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Su M, Lien J, Anilao A, Guo T. Enhanced Single-Strand Breaks of a Nucleic Acid by Gold Nanoparticles under X-ray Irradiation. J Phys Chem Lett 2023; 14:1214-1221. [PMID: 36716218 DOI: 10.1021/acs.jpclett.2c03885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The hydroxyl radical concentration-dependent yield of single-strand breaks (SSBs), obtained through correction of scavenging and hindrance effects caused by gold nanoparticles (AuNPs), for fluorophore- and quencher-labeled DNA on AuNPs was 10 times that of free DNA based on fluorescence measurements of X-ray-irradiated DNA on AuNPs. By comparing the fluorescence data that revealed the number of SSBs with the results of mass spectrometry measurements that detected the total damage to DNA, we found that SSBs dominated DNA damage for DNA on AuNPs whereas non-SSB damage dominated for free DNA. The yield of RNA SSBs under X-ray irradiation was similar to that of DNA in the presence of AuNPs, whereas free RNA was more resistive to radiation than DNA. These results indicated the enhanced SSBs were likely catalyzed through the conversion from nucleobase damage to SSBs by AuNPs. The outcome of this work impacts materials and environmental science, sensing, nanotechnology, biology, and medicine.
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Affiliation(s)
- Mengqi Su
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Jennifer Lien
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Auddy Anilao
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Ting Guo
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
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2
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Advances in the Integration of Nucleic Acid Nanotechnology into CRISPR-Cas System. JOURNAL OF ANALYSIS AND TESTING 2021. [DOI: 10.1007/s41664-021-00180-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Xiao M, Lai W, Yu H, Yu Z, Li L, Fan C, Pei H. Assembly Pathway Selection with DNA Reaction Circuits for Programming Multiple Cell-Cell Interactions. J Am Chem Soc 2021; 143:3448-3454. [PMID: 33631070 DOI: 10.1021/jacs.0c12358] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The manipulation of cell-cell interactions promotes the study of multicellular behavior, but it remains a great challenge for programming multicellular assembly in complex reaction pathways with multiple cell types. Here we report a DNA reaction circuit-based approach to cell-surface engineering for the programmable regulation of multiple cell-cell interactions. The DNA circuits are designed on the basis of a stem-loop-integrated DNA hairpin motif, which has the capability of programming diverse molecular self-assembly and disassembly pathways by sequential allosteric activation. Modifying the cell surface with such DNA reaction circuits allows for performing programmable chemical functions on cell membranes and the control of multicellular self-assembly with selectivity. We demonstrate the selective control of targeting the capability of natural killer (NK) cells to two types of tumor cells, which show selectively enhanced cell-specific adaptive immunotherapy efficacy. We hope that our method provides new ideas for the programmable control of multiple cell-cell interactions in complex reaction pathways and potentially promotes the development of cell immunotherapy.
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Affiliation(s)
- Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Wei Lai
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Huizhen Yu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Zijing Yu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
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Gines G, Menezes R, Nara K, Kirstetter AS, Taly V, Rondelez Y. Isothermal digital detection of microRNAs using background-free molecular circuit. SCIENCE ADVANCES 2020; 6:eaay5952. [PMID: 32010788 PMCID: PMC6976291 DOI: 10.1126/sciadv.aay5952] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 11/20/2019] [Indexed: 05/04/2023]
Abstract
MicroRNAs, a class of transcripts involved in the regulation of gene expression, are emerging as promising disease-specific biomarkers accessible from tissues or bodily fluids. However, their accurate quantification from biological samples remains challenging. We report a sensitive and quantitative microRNA detection method using an isothermal amplification chemistry adapted to a droplet digital readout. Building on molecular programming concepts, we design a DNA circuit that converts, thresholds, amplifies, and reports the presence of a specific microRNA, down to the femtomolar concentration. Using a leak absorption mechanism, we were able to suppress nonspecific amplification, classically encountered in other exponential amplification reactions. As a result, we demonstrate that this isothermal amplification scheme is adapted to digital counting of microRNAs: By partitioning the reaction mixture into water-in-oil droplets, resulting in single microRNA encapsulation and amplification, the method provides absolute target quantification. The modularity of our approach enables to repurpose the assay for various microRNA sequences.
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Affiliation(s)
- Guillaume Gines
- Laboratoire Gulliver, CNRS, ESPCI Paris, PSL Research University, 10 rue Vauquelin, 75005 Paris, France
| | - Roberta Menezes
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université Paris Descartes, Université Paris Diderot, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Kaori Nara
- Laboratoire Gulliver, CNRS, ESPCI Paris, PSL Research University, 10 rue Vauquelin, 75005 Paris, France
| | - Anne-Sophie Kirstetter
- Laboratoire Gulliver, CNRS, ESPCI Paris, PSL Research University, 10 rue Vauquelin, 75005 Paris, France
| | - Valerie Taly
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université Paris Descartes, Université Paris Diderot, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Corresponding author. (Y.R.); (V.T.)
| | - Yannick Rondelez
- Laboratoire Gulliver, CNRS, ESPCI Paris, PSL Research University, 10 rue Vauquelin, 75005 Paris, France
- Corresponding author. (Y.R.); (V.T.)
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Pan J, Zeng L, Chen J. An enzyme-free DNA circuit for the amplified detection of Cd 2+ based on hairpin probe-mediated toehold binding and branch migration. Chem Commun (Camb) 2019; 55:11932-11935. [PMID: 31531427 DOI: 10.1039/c9cc06311k] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
An enzyme-free DNA circuit was designed for the amplified detection of Cd2+ based on hairpin probe-mediated toehold binding and branch migration. A Cd2+-specific aptamer was used to recognize Cd2+ and a G-quadruplex was used to report the detection signal. The assay is sensitive, with a detection limit of 5 pM.
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Affiliation(s)
- Jiafeng Pan
- School of Food Science and Engineering, Foshan University, Foshan 528000, China and Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China.
| | - Lingwen Zeng
- School of Food Science and Engineering, Foshan University, Foshan 528000, China
| | - Junhua Chen
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China.
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Wang B, Song L, Jin B, Deng N, Wu X, He J, Deng Z, Li Y. Base‐Sequence‐Independent Efficient Redox Switching of Self‐Assembled DNA Nanocages. Chembiochem 2019; 20:2743-2746. [DOI: 10.1002/cbic.201900253] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Indexed: 11/11/2022]
Affiliation(s)
- Bang Wang
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction EngineeringSchool of Chemistry and Chemical EngineeringHefei University of Technology Hefei Anhui 230009 P. R. China
| | - Lei Song
- CAS Key Laboratory of Soft Matter ChemistryDepartment of ChemistryUniversity of Science and Technology of China Hefei Anhui 230026 P. R. China
| | - Bang Jin
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction EngineeringSchool of Chemistry and Chemical EngineeringHefei University of Technology Hefei Anhui 230009 P. R. China
| | - Ning Deng
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction EngineeringSchool of Chemistry and Chemical EngineeringHefei University of Technology Hefei Anhui 230009 P. R. China
| | - Xiaojing Wu
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction EngineeringSchool of Chemistry and Chemical EngineeringHefei University of Technology Hefei Anhui 230009 P. R. China
| | - Jianbo He
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction EngineeringSchool of Chemistry and Chemical EngineeringHefei University of Technology Hefei Anhui 230009 P. R. China
| | - Zhaoxiang Deng
- CAS Key Laboratory of Soft Matter ChemistryDepartment of ChemistryUniversity of Science and Technology of China Hefei Anhui 230026 P. R. China
| | - Yulin Li
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction EngineeringSchool of Chemistry and Chemical EngineeringHefei University of Technology Hefei Anhui 230009 P. R. China
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Fan J, Wang HH, Xie S, Wang M, Nie Z. Engineering Cell-Surface Receptors with DNA Nanotechnology for Cell Manipulation. Chembiochem 2019; 21:282-293. [PMID: 31364788 DOI: 10.1002/cbic.201900315] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Revised: 06/19/2019] [Indexed: 12/11/2022]
Abstract
Cell-surface receptors play pivotal roles in the regulation of cell fate. Molecular engineering of cell-surface receptors enables control of cell signaling and manipulation of cell behavior in a user-defined way. Currently, the development of chemical-biological approaches for non-genetic engineering and regulation of membrane receptors is attracting significant interest. Recent research advances in functional nucleic acids and DNA nanotechnology have made it possible to use DNA as a new and promising molecular toolkit for controlling receptor-mediated signaling and cell fates. In this minireview we summarize the advances in the use of DNA nanotechnology for the spatiotemporal regulation of cell receptors and highlight practical applications in manipulating cell functions including cell adhesion, cell-cell contact, cell migration, and cellular immunity. We also provide a perspective on the potential of and challenges facing DNA-based receptor engineering in future applications of cell manipulation and cell-based therapy.
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Affiliation(s)
- Jiahui Fan
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, China
| | - Hong-Hui Wang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, China
| | - Shiyi Xie
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, China
| | - Miao Wang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, China
| | - Zhou Nie
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, China
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