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Tang X, Chen T, Li W, Mao D, Liu C, Wu Q, Huang N, Hu S, Sun F, Pan Q, Zhu X. Throwing and manipulating and cheating with a DNA nano-dice. Nat Commun 2023; 14:2440. [PMID: 37117228 PMCID: PMC10147716 DOI: 10.1038/s41467-023-38164-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 04/18/2023] [Indexed: 04/30/2023] Open
Abstract
Artificial molecular machines have captured the imagination of researchers, given their clear potential to mimic and influence human life. Key to behavior simulation is to reproduce the specific properties of physical or abstract systems. Dice throwing, as a stochastic model, is commonly used for result judgment or plan decision in real life. In this perspective we utilize DNA cube framework for the design of a dice device at the nanoscale to reproduce probabilistic events in different situations: equal probability, high probability, and low probability. We first discuss the randomness of DNA cube, or dice, adsorbing on graphene oxide, or table, and then explore a series of events that change the probability through the way in which the energy released from entropy-driven strand displacement reactions or changes in intermolecular forces. As such, the DNA nano-dice system provides guideline and possibilities for the design, engineering, and quantification of behavioral probability simulation, a currently emerging area of molecular simulation research.
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Affiliation(s)
- Xiaochen Tang
- Department of Clinical Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai, 200127, P. R. China
| | - Tianshu Chen
- Department of Clinical Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai, 200127, P. R. China
| | - Wenxing Li
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, P. R. China
| | - Dongsheng Mao
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, P. R. China
| | - Chenbin Liu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, P. R. China
| | - Qi Wu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, P. R. China
| | - Nan Huang
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, P. R. China
| | - Song Hu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, P. R. China
| | - Fenyong Sun
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, P. R. China.
| | - Qiuhui Pan
- Department of Clinical Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China.
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai, 200127, P. R. China.
| | - Xiaoli Zhu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, P. R. China.
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Wang X, Yao C, Yao X, Lin J, Li R, Huang K, Lin W, Long X, Dai C, Dong J, Yu X, Huang W, Weng W, Wang Q, Ouyang H, Cheng K. Dynamic photoelectrical regulation of ECM protein and cellular behaviors. Bioact Mater 2023; 22:168-179. [PMID: 36203959 PMCID: PMC9529514 DOI: 10.1016/j.bioactmat.2022.09.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 09/07/2022] [Accepted: 09/21/2022] [Indexed: 12/02/2022] Open
Abstract
Dynamic regulation of cell-extracellular matrix (ECM)-material interactions is crucial for various biomedical applications. In this study, a light-activated molecular switch for the modulation of cell attachment/detachment behaviors was established on monolayer graphene (Gr)/n-type Silicon substrates (Gr/Si). Initiated by light illumination at the Gr/Si interface, pre-adsorbed proteins (bovine serum albumin, ECM proteins collagen-1, and fibronectin) underwent protonation to achieve negative charge transfer to Gr films (n-doping) through π-π interactions. This n-doping process stimulated the conformational switches of ECM proteins. The structural alterations in these ECM interactors significantly reduced the specificity of the cell surface receptor-ligand interaction (e.g., integrin recognition), leading to dynamic regulation of cell adhesion and eventual cell detachment. RNA-sequencing results revealed that the detached bone marrow mesenchymal stromal cell sheets from the Gr/Si system manifested regulated immunoregulatory properties and enhanced osteogenic differentiation, implying their potential application in bone tissue regeneration. This work not only provides a fast and feasible method for controllable cells/cell sheets harvesting but also gives new insights into the understanding of cell-ECM-material communications. A light-activated molecular switch for regulation of cell attachment/detachment behaviors was established on (Gr/Si) substrates. Light-induced charge transfer from ECM protein to Gr/Si through π-π interactions, resulting in the conformational alteration of ECM proteins. Structural changes in ECM weakened the binding between RGD and integrin, inducing cell detachment. This work provides a feasible method for cell harvesting and improves the understanding of cell-ECM-material communications.
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Affiliation(s)
- Xiaozhao Wang
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Department of Sports Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, 314400, China
- China Orthopedic Regenerative Medicine Group (CORMed), Hangzhou, 310058, China
| | - Cai Yao
- School of Chemistry, Zhejiang University, Hangzhou, 310027, China
| | - Xudong Yao
- International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, No. N1, Shangcheng Avenue, Yiwu, 322000, China
| | - Junxin Lin
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Department of Sports Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, 314400, China
- China Orthopedic Regenerative Medicine Group (CORMed), Hangzhou, 310058, China
| | - Rui Li
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Department of Sports Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, 314400, China
- China Orthopedic Regenerative Medicine Group (CORMed), Hangzhou, 310058, China
| | - Kun Huang
- School of Materials Science and Engineering, State Key Laboratory of Silicon Materials, Cyrus Tang Center for Sensor Materials and Applications, Zhejiang University, Hangzhou, 310027, China
| | - Weiming Lin
- School of Materials Science and Engineering, State Key Laboratory of Silicon Materials, Cyrus Tang Center for Sensor Materials and Applications, Zhejiang University, Hangzhou, 310027, China
| | - Xiaojun Long
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Department of Sports Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, 314400, China
- China Orthopedic Regenerative Medicine Group (CORMed), Hangzhou, 310058, China
| | - Chao Dai
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, 314400, China
| | - Jiajun Dong
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, 314400, China
| | - Xuegong Yu
- School of Materials Science and Engineering, State Key Laboratory of Silicon Materials, Cyrus Tang Center for Sensor Materials and Applications, Zhejiang University, Hangzhou, 310027, China
| | - Wenwen Huang
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Department of Sports Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, 314400, China
- China Orthopedic Regenerative Medicine Group (CORMed), Hangzhou, 310058, China
| | - Wenjian Weng
- School of Materials Science and Engineering, State Key Laboratory of Silicon Materials, Cyrus Tang Center for Sensor Materials and Applications, Zhejiang University, Hangzhou, 310027, China
| | - Qi Wang
- School of Chemistry, Zhejiang University, Hangzhou, 310027, China
| | - Hongwei Ouyang
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Department of Sports Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, 314400, China
- China Orthopedic Regenerative Medicine Group (CORMed), Hangzhou, 310058, China
- Corresponding author. Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.
| | - Kui Cheng
- School of Materials Science and Engineering, State Key Laboratory of Silicon Materials, Cyrus Tang Center for Sensor Materials and Applications, Zhejiang University, Hangzhou, 310027, China
- Corresponding author.
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Li Y, Gao H, Qi Z, Huang Z, Ma L, Liu J. Freezing-Assisted Conjugation of Unmodified Diblock DNA to Hydrogel Nanoparticles and Monoliths for DNA and Hg 2+ Sensing. Angew Chem Int Ed Engl 2021; 60:12985-12991. [PMID: 33792133 DOI: 10.1002/anie.202102330] [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: 02/15/2021] [Revised: 03/24/2021] [Indexed: 12/22/2022]
Abstract
Acrydite-modified DNA is the most frequently used reagent to prepare DNA-functionalized hydrogels. Herein, we show that unmodified penta-adenine (A5 ) can reach up to 75 % conjugation efficiency in 8 h under a freezing polymerization condition in polyacrylamide hydrogels. DNA incorporation efficiency was reduced by forming duplex or other folded structures and by removing the freezing condition. By designing diblock DNA containing an A5 block, various functional DNA sequences were attached. Such hydrogels were designed for ultrasensitive DNA hybridization and Hg2+ detection, with detection limits of 50 pM and 10 nM, respectively, demonstrating the feasibility of using unmodified DNA to replace acrydite-DNA. The same method worked for both gel nanoparticles and monoliths. This work revealed interesting reaction products by exploiting freezing and has provided a cost-effective way to attach DNA to hydrogels.
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Affiliation(s)
- Yuqing Li
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
| | - Hang Gao
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
| | - Zengyao Qi
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
| | - Zhicheng Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
| | - Lingzi Ma
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada.,Centre for Eye and Vision Research, 17W Hong Kong Science Park, Hong Kong, Hong Kong
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