1
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Huang Z, Liu C, Li Z, Chen Q, Li D, Chen X, Chen Q, Wei J. Multiple DNA cycle amplification for highly efficient detection of mercury pollution in food. Food Chem 2024; 460:140714. [PMID: 39111041 DOI: 10.1016/j.foodchem.2024.140714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 06/16/2024] [Accepted: 07/28/2024] [Indexed: 09/06/2024]
Abstract
Mercury ion (Hg2+), a highly toxic metal pollutant, is widely found in the environment and can enter the human body through the food chain, causing various health issues. Sensitive and accurate methods for monitoring Hg2+ are highly desirable for ensuring food safety. Herein, we propose a self-sustainable multiple amplification system (MAS) for Hg2+ determination through the reciprocal activation between catalytic hairpin assembly (CHA) and rolling circle amplification (RCA). The thymine-encoded recognition element specifically recognizes Hg2+, triggering the exposure of the initiator. The initiator then motivates the mutual activation of CHA and RCA to accelerate the production of an exponentially amplified signal. The MAS method achieved a low detection limit of 11 pM. Due to its reliable target recognition and robust amplification efficiency, the MAS circuit facilitated the highly efficient and accurate analysis of low-abundance Hg2+ in milk and snakehead samples, thus providing a potentially new tool for food safety control.
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Affiliation(s)
- Ziling Huang
- College of Ocean Food and Biological Engineering, Jimei University, Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, 361021, China
| | - Chuanyi Liu
- College of Ocean Food and Biological Engineering, Jimei University, Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, 361021, China
| | - Zhigang Li
- College of Ocean Food and Biological Engineering, Jimei University, Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, 361021, China
| | - Qingmin Chen
- College of Ocean Food and Biological Engineering, Jimei University, Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, 361021, China
| | - Dong Li
- College of Ocean Food and Biological Engineering, Jimei University, Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, 361021, China
| | - Xiaomei Chen
- College of Ocean Food and Biological Engineering, Jimei University, Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, 361021, China
| | - Quansheng Chen
- College of Ocean Food and Biological Engineering, Jimei University, Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, 361021, China
| | - Jie Wei
- College of Ocean Food and Biological Engineering, Jimei University, Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, 361021, China.
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2
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Shi C, Yang D, Ma X, Pan L, Shao Y, Arya G, Ke Y, Zhang C, Wang F, Zuo X, Li M, Wang P. A Programmable DNAzyme for the Sensitive Detection of Nucleic Acids. Angew Chem Int Ed Engl 2024; 63:e202320179. [PMID: 38288561 DOI: 10.1002/anie.202320179] [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: 12/28/2023] [Indexed: 02/17/2024]
Abstract
Nucleic acids in biofluids are emerging biomarkers for the molecular diagnostics of diseases, but their clinical use has been hindered by the lack of sensitive detection assays. Herein, we report the development of a sensitive nucleic acid detection assay named SPOT (sensitive loop-initiated DNAzyme biosensor for nucleic acid detection) by rationally designing a catalytic DNAzyme of endonuclease capability into a unified one-stranded allosteric biosensor. SPOT is activated once a nucleic acid target of a specific sequence binds to its allosteric module to enable continuous cleavage of molecular reporters. SPOT provides a highly robust platform for sensitive, convenient and cost-effective detection of low-abundance nucleic acids. For clinical validation, we demonstrated that SPOT could detect serum miRNAs for the diagnostics of breast cancer, gastric cancer and prostate cancer. Furthermore, SPOT exhibits potent detection performance over SARS-CoV-2 RNA from clinical swabs with high sensitivity and specificity. Finally, SPOT is compatible with point-of-care testing modalities such as lateral flow assays. Hence, we envision that SPOT may serve as a robust assay for the sensitive detection of a variety of nucleic acid targets enabling molecular diagnostics in clinics.
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Affiliation(s)
- Chenzhi Shi
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Donglei Yang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Xiaowei Ma
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Li Pan
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yuanchuan Shao
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708, USA
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina, 27708, USA
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, 30322, USA
| | - Chuan Zhang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Min Li
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Pengfei Wang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
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3
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Wu Q, Yu Y, Chen M, Long J, Yang X. A label-free fluorescence sensing strategy based on GlaI-assisted EXPAR for rapid and accurate quantification of human methyltranferase activity. Talanta 2024; 269:125456. [PMID: 38061202 DOI: 10.1016/j.talanta.2023.125456] [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: 04/25/2023] [Revised: 09/23/2023] [Accepted: 11/20/2023] [Indexed: 01/05/2024]
Abstract
DNA methylation plays an important role in epigenetic modification. DNA methyltransferase (DNMT) is essential in the DNA methylation process, and its abnormal expression is closely related to cancer. In this study, we propose a novel biosensor platform (DS-GlaI-EXPAR) that combines hemi-methylated double-stranded DNA (dsDNA) as the substrate for DNMT1 with GlaI-assisted isothermal exponential amplification reaction (EXPAR) for rapid, simple, and sensitive detection of DNMT1 activity. The hemi-methylated dsDNA is fully methylated by DNMT1, and GlaI recognizes and cleaves the fully methylated sequence, generating terminal fragments that trigger EXPAR for efficient signal amplification. Whereas hemi-methylated dsDNA without DNMT1 will keep intact and cannot initiate EXPAR. DNMT1 activity can therefore be sensitively quantified by the real-time fluorescence signal of the DS-GlaI-EXPAR platform. The high-efficiency amplification of EXPAR and the recognition of GlaI enable the platform to overcome the inherent cumbersome and time-consuming shortcomings of traditional methods while meeting specificity and sensitivity. This DS-GlaI-EXPAR platform offers an impressively low limit of detection of 0.86 pg/μL and the entire detection process can be completed in a short time of 2.5 h in a single tube. Furthermore, DNMT1 activity detected by this platform in MCF-7 cells was significantly higher than that of HEK293 cells, and the inhibition of Apt. #9 was verified. This DNMT1 activity detection platform is very convenient and effective for the discovery of inhibitors and early cancer diagnosis.
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Affiliation(s)
- Qiaomin Wu
- Clinical Laboratory, Dongyang People's Hospital, Dongyang, Zhejiang, 322100, China; Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Yang Yu
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Mengqi Chen
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Jinyan Long
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Xiaolan Yang
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China.
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4
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Zhao QG, Zhou YJ, Cao DX, Tang AN, Kong DM. DNA-Functionalized Porphyrinic Metal-Organic Framework-Based Drug Delivery System for Targeted Bimodal Cancer Therapy. J Med Chem 2023; 66:15370-15379. [PMID: 37963839 DOI: 10.1021/acs.jmedchem.3c01479] [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: 11/16/2023]
Abstract
A DNA-functionalized porphyrinic MOF (porMOF) drug delivery system was successfully constructed. porMOF as a photosensitizer and drug delivery carrier can integrate photodynamic therapy (PDT) and chemotherapy. Via the strong coordination interaction between the zirconium cluster of porMOF and the terminal phosphate group of DNA, the stable modification of the DNA layer on the porMOF surface is achieved. Meanwhile, the introduction of C/G-rich base pairs into the DNA double-stranded structure provides more binding sites of chemotherapeutic drug doxorubicin (DOX). AS1411, an aptamer of nucleolin proteins that are overexpressed by cancer cells, is introduced in the double-stranded terminal, which can endow the nanosystem with the ability to selectively recognize cancer cells. C-rich sequences in DNA double strands form an i-motif structure under acidic conditions to promote the highly efficient release of DOX in cancer cells. In vitro and in vivo experiments demonstrate that the synergistic PDT/chemotherapy modality achieves highly efficient cancer cell killing and tumor ablation without undesirable side effects.
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Affiliation(s)
- Qiu-Ge Zhao
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, People's Republic of China
| | - Yun-Jie Zhou
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, People's Republic of China
| | - Dong-Xiao Cao
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, People's Republic of China
| | - An-Na Tang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, People's Republic of China
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, People's Republic of China
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5
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Dong J, Willner I. Transient Transcription Machineries Modulate Dynamic Functions of G-Quadruplexes: Temporal Regulation of Biocatalytic Circuits, Gene Replication and Transcription. Angew Chem Int Ed Engl 2023; 62:e202307898. [PMID: 37380611 DOI: 10.1002/anie.202307898] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 06/30/2023]
Abstract
Native G-quadruplex-regulated temporal biocatalytic circuits, gene polymerization, and transcription processes are emulated by biomimetic, synthetically engineered transcription machineries coupled to reconfigurable G-quadruplex nanostructures. These are addressed by the following example: (i) A reaction module demonstrates the fuel-triggered transcription machinery-guided transient synthesis of G-quadruplex nanostructures. (ii) A dynamically triggered and modulated transcription machinery that guides the temporal separation and reassembly of the anti-thrombin G-quadruplex aptamer/thrombin complex is introduced, and the transient thrombin-catalyzed coagulation of fibrinogen is demonstrated. (iii) A dynamically fueled transient transcription machinery for the temporal activation of G-quadruplex-topologically blocked gene polymerization circuits is introduced. (iv) Transcription circuits revealing G-quadruplex-promoted or G-quadruplex-inhibited cascaded transcription machineries are presented. Beyond advancing the rapidly developing field of dynamically modulated G-quadruplex DNA nanostructures, the systems introduce potential therapeutic applications.
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Affiliation(s)
- Jiantong Dong
- The Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Itamar Willner
- The Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
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6
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Jiang H, Li Y, Lv X, Deng Y, Li X. Recent advances in cascade isothermal amplification techniques for ultra-sensitive nucleic acid detection. Talanta 2023; 260:124645. [PMID: 37148686 PMCID: PMC10156408 DOI: 10.1016/j.talanta.2023.124645] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/30/2023] [Accepted: 05/03/2023] [Indexed: 05/08/2023]
Abstract
Nucleic acid amplification techniques have always been one of the hot spots of research, especially in the outbreak of COVID-19. From the initial polymerase chain reaction (PCR) to the current popular isothermal amplification, each new amplification techniques provides new ideas and methods for nucleic acid detection. However, limited by thermostable DNA polymerase and expensive thermal cycler, PCR is difficult to achieve point of care testing (POCT). Although isothermal amplification techniques overcome the defects of temperature control, single isothermal amplification is also limited by false positives, nucleic acid sequence compatibility, and signal amplification capability to some extent. Fortunately, efforts to integrating different enzymes or amplification techniques that enable to achieve intercatalyst communication and cascaded biotransformations may overcome the corner of single isothermal amplification. In this review, we systematically summarized the design fundamentals, signal generation, evolution, and application of cascade amplification. More importantly, the challenges and trends of cascade amplification were discussed in depth.
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Affiliation(s)
- Hao Jiang
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Yuan Li
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Xuefei Lv
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China.
| | - Yulin Deng
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Xiaoqiong Li
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
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7
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Li Z, Wang J, Willner B, Willner I. Topologically Triggered Dynamic DNA Frameworks. Isr J Chem 2023. [DOI: 10.1002/ijch.202300013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Affiliation(s)
- Zhenzhen Li
- The Institute of Chemistry The Center for Nanoscience and Nanotechnology The Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Jianbang Wang
- The Institute of Chemistry The Center for Nanoscience and Nanotechnology The Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Bilha Willner
- The Institute of Chemistry The Center for Nanoscience and Nanotechnology The Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Itamar Willner
- The Institute of Chemistry The Center for Nanoscience and Nanotechnology The Hebrew University of Jerusalem Jerusalem 91904 Israel
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8
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Zhang P, Ouyang Y, Zhuo Y, Chai Y, Yuan R. Recent Advances in DNA Nanostructures Applied in Sensing Interfaces and Cellular Imaging. Anal Chem 2023; 95:407-419. [PMID: 36625113 DOI: 10.1021/acs.analchem.2c04540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Pu 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
| | - Yu Ouyang
- 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.,Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - 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
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
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9
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Chakraborty J, Chaudhary AA, Khan SUD, Rudayni HA, Rahaman SM, Sarkar H. CRISPR/Cas-Based Biosensor As a New Age Detection Method for Pathogenic Bacteria. ACS OMEGA 2022; 7:39562-39573. [PMID: 36385843 PMCID: PMC9648122 DOI: 10.1021/acsomega.2c04513] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/03/2022] [Indexed: 05/25/2023]
Abstract
Methods enabling rapid and on-site detection of pathogenic bacteria are a prerequisite for public health assurance, medical diagnostics, ensuring food safety and security, and research. Many current bacteria detection technologies are inconvenient and time-consuming, making them unsuitable for field detection. New technology based on the CRISPR/Cas system has the potential to fill the existing gaps in detection. The clustered regularly interspaced short palindromic repeats (CRISPR) system is a part of the bacterial adaptive immune system to protect them from intruding bacteriophages. The immunological memory is saved by the CRISPR array of bacteria in the form of short DNA sequences (spacers) from invading viruses and incorporated with the CRISPR DNA repeats. Cas proteins are responsible for triggering and initiating the adaptive immune function of CRISPR/Cas systems. In advanced biological research, the CRISPR/Cas system has emerged as a significant tool from genome editing to pathogen detection. By considering its sensitivity and specificity, this system can become one of the leading detection methods for targeting DNA/RNA. This technique is well applied in virus detection like Dengue, ZIKA, SARS-CoV-2, etc., but for bacterial detection, this CRISPR/Cas system is limited to only a few organisms to date. In this review, we have discussed the different techniques based on the CRISPR/Cas system that have been developed for the detection of various pathogenic bacteria like L. monocytogenes, M. tuberculosis, Methicillin-resistant S. aureus, Salmonella, E. coli, P. aeruginosa, and A. baumannii.
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Affiliation(s)
- Joydeep Chakraborty
- Department
of Microbiology, Raiganj University, Raiganj, West Bengal733134, India
| | - Anis Ahmad Chaudhary
- Department
of Biology, College of Science, Imam Mohammad
Ibn Saud Islamic University (IMSIU), Riyadh11623, Saudi
Arabia
| | - Salah-Ud-Din Khan
- Department
of Biochemistry, College of Medicine, Imam
Mohammad Ibn Saud Islamic University (IMSIU), Riyadh11623, Saudi
Arabia
| | - Hassan Ahmad Rudayni
- Department
of Biology, College of Science, Imam Mohammad
Ibn Saud Islamic University (IMSIU), Riyadh11623, Saudi
Arabia
| | | | - Hironmoy Sarkar
- Department
of Microbiology, Raiganj University, Raiganj, West Bengal733134, India
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10
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Kumari R, Lim JW, Sullivan MR, Malampy R, Baush C, Smolina I, Robin H, Demidov VV, Ugolini GS, Auclair JR, Konry T. A Novel Rolling Circle Amplification-Based Detection of SARS-CoV-2 with Multi-Region Padlock Hybridization. Diagnostics (Basel) 2022; 12:diagnostics12092252. [PMID: 36140653 PMCID: PMC9497765 DOI: 10.3390/diagnostics12092252] [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: 08/25/2022] [Revised: 09/09/2022] [Accepted: 09/11/2022] [Indexed: 11/16/2022] Open
Abstract
SARS-CoV-2 has remained a global health burden, primarily due to the continuous evolution of different mutant strains. These mutations present challenges to the detection of the virus, as the target genes of qPCR, the standard diagnostic method, may possess sequence alterations. In this study, we develop an isothermal one-step detection method using rolling circle amplification (RCA) for SARS-CoV-2. This novel strategy utilizes a multi-padlock (MP-RCA) approach to detect viral-RNA via a simplified procedure with the reliable detection of mutated strains over other procedures. We designed 40 padlock-based probes to target different sequences across the SARS-CoV-2 genome. We established an optimal one-step isothermal reaction protocol utilizing a fluorescent output detected via a plate reader to test a variety of padlock combinations. This method was tested on RNA samples collected from nasal swabs and validated via PCR. S-gene target failure (SGTF)-mutated strains of SARS-CoV-2 were included. We demonstrated that the sensitivity of our assay was linearly proportional to the number of padlock probes used. With the 40-padlock combination the MP-RCA assay was able to correctly detect 45 out 55 positive samples (81.8% efficiency). This included 10 samples with SGTF mutations which we were able to detect as positive with 100% efficiency. We found that the MP-RCA approach improves the sensitivity of the MP-RCA assay, and critically, allows for the detection of SARS-CoV-2 variants with SGTF. Our method offers the simplicity of the reaction and requires basic equipment compared to standard qPCR. This method provides an alternative approach to overcome the challenges of detecting SARS-CoV-2 and other rapidly mutating viruses.
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Affiliation(s)
- Rajesh Kumari
- Department of Pharmaceutical Sciences, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
| | - Ji Won Lim
- Department of Pharmaceutical Sciences, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
| | - Matthew Ryan Sullivan
- Department of Pharmaceutical Sciences, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
| | - Rachel Malampy
- Life Science Testing Center, Northeastern University, Burlington, MA 01803, USA
| | - Connor Baush
- Life Science Testing Center, Northeastern University, Burlington, MA 01803, USA
| | | | - Howard Robin
- LJ Pathology Consultants, La Jolla, CA 92037, USA
| | - Vadim V. Demidov
- Biotechnology & Pharmaceuticals Group, Global Prior Art, Inc., Boston, MA 02109, USA
| | - Giovanni Stefano Ugolini
- Department of Pharmaceutical Sciences, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
| | | | - Tania Konry
- Department of Pharmaceutical Sciences, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
- Correspondence:
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11
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Dong J, O'Hagan MP, Willner I. Switchable and dynamic G-quadruplexes and their applications. Chem Soc Rev 2022; 51:7631-7661. [PMID: 35975685 DOI: 10.1039/d2cs00317a] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
G-Quadruplexes attract growing interest as functional constituents in biology, chemistry, nanotechnology, and material science. In particular, the reversible dynamic reconfiguration of G-quadruplexes provides versatile means to switch DNA nanostructures, reversibly control catalytic functions of DNA assemblies, and switch material properties and functions. The present review article discusses the switchable dynamic reconfiguration of G-quadruplexes as central functional and structural motifs that enable diverse applications in DNA nanotechnology and material science. The dynamic reconfiguration of G-quadruplexes has a major impact on the development of DNA switches and DNA machines. The integration of G-quadruplexes with enzymes yields supramolecular assemblies exhibiting switchable catalytic functions guided by dynamic G-quadruplex topologies. In addition, G-quadruplexes act as important building blocks to operate constitutional dynamic networks and transient dissipative networks mimicking complex biological dynamic circuitries. Furthermore, the integration of G-quadruplexes with DNA nanostructures, such as origami tiles, introduces dynamic and mechanical features into these static frameworks. Beyond the dynamic operation of G-quadruplex structures in solution, the assembly of G-quadruplexes on bulk surfaces such as electrodes or nanoparticles provides versatile means to engineer diverse electrochemical and photoelectrochemical devices and to switch the dynamic aggregation/deaggregation of nanoparticles, leading to nanoparticle assemblies that reveal switchable optical properties. Finally, the functionalization of hydrogels, hydrogel microcapsules, or nanoparticle carriers, such as SiO2 nanoparticles or metal-organic framework nanoparticles, yields stimuli-responsive materials exhibiting shape-memory, self-healing, and controlled drug release properties. Indeed, G-quadruplex-modified nanomaterials find growing interest in the area of nanomedicine. Beyond the impressive G-quadruplex-based scientific advances achieved to date, exciting future developments are still anticipated. The review addresses these goals by identifying the potential opportunities and challenges ahead of the field in the coming years.
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Affiliation(s)
- Jiantong Dong
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Michael P O'Hagan
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Itamar Willner
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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12
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Wang Y, Sun W, Wang J, Wang X, Xu Y, Guo Y, Wang Y, Zhang M, Jiang L, Liu S, Huang J. Ultrasensitive Uracil-DNA Glycosylase Activity Assay and Its Inhibitor Screening Based on Primer Remodeling Jointly via Repair Enzyme and Polymerase. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:3868-3875. [PMID: 35298179 DOI: 10.1021/acs.langmuir.2c00115] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The development of isothermal nucleic acid amplification techniques has great significance for highly sensitive biosensing in modern biology and biomedicine. A facile and robust exponential rolling circle amplification (RCA) strategy is proposed based on primer-remodeling amplification jointly via a repair enzyme and polymerase, and uracil-DNA glycosylase (UDG) is selected as a model analyte. Two kinds of complexes, complex I and complex II, are preprepared by hybridizing a circular template (CT) with a uracil-containing hairpin probe and tetrahydrofuran abasic site mimic (AP site)-embedded fluorescence-quenched probe (AFP), respectively. The target UDG specifically binds to complex I, resulting in the generation of an AP site, followed by cleavage via endonuclease IV (Endo IV) and the successive trimming of unmatched 3' terminus via phi29 DNA polymerase, thus producing a useable primer-CT complex that actuates the primary RCA. Then, numerous complex II anneal with the first-generation RCA product (RP), generating a complex II-RP assembly containing AP sites within the DNA duplex. With the aid of Endo IV and phi29, AFP, as a pre-primer in complex II, is converted into a mature primer to initiate additional rounds of RCA. So, countless AFPs are cleaved, releasing remarkably strong fluorescent signals. The biosensor is demonstrated to enable rapid and accurate detection of the UDG activity with an improved detection limit as low as 4.7 × 10-5 U·mL-1. Moreover, this biosensor is successfully applied for UDG inhibitor screening and complicated biological samples analysis. Compared to the previous exponential RCA methods, our proposed strategy offers additional advantages, including excellent stability, optional design of CT, and simplified operating steps. Therefore, this proposed strategy may create a useful and practical platform for ultrasensitive detection of low levels of analytes in clinical diagnosis and fundamental biomedicine research.
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Affiliation(s)
- Yu Wang
- School of Biological Sciences and Technology, University of Jinan, Jinan 250022, P. R. China
| | - Wenyu Sun
- School of Biological Sciences and Technology, University of Jinan, Jinan 250022, P. R. China
| | - Jingfeng Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Xu Wang
- Shandong Institute of Metrology and Science, Jinan 250014, P. R. China
| | - Yicheng Xu
- School of Biological Sciences and Technology, University of Jinan, Jinan 250022, P. R. China
| | - Yuanzhen Guo
- School of Biological Sciences and Technology, University of Jinan, Jinan 250022, P. R. China
| | - Yeru Wang
- School of Biological Sciences and Technology, University of Jinan, Jinan 250022, P. R. China
| | - Manru Zhang
- School of Water Conservancy and Environment, University of Jinan, Jinan 250022, P. R. China
| | - Long Jiang
- School of Water Conservancy and Environment, University of Jinan, Jinan 250022, P. R. China
| | - Su Liu
- School of Water Conservancy and Environment, University of Jinan, Jinan 250022, P. R. China
| | - Jiadong Huang
- School of Biological Sciences and Technology, University of Jinan, Jinan 250022, P. R. China
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13
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Xu Y, Lv Z, Yao C, Yang D. Construction of rolling circle amplification-based DNA nanostructures for biomedical applications. Biomater Sci 2022; 10:3054-3061. [DOI: 10.1039/d2bm00445c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA-based materials exhibit great potential in biomedical applications due to the excellent sequence programmability and unique functional designability. Rolling circle amplification (RCA) is an efficient isothermal enzymatic amplification strategy to...
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14
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Bialy RM, Mainguy A, Li Y, Brennan JD. Functional nucleic acid biosensors utilizing rolling circle amplification. Chem Soc Rev 2022; 51:9009-9067. [DOI: 10.1039/d2cs00613h] [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
Functional nucleic acids regulate rolling circle amplification to produce multiple detection outputs suitable for the development of point-of-care diagnostic devices.
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Affiliation(s)
- Roger M. Bialy
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4O3, Canada
| | - Alexa Mainguy
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4O3, Canada
| | - Yingfu Li
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4O3, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - John D. Brennan
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4O3, Canada
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15
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Zhang P, Fischer A, Ouyang Y, Wang J, Sohn YS, Karmi O, Nechushtai R, Willner I. Biocatalytic cascades and intercommunicated biocatalytic cascades in microcapsule systems. Chem Sci 2022; 13:7437-7448. [PMID: 35872834 PMCID: PMC9241983 DOI: 10.1039/d2sc01542k] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 04/29/2022] [Indexed: 12/13/2022] Open
Abstract
Dynamic dimerization of GOx-loaded microcapsules with β-gal//hemin/G-quadruplex-bridged T1/T2-loaded microcapsules guides the bi-directional intercommunication of the three catalysts cascade.
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Affiliation(s)
- Pu Zhang
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
- Key Laboratory of Luminescence and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People's Republic of China
| | - Amit Fischer
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Yu Ouyang
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Jianbang Wang
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Yang Sung Sohn
- Institute of Life Science, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Ola Karmi
- Institute of Life Science, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Rachel Nechushtai
- Institute of Life Science, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Itamar Willner
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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16
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Garafutdinov RR, Sakhabutdinova AR, Gilvanov AR, Chemeris AV. Rolling Circle Amplification as a Universal Method for the Analysis of a Wide Range of Biological Targets. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021; 47:1172-1189. [PMID: 34931113 PMCID: PMC8675116 DOI: 10.1134/s1068162021060078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/14/2021] [Accepted: 04/16/2021] [Indexed: 11/23/2022]
Abstract
Detection and quantification of biotargets are important analytical tasks, which are solved using a wide range of various methods. In recent years, methods based on the isothermal amplification of nucleic acids (NAs) have been extensively developed. Among them, a special place is occupied by rolling circle amplification (RCA), which is used not only for the detection of a specific NA but also for the analysis of other biomolecules, and is also a versatile platform for the development of highly sensitive methods and convenient diagnostic devices. The present review reveals a number of methodical aspects of RCA-mediated analysis; in particular, the data on its key molecular participants are presented, the methods for increasing the efficiency and productivity of RCA are described, and different variants of reporter systems are briefly characterized. Differences in the techniques of RCA-mediated analysis of biotargets of various types are shown. Some examples of using different RCA variants for the solution of specific diagnostic problems are given.
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Affiliation(s)
- R. R. Garafutdinov
- Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences, 450054 Ufa, Russia
| | - A. R. Sakhabutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences, 450054 Ufa, Russia
| | - A. R. Gilvanov
- Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences, 450054 Ufa, Russia
| | - A. V. Chemeris
- Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences, 450054 Ufa, Russia
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17
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Chen X, Wang L, He F, Chen G, Bai L, He K, Zhang F, Xu X. Label-Free Colorimetric Method for Detection of Vibrio parahaemolyticus by Trimming the G-Quadruplex DNAzyme with CRISPR/Cas12a. Anal Chem 2021; 93:14300-14306. [PMID: 34645259 DOI: 10.1021/acs.analchem.1c03468] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Vibrio parahaemolyticus (V. parahaemolyticus), which may cause gastrointestinal disorders in humans, is a pathogen commonly found in seafood. There are many methods for detecting V. parahaemolyticus, yet they have some shortcomings, such as high cost, labor-intensiveness, and complicated operation, which are impractical for resource-limited settings. Herein, we present a sequence-specific, label-free, and colorimetric method for visual detection of V. parahaemolyticus. This method utilizes CRISPR/Cas12a to specifically recognize the loop-mediated isothermal amplification (LAMP) products for further trans-cleaving the G-quadruplex DNAzyme and depriving its peroxidase-mimicking activity. In this way, the results can be directly observed with the naked eyes via the color development of 2,2'-azino-di-(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS2-), which displays colorless for positive samples while green for target-free samples. We term such Cas12a-crRNA preventing ABTS2- from developing color by trimming the G-quadruplex DNAzyme as Cascade. The proposed method can detect 9.8 CFU (per reaction) of pure cultured V. parahaemolyticus, and the sensitivity is comparable to real-time LAMP. It has been applied for practical use and showed the capability to detect 6.1 × 102 CFU/mL V. parahaemolyticus in shrimp samples. Based on this, the newly established Cascade method can be employed as a universal biosensing strategy for pathogenic bacterial testing in the field.
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Affiliation(s)
- Xueyun Chen
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China.,State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products; Key Laboratory of Information Traceability for Agricultural Products, Ministry of Agriculture and Rural Affairs; Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Liu Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products; Key Laboratory of Information Traceability for Agricultural Products, Ministry of Agriculture and Rural Affairs; Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Fang He
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products; Key Laboratory of Information Traceability for Agricultural Products, Ministry of Agriculture and Rural Affairs; Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Ganghui Chen
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China
| | - Linlin Bai
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China.,State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products; Key Laboratory of Information Traceability for Agricultural Products, Ministry of Agriculture and Rural Affairs; Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Kaiyu He
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products; Key Laboratory of Information Traceability for Agricultural Products, Ministry of Agriculture and Rural Affairs; Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Fang Zhang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China
| | - Xiahong Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products; Key Laboratory of Information Traceability for Agricultural Products, Ministry of Agriculture and Rural Affairs; Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
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18
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Chang WH, Lee YF, Liu YW, Willner I, Liao WC. Stimuli-responsive hydrogel microcapsules for the amplified detection of microRNAs. NANOSCALE 2021; 13:16799-16808. [PMID: 34605515 DOI: 10.1039/d1nr05170a] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
A method for the synthesis of DNA-based acrylamide hydrogel microcapsules loaded with quantum dots as a readout signal is introduced. The shell of DNA-acrylamide hydrogel microcapsules is encoded with microRNA-responsive functionalities, being capable of the detection of cancer-associated microRNA. The microRNA-141 (miR-141), a potential biomarker in prostate cancer, was employed as a model target in the microcapsular biosensor. The sensing principle of the microcapsular biosensor is based on the competitive sequence displacement of target miR-141 with the bridging DNA in the microcapsule's shell, leading to the unlocking of DNA-acrylamide hydrogel microcapsules and the release of the readout signal provided by fluorescent quantum dots. The readout signal is intensified as the concentration of miR-141 increases. While miR-141 was directly measured by DNA-acrylamide hydrogel microcapsules, the linear range for the detection of miR-141 is 2.5 to 50 μM and the limit of detection is 1.69 μM. To improve the sensitivity of the microcapsular biosensor for clinical needs, the isothermal strand displacement polymerization/nicking amplification machinery (SDP/NA) process was coupled to the DNA-acrylamide hydrogel microcapsule sensor for the microRNA detection. The linear range for the detection of miR-141 is improved to the range of 102 to 105 pM and the limit of detection is 44.9 pM. Compared to direct microcapsular biosensing, the detection limit for miR-141 by microcapsules coupled with strand-displacement amplification is enhanced by four orders of magnitude.
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Affiliation(s)
- Wen-Hsin Chang
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei 112, Taiwan.
| | - Yi-Fang Lee
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei 112, Taiwan.
| | - Yen-Wenn Liu
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei 112, Taiwan.
| | - Itamar Willner
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Wei-Ching Liao
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei 112, Taiwan.
- Center for Advanced Pharmaceutics and Drug Delivery Research, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
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19
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Rolling Circle Amplification as an Efficient Analytical Tool for Rapid Detection of Contaminants in Aqueous Environments. BIOSENSORS-BASEL 2021; 11:bios11100352. [PMID: 34677308 PMCID: PMC8533700 DOI: 10.3390/bios11100352] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/16/2021] [Accepted: 09/21/2021] [Indexed: 12/16/2022]
Abstract
Environmental contaminants are a global concern, and an effective strategy for remediation is to develop a rapid, on-site, and affordable monitoring method. However, this remains challenging, especially with regard to the detection of various contaminants in complex water environments. The application of molecular methods has recently attracted increasing attention; for example, rolling circle amplification (RCA) is an isothermal enzymatic process in which a short nucleic acid primer is amplified to form a long single-stranded nucleic acid using a circular template and special nucleic acid polymerases. Furthermore, this approach can be further engineered into a device for point-of-need monitoring of environmental pollutants. In this paper, we describe the fundamental principles of RCA and the advantages and disadvantages of RCA assays. Then, we discuss the recently developed RCA-based tools for environmental analysis to determine various targets, including heavy metals, organic small molecules, nucleic acids, peptides, proteins, and even microorganisms in aqueous environments. Finally, we summarize the challenges and outline strategies for the advancement of this technique for application in contaminant monitoring.
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20
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Wang J, Li Z, Zhou Z, Ouyang Y, Zhang J, Ma X, Tian H, Willner I. DNAzyme- and light-induced dissipative and gated DNA networks. Chem Sci 2021; 12:11204-11212. [PMID: 34522318 PMCID: PMC8386649 DOI: 10.1039/d1sc02091a] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 07/20/2021] [Indexed: 12/20/2022] Open
Abstract
Nucleic acid-based dissipative, out-of-equilibrium systems are introduced as functional assemblies emulating transient dissipative biological transformations. One system involves a Pb2+-ion-dependent DNAzyme fuel strand-driven network leading to the transient cleavage of the fuel strand to “waste” products. Applying the Pb2+-ion-dependent DNAzyme to two competitive fuel strand-driven systems yields two parallel operating networks. Blocking the competitively operating networks with selective inhibitors leads, however, to gated transient operation of dictated networks, yielding gated catalytic operations. A second system introduces a “non-waste” generating out-of-equilibrium, dissipative network driven by light. The system consists of a trans-azobenzene-functionalized photoactive module that is reconfigured by light to an intermediary state consisting of cis-azobenzene units that are thermally recovered to the original trans-azobenzene-modified module. The cyclic transient photoinduced operation of the device is demonstrated. The kinetic simulation of the systems allows the prediction of the transient behavior of the networks under different auxiliary conditions. Functional DNA modules are triggered in the presence of appropriate inhibitors to yield transient gated catalytic functions, and a photoresponsive DNA module leads to “waste-free” operation of transient, dissipative dynamic transitions.![]()
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Affiliation(s)
- Jianbang Wang
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Zhenzhen Li
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Zhixin Zhou
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Yu Ouyang
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Junji Zhang
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology Shanghai 200237 P. R. China
| | - Xiang Ma
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology Shanghai 200237 P. R. China
| | - He Tian
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology Shanghai 200237 P. R. China
| | - Itamar Willner
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem Jerusalem 91904 Israel
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21
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Nawaz N, Abu Bakar NK, Muhammad Ekramul Mahmud HN, Jamaludin NS. Molecularly imprinted polymers-based DNA biosensors. Anal Biochem 2021; 630:114328. [PMID: 34363786 DOI: 10.1016/j.ab.2021.114328] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/26/2021] [Accepted: 08/03/2021] [Indexed: 01/31/2023]
Abstract
In multiple biological processes, molecular recognition performs an integral role in detecting bio analytes. Molecular imprinted polymers (MIPs) are tailored sensing materials that can biomimic the biologic ligands and can detect specific target molecules selectively and sensitively. The formulation of molecularly imprinted polymers is followed by the formulation of a control termed as non-imprinted polymer (NIP), which, in the absence of a template, is commonly formulated to evaluate whether distinctive imprints have been produced for the template. Given the difficulties confronting bioanalytical researchers, it is inevitable that this strategy would come out as a central route of multidisciplinary studies to create extremely promising stable artificial receptors as a replacement or accelerate biological matrices. The ease of synthesis, low cost, capability to 'tailor' recognition element for analyte molecules, and stability under harsh environments make MIPs promising candidates as a recognition tool for biosensing. Compared to biological systems, molecular imprinting techniques have several advantages, including high recognition ability, long-term durability, low cost, and robustness, allowing molecularly imprinted polymers to be employed in drug delivery, biosensor technology, and nanotechnology. Molecular imprinted polymer-based sensors still have certain shortcomings in determining biomacromolecules (nucleic acid, protein, lipids, and carbohydrates), considering the vast volume of the latest literature on biomicromolecules. These potential materials are still required to address a few weaknesses until gaining their position in recognition of biomacromolecules. This review aims to highlight the current progress in molecularly imprinted polymers (MIPs)-based sensors for the determination of deoxyribonucleic acid (DNA) or nucleobases.
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Affiliation(s)
- Noman Nawaz
- Department of Chemistry, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, W.Persekutuan Kuala Lumpur, Malaysia.
| | - Nor Kartini Abu Bakar
- Department of Chemistry, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, W.Persekutuan Kuala Lumpur, Malaysia.
| | | | - Nazzatush Shimar Jamaludin
- Department of Chemistry, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, W.Persekutuan Kuala Lumpur, Malaysia
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22
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Wan Y, Li G, Zou L, Wang H, Wang Q, Tan K, Liu X, Wang F. A Deoxyribozyme-Initiated Self-Catalytic DNA Machine for Amplified Live-Cell Imaging of MicroRNA. Anal Chem 2021; 93:11052-11059. [PMID: 34324305 DOI: 10.1021/acs.analchem.1c02596] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Functional DNA nanostructures have been widely used in various bioassay fields. Yet, the programmable assembly of functional DNA nanostructures in living cells still represents a challenging goal for guaranteeing the sensitive and specific biosensing utility. In this work, we report a self-catalytic DNA assembly (SDA) machine by using a feedback deoxyribozyme (DNAzyme)-amplified branched DNA assembly. This SDA system consists of catalytic self-assembly (CSA) and DNAzyme amplification modules for recognizing and amplifying the target analyte. The analyte initiates the CSA reaction, leading to the formation of Y-shaped DNA that carries two RNA-cleaving DNAzymes. One DNAzyme can then successively cleave the corresponding substrate and generate numerous additional inputs to activate new CSA reactions, thus realizing a self-catalytic amplification reaction. Simultaneously, the other DNAzyme is assembled as a versatile signal transducer for cleaving the fluorophore/quencher-modified substrate, leading to the generation of an amplified fluorescence readout. By incorporating a flexible auxiliary sensing module, the SDA system can be converted into a universal sensing platform for detecting cancerous biomarkers, e.g., a well-known oncogene microRNA-21 (miR-21). Moreover, the SDA system realized the precise intracellular miR-21 imaging in living cells, which is attributed to the reciprocal amplification property between CSA reactions and DNAzyme biocatalysis. This compact SDA amplifier machine provides a universal and facile toolbox for the highly efficient identification of cancerous biomarkers and thus holds great potential for early cancer diagnosis.
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Affiliation(s)
- Yeqing Wan
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Gaiping Li
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China.,College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Lina Zou
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China.,College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Hong Wang
- 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
| | - Kaiyue Tan
- 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
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23
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Tao Y, Lao YH, Yi K, Xu Y, Wang H, Shao D, Wang J, Li M. Noble metal-molybdenum disulfide nanohybrids as dual fluorometric and colorimetric sensor for hepatitis B virus DNA detection. Talanta 2021; 234:122675. [PMID: 34364475 DOI: 10.1016/j.talanta.2021.122675] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/24/2021] [Accepted: 06/27/2021] [Indexed: 12/11/2022]
Abstract
Hepatitis B virus (HBV) infection is one of the global healthcare burdens, and its early diagnosis is crucial for the prevention of HBV-induced chronic hepatitis, liver fibrosis, cirrhosis, and hepatocellular carcinoma. Although different detection approaches have been reported, most of these methods either rely on sophisticated machines or procedures, which limit their use particularly in the high endemic, developing countries. In this work, we report a dual-sensing nanoplatform built on noble metal-molybdenum disulfide (MoS2) nanohybrids, and this platform can detect the HBV DNA target through either fluorometric or colorimetric readouts. The design with the silver nanocluster (AgNC)-MoS2 nanohybrid enables multiplex fluorescent detection, while the HBV DNA-regulated growth of platinum nanoparticles (PtNPs) on the MoS2 nanosheets offers signal-on colorimetric detection. Both AgNC-MoS2 and PtNP-MoS2 nanohybrids show high sensitivity with pico-molar detection limit and single nucleotide specificity, even with the spiked human serum. Collectively, the proposed nanohybrids possess their potential in the use of early HBV diagnosis, particularly suitable for the high endemic areas with limited medical and instrumental supports.
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Affiliation(s)
- Yu Tao
- Laboratory of Biomaterials and Translational Medicine, Center for Nanomedicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
| | - Yeh-Hsing Lao
- Department of Biomedical Engineering, Columbia University, New York, NY, 10027, USA
| | - Ke Yi
- Laboratory of Biomaterials and Translational Medicine, Center for Nanomedicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
| | - Yanteng Xu
- Laboratory of Biomaterials and Translational Medicine, Center for Nanomedicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
| | - Haixia Wang
- Laboratory of Biomaterials and Translational Medicine, Center for Nanomedicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
| | - Dan Shao
- Institutes of Life Sciences, School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Jiasi Wang
- School of Biomedical Engineering, Sun Yat-sen University, Shenzhen, 518107, China
| | - Mingqiang Li
- Laboratory of Biomaterials and Translational Medicine, Center for Nanomedicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China; Guangdong Provincial Key Laboratory of Liver Disease Research, Guangzhou, 510630, China.
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24
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Wang M, Han D, Zhang J, Zhang R, Li J. High-fidelity detection of DNA combining the CRISPR/Cas9 system and hairpin probe. Biosens Bioelectron 2021; 184:113212. [PMID: 33862567 DOI: 10.1016/j.bios.2021.113212] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/13/2021] [Accepted: 03/30/2021] [Indexed: 12/26/2022]
Abstract
Methods that enable specific and sensitive detection of DNA are greatly required for high-fidelity sequence measurement and single-nucleotide variations (SNVs) genotyping. The CRISPR (clustered regularly interspaced short palindromic repeats)/Cas systems have provided revolutionary tools for detecting nucleic acids. However, most of the current CRISPR/Cas-based DNA biosensing platforms suffer from inherent off-target effects of Cas proteins and require pre-amplification processes, which compromise the analytical fidelity. In this work, a CRISPR/Cas9-triggered hairpin probe-mediated biosensing method (namely CHP) was used to directly read the original DNA sequences, while effectively neutralizing the off-target effect and achieving high sensitivity. This technique can quantify DNA targets with a limit of detection (LOD) at the attomole level and identify SNVs with allelic fractions as low as 0.01%~0.1%. Moreover, we show that the CHP system is applicable in detecting mutations in serum samples without DNA isolation steps. Collectively, the CHP system is a sensitive and high-fidelity platform, which promises a great potential for providing robust tool for DNA sequence analysis and SNVs genotyping.
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Affiliation(s)
- Meng Wang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
| | - Dongsheng Han
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
| | - Jiawei Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
| | - Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China.
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China.
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Wang J, Yu S, Wu Q, Gong X, He S, Shang J, Liu X, Wang F. A Self‐Catabolic Multifunctional DNAzyme Nanosponge for Programmable Drug Delivery and Efficient Gene Silencing. Angew Chem Int Ed Engl 2021; 60:10766-10774. [DOI: 10.1002/anie.202101474] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Indexed: 02/06/2023]
Affiliation(s)
- Jing Wang
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
- Oil Crops Research Institute Chinese Academy of Agricultural Sciences Hubei Key Laboratory of Lipid Chemistry and Nutrition, Key Laboratory of Oilseeds Processing Ministry of Agriculture 430062 Wuhan P. R. China
| | - Shanshan Yu
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Qiong Wu
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Xue Gong
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Shizhen He
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Jinhua Shang
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Xiaoqing Liu
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
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Wang J, Yu S, Wu Q, Gong X, He S, Shang J, Liu X, Wang F. A Self‐Catabolic Multifunctional DNAzyme Nanosponge for Programmable Drug Delivery and Efficient Gene Silencing. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202101474] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jing Wang
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
- Oil Crops Research Institute Chinese Academy of Agricultural Sciences Hubei Key Laboratory of Lipid Chemistry and Nutrition, Key Laboratory of Oilseeds Processing Ministry of Agriculture 430062 Wuhan P. R. China
| | - Shanshan Yu
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Qiong Wu
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Xue Gong
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Shizhen He
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Jinhua Shang
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Xiaoqing Liu
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
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27
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Zhang P, Ouyang Y, Willner I. Multiplexed and amplified chemiluminescence resonance energy transfer (CRET) detection of genes and microRNAs using dye-loaded hemin/G-quadruplex-modified UiO-66 metal-organic framework nanoparticles. Chem Sci 2021; 12:4810-4818. [PMID: 34163734 PMCID: PMC8179566 DOI: 10.1039/d0sc06744j] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/07/2021] [Indexed: 01/11/2023] Open
Abstract
Dye-loaded UiO-66 metal-organic framework nanoparticles (NMOFs) modified with catalytic hemin/G-quadruplex DNAzyme labels act as functional hybrid modules for the chemiluminescence resonance energy transfer (CRET) analysis of miRNAs (miRNA-155 or miRNA-21) or genes (p53 or BRCA1). The dye-loaded NMOFs (dye = fluorescein (Fl) or rhodamine 6G (Rh 6G)) are modified with hairpin probes that are engineered to include in their loop domains recognition sequences for the miRNAs or genes, and in their stem regions caged G-quadruplex domains. In the presence of the analytes miRNAs or genes, the hairpin structures are opened, leading, in the presence of hemin, to the self-assembly of hemin/G-quadruplex DNAzyme labels linked to the dye-loaded NMOFs. In the presence of luminol and H2O2, the hemin/G-quadruplex DNAzyme labels catalyze the generation of chemiluminescence that provides radiative energy to stimulate the process of CRET to the dye loaded in the NMOFs, resulting in the luminescence of the loaded dye without external excitation. The resulting CRET signals relate to the concentrations of the miRNAs or the genes and allow the sensitive analysis of miRNAs and genes. In addition, the DNA hairpin-functionalized dye-loaded NMOF sensing modules were further applied to develop amplified miRNA or gene CRET-based sensing platforms. The dye-loaded NMOFs were modified with hairpin probes that include in their loop domain the recognition sequences for miRNA-155 or miRNA-21 or the recognition sequences for the p53 or BRCA1 genes. Subjecting the hairpin-modified NMOFs to the respective miRNAs or genes, in the presence of two hairpins H i and H j that include in their stem regions caged G-quadruplex subunit domains, results in the analyte-triggered opening of the probe hairpin linked to the NMOFs, and the opened hairpin tethers induce the cross-opening of the hairpins H i and H j by the hybridization chain reaction, HCR, resulting in the assembly of G-quadruplex wires tethered to the NMOFs. The binding of hemin to the HCR-generated chains yields hemin/G-quadruplex DNAzyme wires that enhance, in the presence of luminol/H2O2, the CRET processes in the hybrid nanostructures. These amplification platforms lead to the amplified sensing of miRNAs and genes. By mixing the Fl- and Rh 6G-loaded hairpin-functionalized UiO NMOFs, the multiplexed CRET detection of miRNA-155, miRNA-21 and the p53 and BRCA1 genes is demonstrated.
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Affiliation(s)
- Pu Zhang
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Yu Ouyang
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Itamar Willner
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem Jerusalem 91904 Israel
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Shi H, Cui J, Sulemana H, Wang W, Gao L. Protein detection based on rolling circle amplification sensors. LUMINESCENCE 2021; 36:842-848. [PMID: 33502072 DOI: 10.1002/bio.4017] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 01/07/2021] [Accepted: 01/17/2021] [Indexed: 12/22/2022]
Abstract
Rolling circle amplification (RCA) is an isothermal process under the action of DNA polymerases. Large-scale DNA templates have been generated using RCA for target detection. Some signal amplification strategies including optical sensors and electrochemical sensors based on RCA have been applied to achieve sensitive detection. Sensors based on RCA have attracted increasing interest. Advances in RCA-based sensors for protein detection are reviewed in this paper. The advantages and detection mechanisms of sensors based on RCA are revealed and discussed. Finally, possible challenges and future perspectives are also outlined.
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Affiliation(s)
- Haixia Shi
- P. E. Department of Jiangsu University, Zhenjiang, China
| | - Jingjie Cui
- School of Automation, Hangzhou Dianzi University, Hangzhou, China
| | | | - Wunian Wang
- P. E. Department of Jiangsu University, Zhenjiang, China
| | - Li Gao
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
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29
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Zou R, Wang S, Chen C, Chen X, Gong H, Cai C. An enzyme-free DNA circuit-assisted MoS2 nanosheet enhanced fluorescence assay for label-free DNA detection. Talanta 2021; 222:121505. [DOI: 10.1016/j.talanta.2020.121505] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/31/2020] [Accepted: 08/03/2020] [Indexed: 12/23/2022]
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Wang ZY, Li P, Cui L, Qiu JG, Jiang B, Zhang CY. Integration of nanomaterials with nucleic acid amplification approaches for biosensing. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.115959] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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31
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Zhou Z, Sohn YS, Nechushtai R, Willner I. DNA Tetrahedra Modules as Versatile Optical Sensing Platforms for Multiplexed Analysis of miRNAs, Endonucleases, and Aptamer-Ligand Complexes. ACS NANO 2020; 14:9021-9031. [PMID: 32539340 PMCID: PMC7467810 DOI: 10.1021/acsnano.0c04031] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 06/15/2020] [Indexed: 05/21/2023]
Abstract
The sensing modules for analyzing miRNAs or the endonucleases consist of tetrahedra functionalized with three different fluorophore-quencher pairs in spatially quenched configurations and hairpin units acting as recognition elements for the analytes. Three different miRNAs (miRNA-21, miRNA-221, and miRNA-155) or three different endonucleases (Nt.BbvCI, EcoRI, and HindIII) uncage the respective hairpins, leading to the switched-on fluorescence of the respective fluorophores and to the multiplex detection of the respective analytes. In addition, a tetrahedron module for the multiplexed analysis of aptamer ligand complexes (ligands = ATP, thrombin, VEGF) is introduced. The module includes edges modified with three spatially separated fluorophore-quencher pairs that were stretched by the respective aptamer strands to yield a switched-on fluorescent state. Formation of the respective aptamer ligands reconfigures the edges into fluorophore-quenched caged-hairpin structures that enable the multiplexed analysis of the aptamer-ligand complexes. The facile permeation of the tetrahedra structures into cells is used for the imaging of MCF-7 and HepG2 cancer cells and their discrimination from normal epithelial MCF-10A breast cells.
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Affiliation(s)
- Zhixin Zhou
- Institute
of Chemistry, The Minerva Center for Biohybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Yang Sung Sohn
- Institute
of Life Sciences, The Hebrew University
of Jerusalem, Jerusalem 91904, Israel
| | - Rachel Nechushtai
- Institute
of Life Sciences, The Hebrew University
of Jerusalem, Jerusalem 91904, Israel
| | - Itamar Willner
- Institute
of Chemistry, The Minerva Center for Biohybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
- E-mail:
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32
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Sun J, Sun X. Recent advances in the construction of DNA nanostructure with signal amplification and ratiometric response for miRNA sensing and imaging. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.115900] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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33
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Zhou Z, Fan D, Willner I. Modeling Gene Expression Instability by Programmed and Switchable Polymerization/Nicking DNA Nanomachineries. ACS NANO 2020; 14:5046-5052. [PMID: 32250590 DOI: 10.1021/acsnano.0c01583] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Models for gene expression instability by noncanonical DNA-nanostructures are introduced. The systems consist of a promoter-template scaffold that acts as a polymerization/nicking machinery that models, in the presence of polymerase/Nt.BbvCI and dNTPs, the autonomous synthesis of displaced strands mimicking the native "genes". Incorporation of noncanonical DNA structures into the scaffolds consisting of Sr2+-ion-stabilized G-quadruplexes, T-A·T triplexes, or ATP-aptamer complexes results in the perturbation of the polymerization/nicking DNA machineries and the synthesis of displaced strands-"genes" exhibiting other structures. By the dissociation of the noncanonical blockage units, the regeneration of the synthesis of the original intact displaced strands-"genes" is demonstrated. The study introduces conceptual means to eliminate destructive gene expression instability pathways.
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Affiliation(s)
- Zhixin Zhou
- Institute of Chemistry, The Minerva Center for Biohybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Daoqing Fan
- Institute of Chemistry, The Minerva Center for Biohybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Itamar Willner
- Institute of Chemistry, The Minerva Center for Biohybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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34
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Li J, Mohammed-Elsabagh M, Paczkowski F, Li Y. Circular Nucleic Acids: Discovery, Functions and Applications. Chembiochem 2020; 21:1547-1566. [PMID: 32176816 DOI: 10.1002/cbic.202000003] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 02/13/2020] [Indexed: 12/14/2022]
Abstract
Circular nucleic acids (CNAs) are nucleic acid molecules with a closed-loop structure. This feature comes with a number of advantages including complete resistance to exonuclease degradation, much better thermodynamic stability, and the capability of being replicated by a DNA polymerase in a rolling circle manner. Circular functional nucleic acids, CNAs containing at least a ribozyme/DNAzyme or a DNA/RNA aptamer, not only inherit the advantages of CNAs but also offer some unique application opportunities, such as the design of topology-controlled or enabled molecular devices. This article will begin by summarizing the discovery, biogenesis, and applications of naturally occurring CNAs, followed by discussing the methods for constructing artificial CNAs. The exploitation of circular functional nucleic acids for applications in nanodevice engineering, biosensing, and drug delivery will be reviewed next. Finally, the efforts to couple functional nucleic acids with rolling circle amplification for ultra-sensitive biosensing and for synthesizing multivalent molecular scaffolds for unique applications in biosensing and drug delivery will be recapitulated.
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Affiliation(s)
- Jiuxing Li
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Mostafa Mohammed-Elsabagh
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Freeman Paczkowski
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Yingfu Li
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
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35
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Tao G, Lai T, Xu X, Ma Y, Wu X, Pei X, Liu F, Li N. Colocalized Particle Counting Platform for Zeptomole Level Multiplexed Quantification. Anal Chem 2020; 92:3697-3706. [PMID: 32037812 DOI: 10.1021/acs.analchem.9b04823] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
For multiplexed detection, it is important yet challenging to simultaneously meet the requirement of sensitivity, throughput, and implementation convenience for practical applications. Using the detection of DNAs and miRNAs for illustration, we present a colocalized particle counting platform that can realize the separation-free multiplexed detection of 6 nucleic acid targets with a zeptomole sensitivity and a dynamic range of up to 5 orders of magnitude. The presence of target induces the formation of a sandwich nanostructure via hybridization; thus, there is an occurrence of colocalization of two microbeads with two different colors. The sequence specific coding is realized by an arbitrary combination of two fluorescence channels with different emitting colors. The platform presents robustness in detecting multiple nucleic acid targets with a minimal cross talk and matrix effect as well as the ability to distinguish the specific miRNA from members of the same family. The results of simultaneous detection of 3 miRNAs in 3 different cell lines present straight consistency with that of the standard qRT-PCR. This platform can be adapted to other multiplexing designs such as the "turn-off" mode, in which the proportion of colocalized microbeads is decreased due to the strand-displacement reaction initiated by the specific target. This separation-free platform offers the possibility to achieve the on-site multiplexed detection with compatibility to different experimental designs and extensibility to other signal sources for enumeration.
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Affiliation(s)
- Guangyu Tao
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Tiancheng Lai
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiao Xu
- Environmental Metrology Center, National Institute of Metrology, Beijing 100029, China
| | - Yurou Ma
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xi Wu
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiaojing Pei
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Feng Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Na Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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36
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LIU ZL, TAO CA, WANG JF. Progress on Applications of G-quadruplex in Biochemical Analysis. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2020. [DOI: 10.1016/s1872-2040(19)61212-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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37
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Sensitive colorimetric determination of microRNA let-7a through rolling circle amplification and a peroxidase-mimicking system composed of trimeric G-triplex and hemin DNAzyme. Mikrochim Acta 2020; 187:139. [DOI: 10.1007/s00604-019-4093-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 12/22/2019] [Indexed: 01/07/2023]
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38
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Zhang J, He M, Nie C, He M, Pan Q, Liu C, Hu Y, Yi J, Chen T, Chu X. Biomineralized Metal–Organic Framework Nanoparticles Enable Enzymatic Rolling Circle Amplification in Living Cells for Ultrasensitive MicroRNA Imaging. Anal Chem 2019; 91:9049-9057. [DOI: 10.1021/acs.analchem.9b01343] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Juan Zhang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, People’s Republic of China
| | - Mengyun He
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, People’s Republic of China
| | - Cunpeng Nie
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, People’s Republic of China
| | - Manman He
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, People’s Republic of China
| | - Qingshan Pan
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, People’s Republic of China
| | - Chang Liu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, People’s Republic of China
| | - Yanlei Hu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, People’s Republic of China
| | - Jintao Yi
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, People’s Republic of China
| | - Tingting Chen
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, People’s Republic of China
| | - Xia Chu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, People’s Republic of China
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Ma H, Guo B, Yan X, Wang T, Que H, Gan X, Liu P, Yan Y. A smart fluorescent biosensor for the highly sensitive detection of BRCA1 based on a 3D DNA walker and ESDR cascade amplification. RSC Adv 2019; 9:19347-19353. [PMID: 35519381 PMCID: PMC9064877 DOI: 10.1039/c9ra02401h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 06/06/2019] [Indexed: 11/21/2022] Open
Abstract
Nucleic acid analysis plays an important role in the diagnosis of diseases. There is a continuous demand to develop rapid and sensitive methods for the specific detection of nucleic acids. Herein, we constructed a highly sensitive and rapid fluorescent biosensor for the detection of BRCA1 by coupling a 3D DNA walker machine with spontaneous entropy-driven strand displacement reactions (ESDRs). In this study, the 3D DNA walker machine was well activated by the target DNA; this resulted in the cyclic utilization of the target DNA and the release of intermediate DNAs. Subsequently, the free intermediate DNAs triggered the circulation process of ESDRs with the help of the assistant probe A, leading to a significant enhancement of the fluorescence intensity. Due to the robust execution of the 3D DNA walker machine and highly efficient amplification capability of ESDRs, the developed biosensing method shows a wide linear range from 0.1 pM to 10 nM with the detection limit as low as 41.44 fM (S/N = 3). Moreover, the constructed biosensor displays superior specificity and has been applied to monitor BRCA1 in complex matrices. Thus, this elaborated cascade amplification biosensing strategy provides a potential platform for the bioassays of nucleic acids and the clinical diagnosis of diseases.
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Affiliation(s)
- Hongmin Ma
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University Chongqing 400016 China +86-23-68485786 +86-23-68485688
| | - Bin Guo
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University Chongqing 400016 China +86-23-68485786 +86-23-68485688
| | - Xiaoyu Yan
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University Chongqing 400016 China +86-23-68485786 +86-23-68485688
| | - Tong Wang
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University Chongqing 400016 China +86-23-68485786 +86-23-68485688
| | - Haiying Que
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University Chongqing 400016 China +86-23-68485786 +86-23-68485688
| | - Xiufeng Gan
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University Chongqing 400016 China +86-23-68485786 +86-23-68485688
| | - Ping Liu
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University Chongqing 400016 China +86-23-68485786 +86-23-68485688
| | - Yurong Yan
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University Chongqing 400016 China +86-23-68485786 +86-23-68485688
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40
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Xiong E, Zhen D, Jiang L. Cascade signal amplified assay of nucleic acids based on entropy-driven amplification strategy and Mg2+-dependent DNAzyme cleavage. Talanta 2019; 198:179-184. [DOI: 10.1016/j.talanta.2019.02.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/27/2019] [Accepted: 02/03/2019] [Indexed: 12/15/2022]
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41
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Ma X, Miao P. Silver nanoparticle@DNA tetrahedron-based colorimetric detection of HIV-related DNA with cascade strand displacement amplification. J Mater Chem B 2019; 7:2608-2612. [PMID: 32254992 DOI: 10.1039/c9tb00274j] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
DNA tetrahedron-modified silver nanoparticles (AgNPs) were achieved via amino-silver chemistry for the first time and were applied as a colorimetric biosensor for detecting HIV-related DNA. Target DNA initiated strand displacement polymerization and nicking endonuclease-aided cycles were involved to link DNA tetrahedron-modified AgNPs, reporting colorimetric responses. This developed method showed excellent specificity and sensitivity. A wide linear range from 1 to 15 000 nM was achieved with a limit of detection of 0.84 nM. Moreover, it was successfully applied to determine DNA in blood serum samples.
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Affiliation(s)
- Xiaoyi Ma
- University of Science and Technology of China, Hefei 230026, China.
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42
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Zhang H, Song Z, Pan F, He F. A surface-confined DNA assembly enabled target recycling amplification for multiplexed electrochemical DNA detection. J Electroanal Chem (Lausanne) 2019. [DOI: 10.1016/j.jelechem.2018.09.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Pan M, Liang M, Sun J, Liu X, Wang F. Lighting Up Fluorescent Silver Clusters via Target-Catalyzed Hairpin Assembly for Amplified Biosensing. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14851-14857. [PMID: 30044098 DOI: 10.1021/acs.langmuir.8b01576] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Isothermal enzyme-free nucleic acid circuits have been developed for carrying out diverse functions ranging from dictate biocomputing to amplified biosensing. Catalytic hairpin assembly (CHA), the catalyzed cross-opening of two hairpin substrates by an initiator, has attracted increasing attention because of its facile design and high amplification capacity. The complex labeling and frequent photobleaching of a conventional fluorescent CHA biosensor still remains a challenge that needs to be solved. Herein, we constructed a new label-free and enzyme-free isothermal CHA lighting up AgNCs strategy for amplified nucleic acid assay by integrating the interfacially and spatially sensitive feature of DNA-templated fluorescent silver nanoclusters (DNA-AgNCs) and the high signal amplification capability of the CHA circuit. In this strategy, one polyguanine-grafted hairpin and the other AgNCs-capturing hairpin were engineered as assembly constitutes, which were kinetically impeded from cross-hybridizations without target. However, in the presence of target, the CHA-catalyzed assembly of two functional hairpins was successively progressed and concomitantly accompanied by an efficient accommodation of AgNCs to the polyguanine-elongated dsDNA product, leading to highly efficient AgNCs-lighting up and to the generation of an amplified fluorescence signal. As a simple mix-and-detect strategy, the isothermal enzyme-free CHA-mediated lighting up AgNCs (CHA-AgNCs) system provided a facile visualization way for amplified detection of DNA with a detection limit of 20 pM, which was comparable to or even better than some enzyme-involved amplification methods. The homogeneous CHA-AgNCs system can be used as a general sensing platform and be easily adapted for analyzing other biologically important analytes, for example, microRNA (miRNA), by introducing the sensing module consisting of an auxiliary hairpin through an easy-to-integrate procedure. By taking advantage of the signal amplification features of CHA and the robust AgNCs-lighting up procedure, we anticipate that the CHA-lighting up AgNCs system can provide an important tool for biomedicine and bioimaging applications and thus should hold great promise in clinical diagnoses and treatment fields.
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Affiliation(s)
- Min Pan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , Hubei 430072 , P. R. China
| | - Meijuan Liang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , Hubei 430072 , P. R. China
| | - Junlin Sun
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , Hubei 430072 , P. R. China
| | - Xiaoqing Liu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , Hubei 430072 , P. R. China
| | - Fuan Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , Hubei 430072 , P. R. China
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Vázquez-González M, Willner I. DNA-Responsive SiO 2 Nanoparticles, Metal-Organic Frameworks, and Microcapsules for Controlled Drug Release. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14692-14710. [PMID: 29870667 DOI: 10.1021/acs.langmuir.8b00478] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Recent advances addressing the development of stimuli-responsive nucleic acid (DNA)-functionalized micro/nanocarriers for the controlled release of drugs are presented. The DNA associated with the drug-loaded carriers acts as capping units that lock the drugs in the carriers. In the presence of appropriate triggers, the capping units are unlocked, resulting in the release of the drugs. Three types of DNA-modified carriers are discussed, including mesoporous SiO2 nanoparticles (MP SiO2 NPs), metal-organic framework nanoparticles (NMOFs) and micro/nanocapsules. The triggers to unlock the DNA gating units include pH, the dissociation of K+-stabilized G-quadruplexes in the presence of crown ethers, the catalytic dissociation of the capping units by enzymes or DNAzymes, the dissociation of capping units by the formation of aptamer-ligand complexes (particularly ligands acting as biomarkers for different diseases), and the use of light for the photochemical unlocking of the DNA gates. Different issues related to the targeting of the different drug-loaded carriers to cancer cells, the switchable ON/OFF release of the drug loads, and the selective cytotoxicity of the drug-loaded carriers toward cancer cells are discussed. Finally, the future perspectives of the stimuli-responsive DNA-based, drug-loaded micro/nanocarriers for future nanomedicine and, in particular, the development of autonomous sense-and-treat systems are addressed.
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Affiliation(s)
- Margarita Vázquez-González
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| | - Itamar Willner
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
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Qin Y, Liao S, Huang Y, Zhao J, Zhao S. Ultrasensitive fluorescent detection of nucleic acids based on label-free enzymatic-assisted cascade signal amplification. Anal Chim Acta 2018; 1039:91-97. [DOI: 10.1016/j.aca.2018.07.038] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 07/01/2018] [Accepted: 07/17/2018] [Indexed: 01/21/2023]
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Kim J, Jang D, Park H, Jung S, Kim DH, Kim WJ. Functional-DNA-Driven Dynamic Nanoconstructs for Biomolecule Capture and Drug Delivery. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1707351. [PMID: 30062803 DOI: 10.1002/adma.201707351] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 03/13/2018] [Indexed: 06/08/2023]
Abstract
The discovery of sequence-specific hybridization has allowed the development of DNA nanotechnology, which is divided into two categories: 1) structural DNA nanotechnology, which utilizes DNA as a biopolymer; and 2) dynamic DNA nanotechnology, which focuses on the catalytic reactions or displacement of DNA structures. Recently, numerous attempts have been made to combine DNA nanotechnologies with functional DNAs such as aptamers, DNAzymes, amplified DNA, polymer-conjugated DNA, and DNA loaded on functional nanoparticles for various applications; thus, the new interdisciplinary research field of "functional DNA nanotechnology" is initiated. In particular, a fine-tuned nanostructure composed of functional DNAs has shown immense potential as a programmable nanomachine by controlling DNA dynamics triggered by specific environments. Moreover, the programmability and predictability of functional DNA have enabled the use of DNA nanostructures as nanomedicines for various biomedical applications, such as cargo delivery and molecular drugs via stimuli-mediated dynamic structural changes of functional DNAs. Here, the concepts and recent case studies of functional DNA nanotechnology and nanostructures in nanomedicine are reviewed, and future prospects of functional DNA for nanomedicine are indicated.
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Affiliation(s)
- Jinhwan Kim
- Center for Self-Assembly and Complexity, Institute for Basic Science (IBS), Pohang, 37673, Korea
| | - Donghyun Jang
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea
| | - Hyeongmok Park
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea
| | - Sungjin Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea
| | - Dae Heon Kim
- Department of Biology, Sunchon National University, Sunchon, 57922, Korea
| | - Won Jong Kim
- Center for Self-Assembly and Complexity, Institute for Basic Science (IBS), Pohang, 37673, Korea
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea
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Xu Q, Zhang Y, Xiang D, Li CC, Zhang CY. A universal DNAzyme-based bioluminescent sensor for label-free detection of biomolecules. Anal Chim Acta 2018; 1043:81-88. [PMID: 30392672 DOI: 10.1016/j.aca.2018.08.059] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 08/27/2018] [Accepted: 08/30/2018] [Indexed: 12/28/2022]
Abstract
We demonstrate for the first time the development of a universal DNAzyme-based bioluminescent sensor for label-free detection of various biomolecules including DNAzyme and DNA. The presence of DNAzyme may induce the cyclic cleavage of riboadenosine (rA)-containing substrates, and the subsequent digestion of the cleaved substrates by exonuclease III (Exo III) releases abundant AMPs to initiate cyclic AMP pyrophosphorylation-ATP depyrophosphorylation for the generation of an enhanced bioluminescence signal. This sensor can real-time monitor the DNAzyme activity with a detection limit of 3.16 × 10-12 M. Moreover, the DNAzyme may be divided into two subunits for sensitive detection of target DNA. In the presence of target DNA, the two separated subunits may assemble into an active DNAzyme which can catalyze the cyclic cleavage of substrates and initiate the digestion of cleaved substrates by Exo III for the generation of an enhanced bioluminescence signal. This sensor can sensitively detect target DNA with a detection limit of 3.31 × 10-12 M. Importantly, this bioluminescent sensor can achieve a zero-background signal, and its output signal originates from the release of AMP for the generation of self-illuminating light emission without the requirement of either the external labels or the reporting reagents.
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Affiliation(s)
- Qinfeng Xu
- College of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China
| | - Yan Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, China
| | - Dongxue Xiang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, China
| | - Chen-Chen Li
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, China.
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Li P, Zhang H, Wang D, Tao Y, Zhang L, Zhang W, Wang X. An efficient nonlinear hybridization chain reaction-based sensitive fluorescent assay for in situ estimation of calcium channel protein expression on bone marrow cells. Anal Chim Acta 2018; 1041:25-32. [PMID: 30340687 DOI: 10.1016/j.aca.2018.08.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 08/13/2018] [Accepted: 08/15/2018] [Indexed: 02/03/2023]
Abstract
A sensitive and highly efficient approach to monitor the expression of proteins on live cells was urgently needed to demonstrate its factor and mechanism and most important for clinical diagnostics and molecular biology. Herein, we developed a simple and highly efficient strategy, nonlinear hybridization chain reaction (nonlinear HCR), for the sensitive determination of proteins on live cells with transient receptor potential vanilloid 4 (TRPV4) and RAW264.7 cells as a model. Unlike the normal hybridization chain reaction (HCR) with multiplicative amplification, an exponential amplified fluorescent response could be obtained in theory based on the proposed nonlinear HCR. As a result, the nonlinear HCR generated a significant enhancement about 3 times compared with the normal HCR and 10 times compared with the directly immunofluorescence assay. Based on the proposed nonlinear HCR, the fluorescent signals increased with the concentration of TRPV4 in the range from 10 pg/mL to 100 ng/mL with a detection limit of 2.8 pg/mL, which would be useful for the sensitive detection of proteins in cell lysis or on cell surface. At the same time, the significant improvements via nonlinear HCR were achieved in the fluorescent imaging system compared with traditional immunofluorescence staining and normal HCR, proving the significant value of nonlinear HCR-based amplification strategy. Success in the establishment of the highly efficient nonlinear HCR strategy offered a simple and sensitive approach to demonstrate the concentration of special proteins on cell and other proteins and nucleotide potentially, revealing a simple and efficient technology for research fields of clinical diagnostics and molecular biology.
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Affiliation(s)
- Ping Li
- Department of Maxillofacial &E.N.T Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300020, PR China
| | - Hua Zhang
- Department of Maxillofacial &E.N.T Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300020, PR China
| | - Dong Wang
- Department of Maxillofacial &E.N.T Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300020, PR China
| | - Yingjie Tao
- Department of Maxillofacial &E.N.T Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300020, PR China
| | - Lun Zhang
- Department of Maxillofacial &E.N.T Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300020, PR China
| | - Wenchao Zhang
- Department of Maxillofacial &E.N.T Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300020, PR China.
| | - Xudong Wang
- Department of Maxillofacial &E.N.T Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300020, PR China.
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Zhang Z, Zhang H, Wang F, Zhang G, Zhou T, Wang X, Liu S, Liu T. DNA Block Macromolecules Based on Rolling Circle Amplification Act as Scaffolds to Build Large-Scale Origami Nanostructures. Macromol Rapid Commun 2018; 39:e1800263. [PMID: 29952041 DOI: 10.1002/marc.201800263] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 05/15/2018] [Indexed: 01/26/2023]
Affiliation(s)
- Zhiqing Zhang
- College of Science; China University of Petroleum; No. 66, West Changjiang Road Qingdao 266580 China
| | - Hongzhi Zhang
- College of Science; China University of Petroleum; No. 66, West Changjiang Road Qingdao 266580 China
| | - Fang Wang
- College of Science; China University of Petroleum; No. 66, West Changjiang Road Qingdao 266580 China
| | - Guodong Zhang
- College of Science; China University of Petroleum; No. 66, West Changjiang Road Qingdao 266580 China
| | - Ting Zhou
- College of Science; China University of Petroleum; No. 66, West Changjiang Road Qingdao 266580 China
| | - Xiufeng Wang
- College of Science; China University of Petroleum; No. 66, West Changjiang Road Qingdao 266580 China
| | - Shuzhen Liu
- College of Science; China University of Petroleum; No. 66, West Changjiang Road Qingdao 266580 China
| | - Tingting Liu
- College of Science; China University of Petroleum; No. 66, West Changjiang Road Qingdao 266580 China
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50
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Huang DJ, Huang ZM, Xiao HY, Wu ZK, Tang LJ, Jiang JH. Protein scaffolded DNA tetrads enable efficient delivery and ultrasensitive imaging of miRNA through crosslinking hybridization chain reaction. Chem Sci 2018; 9:4892-4897. [PMID: 29910942 PMCID: PMC5982210 DOI: 10.1039/c8sc01001c] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 05/04/2018] [Indexed: 12/28/2022] Open
Abstract
Efficient intracellular delivery of nucleic acids to achieve sensitive detection and gene regulation is essential for chemistry and biology. Here we developed a novel protein scaffolded DNA tetrad, a four-arm DNA nanostructure constructed using streptavidin (SA) protein and four biotinylated hairpin DNA probes for efficient nucleic acid delivery and ultrasensitive miRNA imaging through crosslinking hybridization chain reaction (cHCR). DNA tetrads were easy to prepare and allowed precise control of the structure of the probes. DNA tetrads showed rapid intracellular delivery of DNA probes and high efficiency in lysosome escape by using confocal images for individual cells and flow cytometry for a large population of cells. cHCR allowed generating clumps of crosslinked hydrogel networks specifically to target miRNA, affording high sensitivity and spatial resolution for imaging. To our knowledge, this is the first time that HCR amplification has been realized in situ on nanostructures. Moreover, the FRET based design of cHCR conferred improved precision with the use of dual-emission ratiometric imaging to avoid false signals in biological systems. Intracellular imaging experiments further showed that DNA tetrad based cHCR could realize ultrasensitive and accurate miRNA imaging in living cells. Moreover, DNA tetrad based cHCR provided a potential tool for quantitative measurement of intracellular miRNA. The results suggested that this developed strategy provided a useful platform for nucleic acid delivery and low level biomarker imaging.
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Affiliation(s)
- Du-Juan Huang
- Institute of Chemical Biology & Nanomedicine , State Key Laboratory of Chemo/Biosensing & Chemometrics , College of Chemistry & Chemical Engineering , Hunan University , Changsha 410082 , China . ;
| | - Zhi-Mei Huang
- Institute of Chemical Biology & Nanomedicine , State Key Laboratory of Chemo/Biosensing & Chemometrics , College of Chemistry & Chemical Engineering , Hunan University , Changsha 410082 , China . ;
| | - Hu-Yan Xiao
- Institute of Chemical Biology & Nanomedicine , State Key Laboratory of Chemo/Biosensing & Chemometrics , College of Chemistry & Chemical Engineering , Hunan University , Changsha 410082 , China . ;
| | - Zhen-Kun Wu
- Institute of Chemical Biology & Nanomedicine , State Key Laboratory of Chemo/Biosensing & Chemometrics , College of Chemistry & Chemical Engineering , Hunan University , Changsha 410082 , China . ;
| | - Li-Juan Tang
- Institute of Chemical Biology & Nanomedicine , State Key Laboratory of Chemo/Biosensing & Chemometrics , College of Chemistry & Chemical Engineering , Hunan University , Changsha 410082 , China . ;
| | - Jian-Hui Jiang
- Institute of Chemical Biology & Nanomedicine , State Key Laboratory of Chemo/Biosensing & Chemometrics , College of Chemistry & Chemical Engineering , Hunan University , Changsha 410082 , China . ;
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