpressed DNA repairing enzyme apurinic/apyrimidinic endonuclease 1 (APE1) and miR-21 could synergistically activate a DNA circuit via cascaded localized toehold-mediated strand displacement (TMSD) reactions, resulting in amplified fluorescence resonance energy transfer (FRET) signal. In this strategy, both endogenous APE1 and miR-21, served as two "keys" to activate the AND logic operation in cancer cells to reduce off-tumor signal leakage. Such a multiplied molecular recognition/activation nanomachine as a powerful toolbox realized specific capture and reliable imaging of biomolecules in living cancer cells.
Collapse
Affiliation(s)
- Yu-Wen Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Shu-Min Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xiao-Qiong Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Bin Kang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jing-Juan Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| |
Collapse
|
5
|
Bardales AC, Smirnov V, Taylor K, Kolpashchikov DM. DNA Logic Gates Integrated on DNA Substrates in Molecular Computing. Chembiochem 2024; 25:e202400080. [PMID: 38385968 DOI: 10.1002/cbic.202400080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 02/23/2024]
Abstract
Due to nucleic acid's programmability, it is possible to realize DNA structures with computing functions, and thus a new generation of molecular computers is evolving to solve biological and medical problems. Pioneered by Milan Stojanovic, Boolean DNA logic gates created the foundation for the development of DNA computers. Similar to electronic computers, the field is evolving towards integrating DNA logic gates and circuits by positioning them on substrates to increase circuit density and minimize gate distance and undesired crosstalk. In this minireview, we summarize recent developments in the integration of DNA logic gates into circuits localized on DNA substrates. This approach of all-DNA integrated circuits (DNA ICs) offers the advantages of biocompatibility, increased circuit response, increased circuit density, reduced unit concentration, facilitated circuit isolation, and facilitated cell uptake. DNA ICs can face similar challenges as their equivalent circuits operating in bulk solution (bulk circuits), and new physical challenges inherent in spatial localization. We discuss possible avenues to overcome these obstacles.
Collapse
Affiliation(s)
- Andrea C Bardales
- Chemistry Department, University of Central Florida, 4111 Libra Drive, Physical Sciences Bld. Rm. 255, Orlando, FL 32816-2366, Florida
| | - Viktor Smirnov
- Laboratory of Molecular Robotics and Biosensor Materials, SCAMT Institute, ITMO University, 9 Lomonosova Str., St. Petersburg, Russian Federation
| | - Katherine Taylor
- Chemistry Department, University of Central Florida, 4111 Libra Drive, Physical Sciences Bld. Rm. 255, Orlando, FL 32816-2366, Florida
| | - Dmitry M Kolpashchikov
- Chemistry Department, University of Central Florida, 4111 Libra Drive, Physical Sciences Bld. Rm. 255, Orlando, FL 32816-2366, Florida
| |
Collapse
|
6
|
Wu C, Yan L, Zhan Z, Qu R, Wang Y, Zeng X, Yang H, Feng P, Wei Z, Chen P. Biomolecules-mediated electrochemical signals of Cu 2+: Y-DNA nanomachines enable homogeneous rapid one-step assay of lung cancer circulating tumor cells. Biosens Bioelectron 2024; 249:116030. [PMID: 38241796 DOI: 10.1016/j.bios.2024.116030] [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: 11/26/2023] [Revised: 01/01/2024] [Accepted: 01/10/2024] [Indexed: 01/21/2024]
Abstract
This study presents a straightforward efficient technique for extracting circulating tumor cells (CTCs) and a rapid one-step electrochemical method (45 min) for detecting lung cancer A549 cells based on the specific recognition of mucin 1 using aptamers and the modulation of Cu2+ electrochemical signals by biomolecules. The CTCs separation and enrichment process can be completed within 45 min using lymphocyte separation solution (LSS), erythrocyte lysis solution (ELS), and three centrifugations. Besides, the influence of various biomolecules on Cu2+ electrochemical signals is comprehensively discussed, with DNA nanospheres selected as the medium. Three single-stranded DNA sequences were hybridized to form Y-shaped DNA (Y-DNA), creating DNA nanospheres. Upon specific capture of mucin 1 by the aptamer, most DNA nanospheres could form complexes with Cu2+ (DNA nanosphere-Cu2+), significantly reducing the concentration of free Cu2+. Our approach yielded the limit of detection (LOD) of 2 ag/mL for mucin 1 and 1 cell/mL for A549 cells. 39 clinical blood samples were used for further validation, yielding results closely correlated with pathological, computed tomography (CT) scan findings and folate receptor-polymerase chain reaction (FR-PCR) kits. The receiver operating characteristic (ROC) curve displayed an area under the curve (AUC) value of 0.960, demonstrating 100% specificity and 93.1% sensitivity for the assay. Taken together, our findings indicate that this straightforward and efficient pretreatment and rapid, highly sensitive electrochemical assay holds great promise for liquid biopsy-based tumor detection using CTCs.
Collapse
Affiliation(s)
- Chengyong Wu
- Department of Laboratory Medicine, Med+X Center for Manufacturing, Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, National Clinical Research Center for Geriatrics, Out-patient Department, Core Facilities of West China Hospital, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Li Yan
- Department of Laboratory Medicine, Med+X Center for Manufacturing, Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, National Clinical Research Center for Geriatrics, Out-patient Department, Core Facilities of West China Hospital, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Zixuan Zhan
- Department of Laboratory Medicine, Med+X Center for Manufacturing, Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, National Clinical Research Center for Geriatrics, Out-patient Department, Core Facilities of West China Hospital, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Runlian Qu
- Department of Laboratory Medicine, Med+X Center for Manufacturing, Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, National Clinical Research Center for Geriatrics, Out-patient Department, Core Facilities of West China Hospital, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yue Wang
- Department of Laboratory Medicine, Med+X Center for Manufacturing, Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, National Clinical Research Center for Geriatrics, Out-patient Department, Core Facilities of West China Hospital, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Xianghu Zeng
- Department of Laboratory Medicine, Med+X Center for Manufacturing, Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, National Clinical Research Center for Geriatrics, Out-patient Department, Core Facilities of West China Hospital, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Haihui Yang
- Department of Laboratory Medicine, Med+X Center for Manufacturing, Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, National Clinical Research Center for Geriatrics, Out-patient Department, Core Facilities of West China Hospital, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Pan Feng
- Department of Laboratory Medicine, Med+X Center for Manufacturing, Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, National Clinical Research Center for Geriatrics, Out-patient Department, Core Facilities of West China Hospital, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Zeliang Wei
- Department of Laboratory Medicine, Med+X Center for Manufacturing, Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, National Clinical Research Center for Geriatrics, Out-patient Department, Core Facilities of West China Hospital, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Piaopiao Chen
- Department of Laboratory Medicine, Med+X Center for Manufacturing, Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, National Clinical Research Center for Geriatrics, Out-patient Department, Core Facilities of West China Hospital, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Li XQ, Jia YL, Zhang YW, Shi PF, Chen HY, Xu JJ. Simulation-Assisted DNA Nanodevice Serve as a General Optical Platform for Multiplexed Analysis of Micrornas. Adv Healthc Mater 2024; 13:e2302652. [PMID: 37794560 DOI: 10.1002/adhm.202302652] [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: 08/24/2023] [Revised: 09/29/2023] [Indexed: 10/06/2023]
Abstract
Small frame nucleic acids (FNAs) serve as excellent carrier materials for various functional nucleic acid molecules, showcasing extensive potential applications in biomedicine development. The carrier module and function module combination is crucial for probe design, where an improper combination can significantly impede the functionality of sensing platforms. This study explores the effect of various combinations on the sensing performance of nanodevices through simulations and experimental approaches. Variances in response velocities, sensitivities, and cell uptake efficiencies across different structures are observed. Factors such as the number of functional molecules loaded, loading positions, and intermodular distances affect the rigidity and stability of the nanostructure. The findings reveal that the structures with full loads and moderate distances between modules have the lowest potential energy. Based on these insights, a multisignal detection platform that offers optimal sensitivity and response speed is developed. This research offers valuable insights for designing FNAs-based probes and presents a streamlined method for the conceptualization and optimization of DNA nanodevices.
Collapse
Affiliation(s)
- Xiao-Qiong Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Yi-Lei Jia
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Yu-Wen Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Peng-Fei Shi
- College of Medicine, Linyi University, Linyi, 276005, China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Jing-Juan Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| |
Collapse
|
9
|
Ding M, Xiao X, Yang Y, Yao Z, Dong Z, Gao Q, Tian B. AND-Logic Cascade Rolling Circle Amplification for Optomagnetic Detection of Dual Target SARS-CoV-2 Sequences. Anal Chem 2024; 96:455-462. [PMID: 38123506 DOI: 10.1021/acs.analchem.3c04533] [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: 12/23/2023]
Abstract
DNA logic operations are accurate and specific molecular strategies that are appreciated in target multiplexing and intelligent diagnostics. However, most of the reported DNA logic operation-based assays lack amplifiers prior to logic operation, resulting in detection limits at the subpicomolar to nanomolar level. Herein, a homogeneous and isothermal AND-logic cascade amplification strategy is demonstrated for optomagnetic biosensing of two different DNA inputs corresponding to a variant of concern sequence (containing spike L452R) and a highly conserved sequence from SARS-CoV-2. With an "amplifiers-before-operator" configuration, two input sequences are recognized by different padlock probes for amplification reactions, which generate amplicons used, respectively, as primers and templates for secondary amplification, achieving the AND-logic operation. Cascade amplification products can hybridize with detection probes grafted onto magnetic nanoparticles (MNPs), leading to hydrodynamic size increases and/or aggregation of MNPs. Real-time optomagnetic MNP analysis offers a detection limit of 8.6 fM with a dynamic detection range spanning more than 3 orders of magnitude. The accuracy, stability, and specificity of the system are validated by testing samples containing serum, salmon sperm, a single-nucleotide variant, and biases of the inputs. Clinical samples are tested with both quantitative reverse transcription-PCR and our approach, showing highly consistent measurement results.
Collapse
Affiliation(s)
- Mingming Ding
- Department of Biomedical Engineering, School of Basic Medical Sciences, Central South University, Changsha 410013, China
| | - Xiaozhou Xiao
- Department of Biomedical Engineering, School of Basic Medical Sciences, Central South University, Changsha 410013, China
| | - Yulin Yang
- Department of Biomedical Engineering, School of Basic Medical Sciences, Central South University, Changsha 410013, China
| | - Ziyang Yao
- Department of Biomedical Engineering, School of Basic Medical Sciences, Central South University, Changsha 410013, China
| | - Zhuxin Dong
- Department of Biomedical Engineering, School of Basic Medical Sciences, Central South University, Changsha 410013, China
- Furong Laboratory, Changsha 410008, China
| | - Qian Gao
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Bo Tian
- Department of Biomedical Engineering, School of Basic Medical Sciences, Central South University, Changsha 410013, China
- Furong Laboratory, Changsha 410008, China
| |
Collapse
|
10
|
Wu Q, Wei X, Chen F, Huang M, Zhang S, Zhu L, Zhou L, Yang C, Song Y. Aptamer-Assisted Blockade of the Immune Suppressor Sialic Acid-Binding Immunoglobulin-Like Lectin-15 for Cancer Immunotherapy. Angew Chem Int Ed Engl 2023; 62:e202312609. [PMID: 37955317 DOI: 10.1002/anie.202312609] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/12/2023] [Accepted: 11/13/2023] [Indexed: 11/14/2023]
Abstract
The percentage of low response and adaptive resistance to current antibody-based immune checkpoint blockade (ICB) therapy requires the development of novel immunotherapy strategies. Here, we developed an aptamer-assisted immune checkpoint blockade (Ap-ICB) against sialic acid-binding immunoglobulin-like lectin-15 (Siglec-15), a novel immune suppressor broadly upregulated on cancer cells and tumor infiltrating myeloid cells, which is mutually exclusive of programmed cell death ligand 1 (PD-L1). Using protein aptamer selection, we identified WXY3 aptamer with high affinity against Siglec-15 protein/Siglec-15 positive cells. We demonstrated that WXY3 aptamer rescued antigen-specific T cell responses in vitro and in vivo. Importantly, the WXY3 Ap-ICB against Siglec-15 amplified anti-tumor immunity in the tumor microenvironment and inhibited tumor growth/metastasis in syngeneic mouse model, which may result from enhanced macrophage and T cell functionality. In addition, by using aptamer-based spherical nucleic acids, we developed a synergetic ICB strategy of multivalent binding and steric hindrance, which further improves the in vivo anti-tumor effect. Taken together, our results support Ap-ICB targeted Siglec-15 as a potential strategy for normalization cancer immunotherapy.
Collapse
Affiliation(s)
- Qiuyue Wu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, 361005, Xiamen, Fujian, China
| | - Xinyu Wei
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, 361005, Xiamen, Fujian, China
| | - Fude Chen
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, 361005, Xiamen, Fujian, China
| | - Mengjiao Huang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, 361005, Xiamen, Fujian, China
| | - Suhui Zhang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, 361005, Xiamen, Fujian, China
| | - Lin Zhu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, 361005, Xiamen, Fujian, China
| | - Leiji Zhou
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, 361005, Xiamen, Fujian, China
| | - Chaoyong Yang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, 361005, Xiamen, Fujian, China
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China
| | - Yanling Song
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, 361005, Xiamen, Fujian, China
| |
Collapse
|
11
|
Yang H, Dong Q, Xu D, Feng X, He P, Song W, Zhou H. An "off-on-off" type electrochemical biosensor for detecting multiple biomarkers with DNAzyme-mediated entropy-driven catalytic and DSN enzyme-assisted recycling amplification. Anal Chim Acta 2023; 1283:341978. [PMID: 37977795 DOI: 10.1016/j.aca.2023.341978] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/06/2023] [Accepted: 10/27/2023] [Indexed: 11/19/2023]
Abstract
In this work, an intelligent and versatile electrochemical biosensor was constructed to detect two types of biomarkers by utilizing "off-on-off" switching. Firstly, human apurinic/apyrimidinic endonuclease1(APE1) mediated specific cleavage of the AP site, initiating activation DNAzyme and entropy-driven catalytic (EDC) reaction. Subsequently, large amounts of ferrocene labeled single-stranded DNA was released and captured with a remarkable electrochemical signal, achieving "off-on" state. In the presence of microRNA 21(miRNA-21), the DNA/RNA heteroduplexes were formed and cleaved by duplex-specific nuclease (DSN) with recovery the target miRNA-21, causing the current suppression in an "on-off" state. This sensor achieved highly sensitive detection of APE1 and miRNA-21 with a detection limit of 2.5 mU·mL-1 and 1.33 × 10-20 M, respectively, and also exhibited good selectivity, reproducibility and stability. Moreover, this proposed biosensor made it possible to realize analysis of multiple types of biomarkers on a single sensor, which improved utilization and analysis efficiency compared to traditional sensors. This study might open a new avenue to design multifunctional sensing platform for biological research and early disease diagnosis.
Collapse
Affiliation(s)
- Huan Yang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, PR China; Shandong Key Laboratory of Biochemical Analysis, PR China; Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, PR China; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Qi Dong
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, PR China; Shandong Key Laboratory of Biochemical Analysis, PR China; Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, PR China; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Dandan Xu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, PR China; Shandong Key Laboratory of Biochemical Analysis, PR China; Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, PR China; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Xinmiao Feng
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, PR China; Shandong Key Laboratory of Biochemical Analysis, PR China; Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, PR China; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Peng He
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, PR China; Shandong Key Laboratory of Biochemical Analysis, PR China; Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, PR China; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Weiling Song
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, PR China; Shandong Key Laboratory of Biochemical Analysis, PR China; Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, PR China; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China.
| | - Hong Zhou
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, PR China; Shandong Key Laboratory of Biochemical Analysis, PR China; Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, PR China; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China.
| |
Collapse
|
12
|
Zhu X, Xu J, Ling G, Zhang P. Tunable metal-organic frameworks assist in catalyzing DNAzymes with amplification platforms for biomedical applications. Chem Soc Rev 2023; 52:7549-7578. [PMID: 37817667 DOI: 10.1039/d3cs00386h] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/12/2023]
Abstract
Various binding modes of tunable metal organic frameworks (MOFs) and functional DNAzymes (Dzs) synergistically catalyze the emergence of abundant functional nanoplatforms. Given their serial variability in formation, structural designability, and functional controllability, Dzs@MOFs tend to be excellent building blocks for the precise "intelligent" manufacture of functional materials. To present a clear outline of this new field, this review systematically summarizes the progress of Dz integration into MOFs (MOFs@Dzs) through different methods, including various surface infiltration, pore encapsulation, covalent binding, and biomimetic mineralization methods. Atomic-level and time-resolved catalytic mechanisms for biosensing and imaging are made possible by the complex interplay of the distinct molecular structure of Dzs@MOF, conformational flexibility, and dynamic regulation of metal ions. Exploiting the precision of DNAzymes, MOFs@Dzs constructed a combined nanotherapy platform to guide intracellular drug synthesis, photodynamic therapy, catalytic therapy, and immunotherapy to enhance gene therapy in different ways, solving the problems of intracellular delivery inefficiency and insufficient supply of cofactors. MOFs@Dzs nanostructures have become excellent candidates for biosensing, bioimaging, amplification delivery, and targeted cancer gene therapy while emphasizing major advancements and seminal endeavors in the fields of biosensing (nucleic acid, protein, enzyme activity, small molecules, and cancer cells), biological imaging, and targeted cancer gene delivery and gene therapy. Overall, based on the results demonstrated to date, we discuss the challenges that the emerging MOFs@Dzs might encounter in practical future applications and briefly look forward to their bright prospects in other fields.
Collapse
Affiliation(s)
- Xiaoguang Zhu
- Wuya College of Innovation, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang 110016, China.
| | - Jiaqi Xu
- Wuya College of Innovation, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang 110016, China.
| | - Guixia Ling
- Wuya College of Innovation, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang 110016, China.
| | - Peng Zhang
- Wuya College of Innovation, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang 110016, China.
| |
Collapse
|
13
|
Wei K, He M, Zhang J, Zhao C, Nie C, Zhang T, Liu Y, Chen T, Jiang J, Chu X. A DNA Logic Circuit Equipped with a Biological Amplifier Loaded into Biomimetic ZIF-8 Nanoparticles Enables Accurate Identification of Specific Cancers In Vivo. Angew Chem Int Ed Engl 2023; 62:e202307025. [PMID: 37615278 DOI: 10.1002/anie.202307025] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 08/11/2023] [Accepted: 08/23/2023] [Indexed: 08/25/2023]
Abstract
DNA logic circuits (DLC) enable the accurate identification of specific cell types, such as cancer cells, but they face the challenges of weak output signals and a lack of competent platforms that can efficiently deliver DLC components to the target site in the living body. To address these issues, we rationally introduced a cascaded biological amplifier module based on the Primer Exchange Reaction inspired by electronic circuit amplifier devices. As a paradigm, three abnormally expressed Hela cell microRNAs (-30a, -17, and -21) were chosen as "AND" gate inputs. DLC response to these inputs was boosted by the amplifier markedly enhancing the output signal. More importantly, the encapsulation of DLC and amplifier components into ZIF-8 nanoparticles resulted in their efficient delivery to the target site, successfully distinguishing the Hela tumor subtype from other tumors in vivo. Thus, we envision that this strategy has great potential for clinical cancer diagnosis.
Collapse
Affiliation(s)
- Kaiji Wei
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Mengyun He
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Juan Zhang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Chuan Zhao
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Cunpeng Nie
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Tong Zhang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Yi Liu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Tingting Chen
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Jianhui Jiang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Xia Chu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| |
Collapse
|
14
|
Huang X, Chen M, Huang Z, Zhang Y, Shen T, Shi Y, Tong Y, Zou X, Liu SY, Guo J, Dai Z. On-Site-Activated Transmembrane Logic DNA Nanodevice Enables Highly Specific Imaging of Cancer Cells by Targeting Tumor-Related Nucleolin and Intracellular MicroRNA. Anal Chem 2023; 95:14746-14753. [PMID: 37723832 DOI: 10.1021/acs.analchem.3c02868] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/20/2023]
Abstract
The ability to specifically image cancer cells is essential for cancer diagnosis; however, this ability is limited by the false positive associated with single-biomarker sensors and off-site activation of "always active" nucleic acid probes. Herein, we propose an on-site, activatable, transmembrane logic DNA (TLD) nanodevice that enables dual-biomarker sensing of tumor-related nucleolin and intracellular microRNA for highly specific cancer cell imaging. The TLD nanodevice is constructed by assembling a tetrahedral DNA nanostructure containing a linker (L)-blocker (B)-DNAzyme (D)-substrate (S) unit. AS-apt, a DNA strand containing an elongated segment and the AS1411 aptamer, is pre-anchored to nucleolin protein, which is specifically expressed on the membrane of cancer cells. Initially, the TLD nanodevice is firmly sealed by the blocker containing an AS-apt recognition zone, which prevents off-site activation. When the nanodevice encounters a target cancer cell, AS-apt (input 1) binds to the blocker and unlocks the sensing ability of the nanodevice for miR-21 (input 2). The TLD nanodevice achieves dual-biomarker sensing from the cell membrane to the cytoplasm, thereby ensuring cancer cell-specific imaging. This TLD nanodevice represents a promising strategy for the highly reliable analysis of intracellular biomarkers and a promising platform for cancer diagnosis and related biomedical applications.
Collapse
Affiliation(s)
- Xing Huang
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen Campus of Sun Yat-Sen University, Shenzhen 518107, China
| | - Meng Chen
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen Campus of Sun Yat-Sen University, Shenzhen 518107, China
| | - Zhan Huang
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yanfei Zhang
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Taorong Shen
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yakun Shi
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen Campus of Sun Yat-Sen University, Shenzhen 518107, China
| | - Yanli Tong
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen Campus of Sun Yat-Sen University, Shenzhen 518107, China
| | - Xiaoyong Zou
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Si-Yang Liu
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen Campus of Sun Yat-Sen University, Shenzhen 518107, China
| | - Jianhe Guo
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen Campus of Sun Yat-Sen University, Shenzhen 518107, China
| | - Zong Dai
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen Campus of Sun Yat-Sen University, Shenzhen 518107, China
| |
Collapse
|
15
|
Hou TL, Zhang XL, Zhou J, Chai YQ, Yuan R. Near-Infrared-Driven Nanorocket for Rapid and Ultrasensitive Detection of MicroRNA. Anal Chem 2023; 95:13156-13162. [PMID: 37606955 DOI: 10.1021/acs.analchem.3c01962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
Herein, by introducing gold nanostars (AuNSs) as fuel core, a near-infrared-driven nanorocket (NIDNR) with pretty fast walking was exploited for ultrasensitive miRNA detection. Compared with traditional nanomaterials-comprised nanomachines (NMs), the NIDNR possesses much better kinetic and thermodynamic performance owing to the extra photothermal driving force from localized surface plasmon (LSP). Impressively, the whole reaction time of NIDNR down to 15 min was realized, which is almost more than 8 times beyond those of conventional DNA-based NMs. This way, the inherent obstacle of traditional NMs, including long reaction time and low efficiency, could be easily addressed. As a proof of concept, the NIDNR was successfully applied to develop an electrochemical biosensing platform for rapid and sensitive detection of miRNA with an LOD down to 2.95 aM and achieved the real-time assay of real biological samples from human hepatocellular carcinoma cells (MHCC97L) and HeLa, thus providing an innovative insight to design more versatile DNA nanomachines for ultimate application in biosensing platform construction and clinical sample detection.
Collapse
Affiliation(s)
- Tong-Lin Hou
- 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
| | - Xiao-Long Zhang
- 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
| | - Ya-Qin 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
| |
Collapse
|
16
|
Wu K, Ma C, Wang Y. Functional Nucleic Acid Probes Based on Two-Photon for Biosensing. BIOSENSORS 2023; 13:836. [PMID: 37754070 PMCID: PMC10527542 DOI: 10.3390/bios13090836] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/18/2023] [Accepted: 08/18/2023] [Indexed: 09/28/2023]
Abstract
Functional nucleic acid (FNA) probes have been widely used in environmental monitoring, food analysis, clinical diagnosis, and biological imaging because of their easy synthesis, functional modification, flexible design, and stable properties. However, most FNA probes are designed based on one-photon (OP) in the ultraviolet or visible regions, and the effectiveness of these OP-based FNA probes may be hindered by certain factors, such as their potential for photodamage and limited light tissue penetration. Two-photon (TP) is characterized by the nonlinear absorption of two relatively low-energy photons of near-infrared (NIR) light with the resulting emission of high-energy ultraviolet or visible light. TP-based FNA probes have excellent properties, including lower tissue self-absorption and autofluorescence, reduced photodamage and photobleaching, and higher spatial resolution, making them more advantageous than the conventional OP-based FNA probes in biomedical sensing. In this review, we summarize the recent advances of TP-excited and -activated FNA probes and detail their applications in biomolecular detection. In addition, we also share our views on the highlights and limitations of TP-based FNA probes. The ultimate goal is to provide design approaches for the development of high-performance TP-based FNA probes, thereby promoting their biological applications.
Collapse
Affiliation(s)
- Kefeng Wu
- GBA Branch of Aerospace Information Research Institute, Chinese Academy of Sciences, Guangzhou 510700, China
- Guangdong Provincial Key Laboratory of Terahertz Quantum Electromagnetics, Guangzhou 510700, China
| | - Changbei Ma
- School of Life Sciences, Central South University, Changsha 410013, China
| | - Yisen Wang
- GBA Branch of Aerospace Information Research Institute, Chinese Academy of Sciences, Guangzhou 510700, China
- Guangdong Provincial Key Laboratory of Terahertz Quantum Electromagnetics, Guangzhou 510700, China
| |
Collapse
|
17
|
Zhao Y, Li Z, Li B, Wang C. DNA Windmill Probe for Multiplexed mRNA Detection and Cell Type Discrimination. Chemistry 2023; 29:e202301300. [PMID: 37314386 DOI: 10.1002/chem.202301300] [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: 04/25/2023] [Revised: 05/29/2023] [Accepted: 06/14/2023] [Indexed: 06/15/2023]
Abstract
Accurate cancer diagnosis especially early diagnosis is of great importance for prompt therapy and elevated survival rate. mRNAs are widely used as biomarkers for cancer identification and treatment. mRNA expression levels are highly associated with cancer stage and malignant progression. Nevertheless, single type mRNA detection is insufficient and unreliable. Herein, we developed a DNA nano-windmill probe for in situ multiplexed mRNAs detection and imaging in this paper. The probe is designed to simultaneously target four types of mRNA through wind blades. Importantly, recognition of targets is independent from each other, which further facilitate cell type discrimination. The probe can specifically distinguish cancer cell lines from normal cells. In addition, it can identify changes in mRNA expression levels in living cells. The current strategy enriches the toolbox for improving the accuracy of cancer diagnosis and therapeutic solutions.
Collapse
Affiliation(s)
- Yu Zhao
- Department of Chemistry and Chemical Engineering, Inner Mongolia University, Hohhot, 010020, China
| | - Zhihao Li
- Department of Chemistry and Chemical Engineering, Inner Mongolia University, Hohhot, 010020, China
| | - Bo Li
- Department of Chemistry and Chemical Engineering, Inner Mongolia University, Hohhot, 010020, China
| | - Chunyan Wang
- Department of Chemistry and Chemical Engineering, Inner Mongolia University, Hohhot, 010020, China
| |
Collapse
|
18
|
Kim M, Jo H, Jung GY, Oh SS. Molecular Complementarity of Proteomimetic Materials for Target-Specific Recognition and Recognition-Mediated Complex Functions. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2208309. [PMID: 36525617 DOI: 10.1002/adma.202208309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/29/2022] [Indexed: 06/02/2023]
Abstract
As biomolecules essential for sustaining life, proteins are generated from long chains of 20 different α-amino acids that are folded into unique 3D structures. In particular, many proteins have molecular recognition functions owing to their binding pockets, which have complementary shapes, charges, and polarities for specific targets, making these biopolymers unique and highly valuable for biomedical and biocatalytic applications. Based on the understanding of protein structures and microenvironments, molecular complementarity can be exhibited by synthesizable and modifiable materials. This has prompted researchers to explore the proteomimetic potentials of a diverse range of materials, including biologically available peptides and oligonucleotides, synthetic supramolecules, inorganic molecules, and related coordination networks. To fully resemble a protein, proteomimetic materials perform the molecular recognition to mediate complex molecular functions, such as allosteric regulation, signal transduction, enzymatic reactions, and stimuli-responsive motions; this can also expand the landscape of their potential bio-applications. This review focuses on the recognitive aspects of proteomimetic designs derived for individual materials and their conformations. Recent progress provides insights to help guide the development of advanced protein mimicry with material heterogeneity, design modularity, and tailored functionality. The perspectives and challenges of current proteomimetic designs and tools are also discussed in relation to future applications.
Collapse
Affiliation(s)
- Minsun Kim
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Hyesung Jo
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, South Korea
| | - Gyoo Yeol Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, South Korea
| | - Seung Soo Oh
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, South Korea
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, South Korea
| |
Collapse
|
19
|
Yang Y, Hu T, Bian Y, Meng F, Yu S, Li H, Zhang Q, Gu L, Weng X, Tan C, Liang R. Coupling Probiotics with 2D CoCuMo-LDH Nanosheets as a Tumor-Microenvironment-Responsive Platform for Precise NIR-II Photodynamic Therapy. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2211205. [PMID: 36913539 DOI: 10.1002/adma.202211205] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/07/2023] [Indexed: 06/09/2023]
Abstract
Photodynamic therapy (PDT) has become a promising cancer treatment approach with superior advantages. However, it remains a grand challenge to develop tumor microenvironment (TME)-responsive photosensitizers (PSs) for tumor-targeting precise PDT. Herein, the coupling Lactobacillus acidophilus (LA) probiotics with 2D CoCuMo layered-double-hydroxide (LDH) nanosheets (LA&LDH) is reported as a TME-responsive platform for precise NIR-II PDT. The CoCuMo-LDH nanosheets loaded on LA can be transformed from crystalline into amorphous through etching by the LA-metabolite-enabled low pH and overexpressed glutathione. The TME-induced in situ amorphization of CoCuMo-LDH nanosheets can boost its photodynamic activity for singlet oxygen (1 O2 ) generation under 1270 nm laser irradiation with relative 1 O2 quantum yield of 1.06, which is the highest among previously reported NIR-excited PSs. In vitro and in vivo assays prove that the LA&LDH can effectively achieve complete cell apoptosis and tumor eradication under 1270 nm laser irradiation. This study proves that the probiotics can be used as a tumor-targeting platform for highly efficient precise NIR-II PDT.
Collapse
Affiliation(s)
- Yu Yang
- State Key Laboratory of Chemical Resource Engineering, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Tingting Hu
- State Key Laboratory of Chemical Resource Engineering, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Yixin Bian
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100730, P. R. China
| | - Fanqi Meng
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Shilong Yu
- Institute of Advanced Materials (IAM) and Key Laboratory of Flexible Electronics (KLoFE), Nanjing Tech University (NanjingTech), 30 South Puzhu Road, Nanjing, 211816, P. R. China
| | - Hai Li
- Institute of Advanced Materials (IAM) and Key Laboratory of Flexible Electronics (KLoFE), Nanjing Tech University (NanjingTech), 30 South Puzhu Road, Nanjing, 211816, P. R. China
| | - Qinghua Zhang
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Lin Gu
- School of Materials Science and Engineering, Tsinghua University, Beijing, 100084, P. R. China
| | - Xisheng Weng
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100730, P. R. China
| | - Chaoliang Tan
- Department of Chemistry and Center of Super-Diamond and Advanced Films (COSDAF), City University of Hong Kong, Kowloon, Hong Kong SAR, 999077, P. R. China
- Shenzhen Research Institute, City University of Hong Kong, Shenzhen, 518057, P. R. China
| | - Ruizheng Liang
- State Key Laboratory of Chemical Resource Engineering, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| |
Collapse
|
20
|
Xi X, Wu Z, Zhang X, Li Y, Zhao Y, Wen W, Wang S. Endogenous Protease-Activatable Nanosensor Based on PNA-Peptide-DNA Engineering for AND-Gated and Dual-Model Detection of MicroRNA in Single Living Tumor Cells. ACS APPLIED MATERIALS & INTERFACES 2023; 15:21917-21928. [PMID: 37105764 DOI: 10.1021/acsami.3c02012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The in situ detection of low-content cancer biomarkers by an endogenous activator instead of an exogenous initiator in vitro remains a great challenge, leaving a gap in the development of a tumor-specific nanosensor with an endogenous protease-activatable manner. Herein, we proposed an endogenous protease-activatable nanosensor (PA-NS) guided by peptide nucleic acid-peptide-DNA copolymers to realize AND-gated and dual-model sensing of miRNA-21 (miR-21) by combining electrochemical detection with optical imaging in living tumor cells, without an additional introduction of an exogenous activator or nanomaterials. Moreover, the PA-NS can only be activated by "dual keys" (overexpressed miR-21 and cathepsin B protease in tumor cells) simultaneously, which enables effective improvement of the tumor-to-healthy cells ratio. The fluorescence intensity measured in single tumor cells was ∼3.5-fold higher than that in single healthy cells, and the electrochemical response decreased ∼30% in the presence of target miRNA. Furthermore, studies on regulation of the protease activity and miR-21 fluctuation under external stimulation have contributed to our understanding of the biological processes and drug screenings underlying disease development. This specific endogenous protease-mediated manner for dual-model detection of miRNA guarantees excellent tumor-selective capability, which offers new opportunities to study cell heterogeneity and provides more reliable fundamentals for the diagnosis and treatment of cancer down to the single-cell level.
Collapse
Affiliation(s)
- Xiaoxue Xi
- Collaborative Innovation Center for Advanced Organic Chemical Materials, Coconstruted by the Province and Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering. Hubei University, Wuhan 430062, P. R. China
| | - Zhen Wu
- Collaborative Innovation Center for Advanced Organic Chemical Materials, Coconstruted by the Province and Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering. Hubei University, Wuhan 430062, P. R. China
| | - Xiuhua Zhang
- Collaborative Innovation Center for Advanced Organic Chemical Materials, Coconstruted by the Province and Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering. Hubei University, Wuhan 430062, P. R. China
| | - Yuebin Li
- Faculty of Physics and Electronic Sciences, Wuhan 430062, Hubei, P. R. China
| | - Yuandi Zhao
- Britton Chance Center for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics-Hubei Bioformatics and Molecular Imaging Key Laboratory, Department of Biomedicine Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, P. R. China
| | - Wei Wen
- Collaborative Innovation Center for Advanced Organic Chemical Materials, Coconstruted by the Province and Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering. Hubei University, Wuhan 430062, P. R. China
| | - Shengfu Wang
- Collaborative Innovation Center for Advanced Organic Chemical Materials, Coconstruted by the Province and Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering. Hubei University, Wuhan 430062, P. R. China
| |
Collapse
|
21
|
Chao Q, Zhang Y, Li Q, Jiao L, Sun X, Chen X, Zhu L, Yang Q, Shang C, Kong RM, Fan GC, Song ZL, Luo X. Compute-and-Release Logic-Gated DNA Cascade Circuit for Accurate Cancer Cell Imaging. Anal Chem 2023; 95:7723-7734. [PMID: 37133978 DOI: 10.1021/acs.analchem.3c00898] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Accurate identification of cancer cells is an essential prerequisite for cancer diagnosis and subsequent effective curative interventions. The logic-gate-assisted cancer imaging system that allows a comparison of expression levels between biomarkers, rather than just reading biomarkers as inputs, returns a more comprehensive logical output, improving its accuracy for cell identification. To fulfill this key criterion, we develop a compute-and-release logic-gated double-amplified DNA cascade circuit. This novel system, CAR-CHA-HCR, consists of a compute-and-release (CAR) logic gate, a double-amplified DNA cascade circuit (termed CHA-HCR), and a MnO2 nanocarrier. CAR-CHA-HCR, a novel adaptive logic system, is designed to logically output the fluorescence signals after computing the expression levels of intracellular miR-21 and miR-892b. Only when miR-21 is present and its expression level is above the threshold CmiR-21 > CmiR-892b, the CAR-CHA-HCR circuit performs a compute-and-release operation on free miR-21, thereby outputting enhanced fluorescence signals to accurately image positive cells. It is capable of comparing the relative concentrations of two biomarkers while sensing them, thus allowing accurate identification of positive cancer cells, even in mixed cell populations. Such an intelligent system provides an avenue for highly accurate cancer imaging and is potentially envisioned to perform more complex tasks in biomedical studies.
Collapse
Affiliation(s)
- Qiqi Chao
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Yuxi Zhang
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Qian Li
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Luzhen Jiao
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Xufeng Sun
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Xuxu Chen
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Lina Zhu
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Qian Yang
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Chengwen Shang
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Rong-Mei Kong
- School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, Shandong 273165, China
| | - Gao-Chao Fan
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Zhi-Ling Song
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, East China University of Technology, Nanchang 330013, China
| | - Xiliang Luo
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| |
Collapse
|
22
|
Liu J, Zhang C, Song J, Zhang Q, Zhang R, Zhang M, Han D, Tan W. Unlocking Genetic Profiles with a Programmable DNA-Powered Decoding Circuit. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023:e2206343. [PMID: 37116171 PMCID: PMC10369254 DOI: 10.1002/advs.202206343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 04/12/2023] [Indexed: 06/19/2023]
Abstract
Human genetic architecture provides remarkable insights into disease risk prediction and personalized medication. Advances in genomics have boosted the fine-mapping of disease-associated genetic variants across human genome. In healthcare practice, interpreting intricate genetic profiles into actionable medical decisions can improve health outcomes but remains challenging. Here an intelligent genetic decoder is engineered with programmable DNA computation to automate clinical analyses and interpretations. The DNA-based decoder recognizes multiplex genetic information by one-pot ligase-dependent reactions and interprets implicit genetic profiles into explicit decision reports. It is shown that the DNA decoder implements intended computation on genetic profiles and outputs a corresponding answer within hours. Effectiveness in 30 human genomic samples is validated and it is shown that it achieves desirable performance on the interpretation of CYP2C19 genetic profiles into drug responses, with accuracy equivalent to that of Sanger sequencing. Circuit modules of the DNA decoder can also be readily reprogrammed to interpret another pharmacogenetics genes, provide drug dosing recommendations, and implement reliable molecular calculation of polygenic risk score (PRS) and PRS-informed cancer risk assessment. The DNA-powered intelligent decoder provides a general solution to the translation of complex genetic profiles into actionable healthcare decisions and will facilitate personalized healthcare in primary care.
Collapse
Affiliation(s)
- Junlan Liu
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chao Zhang
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jinxing Song
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qing Zhang
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Rongjun Zhang
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Mingzhi Zhang
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Da Han
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
| | - Weihong Tan
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| |
Collapse
|
23
|
Gao P, Wei R, Chen Y, Li X, Pan W, Li N, Tang B. Pt nanozyme-bridged covalent organic framework-aptamer nanoplatform for tumor targeted self-strengthening photocatalytic therapy. Biomaterials 2023; 297:122109. [PMID: 37058901 DOI: 10.1016/j.biomaterials.2023.122109] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/29/2023] [Accepted: 04/01/2023] [Indexed: 04/05/2023]
Abstract
Covalent organic frameworks (COFs) have emerged as a promising platform for nanomedicine, while developing multifunctional COF nanoplatforms remains challenging due to the lack of efficient strategies for COF modification. Herein, we propose a nanozyme bridging (NZB) strategy for COF functionalization. Platinum nanoparticles (Pt NPs) as catalase mimics were in situ grown on the surface of COF NPs without reducing their drug loading capacity (CP), and thiol-terminated aptamer was further densely decorated onto CP NPs via a stable Pt-S bond (CPA). Pt nanozyme engineering and aptamer functionalization rendered the nanoplatform with excellent photothermal conversion, tumor targeting, and catalase-like catalytic performances. Using clinical-approved photosensitizer indocyanine green (ICG) as a model drug, we fabricated a nanosystem (ICPA) for tumor-targeted self-strengthening therapy. ICPA can effectively accumulate into tumor tissue and relieve the hypoxia microenvironment by decomposing the overexpressed H2O2 and generating O2. Under monowavelength NIR light irradiation, the catalase-like catalytic and singlet oxygen generation activities of ICPA can be significantly strengthened, leading to admirable photocatalytic treatment effects against malignant cells as well as tumor-bearing mice in a self-strengthening manner.
Collapse
Affiliation(s)
- Peng Gao
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan, 250014, PR China
| | - Ruyue Wei
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan, 250014, PR China
| | - Yuanyuan Chen
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan, 250014, PR China
| | - Xiaoyu Li
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan, 250014, PR China
| | - Wei Pan
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan, 250014, PR China
| | - Na Li
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan, 250014, PR China.
| | - Bo Tang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan, 250014, PR China.
| |
Collapse
|
24
|
Bohrmann L, Burghardt T, Rodríguez-Rodríguez C, Herth MM, Saatchi K, Häfeli UO. Quantitative Evaluation of a Multimodal Aptamer-Targeted Long-Circulating Polymer for Tumor Targeting. ACS OMEGA 2023; 8:11003-11020. [PMID: 37008162 PMCID: PMC10061651 DOI: 10.1021/acsomega.2c07762] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 02/23/2023] [Indexed: 06/19/2023]
Abstract
Aptamers are promising targeting agents for imaging and therapy of numerous diseases, including cancer. However, a significant shortcoming of aptamers is their poor stability and fast excretion, limiting their application in vivo. Common strategies to overcome these challenges is to chemically modify aptamers in order to increase their stability and/or to apply formulation technologies such as conjugating them to polymers or nanocarriers in order to increase their circulation half-life. This is expected to result in improved cellular uptake or retention to passively targeted nanomedicines. Herein, we report a modular conjugation strategy based on click chemistry between functionalized tetrazines and trans-cyclooctene (TCO), for the modification of high molecular weight hyperbranched polyglycerol (HPG) with sgc8 aptamer, fluorescent dyes, and 111In. Our data indicate strong affinity of sgc8 against a range of solid tumor-derived cell lines that have previously not been tested with this aptamer. Nevertheless, nonspecific uptake of scrambled ssDNA-functionalized HPG in cells highlights inherent challenges of aptamer-targeted probes that remain to be solved for clinical translation. We validate HPG-sgc8 as a nontoxic nanoprobe with high affinity against MDA-MB-468 breast and A431 lung cancer cells and show significantly increased plasma stability compared to free sgc8. In vivo quantitative SPECT/CT imaging indicates EPR-mediated tumor uptake of HPG-sgc8 and nontargeted or scrambled ssDNA-conjugated HPG but no statistically significant difference between these formulations in terms of total tumor uptake or retention. Our study emphasizes the need for stringent controls and quantification in the evaluation of aptamer-targeted probes. For this purpose, our versatile synthesis strategy provides a simple approach for the design and evaluation of long-circulating aptamer-conjugated nanoformulations.
Collapse
Affiliation(s)
- Lennart Bohrmann
- Faculty
of Pharmaceutical Sciences, University of
British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
- Department
of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Tobias Burghardt
- Faculty
of Pharmaceutical Sciences, University of
British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | | | - Matthias M. Herth
- Department
of Drug Design and Pharmacology, Faculty of Health and Medicinal Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
- Department
of Clinical Physiology, Nuclear Medicine & PET, Rigshospitalet, Blegdamsvej
9, 2100 Copenhagen, Denmark
| | - Katayoun Saatchi
- Faculty
of Pharmaceutical Sciences, University of
British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Urs O. Häfeli
- Faculty
of Pharmaceutical Sciences, University of
British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
- Department
of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| |
Collapse
|
25
|
Li JH, Liu JL, Zhang XL, Zhu XC, Yuan R, Chai YQ. Ultrasensitive Electrochemiluminescence Biosensor Based on 2D Co 3O 4 Nanosheets as a Coreaction Accelerator and Highly Ordered Rolling DNA Nanomachine as a Signal Amplifier for the Detection of MicroRNA. Anal Chem 2023; 95:4131-4137. [PMID: 36799666 DOI: 10.1021/acs.analchem.2c05116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
A novel ultrasensitive electrochemiluminescence (ECL) biosensor was constructed using two-dimensional (2D) Co3O4 nanosheets as a novel coreaction accelerator of the luminol/H2O2 ECL system for the detection of microRNA-21 (miRNA-21). Impressively, coreaction accelerator 2D Co3O4 nanosheets with effective mutual conversion of the Co2+/Co3+ redox pair and abundant active sites could promote the decomposition of coreactant H2O2 to generate more superoxide anion radicals (O2•-), which reacted with luminol for significantly enhancing ECL signals. Furthermore, the trace target miRNA-21 was transformed into a large number of G-wires through the strand displacement amplification (SDA) process to self-assemble the highly ordered rolling DNA nanomachine (HORDNM), which could tremendously improve the detection sensitivity of biosensors. Hence, on the basis of the novel luminol/H2O2/2D Co3O4 nanosheet ternary ECL system, the biosensor implemented ultrasensitive detection of miRNA-21 with a detection limit as low as 4.1 aM, which provided a novel strategy to design an effective ECL emitter for ultrasensitive detection of biomarkers for early disease diagnosis.
Collapse
Affiliation(s)
- Jia-Hang Li
- 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
| | - Jia-Li Liu
- 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
| | - Xiao-Long Zhang
- 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
| | - Xiao-Chun Zhu
- 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
| | - Ya-Qin 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
| |
Collapse
|
26
|
Zhang Q, Wang Y, Wang W, Min Q, Zhang JR, Zhu JJ. A Telomerase-Assisted Strategy for Regeneration of DNA Nanomachines in Living Cells. Angew Chem Int Ed Engl 2023; 62:e202213884. [PMID: 36478372 DOI: 10.1002/anie.202213884] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 12/04/2022] [Accepted: 12/06/2022] [Indexed: 12/12/2022]
Abstract
DNA nanomachines have been engineered into diverse personalized devices for diagnostic imaging of biomarkers; however, the regeneration of DNA nanomachines in living cells remains challenging. Here, we report an ingenious DNA nanomachine that can implement telomerase (TE)-activated regeneration in living cells. Upon apurinic/apyrimidinic endonuclease 1 (APE1)-responsive initiation of the nanomachine, the walker of the nanomachine moves along tracks regenerated by TE, generating multiply amplified signals through which APE1 can be imaged in situ. Additionally, augmentation of the signal due to the regeneration of the nanomachines could reveal differential expression of TE in different cell lines. To the best of our knowledge, this is the first proof-of-concept demonstration of the use of biomarkers to assist in the regeneration of nanomachines in living cells. This study offers a new paradigm for the development of more applicable and efficient DNA nanomachines.
Collapse
Affiliation(s)
- Qianying Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Yihan Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Wenjing Wang
- State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qianhao Min
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Jian-Rong Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China.,School of Chemistry and Life Science, Nanjing University Jinling College, Nanjing, 210089, China
| | - Jun-Jie Zhu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| |
Collapse
|
27
|
Zhou C, Song Y, Jin X, Li B, Pang C. Construction of a scalable DNA computing nano-system for large-scale and complex logical operations. NANOSCALE HORIZONS 2023; 8:176-184. [PMID: 36524605 DOI: 10.1039/d2nh00525e] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The predictability of Watson-Crick base pairing provides unique structural programmability to DNA, facilitating the development and application of biomolecules in biocomputing. However, in DNA-based biocomputing, the scale of operation that can be achieved by an existing reaction system is very limited. How to expand the operation range of a logic circuit and realize the integration and extensibility of circuits is always the key problem to be solved in this field. In this work, by designing a multifunctional DNA-nanostructure-based reaction platform, which can realize an output of up to 2n scalable fluorescence signals, combined with the construction of an input "library" and a modular distribution strategy of output signals, for the first time, we successfully performed the calculation of both square roots and cube roots of consecutive integers within a decimal number of "10" and in each result of the operation, two digits after the decimal point are preserved (). We believe that the design concept presented in this work can help effectively solve the urgent problems of biological computing in terms of computational scaling, integration and scalability, and can open up new horizons for the design of new functional devices and complex computing circuits.
Collapse
Affiliation(s)
- Chunyang Zhou
- Biomedical Engineering, School of Life Science and Technology, Changchun University of Science and Technology, Changchun, 130031, China.
| | - Yiwei Song
- Biomedical Engineering, School of Life Science and Technology, Changchun University of Science and Technology, Changchun, 130031, China.
| | - Xiuyan Jin
- Biomedical Engineering, School of Life Science and Technology, Changchun University of Science and Technology, Changchun, 130031, China.
| | - Bei Li
- Changchun Institute of Optics, Precision Machinery and Physics, Chinese Academy of Sciences, Changchun, 130031, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunying Pang
- Biomedical Engineering, School of Life Science and Technology, Changchun University of Science and Technology, Changchun, 130031, China.
| |
Collapse
|
28
|
Wang L, Wang K, Wang X, Niu R, Chen X, Zhu Y, Sun Z, Yang J, Liu G, Luo Y. Intelligent Dual-Lock Deoxyribonucleic Acid Automatons Boosting Precise Tumor Imaging. ACS APPLIED MATERIALS & INTERFACES 2023; 15:3826-3838. [PMID: 36625537 DOI: 10.1021/acsami.2c20024] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
An early and accurate cancer diagnosis holds the potential to improve treatment and prognosis. Nevertheless, the complexity of the biological system limits the selectivity of existing approaches and makes tumor imaging in vivo particularly challenging. In this study, tumor-specific fluorescence imaging was achieved by building intelligent dual-lock deoxyribonucleic acid automatons (IDEAs) that employed a DNA walking system standing on ZrMOF@MnO2 multifunctional nanocomposites for controllable molecular recognition. The IDEAs exhibited significantly enhanced fluorescence signals only in the coexistence of both miRNA and GSH of tumor cells, enabling accurate distinguishing of tumor cells from healthy ones. Furthermore, the feasibility and specificity of IDEAs were also validated in vivo with tumor bearing mice successfully. This work highlights the potential of the proposed IDEA strategy for tumor-specific imaging, paving the way for successful precision diagnosis and treatment.
Collapse
Affiliation(s)
- Liu Wang
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing400044, P. R. China
| | - Kang Wang
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing400044, P. R. China
- College of Bioengineering, Chongqing University, Chongqing400044, P. R. China
| | - Xiaohui Wang
- Department of Oncology, Jiangjin Hospital, Chongqing University, Chongqing402260, P. R. China
| | - Ruyan Niu
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing400044, P. R. China
- College of Bioengineering, Chongqing University, Chongqing400044, P. R. China
| | - Xiaohui Chen
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing400044, P. R. China
- College of Bioengineering, Chongqing University, Chongqing400044, P. R. China
| | - Ying Zhu
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing400044, P. R. China
| | - Zixin Sun
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing400044, P. R. China
| | - Jichun Yang
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing400044, P. R. China
| | - Guoxiang Liu
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing400044, P. R. China
| | - Yang Luo
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing400044, P. R. China
| |
Collapse
|
29
|
Qi M, Shi P, Zhang X, Cui S, Liu Y, Zhou S, Zhang Q. Reconfigurable DNA triplex structure for pH responsive logic gates †. RSC Adv 2023; 13:9864-9870. [PMID: 36998523 PMCID: PMC10043996 DOI: 10.1039/d3ra00536d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
The DNA triplex is a special DNA structure often used as a logic gate substrate due to its high stability, programmability, and pH responsiveness. However, multiple triplex structures with different C−G−C+ proportions must be introduced into existing triplex logic gates due to the numerous logic calculations involved. This requirement complicates circuit design and results in many reaction by-products, greatly restricting the construction of large-scale logic circuits. Thus, we designed a new reconfigurable DNA triplex structure (RDTS) and constructed the pH-responsive logic gates through its conformational change that uses two types of logic calculations, ‘AND’ and ‘OR’. The use of these logic calculations necessitates fewer substrates, further enhancing the extensibility of the logic circuit. This result is expected to promote the development of the triplex in molecular computing and facilitate the completion of large-scale computing networks. We constructed pH-responsive logic gates through substrate conformational change that uses two types of logic calculations, ‘AND’ and ‘OR’. Our logic gates necessitate fewer substrates when two types of logic calculations are needed.![]()
Collapse
Affiliation(s)
- Mingxuan Qi
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian UniversityDalian 116622China
| | - Peijun Shi
- School of Computer Science and Technology, Dalian University of TechnologyDalian 116024China
| | - Xiaokang Zhang
- School of Computer Science and Technology, Dalian University of TechnologyDalian 116024China
| | - Shuang Cui
- School of Computer Science and Technology, Dalian University of TechnologyDalian 116024China
| | - Yuan Liu
- School of Computer Science and Technology, Dalian University of TechnologyDalian 116024China
| | - Shihua Zhou
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian UniversityDalian 116622China
| | - Qiang Zhang
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian UniversityDalian 116622China
| |
Collapse
|
30
|
Yin N, Wang Y, Huang Y, Cao Y, Jin L, Liu J, Zhang T, Song S, Liu X, Zhang H. Modulating Nanozyme-Based Nanomachines via Microenvironmental Feedback for Differential Photothermal Therapy of Orthotopic Gliomas. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2204937. [PMID: 36437111 PMCID: PMC9875674 DOI: 10.1002/advs.202204937] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 10/03/2022] [Indexed: 05/20/2023]
Abstract
Gliomas are common and refractory primary tumors closely associated with the fine structures of the brain. Photothermal therapy (PTT) has recently shown promise as an effective treatment for gliomas. However, nonspecific accumulation of photothermal agents may affect adjacent normal brain structures, and the inflammatory response induced during PTT may result in an increased risk of brain tumor recurrence or metastasis. Here, the design and fabrication of an intelligent nanomachine is reported based on Gd2 O3 @Ir/TMB-RVG29 (G@IT-R) hybrid nanomaterials. These nanomaterials enable tumor-specific PTT and eliminate inflammation to protect normal brain tissue. The mechanism involves the rabies virus glycopeptide-29 peptide (RVG29) passing through the blood-brain barrier (BBB) and targeting gliomas. In the tumor microenvironment, Ir nanozymes can act as logic control systems to trigger chromogenic reaction amplification of 3,3',5,5'-tetramethylbenzidine (TMB) for tumor-specific PTT, whereas in normal brain tissues, they scavenge reactive oxygen species (ROS) generated by poor therapy and function as protective agents. Autophagy inhibition of Gd2 O3 enables excellent photothermal therapeutic effects on orthotopic gliomas and protection against inflammation in normal cells. The results of this study may prove useful in developing highly efficient nanomedicines for glioma treatment.
Collapse
Affiliation(s)
- Na Yin
- State Key Laboratory of Rare Earth Resource UtilizationChangchun Institute of Applied ChemistryChinese Academy of SciencesChangchunJilin130022China
- School of Applied Chemistry and EngineeringUniversity of Science and Technology of ChinaHefeiAnhui230026China
| | - Yinghui Wang
- State Key Laboratory of Rare Earth Resource UtilizationChangchun Institute of Applied ChemistryChinese Academy of SciencesChangchunJilin130022China
- School of Applied Chemistry and EngineeringUniversity of Science and Technology of ChinaHefeiAnhui230026China
| | - Ying Huang
- School of Applied Chemistry and EngineeringUniversity of Science and Technology of ChinaHefeiAnhui230026China
| | - Yue Cao
- Department of NeurosurgeryThe First Hospital of Jilin UniversityChangchunJilin130061China
| | - Longhai Jin
- Department of RadiologyThe Second Hospital of Jilin UniversityChangchunJilin130041China
| | - Jianhua Liu
- Department of RadiologyThe Second Hospital of Jilin UniversityChangchunJilin130041China
| | - Tianqi Zhang
- Department of RadiologyThe Second Hospital of Jilin UniversityChangchunJilin130041China
| | - Shuyan Song
- State Key Laboratory of Rare Earth Resource UtilizationChangchun Institute of Applied ChemistryChinese Academy of SciencesChangchunJilin130022China
- School of Applied Chemistry and EngineeringUniversity of Science and Technology of ChinaHefeiAnhui230026China
| | - Xiaogang Liu
- Department of ChemistryNational University of SingaporeSingapore117543Singapore
| | - Hongjie Zhang
- State Key Laboratory of Rare Earth Resource UtilizationChangchun Institute of Applied ChemistryChinese Academy of SciencesChangchunJilin130022China
- School of Applied Chemistry and EngineeringUniversity of Science and Technology of ChinaHefeiAnhui230026China
- Department of ChemistryTsinghua University100084BeijingChina
| |
Collapse
|
31
|
Liu H, Chen Y, Ju H. Functional DNA structures for cytosensing. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
|
32
|
Gauci G, Magri DC. Solvent-polarity reconfigurable fluorescent 4-piperazino- N-aryl-1,8-naphthalimide crown ether logic gates. RSC Adv 2022; 12:35270-35278. [PMID: 36540226 PMCID: PMC9732761 DOI: 10.1039/d2ra07568g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 09/19/2023] Open
Abstract
Four compounds 1-4 were designed and synthesised, comprising a 4-amino-N-aryl-1,8-naphthalimide fluorophore, a piperazine receptor, and an aryl group, as fluorescent logic gates. At the imide position, the substituent is phenyl (1), 1,2-dimethoxyphenyl (2), benzo-15-crown-5 (3), or benzo-18-crown-6 (4). Molecules 1 and 2 are constructed according to a fluorophore-spacer-receptor format, while 3 and 4 are engineered according to a receptor1-spacer1-fluorophore-spacer2-receptor2 format based on photoinduced electron transfer and internal charge transfer mechanisms. The compounds were studied in water, water/methanol mixtures of different ratios, and methanol by UV-visible absorption and steady-state fluorescence spectroscopy, as a function of pH, metal ions and solvent polarity. The excited state of 1-4 is 8.4 ± 0.2 in water, 7.6 ± 0.1 in 1 : 1 (v/v) water/methanol, and 7.1 ± 0.3 in methanol. The of 3 in water is 0.92 and the and of 4 in water are 2.3 and 2.9. 1H NMR data in D2O and CD3OD confirm H+ interaction at the piperazine moiety, and Na+ and Ba2+ binding at the benzo-15-crown-5 and benzo-18-crown-6 moieties of 3 and 4. By altering the solvent polarity, the fluorescent logic gates can be reconfigured between TRANSFER logic and AND logic. Molecules with polarity reconfigurable logic could be useful tools for probing the microenvironment of cellular membranes and protein interfaces.
Collapse
Affiliation(s)
- Gabriel Gauci
- Department of Chemistry, Faculty of Science, University of Malta Msida MSD 2080 Malta
| | - David C Magri
- Department of Chemistry, Faculty of Science, University of Malta Msida MSD 2080 Malta
| |
Collapse
|
33
|
Yao C, de Silva AP. A Tool, an App and a Field: Fluorescent PET Sensors, Blood Electrolyte Analysis and Molecular Logic as Products of Supramolecular Photoscience from Northern Ireland and Sri Lanka. Chempluschem 2022; 88:e202200362. [PMID: 36456470 DOI: 10.1002/cplu.202200362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/22/2022] [Indexed: 12/05/2022]
Abstract
The general tool of fluorescent PET (photoinduced electron transfer) sensors/switches - a molecular design principle with engineering features - is outlined, with the aid of frontier orbital energy diagrams. Fluorophores such as anthracene, 1,3-diaryl-Δ2 -pyrazolines and 4-amino-1,8-naphthalimides are employed within this system, alongside receptors such as amines, carboxylates, crown ethers and amino acids. This tool appealed to a multinational corporation for building a medical analyzer for electrolytes such as Na+ , K+ , Ca2+ and gases like CO2 , which became a commercially successful application. Finally, the tool was a springboard for chemistry to cross into computer science. The field of molecular logic can elucidate how molecules inside us handle information. Molecular examples of the simplest logic gates such as YES, NOT, OR, AND are described. A case of a human-level computation - visual edge detection - is also included.
Collapse
Affiliation(s)
- Chao‐Yi Yao
- School of Chemistry and Chemical Engineering Queen's University Belfast BT9 5AG Northern Ireland
| | - A. Prasanna de Silva
- School of Chemistry and Chemical Engineering Queen's University Belfast BT9 5AG Northern Ireland
| |
Collapse
|
34
|
Dong H, Zheng M, Chen M, Song D, Huang R, Zhang A, Wen H, Jia L, Zhuang J. Exploiting the size exclusion effect of protein adsorption layers for electrochemical detection of microRNA: A new mechanism for design of E-DNA sensor. Biosens Bioelectron 2022; 220:114911. [DOI: 10.1016/j.bios.2022.114911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 10/30/2022] [Accepted: 11/10/2022] [Indexed: 11/18/2022]
|
35
|
Wang J, Li J, Chen Y, Liu R, Wu Y, Liu J, Yang X, Wang K, Huang J. Size-Controllable and Self-Assembled DNA Nanosphere for Amplified MicroRNA Imaging through ATP-Fueled Cyclic Dissociation. NANO LETTERS 2022; 22:8216-8223. [PMID: 36194690 DOI: 10.1021/acs.nanolett.2c02934] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Visualizing intracellular microRNA (miRNA) is of great importance for revealing its roles in the development of disease. However, cell membrane barrier, complex intracellular environment and low abundance of target miRNA are three main challenges for efficient imaging of intracellular miRNA. Here, we report a size-controllable and self-assembled DNA nanosphere with ATP-fueled dissociation property for amplified miRNA imaging in live cells and mice. The DNA nanosphere was self-assembled from Y-shaped DNA (Y-DNA) monomers through predesigned base pair hybridization, and the size could be easily controlled by varying the concentration of Y-DNA. Once the nanosphere was internalized into cells, the intracellular specific target miRNA would trigger the cyclic dissociation of the DNA nanosphere driven by ATP, resulting in amplified FRET signal. The programmable DNA nanosphere has been proven to work well for detecting the expression of miRNA in cancer cells and in mice, which demonstrates its fairish cell penetration, stability and sensitivity.
Collapse
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 410082, P.R. China
| | - Juan Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, P.R. China
| | - Yu Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, P.R. China
| | - 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 410082, P.R. China
| | - Yixuan Wu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, P.R. China
| | - Jianbo 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 410082, P.R. China
| | - Xiaohai Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, P.R. China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, P.R. China
| | - 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 410082, P.R. China
| |
Collapse
|
36
|
Yan C, Shi G, Chen J. Fluorescent Detection of Two Pesticides Based on CRISPR-Cas12a and Its Application for the Construction of Four Molecular Logic Gates. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:12700-12707. [PMID: 36128975 DOI: 10.1021/acs.jafc.2c04548] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
An intelligent detection platform was developed through molecular logic gate operation based on CRISPR-Cas12a and signal amplification circuits using two kinds of pesticides [acetamiprid (ACE) and atrazine (ATR)] as inputs. The pesticide-aptamer bindings activate the signal amplification process to produce numerous double-stranded DNA, which can be identified by CRISPR-Cas12a. Under the optimal assay conditions, the sensor exhibits excellent analytical performance, with the detection limits for ACE and ATR of 2.5 and 0.2 pM, respectively. The practicality of the platform was verified by testing pesticide concentrations in food samples. Several molecular logic gates (OR, AND, XOR, and INHIBIT) were constructed using "0" and "1" to encode the target pesticides and the fluorescence readout. The logic detection platform with simple operation, high sensitivity, and multiple logic functions is promising to become a powerful sensing system for the intelligent assay of different pesticides in food samples.
Collapse
Affiliation(s)
- Chong Yan
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, Guangdong 510650, People's Republic of China
| | - Gu Shi
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, Guangdong 510650, People's Republic of China
| | - Junhua Chen
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, Guangdong 510650, People's Republic of China
| |
Collapse
|
37
|
Wang Z, Yang J, Qin G, Zhao C, Ren J, Qu X. An Intelligent Nanomachine Guided by DNAzyme Logic System for Precise Chemodynamic Therapy. Angew Chem Int Ed Engl 2022; 61:e202204291. [DOI: 10.1002/anie.202204291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Zhao Wang
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
- University of Science and Technology of China Hefei Anhui 230026 P. R. China
| | - Jie Yang
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
- University of Science and Technology of China Hefei Anhui 230026 P. R. China
| | - Geng Qin
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
- University of Science and Technology of China Hefei Anhui 230026 P. R. China
| | - Chuanqi Zhao
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
- University of Science and Technology of China Hefei Anhui 230026 P. R. China
| | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
- University of Science and Technology of China Hefei Anhui 230026 P. R. China
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
- University of Science and Technology of China Hefei Anhui 230026 P. R. China
| |
Collapse
|
38
|
Huang X, Zhang Y, Chen J, Zhang L, Xu Y, Yin W, Shi Y, Liu SY, Zou X, Dai Z. Dual-Locked DNAzyme Platform for In Vitro and In Vivo Discrimination of Cancer Cells. Anal Chem 2022; 94:12221-12230. [PMID: 36000958 DOI: 10.1021/acs.analchem.2c02788] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Imaging of tumor-associated microRNAs (miRNAs) can provide abundant information for cancer diagnosis, whereas the occurrence of trace amounts of miRNAs in normal cells inevitably causes an undesired false-positive signal in the discrimination of cancer cells during miRNA imaging. In this study, we propose a dual-locked (D-locked) platform consisting of the enzyme/miRNA-D-locked DNAzyme sensor and the honeycomb MnO2 nanosponge (hMNS) nanocarrier for highly specific cancer cell imaging. For a proof-of-concept demonstration, apurinic/apyrimidinic endonuclease 1 (APE1) and miR-21 were chosen as key models. The hMNS nanocarrier can efficiently release the D-locked DNAzyme sensor in living cells due to the decomposition of hMNS by glutathione, which can also supply Mn2+ for DNAzyme cleavage. Ascribing to the smart design of the D-locked DNAzyme sensor, the fluorescence signal can only be generated by the synergistic response of APE1 and miR-21 that are overexpressed in cancer cells. Compared with the miRNA single-locked DNAzyme sensor and the small-molecule (ATP)/miRNA D-locked DNAzyme sensor, the proposed enzyme (APE1)/miRNA D-locked DNAzyme sensor exhibited 2.6-fold and 2.4-fold higher discrimination ratio (Fcancer/Fnormal) for cancer cell discrimination, respectively. Owing to the superior performance, the D-locked strategy can selectively generate a fluorescence signal in cancer cells, facilitating accurate discrimination of cancer both in vitro and in vivo. Furthermore, this D-locked platform is easily adaptable toward other target molecules by redesigning the DNA sequences. The outstanding performance and expansibility of this D-locked platform holds promising prospects for cancer diagnosis and related biomedical applications.
Collapse
Affiliation(s)
- Xing Huang
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Yanfei Zhang
- School of Chemistry, Sun Yat-sen University, Guangzhou 510275, China
| | - Jun Chen
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Lang Zhang
- School of Chemistry, Sun Yat-sen University, Guangzhou 510275, China
| | - Yuzhi Xu
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518107, China
| | - Wen Yin
- School of Chemistry, Sun Yat-sen University, Guangzhou 510275, China
| | - Yakun Shi
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Si-Yang Liu
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Xiaoyong Zou
- School of Chemistry, Sun Yat-sen University, Guangzhou 510275, China
| | - Zong Dai
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| |
Collapse
|
39
|
Kong L, Han Z, Zhao M, Zhang X, Zhuo Y, Chai Y, Li Z, Yuan R. Versatile Electrochemical Biosensor Based on the Target-Controlled Capture and Release of DNA Nanotubes for the Ultrasensitive Detection of Multiplexed Biomarkers. Anal Chem 2022; 94:11416-11424. [PMID: 35930307 DOI: 10.1021/acs.analchem.2c02541] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Herein, an ultrasensitive and versatile electrochemical biosensor was developed through the target-controlled capture and release of signal probe-loaded DNA nanotube for the ultrasensitive detection of two different types of cancer-related biomarkers, microRNA-21 (miRNA-21) and glutathione (GSH). In this system, target 1 (miRNA-21) first triggered duplex-specific nuclease (DSN)-assisted recycle amplification to generate numerous disulfide-linked DNA strands (DL), which could effectively capture DNA nanotube to immobilize methylene blue (MB) to produce remarkable electrochemical signals and achieve the ultrasensitive detection of miRNA-21 with a detection limit down to 32.6 aM. Furthermore, in the presence of target 2 (GSH), the electrochemical signal was significantly reduced by a thiol-disulfide bond exchange reaction on DL to release MB-immobilized DNA nanotubes away from the sensing interface, which enabled the sensitive analysis of GSH with a detection limit of 0.379 nM. Impressively, this strategy could achieve ultrasensitive detection of different types of biomarkers to prominently lessen false-positive responses from the current sensing methods toward a single biomarker or the same type of biomarker and remarkably heighten the accuracy and precision of early cancer diagnosis. Meanwhile, the proposed electrochemical biosensor made it possible to realize the regenerative analysis of targets over four times without extra fuel, which could conspicuously improve the analytical efficiency compared with that of traditional biosensing assays. As a result, this study might open up novel insights to design a versatile and multifunctional sensing platform and encourage deeper exploration for detecting different types of biomarkers in the fields of early disease diagnosis and biochemical research.
Collapse
Affiliation(s)
- Lingqi Kong
- 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
| | - Zeshuai Han
- 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
| | - Mingzhou Zhao
- 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
| | - Xiaolong Zhang
- 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
| | - Ying Zhuo
- 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
| | - Zhaohui Li
- Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, College of Chemistry, Zhengzhou University, Zhengzhou 450001, 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
| |
Collapse
|
40
|
Wang Z, Yang J, Qin G, Zhao C, Ren J, Qu X. An Intelligent Nanomachine Guided by DNAzyme Logic System for Precise Chemodynamic Therapy. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202204291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Zhao Wang
- Changchun Institute of Applied Chemistry Chinese Academy of Sciences: Chang Chun Institute of Applied Chemistry Chinese Academy of Sciences Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization CHINA
| | - Jie Yang
- Changchun Institute of Applied Chemistry Chinese Academy of Sciences: Chang Chun Institute of Applied Chemistry Chinese Academy of Sciences Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization CHINA
| | - Geng Qin
- Changchun Institute of Applied Chemistry Chinese Academy of Sciences: Chang Chun Institute of Applied Chemistry Chinese Academy of Sciences Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization CHINA
| | - Chuanqi Zhao
- Changchun Institute of Applied Chemistry Chinese Academy of Sciences: Chang Chun Institute of Applied Chemistry Chinese Academy of Sciences Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization CHINA
| | - Jinsong Ren
- Changchun Institute of Applied Chemistry Chinese Academy of Sciences: Chang Chun Institute of Applied Chemistry Chinese Academy of Sciences Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization CHINA
| | - Xiaogang Qu
- Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Laboratory of Chemical Biology, Division of Biological Inorganic Chemistry 5625 Renmin Street 130022 Changchun CHINA
| |
Collapse
|
41
|
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.
Collapse
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
| |
Collapse
|
42
|
Chen H, Ding B, Ma P, Lin J. Recent progress in upconversion nanomaterials for emerging optical biological applications. Adv Drug Deliv Rev 2022; 188:114414. [PMID: 35809867 DOI: 10.1016/j.addr.2022.114414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/19/2022] [Accepted: 06/26/2022] [Indexed: 02/08/2023]
Abstract
The recent advances of upconversion nanoparticles (UCNPs) have made them the ideal "partner" for a variety of biological applications. In this review, we describe the emerging biological optical applications of UCNPs, focus on their potential therapeutic advantages. Firstly, we briefly review the development and mechanisms of upconversion luminescence, including organic and inorganic UCNPs. Next, in the section on UCNPs for imaging and detection, we list the development of UCNPs in visualization, temperature sensing, and detection. In the section on therapy, recent results are described concerning optogenetics and neurotherapy. Tumor therapy is another major part of this section, including the synergistic application of phototherapy such as photoimmunotherapy. In a special section, we briefly cover the integration of UCNPs in therapeutics. Finally, we present our understanding of the limitations and prospects of applications of UCNPs in biological fields, hoping to provide a more comprehensive understanding of UCNPs and attract more attention.
Collapse
Affiliation(s)
- Hao Chen
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China; School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Binbin Ding
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China.
| | - Ping'an Ma
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China; School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei 230026, China.
| | - Jun Lin
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China; School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei 230026, China.
| |
Collapse
|
43
|
Li ZY, Li DY, Huang L, Hu R, Yang T, Yang YH. An electrochemical aptasensor based on intelligent walking DNA nanomachine with cascade signal amplification powered by nuclease for Mucin 1 assay. Anal Chim Acta 2022; 1214:339964. [DOI: 10.1016/j.aca.2022.339964] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/05/2022] [Accepted: 05/18/2022] [Indexed: 02/01/2023]
|
44
|
A Target-Feedback Rolling-Cleavage Signal Amplifier for Ultrasensitive Electrochemical Detection of miRNA with Self-Assembled CeO2@Ag Hybrid Nanoflowers. Bioelectrochemistry 2022; 146:108152. [DOI: 10.1016/j.bioelechem.2022.108152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/30/2022] [Accepted: 04/30/2022] [Indexed: 01/15/2023]
|
45
|
Chen J, Fu S, Zhang C, Liu H, Su X. DNA Logic Circuits for Cancer Theranostics. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2108008. [PMID: 35254723 DOI: 10.1002/smll.202108008] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 02/08/2022] [Indexed: 06/14/2023]
Abstract
Cancer diagnosis and therapeutics (theranostics) based on the tumor microenvironment (TME) and biomarkers has been an emerging approach for precision medicine. DNA nanotechnology dynamically controls the self-assembly of DNA molecules at the nanometer scale to construct intelligent DNA chemical reaction systems. The DNA logic circuit is a particularly emerging approach for computing within the DNA chemical systems. DNA logic circuits can sensitively respond to tumor-specific markers and the TME through logic operations and signal amplification, to generate detectable signals or to release anti-cancer agents. In this review, the fundamental concepts of DNA logic circuits are clarified, the basic modules in the circuit are summarized, and how this advanced nano-assembly circuit responds to tumor-related molecules, how to perform logic operations, to realize signal amplification, and selectively release drugs through discussing over 30 application examples, are demonstrated. This review shows that DNA logic circuits have powerful logic judgment and signal amplification functions in improving the specificity and sensitivity of cancer diagnosis and making cancer treatment controllable. In the future, researchers are expected to overcome the existing shortcomings of DNA logic circuits and design smarter DNA devices with better biocompatibility and stability, which will further promote the development of cancer theranostics.
Collapse
Affiliation(s)
- Jing Chen
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Shengnan Fu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Chunyi Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Huiyu Liu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Xin Su
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| |
Collapse
|
46
|
Kong L, Li H, Zhang X, Zhuo Y, Chai Y, Yuan R. A Novel Ratiometric Electrochemical Biosensor Using Only One Signal Tag for Highly Reliable and Ultrasensitive Detection of miRNA-21. Anal Chem 2022; 94:5167-5172. [PMID: 35298124 DOI: 10.1021/acs.analchem.2c00190] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Herein, a novel ratiometric electrochemical biosensor with methylene blue (MB) as the only one signal tag was proposed for highly reliable and ultrasensitive detection of microRNA-21 (miRNA-21) under the assistance of an intelligent target-induced dual signal amplification (T-DSA). First, a small amount of target miRNA-21 could produce abundant mimic targets DNA S1 and Zn2+ through target-induced recycle and acid dissolution, respectively. Then, S1 triggered rolling circle amplification (RCA) to generate functional DNA nanospheres (DSP) encoded by DNAzyme and substrate sequence for loading numerous signal tag MB with a remarkable electrochemical signal (signal on), and the Zn2+ cofactor mediated the nonviolent DNAzyme-catalyzed cleavage of DSP to sharply release MB with obviously reduced electrochemical responses (signal off). Impressively, our strategy could controllably load and release the only signal tag MB through the well-designed DSP to effectively avoid the false positive responses caused by the non-ideal upright state of DNA probes connected to electrodes in traditional distance-dependent signal adjustment ratiometric strategies with two different signal tags. Meanwhile, with the aid of innovative T-DSA recycle and RCA-produced functional DSP, the detection sensitivity of this sensing platform was significantly improved. As a result, the proposed biosensor successfully realized highly reliable and ultrasensitive detection of miRNA-21 with a detection limit down to 26.7 aM, which shows exceptional promise in biological analysis and medical diagnosis.
Collapse
Affiliation(s)
- Lingqi Kong
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Hao Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Xiaolong Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ying Zhuo
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR 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, PR 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, PR China
| |
Collapse
|
47
|
Catalytic hairpin assembly as cascade nucleic acid circuits for fluorescent biosensor: design, evolution and application. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116582] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
48
|
Wang Y, Li B, Tian T, Liu Y, Zhang J, Qian K. Advanced on-site and in vitro signal amplification biosensors for biomolecule analysis. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
49
|
Li Z, Li Q, Wu Y, Yuan K, Shi M, Li Y, Meng HM, Li Z. Multivalent self-assembled nano string lights for tumor-targeted delivery and accelerated biomarker imaging in living cells and in vivo. Analyst 2022; 147:811-818. [DOI: 10.1039/d1an02363b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Multivalent self-assembled nano string lights for tumor-targeted delivery with high efficiency and accelerated biomarker imaging in living cells and in vivo.
Collapse
Affiliation(s)
- Zhijun Li
- College of Chemistry, Institute of Analytical Chemistry for Life Science, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China
| | - Qiannan Li
- College of Chemistry, Institute of Analytical Chemistry for Life Science, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China
| | - Yanan Wu
- College of Chemistry, Institute of Analytical Chemistry for Life Science, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China
| | - Kun Yuan
- College of Chemistry, Institute of Analytical Chemistry for Life Science, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China
| | - Mingqing Shi
- College of Chemistry, Institute of Analytical Chemistry for Life Science, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China
| | - Yiwei Li
- College of Chemistry, Institute of Analytical Chemistry for Life Science, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China
| | - Hong-Min Meng
- College of Chemistry, Institute of Analytical Chemistry for Life Science, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China
| | - Zhaohui Li
- College of Chemistry, Institute of Analytical Chemistry for Life Science, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China
| |
Collapse
|
50
|
Biosupramolecular networks: Taking inspiration from nature to create powerful synthetic platforms. Curr Opin Chem Biol 2021; 66:102104. [PMID: 34936943 DOI: 10.1016/j.cbpa.2021.102104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/10/2021] [Accepted: 11/18/2021] [Indexed: 12/19/2022]
Abstract
Nature is predicated on the ability to process large number of parallel signals to produce specific downstream outputs. Biosupramolecular networks are beginning to allow such processing power in synthetic systems, particularly through harnessing the recognition power of biomolecules. Such systems can be summarised through the reductionist view of containing inputs, circuitry motifs and functional outputs, with each of these elements able to be readily combined in a modular approach. Through the inherent 'plug and play' nature of these systems the field continues to rapidly expand, providing a wealth of new smart diagnostic and therapeutic systems.
Collapse
|