1
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Iwabuchi S, Nomura SIM, Sato Y. Surfactant-Assisted Purification of Hydrophobic DNA Nanostructures. Chembiochem 2023; 24:e202200568. [PMID: 36470849 DOI: 10.1002/cbic.202200568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 12/04/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022]
Abstract
Purification of functional DNA nanostructures is an essential step in achieving intended functions because misfolded structures and the remaining free DNA strands in a solution can interact and affect their behavior. However, due to hydrophobicity-mediated aggregation, it is difficult to purify DNA nanostructures modified with hydrophobic molecules by conventional methods. Herein, we report the purification of cholesterol-modified DNA nanostructures by using a novel surfactant-assisted gel extraction. The addition of sodium cholate (SC) to the sample solution before structure folding prevented aggregation; this was confirmed by gel electrophoresis. We also found that adding sodium dodecyl sulfate (SDS) to the sample inhibited structural folding. The cholesterol-modified DNA nanostructures prepared with SC were successfully purified by gel extraction, and their ability to bind to the lipid membrane surfaces was maintained. This method will facilitate the purification of DNA nanostructures modified with hydrophobic molecules and expand their applicability in the construction of artificial cell-like systems.
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Affiliation(s)
- Shoji Iwabuchi
- Department of Robotics, Tohoku University, 6-6-01 Aramaki Aoba-ku, Sendai, 980-0845, Japan
| | - Shin-Ichiro M Nomura
- Department of Robotics, Tohoku University, 6-6-01 Aramaki Aoba-ku, Sendai, 980-0845, Japan
| | - Yusuke Sato
- Department of Intelligent and Control Systems, Kyushu Institute of Technology, 680-4 kawazu, lizuka, 820-8502, Japan
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2
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Hao P, Niu L, Luo Y, Wu N, Zhao Y. Surface Engineering of Lipid Vesicles Based on DNA Nanotechnology. Chempluschem 2022; 87:e202200074. [PMID: 35604011 DOI: 10.1002/cplu.202200074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/01/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Pengyan Hao
- Xi'an Jiaotong University School of Life Science and Technology CHINA
| | - Liqiong Niu
- Xi'an Jiaotong University School of Life Science and Technology CHINA
| | - Yuanyuan Luo
- Xi'an Jiaotong University School of Life Science and Technology CHINA
| | - Na Wu
- Xi'an Jiaotong University School of Life Science and Technology No.28, West Xianning Road 710049 Xi'an CHINA
| | - Yongxi Zhao
- Xi'an Jiaotong University School of Life Science and Technology CHINA
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3
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Guo Z, Zhang L, Yang Q, Peng R, Yuan X, Xu L, Wang Z, Chen F, Huang H, Liu Q, Tan W. Manipulation of Multiple Cell–Cell Interactions by Tunable DNA Scaffold Networks. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202111151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Zhenzhen Guo
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Biology Aptamer Engineering Center of Hunan Province Hunan University Changsha Hunan 410082 China
| | - Lili Zhang
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Biology Aptamer Engineering Center of Hunan Province Hunan University Changsha Hunan 410082 China
| | - Qiuxia Yang
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Biology Aptamer Engineering Center of Hunan Province Hunan University Changsha Hunan 410082 China
| | - Ruizi Peng
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Biology Aptamer Engineering Center of Hunan Province Hunan University Changsha Hunan 410082 China
- The Cancer Hospital of the University of Chinese Academy of Sciences Zhejiang Cancer Hospital) Institute of Basic Medicine and Cancer (IBMC) Chinese Academy of Sciences Hangzhou Zhejiang 310022 China
| | - Xi Yuan
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Biology Aptamer Engineering Center of Hunan Province Hunan University Changsha Hunan 410082 China
| | - Liujun Xu
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Biology Aptamer Engineering Center of Hunan Province Hunan University Changsha Hunan 410082 China
| | - Zhimin Wang
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Biology Aptamer Engineering Center of Hunan Province Hunan University Changsha Hunan 410082 China
| | - Fengming Chen
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Biology Aptamer Engineering Center of Hunan Province Hunan University Changsha Hunan 410082 China
| | - Huidong Huang
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Biology Aptamer Engineering Center of Hunan Province Hunan University Changsha Hunan 410082 China
| | - Qiaoling Liu
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Biology Aptamer Engineering Center of Hunan Province Hunan University Changsha Hunan 410082 China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Biology Aptamer Engineering Center of Hunan Province Hunan University Changsha Hunan 410082 China
- The Cancer Hospital of the University of Chinese Academy of Sciences Zhejiang Cancer Hospital) Institute of Basic Medicine and Cancer (IBMC) Chinese Academy of Sciences Hangzhou Zhejiang 310022 China
- Institute of Molecular Medicine (IMM) Renji Hospital Shanghai Jiao Tong University School of Medicine Shanghai Jiao Tong University Shanghai 200240 China
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4
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Guo Z, Zhang L, Yang Q, Peng R, Yuan X, Xu L, Wang Z, Chen F, Huang H, Liu Q, Tan W. Manipulation of Multiple Cell-Cell Interactions by Tunable DNA Scaffold Networks. Angew Chem Int Ed Engl 2021; 61:e202111151. [PMID: 34873818 DOI: 10.1002/anie.202111151] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Indexed: 12/15/2022]
Abstract
Manipulation of cell-cell interactions via cell surface engineering has potential biomedical applications in tissue engineering and cell therapy. However, manipulation of the comprehensive and multiple intercellular interactions remains a challenge and missing elements. Herein, utilizing a DNA triangular prism (TP) and a branched polymer (BP) as functional modules, we fabricate tunable DNA scaffold networks on the cell surface. The responsiveness of cell-cell recognition, aggregation and dissociation could be modulated by aptamer-functionalized DNA scaffold networks with high accuracy and specificity. By regulating the DNA scaffold networks coated on the cell surface, controlled intercellular molecular transportation is achieved. Our tunable network provides a simple and extendible strategy which addresses a current need in cell surface engineering to precisely manipulate cell-cell interactions and shows promise as a general tool for controllable cell behavior.
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Affiliation(s)
- Zhenzhen Guo
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Lili Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Qiuxia Yang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Ruizi Peng
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China.,The Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
| | - Xi Yuan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Liujun Xu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Zhimin Wang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Fengming Chen
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Huidong Huang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Qiaoling Liu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China.,The Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China.,Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
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5
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Feng L, Li J, Sun J, Wang L, Fan C, Shen J. Recent Advances of DNA Nanostructure-Based Cell Membrane Engineering. Adv Healthc Mater 2021; 10:e2001718. [PMID: 33458966 DOI: 10.1002/adhm.202001718] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/20/2020] [Indexed: 01/30/2023]
Abstract
Materials that can regulate the composition and structure of the cell membrane to fabricate engineered cells with defined functions are in high demand. Compared with other biomolecules, DNA has unique advantages in cell membrane engineering due to its excellent programmability and biocompatibility. Especially, the near-atomic scale precision of DNA nanostructures facilitates the investigation of structure-property relations on the cell membrane. In this review, first the state of the art of functional DNA nanostructures is summarized, and then the overview of the use of DNA nanostructures to engineer the cell membrane is presented. Subsequently, applications of DNA nanostructures in modifying cell membrane morphology, controlling ions transport, and synthesizing high precise liposomes are highlighted. Finally, the challenges and outlook on using DNA nanostructures for cell membrane engineering are discussed.
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Affiliation(s)
- Lingyu Feng
- Division of Physical Biology CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Jiang Li
- Division of Physical Biology CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China
- University of Chinese Academy of Sciences Beijing 100049 China
- Bioimaging Center Shanghai Synchrotron Radiation Facility Zhangjiang Laboratory Shanghai Advanced Research Institute Chinese Academy of Sciences Shanghai 201210 China
| | - Jielin Sun
- Key Laboratory of Systems Biomedicine (Ministry of Education) Shanghai Center for Systems Biomedicine Shanghai Jiao Tong University Shanghai 200240 China
| | - Lihua Wang
- Division of Physical Biology CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China
- University of Chinese Academy of Sciences Beijing 100049 China
- Bioimaging Center Shanghai Synchrotron Radiation Facility Zhangjiang Laboratory Shanghai Advanced Research Institute Chinese Academy of Sciences Shanghai 201210 China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine Shanghai Jiao Tong University Shanghai 200240 China
| | - Jianlei Shen
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine Shanghai Jiao Tong University Shanghai 200240 China
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6
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Bhatia D, Wunder C, Johannes L. Self-assembled, Programmable DNA Nanodevices for Biological and Biomedical Applications. Chembiochem 2021; 22:763-778. [PMID: 32961015 DOI: 10.1002/cbic.202000372] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 09/19/2020] [Indexed: 12/28/2022]
Abstract
The broad field of structural DNA nanotechnology has diverged into various areas of applications ranging from computing, photonics, synthetic biology, and biosensing to in-vivo bioimaging and therapeutic delivery, to name but a few. Though the field began to exploit DNA to build various nanoscale architectures, it has now taken a new path to diverge from structural DNA nanotechnology to functional or applied DNA nanotechnology. More recently a third sub-branch has emerged-biologically oriented DNA nanotechnology, which seeks to explore the functionalities of combinatorial DNA devices in various biological systems. In this review, we summarize the key developments in DNA nanotechnology revealing a current trend that merges the functionality of DNA devices with the specificity of biomolecules to access a range of functions in biological systems. This review seeks to provide a perspective on the evolution and biological applications of DNA nanotechnology, where the integration of DNA structures with biomolecules can now uncover phenomena of interest to biologists and biomedical scientists. Finally, we conclude with the challenges, limitations, and perspectives of DNA nanodevices in fundamental and applied research.
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Affiliation(s)
- Dhiraj Bhatia
- Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, 382330, Gandhinagar, India
| | - Christian Wunder
- Cellular and Chemical Biology Unit, Endocytic Trafficking and Intracellular Delivery Team U1143 INSERM UMR 3666 CNRS, Institut Curie, PSL Research University, 26 rue d'Ulm, 75248, Paris Cedex 05, France
| | - Ludger Johannes
- Cellular and Chemical Biology Unit, Endocytic Trafficking and Intracellular Delivery Team U1143 INSERM UMR 3666 CNRS, Institut Curie, PSL Research University, 26 rue d'Ulm, 75248, Paris Cedex 05, France
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7
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Extracting lipid vesicles from plasma membranes via self-assembly of clathrin-inspired scaffolding nanoparticles. Colloids Surf B Biointerfaces 2019; 176:239-248. [PMID: 30623811 DOI: 10.1016/j.colsurfb.2019.01.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/27/2018] [Accepted: 01/02/2019] [Indexed: 11/22/2022]
Abstract
Single-cell analysis is a new and rapidly expanding field, the goal of which is obtaining fresh information from individual cells to understand the regulatory mechanisms of cell development and diseases. Conventional approaches generally rely on the cell lysis which, however, is destructive to cells and against multiple sampling from the living cell. Here, we propose and design a scaffolding nanoparticle (NP) system that enables us to sample cytoplasmic contents without rupturing the cellular membrane, by mimicking the unusual features of clathrin. Our simulation results reveal the design principles, following which scaffolding NPs can extract lipid vesicles from plasma membranes, with both the pathway and the mechanism resembling the clathrin-mediated endocytosis, i.e. multiple NPs deposit at the membrane, assembling into cage-like structures to deform the membrane into a vesicle shape. As important design parameters, the interaction between different NPs should be properly stronger than that between each NP and the membrane to ensure the cage formation, and optimal NP concentration and the membrane surface tension are also requisite for extracting lipid vesicles. Our results provide useful guidelines for design of bio-inspired scaffolding NPs as an intelligent machine for practical use in but not limited to the single-cell analysis.
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8
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Yang J, Meng Z, Liu Q, Shimada Y, Olsthoorn RCL, Spaink HP, Herrmann A, Kros A. Performing DNA nanotechnology operations on a zebrafish. Chem Sci 2018; 9:7271-7276. [PMID: 30288248 PMCID: PMC6148687 DOI: 10.1039/c8sc01771a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 07/16/2018] [Indexed: 12/18/2022] Open
Abstract
Nanoscale engineering of surfaces is becoming an indispensable technique to modify membranes and, thus cellular behaviour. Here, such membrane engineering related was explored on the surface of a living animal using DNA nanotechnology. We demonstrate the immobilization of oligonucleotides functionalized with a membrane anchor on 2 day old zebrafish. The protruding single-stranded DNA on the skin of zebrafish served as a handle for complementary DNAs, which allowed the attachment of small molecule cargo, liposomes and dynamic relabeling by DNA hybridization protocols. Robust anchoring of the oligonucleotides was proven as DNA-based amplification processes were successfully performed on the outer membrane of the zebrafish enabling the multiplication of surface functionalities from a single DNA-anchoring unit and the dramatic improvement of fluorescent labeling of these animals. As zebrafish are becoming an alternative to animal models in drug development, toxicology and nanoparticles characterization, we believe the platform presented here allows amalgamation of DNA nanotechnology tools with live animals and this opens up yet unexplored avenues like efficient bio-barcoding as well as in vivo tracking.
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Affiliation(s)
- Jian Yang
- Supramolecular & Biomaterials Chemistry , Leiden Institute of Chemistry , Leiden University , P.O. Box 9502 , 2300 RA Leiden , The Netherlands .
| | - Zhuojun Meng
- Zernike Institute for Advanced Materials , University of Groningen , Nijenborgh 4 , 9747 AG Groningen , The Netherlands .
| | - Qing Liu
- Zernike Institute for Advanced Materials , University of Groningen , Nijenborgh 4 , 9747 AG Groningen , The Netherlands .
| | - Yasuhito Shimada
- Institute of Biology , Leiden University , Leiden , The Netherlands
- Department of Integrative Pharmacology , Mie University Graduate School of Medicine , Mie , Japan .
| | - René C L Olsthoorn
- Supramolecular & Biomaterials Chemistry , Leiden Institute of Chemistry , Leiden University , P.O. Box 9502 , 2300 RA Leiden , The Netherlands .
| | - Herman P Spaink
- Institute of Biology , Leiden University , Leiden , The Netherlands
| | - Andreas Herrmann
- Zernike Institute for Advanced Materials , University of Groningen , Nijenborgh 4 , 9747 AG Groningen , The Netherlands .
- DWI-Leibniz Institute for Interactive Materials , Forckenbeckstr. 50 , 52056 Aachen , Germany
- Institute of Technical and Macromolecular Chemistry , RWTH Aachen University , Worringerweg 2 , 52074 , Aachen , Germany
| | - Alexander Kros
- Supramolecular & Biomaterials Chemistry , Leiden Institute of Chemistry , Leiden University , P.O. Box 9502 , 2300 RA Leiden , The Netherlands .
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9
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Grome MW, Zhang Z, Pincet F, Lin C. Vesicle Tubulation with Self-Assembling DNA Nanosprings. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201800141] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Michael W. Grome
- Department of Cell Biology & Nanobiology Institute; Yale University; 850 West Campus Drive West Haven CT 06516 USA
| | - Zhao Zhang
- Department of Cell Biology & Nanobiology Institute; Yale University; 850 West Campus Drive West Haven CT 06516 USA
| | - Frédéric Pincet
- Department of Cell Biology & Nanobiology Institute; Yale University; 850 West Campus Drive West Haven CT 06516 USA
- Laboratoire de Physique Statistique; Ecole Normale Supérieure; PSL Research University; Université Paris Diderot Sorbonne Paris Cité; Sorbonne Universités UPMC Univ Paris 06, CNRS; 24 rue Lhomond 75005 Paris France
| | - Chenxiang Lin
- Department of Cell Biology & Nanobiology Institute; Yale University; 850 West Campus Drive West Haven CT 06516 USA
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10
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Grome MW, Zhang Z, Pincet F, Lin C. Vesicle Tubulation with Self-Assembling DNA Nanosprings. Angew Chem Int Ed Engl 2018; 57:5330-5334. [PMID: 29575478 DOI: 10.1002/anie.201800141] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 02/23/2018] [Indexed: 12/22/2022]
Affiliation(s)
- Michael W. Grome
- Department of Cell Biology & Nanobiology Institute; Yale University; 850 West Campus Drive West Haven CT 06516 USA
| | - Zhao Zhang
- Department of Cell Biology & Nanobiology Institute; Yale University; 850 West Campus Drive West Haven CT 06516 USA
| | - Frédéric Pincet
- Department of Cell Biology & Nanobiology Institute; Yale University; 850 West Campus Drive West Haven CT 06516 USA
- Laboratoire de Physique Statistique; Ecole Normale Supérieure; PSL Research University; Université Paris Diderot Sorbonne Paris Cité; Sorbonne Universités UPMC Univ Paris 06, CNRS; 24 rue Lhomond 75005 Paris France
| | - Chenxiang Lin
- Department of Cell Biology & Nanobiology Institute; Yale University; 850 West Campus Drive West Haven CT 06516 USA
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11
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Hong F, Zhang F, Liu Y, Yan H. DNA Origami: Scaffolds for Creating Higher Order Structures. Chem Rev 2017; 117:12584-12640. [DOI: 10.1021/acs.chemrev.6b00825] [Citation(s) in RCA: 645] [Impact Index Per Article: 92.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Fan Hong
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Fei Zhang
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Yan Liu
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Hao Yan
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
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12
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Dong Y, Yang YR, Zhang Y, Wang D, Wei X, Banerjee S, Liu Y, Yang Z, Yan H, Liu D. Cuboid Vesicles Formed by Frame‐Guided Assembly on DNA Origami Scaffolds. Angew Chem Int Ed Engl 2017; 56:1586-1589. [DOI: 10.1002/anie.201610133] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 11/16/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Yuanchen Dong
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of ChemistryTsinghua University Beijing 100084 China
| | - Yuhe Renee Yang
- School of Molecular Sciences and Center of Molecular Design & Biomimetics at Biodesign InstituteArizona State University Tempe AZ 85287 USA
| | - Yiyang Zhang
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of ChemistryTsinghua University Beijing 100084 China
| | - Dianming Wang
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of ChemistryTsinghua University Beijing 100084 China
| | - Xixi Wei
- School of Molecular Sciences and Center of Molecular Design & Biomimetics at Biodesign InstituteArizona State University Tempe AZ 85287 USA
| | - Saswata Banerjee
- School of Molecular Sciences and Center of Molecular Design & Biomimetics at Biodesign InstituteArizona State University Tempe AZ 85287 USA
| | - Yan Liu
- School of Molecular Sciences and Center of Molecular Design & Biomimetics at Biodesign InstituteArizona State University Tempe AZ 85287 USA
| | - Zhongqiang Yang
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of ChemistryTsinghua University Beijing 100084 China
| | - Hao Yan
- School of Molecular Sciences and Center of Molecular Design & Biomimetics at Biodesign InstituteArizona State University Tempe AZ 85287 USA
| | - Dongsheng Liu
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of ChemistryTsinghua University Beijing 100084 China
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13
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Dong Y, Yang YR, Zhang Y, Wang D, Wei X, Banerjee S, Liu Y, Yang Z, Yan H, Liu D. Cuboid Vesicles Formed by Frame-Guided Assembly on DNA Origami Scaffolds. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201610133] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yuanchen Dong
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Yuhe Renee Yang
- School of Molecular Sciences and Center of Molecular Design & Biomimetics at Biodesign Institute; Arizona State University; Tempe AZ 85287 USA
| | - Yiyang Zhang
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Dianming Wang
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Xixi Wei
- School of Molecular Sciences and Center of Molecular Design & Biomimetics at Biodesign Institute; Arizona State University; Tempe AZ 85287 USA
| | - Saswata Banerjee
- School of Molecular Sciences and Center of Molecular Design & Biomimetics at Biodesign Institute; Arizona State University; Tempe AZ 85287 USA
| | - Yan Liu
- School of Molecular Sciences and Center of Molecular Design & Biomimetics at Biodesign Institute; Arizona State University; Tempe AZ 85287 USA
| | - Zhongqiang Yang
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Hao Yan
- School of Molecular Sciences and Center of Molecular Design & Biomimetics at Biodesign Institute; Arizona State University; Tempe AZ 85287 USA
| | - Dongsheng Liu
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of Chemistry; Tsinghua University; Beijing 100084 China
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14
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Multiscale simulations of protein-facilitated membrane remodeling. J Struct Biol 2016; 196:57-63. [PMID: 27327264 DOI: 10.1016/j.jsb.2016.06.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 06/14/2016] [Accepted: 06/15/2016] [Indexed: 12/19/2022]
Abstract
Protein-facilitated shape and topology changes of cell membranes are crucial for many biological processes, such as cell division, protein trafficking, and cell signaling. However, the inherently multiscale nature of membrane remodeling presents a considerable challenge for understanding the mechanisms and physics that drive this process. To address this problem, a multiscale approach that makes use of a diverse set of computational and experimental techniques is required. The atomistic simulations provide high-resolution information on protein-membrane interactions. Experimental techniques, like electron microscopy, on the other hand, resolve high-order organization of proteins on the membrane. Coarse-grained (CG) and mesoscale computational techniques provide the intermediate link between the two scales and can give new insights into the underlying mechanisms. In this Review, we present the recent advances in multiscale computational approaches established in our group. We discuss various CG and mesoscale approaches in studying the protein-mediated large-scale membrane remodeling.
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