1
|
Zhou L, Ren L, Bai Z, Xia Q, Wang Y, Peng H, Yan Q, Shi J, Li B, Guo L, Wang L. DNA Framework Programmed Conformational Reconstruction of Antibody Complementary Determining Region. JACS AU 2023; 3:2709-2714. [PMID: 37885585 PMCID: PMC10598557 DOI: 10.1021/jacsau.3c00492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/18/2023] [Accepted: 09/18/2023] [Indexed: 10/28/2023]
Abstract
The conformation of complementary determining region (CDR) is crucial in dictating its specificity and affinity for binding with an antigen, making it a focal point in artificial antibody engineering. Although desirable, programmable scaffolds that can regulate the conformation of individual CDRs with nanometer precision are still lacking. Here, we devise a strategy to program the CDR conformation by anchoring both ends of a free CDR loop to specific sites of a DNA framework structure. This method allows us to define the span of a single CDR loop with an ∼2 nm resolution. Using this approach, we create a series of DNA framework based artificial antibodies (DNFbodies) with varied CDR loop spans, leading to different antibody-antigen binding affinities. We find that an optimized single CDR loop (∼2.3 nm span) exhibits ∼3-fold improved affinity relative to natural antibodies, confirming the critical role of the CDR conformation. This study may inspire the rational design of artificial antibodies.
Collapse
Affiliation(s)
- Liqi Zhou
- National
Laboratory of Solid State Microstructures, Jiangsu Key Laboratory
of Artificial Functional Materials, College of Engineering and Applied
Sciences and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, People’s Republic of China
- Institute
of Materiobiology, College of Science, Shanghai
University, Shanghai 200444, People’s Republic
of China
| | - Lei Ren
- Institute
of Materiobiology, College of Science, Shanghai
University, Shanghai 200444, People’s Republic
of China
- CAS
Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
| | - Zhiang Bai
- Institute
of Materiobiology, College of Science, Shanghai
University, Shanghai 200444, People’s Republic
of China
| | - Qinglin Xia
- Institute
of Materiobiology, College of Science, Shanghai
University, Shanghai 200444, People’s Republic
of China
- CAS
Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
| | - Yue Wang
- Institute
of Materiobiology, College of Science, Shanghai
University, Shanghai 200444, People’s Republic
of China
- CAS
Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
| | - Hongzhen Peng
- Institute
of Materiobiology, College of Science, Shanghai
University, Shanghai 200444, People’s Republic
of China
| | - Qinglong Yan
- Xiangfu
Laboratory, Jiashan 314102, People’s Republic
of China
| | - Jiye Shi
- CAS
Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
| | - Bin Li
- CAS
Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
- The
Interdisciplinary Research Center, Shanghai Synchrotron Radiation
Facility, Shanghai Advanced Research Institute,
Chinese Academy of Sciences, Shanghai 201210, People’s
Republic of China
| | - Linjie Guo
- Institute
of Materiobiology, College of Science, Shanghai
University, Shanghai 200444, People’s Republic
of China
| | - Lihua Wang
- Institute
of Materiobiology, College of Science, Shanghai
University, Shanghai 200444, People’s Republic
of China
- CAS
Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
- The
Interdisciplinary Research Center, Shanghai Synchrotron Radiation
Facility, Shanghai Advanced Research Institute,
Chinese Academy of Sciences, Shanghai 201210, People’s
Republic of China
| |
Collapse
|
2
|
Zheng H, Li H, Li M, Zhai T, Xie X, Li C, Jing X, Liang C, Li Q, Zuo X, Li J, Fan J, Shen J, Peng X, Fan C. A Membrane Tension-Responsive Mechanosensitive DNA Nanomachine. Angew Chem Int Ed Engl 2023; 62:e202305896. [PMID: 37438325 DOI: 10.1002/anie.202305896] [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: 04/27/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 07/14/2023]
Abstract
Membrane curvature reflects physical forces operating on the lipid membrane, which plays important roles in cellular processes. Here, we design a mechanosensitive DNA (MSD) nanomachine that mimics natural mechanosensitive PIEZO channels to convert the membrane tension changes of lipid vesicles with different sizes into fluorescence signals in real time. The MSD nanomachine consists of an archetypical six-helix-bundle DNA nanopore, cholesterol-based membrane anchors, and a solvatochromic fluorophore, spiropyran (SP). We find that the DNA nanopore effectively amplifies subtle variations of the membrane tension, which effectively induces the isomerization of weakly emissive SP into highly emissive merocyanine isomers for visualizing membrane tension changes. By measuring the membrane tension via the fluorescence of MSD nanomachine, we establish the correlation between the membrane tension and the curvature that follows the Young-Laplace equation. This DNA nanotechnology-enabled strategy opens new routes to studying membrane mechanics in physiological and pathological settings.
Collapse
Affiliation(s)
- Haoran Zheng
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Haidong Li
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian, 116024, China
| | - Mingqiang Li
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Tingting Zhai
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaodong Xie
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Cong Li
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xinxin Jing
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Chengpin Liang
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Jiang Li
- Institute of Materiobiology, Department of Chemistry, College of Science, Shanghai University, Shanghai, 200444, China
| | - Jiangli Fan
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian, 116024, China
- Ningbo Institute of Dalian University of Technology, Ningbo, 315016, China
| | - Jianlei Shen
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaojun Peng
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian, 116024, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| |
Collapse
|
3
|
Gao D, Tang Z, Chen X, Wu R, Tian Y, Min Q, Zhang JR, Chen Z, Zhu JJ. Reversible Regulation of Long-Distance Charge Transport in DNA Nanowires by Dynamically Controlling Steric Conformation. NANO LETTERS 2023; 23:4201-4208. [PMID: 37188354 DOI: 10.1021/acs.nanolett.3c00102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Understanding of DNA-mediated charge transport (CT) is significant for exploring circuits at the molecular scale. However, the fabrication of robust DNA wires remains challenging due to the persistence length and natural flexibility of DNA molecules. Moreover, CT regulation in DNA wires often relies on predesigned sequences, which limit their application and scalability. Here, we addressed these issues by preparing self-assembled DNA nanowires with lengths of 30-120 nm using structural DNA nanotechnology. We employed these nanowires to plug individual gold nanoparticles into a circuit and measured the transport current in nanowires with an optical imaging technique. Contrary to the reported cases with shallow or no length dependence, a fair current attenuation was observed with increasing nanowire length, which experimentally confirmed the prediction of the incoherent hopping model. We also reported a mechanism for the reversible CT regulation in DNA nanowires, which involves dynamic transitions in the steric conformation.
Collapse
Affiliation(s)
- Di Gao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Zhuodong Tang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Xueqin Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Rong Wu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Ye Tian
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Qianhao Min
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Jian-Rong Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Zixuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Jun-Jie Zhu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
- Shenzhen Research Institute of Nanjing University, Shenzhen 518000, People's Republic of China
| |
Collapse
|
4
|
Zhao Y, Guo L, Cao S, Xie M, Peng H, Li J, Luo S, Ma L, Wang L. DNA framework carriers with asymmetric hydrophobic drug patterns for enhanced cellular cytotoxicity. Chem Commun (Camb) 2023; 59:306-309. [PMID: 36507912 DOI: 10.1039/d2cc05763h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We devise a class of amphiphilic drug complexes by programming hydrophobic drug patterns (HDPs) on DNA frameworks. We investigate the effect of HDPs on cellular uptake efficiency and drug potency. We achieve enhanced cytotoxicity against tumor cells by using an asymmetric HDP.
Collapse
Affiliation(s)
- Yan Zhao
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen 518132, China.,Division of Physical Biology Department, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.
| | - Linjie Guo
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China.,Zhangjiang Laboratory, Shanghai 201210, China
| | - Shuting Cao
- Division of Physical Biology Department, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.
| | - Mo Xie
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, Nanjing, Jiangsu 210023, China
| | - Hongzhen Peng
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China.,Zhangjiang Laboratory, Shanghai 201210, China
| | - Jiang Li
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China.,Zhangjiang Laboratory, Shanghai 201210, China
| | - Shihua Luo
- Department of Traumatology, Rui Jin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Lan Ma
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen 518132, China.,Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Lihua Wang
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China.,Zhangjiang Laboratory, Shanghai 201210, China
| |
Collapse
|
5
|
Ma J, Yao M, Yang Y, Zhang X. Comprehensive review on stability and demulsification of unconventional heavy oil-water emulsions. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.118510] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
6
|
He Q, Liu Y, Li K, Wu Y, Wang T, Tan Y, Jiang T, Liu X, Liu Z. Deoxyribonucleic acid anchored on cell membranes for biomedical application. Biomater Sci 2021; 9:6691-6717. [PMID: 34494042 DOI: 10.1039/d1bm01057c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Engineering cellular membranes with functional molecules provides an attractive strategy to manipulate cellular behaviors and functionalities. Currently, synthetic deoxyribonucleic acid (DNA) has emerged as a promising molecular tool to engineer cellular membranes for biomedical applications due to its molecular recognition and programmable properties. In this review, we summarized the recent advances in anchoring DNA on the cellular membranes and their applications. The strategies for anchoring DNA on cell membranes were summarized. Then their applications, such as immune response activation, receptor oligomerization regulation, membrane structure mimicking, cell-surface biosensing, and construction of cell clusters, were listed. The DNA-enabled intelligent systems which were able to sense stimuli such as DNA strands, light, and metal ions were highlighted. Finally, insights regarding the remaining challenges and possible future directions were provided.
Collapse
Affiliation(s)
- Qunye He
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, P. R. China.
| | - Yanfei Liu
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, Hunan Province, P. R. China
| | - Ke Li
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, P. R. China.
| | - Yuwei Wu
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, P. R. China.
| | - Ting Wang
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, P. R. China.
| | - Yifu Tan
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, Hunan Province, P. R. China
| | - Ting Jiang
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, Hunan Province, P. R. China
| | - Xiaoqin Liu
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, Hunan Province, P. R. China
| | - Zhenbao Liu
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, P. R. China. .,Molecular Imaging Research Center of Central South University, Changsha 410008, Hunan, P. R. China
| |
Collapse
|
7
|
Lu S, Shen J, Fan C, Li Q, Yang X. DNA Assembly-Based Stimuli-Responsive Systems. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2100328. [PMID: 34258165 PMCID: PMC8261508 DOI: 10.1002/advs.202100328] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/05/2021] [Indexed: 05/06/2023]
Abstract
Stimuli-responsive designs with exogenous stimuli enable remote and reversible control of DNA nanostructures, which break many limitations of static nanostructures and inspired development of dynamic DNA nanotechnology. Moreover, the introduction of various types of organic molecules, polymers, chemical bonds, and chemical reactions with stimuli-responsive properties development has greatly expand the application scope of dynamic DNA nanotechnology. Here, DNA assembly-based stimuli-responsive systems are reviewed, with the focus on response units and mechanisms that depend on different exogenous stimuli (DNA strand, pH, light, temperature, electricity, metal ions, etc.), and their applications in fields of nanofabrication (DNA architectures, hybrid architectures, nanomachines, and constitutional dynamic networks) and biomedical research (biosensing, bioimaging, therapeutics, and theranostics) are discussed. Finally, the opportunities and challenges for DNA assembly-based stimuli-responsive systems are overviewed and discussed.
Collapse
Affiliation(s)
- Shasha Lu
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesInstitute of Translational MedicineShanghai Jiao Tong UniversityShanghai200240China
| | - Jianlei Shen
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesInstitute of Translational MedicineShanghai Jiao Tong UniversityShanghai200240China
| | - Chunhai Fan
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesInstitute of Translational MedicineShanghai Jiao Tong UniversityShanghai200240China
- Institute of Molecular MedicineShanghai Key Laboratory for Nucleic Acid Chemistry and NanomedicineDepartment of UrologyRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Qian Li
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesInstitute of Translational MedicineShanghai Jiao Tong UniversityShanghai200240China
| | - Xiurong Yang
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesInstitute of Translational MedicineShanghai Jiao Tong UniversityShanghai200240China
| |
Collapse
|
8
|
Naskar S, Maiti PK. Mechanical properties of DNA and DNA nanostructures: comparison of atomistic, Martini and oxDNA models. J Mater Chem B 2021; 9:5102-5113. [PMID: 34127998 DOI: 10.1039/d0tb02970j] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The flexibility and stiffness of small DNA molecules play a fundamental role ranging from several biophysical processes to nano-technological applications. Here, we estimate the mechanical properties of short double-stranded DNA (dsDNA) with lengths ranging from 12 base-pairs (bp) to 56 bp, paranemic crossover (PX) DNA and hexagonal DNA nanotubes (DNTs) using two widely used coarse-grained models - Martini and oxDNA. To calculate the persistence length (Lp) and the stretch modulus (γ) of the dsDNA, we incorporate the worm-like chain and elastic rod model, while for the DNTs, we implement our previously developed theoretical framework. We compare and contrast all of the results with previously reported all-atom molecular dynamics (MD) simulations and experimental results. The mechanical properties of dsDNA (Lp ∼ 50 nm, γ ∼ 800-1500 pN), PX DNA (γ ∼ 1600-2000 pN) and DNTs (Lp ∼ 1-10 μm, γ ∼ 6000-8000 pN) estimated using the Martini soft elastic network and oxDNA are in very good agreement with the all-atom MD and experimental values, while the stiff elastic network Martini reproduces values of Lp and γ which are an order of magnitude higher. The high flexibility of small dsDNA is also depicted in our calculations. However, Martini models proved inadequate to capture the salt concentration effects on the mechanical properties with increasing salt molarity. oxDNA captures the salt concentration effect on the small dsDNA mechanics. But it is found to be ineffective for reproducing the salt-dependent mechanical properties of DNTs. Also, unlike Martini, the time evolved PX DNA and DNT structures from the oxDNA models are comparable to the all-atom MD simulated structures. Our findings provide a route to study the mechanical properties of DNA and DNA based nanostructures with increased time and length scales and has a remarkable implication in the context of DNA nanotechnology.
Collapse
Affiliation(s)
- Supriyo Naskar
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore, 560012, India.
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore, 560012, India.
| |
Collapse
|
9
|
Jones S, Joshi H, Terry SJ, Burns JR, Aksimentiev A, Eggert US, Howorka S. Hydrophobic Interactions between DNA Duplexes and Synthetic and Biological Membranes. J Am Chem Soc 2021; 143:8305-8313. [PMID: 34015219 PMCID: PMC8193631 DOI: 10.1021/jacs.0c13235] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Indexed: 12/18/2022]
Abstract
Equipping DNA with hydrophobic anchors enables targeted interaction with lipid bilayers for applications in biophysics, cell biology, and synthetic biology. Understanding DNA-membrane interactions is crucial for rationally designing functional DNA. Here we study the interactions of hydrophobically tagged DNA with synthetic and cell membranes using a combination of experiments and atomistic molecular dynamics (MD) simulations. The DNA duplexes are rendered hydrophobic by conjugation to a terminal cholesterol anchor or by chemical synthesis of a charge-neutralized alkyl-phosphorothioate (PPT) belt. Cholesterol-DNA tethers to lipid vesicles of different lipid compositions and charges, while PPT DNA binding strongly depends on alkyl length, belt position, and headgroup charge. Divalent cations in the buffer can also influence binding. Our MD simulations directly reveal the complex structure and energetics of PPT DNA within a lipid membrane, demonstrating that longer alkyl-PPT chains provide the most stable membrane anchoring but may disrupt DNA base paring in solution. When tested on cells, cholesterol-DNA is homogeneously distributed on the cell surface, while alkyl-PPT DNA accumulates in clustered structures on the plasma membrane. DNA tethered to the outside of the cell membrane is distinguished from DNA spanning the membrane by nuclease and sphingomyelinase digestion assays. The gained fundamental insight on DNA-bilayer interactions will guide the rational design of membrane-targeting nanostructures.
Collapse
Affiliation(s)
- Sioned
F. Jones
- Department
of Chemistry, Institute of Structural and Molecular Biology, University College London, London WC1H 0AJ, United Kingdom
- Randall
Centre for Cell and Molecular Biophysics, School of Basic and Medical
Biosciences, and Department of Chemistry, King’s College London, London SE1 1UL, United Kingdom
| | - Himanshu Joshi
- Department
of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Stephen J. Terry
- Randall
Centre for Cell and Molecular Biophysics, School of Basic and Medical
Biosciences, and Department of Chemistry, King’s College London, London SE1 1UL, United Kingdom
- UCL
Ear Institute, London WC1X 8EE, United Kingdom
| | - Jonathan R. Burns
- Department
of Chemistry, Institute of Structural and Molecular Biology, University College London, London WC1H 0AJ, United Kingdom
| | - Aleksei Aksimentiev
- Department
of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Ulrike S. Eggert
- Randall
Centre for Cell and Molecular Biophysics, School of Basic and Medical
Biosciences, and Department of Chemistry, King’s College London, London SE1 1UL, United Kingdom
| | - Stefan Howorka
- Department
of Chemistry, Institute of Structural and Molecular Biology, University College London, London WC1H 0AJ, United Kingdom
| |
Collapse
|
10
|
Li C, Hofmeister E, Krivtsov I, Mitoraj D, Adler C, Beranek R, Dietzek B. Photodriven Charge Accumulation and Carrier Dynamics in a Water-Soluble Carbon Nitride Photocatalyst. CHEMSUSCHEM 2021; 14:1728-1736. [PMID: 33586917 PMCID: PMC8048561 DOI: 10.1002/cssc.202002921] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/15/2021] [Indexed: 05/21/2023]
Abstract
Charge accumulation in photoactive molecules and materials holds great promise in solar energy conversion as it allows for decoupling solar-driven charging from (dark) redox reactions. In this contribution, light-driven charge accumulation was investigated for a recently reported novel water-soluble carbon nitride [K,Na-poly(heptazine imide); K,Na-PHI] photocatalyst, which exhibits excellent activity and stability in highly selective photocatalytic oxidation of alcohols and concurrent reduction of dioxygen to H2 O2 under quasi-homogeneous conditions. An excellent charge storage ability of the K,Na-PHI material was demonstrated, showing an optimal density of accumulated electrons (32.2 μmol of electrons per gram) in the presence of 10 vol % MeOH as a sacrificial electron donor. The long-lived electrons accumulated under anaerobic conditions as K,Na-PHI.- radical ions were utilized in interfacial electron transfer to O2 or methyl viologen in a subsequent dark reaction. Ultrafast time-resolved spectroscopy was employed to reveal the kinetics of charge-carrier recombination and methanol oxidation. Geminate recombination of electrons and holes within approximately 100 ps was followed by trap-assisted recombination. The presence of methanol as a sacrificial electron donor accelerated the decay of the transient absorption signal when a static sample was used. This behavior was ascribed to the faster charge recombination in the presence of the radical anions generated after hole extraction. The work suggests that photodriven electron storage in the water-soluble carbon nitride is enabled by localized trap states, and highlights the importance of the effective electron donor for creating long-lived photo-generated carbon nitride radicals.
Collapse
Affiliation(s)
- Chunyu Li
- Department Functional InterfacesLeibniz Institute of Photonic Technology Jena (IPHT)Albert-Einstein-Straße 907745JenaGermany
- Institute of Physical ChemistryFriedrich-Schiller University JenaHelmholtzweg 407743JenaGermany
| | - Elisabeth Hofmeister
- Department Functional InterfacesLeibniz Institute of Photonic Technology Jena (IPHT)Albert-Einstein-Straße 907745JenaGermany
- Institute of Physical ChemistryFriedrich-Schiller University JenaHelmholtzweg 407743JenaGermany
| | - Igor Krivtsov
- Institute of ElectrochemistryUlm UniversityAlbert-Einstein-Allee 4789081UlmGermany
| | - Dariusz Mitoraj
- Institute of ElectrochemistryUlm UniversityAlbert-Einstein-Allee 4789081UlmGermany
| | - Christiane Adler
- Institute of ElectrochemistryUlm UniversityAlbert-Einstein-Allee 4789081UlmGermany
| | - Radim Beranek
- Institute of ElectrochemistryUlm UniversityAlbert-Einstein-Allee 4789081UlmGermany
| | - Benjamin Dietzek
- Department Functional InterfacesLeibniz Institute of Photonic Technology Jena (IPHT)Albert-Einstein-Straße 907745JenaGermany
- Institute of Physical ChemistryFriedrich-Schiller University JenaHelmholtzweg 407743JenaGermany
- Centre for Energy and Environmental Chemistry Jena (CEEC Jena)Friedrich-Schiller University JenaPhilosophenweg 7a07743JenaGermany
| |
Collapse
|
11
|
Lanphere C, Offenbartl-Stiegert D, Dorey A, Pugh G, Georgiou E, Xing Y, Burns JR, Howorka S. Design, assembly, and characterization of membrane-spanning DNA nanopores. Nat Protoc 2020; 16:86-130. [PMID: 33349702 DOI: 10.1038/s41596-020-0331-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 04/06/2020] [Indexed: 01/08/2023]
Abstract
DNA nanopores are bio-inspired nanostructures that control molecular transport across lipid bilayer membranes. Researchers can readily engineer the structure and function of DNA nanopores to synergistically combine the strengths of DNA nanotechnology and nanopores. The pores can be harnessed in a wide range of areas, including biosensing, single-molecule chemistry, and single-molecule biophysics, as well as in cell biology and synthetic biology. Here, we provide a protocol for the rational design of nanobarrel-like DNA pores and larger DNA origami nanopores for targeted applications. We discuss strategies for the pores' chemical modification with lipid anchors to enable them to be inserted into membranes such as small unilamellar vesicles (SUVs) and planar lipid bilayers. The procedure covers the self-assembly of DNA nanopores via thermal annealing, their characterization using gel electrophoresis, purification, and direct visualization with transmission electron microscopy and atomic force microscopy. We also describe a gel assay to determine pore-membrane binding and discuss how to use single-channel current recordings and dye flux assays to confirm transport through the pores. We expect this protocol to take approximately 1 week to complete for DNA nanobarrel pores and 2-3 weeks for DNA origami pores.
Collapse
Affiliation(s)
- Conor Lanphere
- Department of Chemistry & Institute of Structural Molecular Biology, University College London, London, UK
| | - Daniel Offenbartl-Stiegert
- Department of Chemistry & Institute of Structural Molecular Biology, University College London, London, UK
| | - Adam Dorey
- Department of Chemistry & Institute of Structural Molecular Biology, University College London, London, UK
| | - Genevieve Pugh
- Department of Chemistry & Institute of Structural Molecular Biology, University College London, London, UK
| | - Elena Georgiou
- Department of Chemistry & Institute of Structural Molecular Biology, University College London, London, UK
| | - Yongzheng Xing
- Department of Chemistry & Institute of Structural Molecular Biology, University College London, London, UK
| | - Jonathan R Burns
- Department of Chemistry & Institute of Structural Molecular Biology, University College London, London, UK.
| | - Stefan Howorka
- Department of Chemistry & Institute of Structural Molecular Biology, University College London, London, UK.
| |
Collapse
|
12
|
Lv C, Gu X, Li H, Zhao Y, Yang D, Yu W, Han D, Li J, Tan W. Molecular Transport through a Biomimetic DNA Channel on Live Cell Membranes. ACS NANO 2020; 14:14616-14626. [PMID: 32897687 DOI: 10.1021/acsnano.0c03105] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Biological membrane channels, considered as molecular gatekeepers, control the transportation of molecules and ions across live cell membranes. Developing synthetic passable channels with predictable structures, high transport efficiency, and low cytotoxicity on live cells is of great interest for replicating the functions of endogenous protein channels, but remains challenging. The development of DNA nanotechnology provides possible solutions for making synthetic channels with precise structures and controllable functionalization. Therefore, in this work, we constructed a phosphorothioate-modified DNA nanopore able to structurally mimic biological channels for molecular transport across live cell membranes. With its stable structure with small hollow size (<2 nm) and the ability to interact with the lipid molecules, this DNA nanopore could show stable insertion into the plasma membrane. We further proved that this membrane-spanning channel could transport ions and antitumor drugs to neurons and cancer cells, respectively, and do so within a certain time window. We expect that this live cell membrane-spanning synthetic DNA nanopore will provide a tool for studying cellular communication, building synthetic cells, and achieving controlled transmembrane transport to cells.
Collapse
Affiliation(s)
- Cheng Lv
- Institute of Molecular Medicine (IMM), Department of Anesthesiology, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, State Key Laboratory of Oncogenes and Related Genes, School of Medicine and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Xiyao Gu
- Institute of Molecular Medicine (IMM), Department of Anesthesiology, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, State Key Laboratory of Oncogenes and Related Genes, School of Medicine and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Haowen Li
- Institute of Molecular Medicine (IMM), Department of Anesthesiology, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, State Key Laboratory of Oncogenes and Related Genes, School of Medicine and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yumeng Zhao
- Institute of Molecular Medicine (IMM), Department of Anesthesiology, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, State Key Laboratory of Oncogenes and Related Genes, School of Medicine and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Donglei Yang
- Institute of Molecular Medicine (IMM), Department of Anesthesiology, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, State Key Laboratory of Oncogenes and Related Genes, School of Medicine and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Weifeng Yu
- Institute of Molecular Medicine (IMM), Department of Anesthesiology, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, State Key Laboratory of Oncogenes and Related Genes, School of Medicine and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Da Han
- Institute of Molecular Medicine (IMM), Department of Anesthesiology, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, State Key Laboratory of Oncogenes and Related Genes, School of Medicine and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Juan Li
- Institute of Molecular Medicine (IMM), Department of Anesthesiology, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, State Key Laboratory of Oncogenes and Related Genes, School of Medicine and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200127, China
- The Cancer Hospital of the University of Chinese Academy of Sciences, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Weihong Tan
- Institute of Molecular Medicine (IMM), Department of Anesthesiology, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, State Key Laboratory of Oncogenes and Related Genes, School of Medicine and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200127, China
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China
- The Cancer Hospital of the University of Chinese Academy of Sciences, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| |
Collapse
|
13
|
Zhao N, Chen Y, Chen G, Xiao Z. Artificial Cells Based on DNA Nanotechnology. ACS APPLIED BIO MATERIALS 2020; 3:3928-3934. [PMID: 35025469 DOI: 10.1021/acsabm.0c00149] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Artificial cells have led to many potential applications in synthetic biology and served as useful platforms to study biological phenomena. With increasing development of DNA nanotechnology, DNA-based nanostructures with various morphologies have been constructed for protein mimicking. These biomimicking elements can be assembled on cell membrane involved in various cellular activities, as well as be constructed as signaling networks inside cells. DNA nanotechnology provides an efficient approach to accomplish multiple functions, including signal recognition, transduction, and output. Here, we review a myriad of predominant studies on the construction of artificial cells based on DNA nanotechnology, including the morphological and functional mimic of membrane proteins, biosensors for monitoring the cellular microenvironment, and construction of DNA-based signal feedback networks. We also provide a comprehensive insight into DNA-based artificial cells, on the basis of current challenges and scientific requirements, which will prompt their reasonable designs in the future.
Collapse
Affiliation(s)
- Na Zhao
- Department of Pharmacology and Chemical Biology, & Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Clinical and Fundamental Research Center, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yingzhi Chen
- Department of Pharmacology and Chemical Biology, & Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Clinical and Fundamental Research Center, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Gaoxian Chen
- Department of Pharmacology and Chemical Biology, & Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Clinical and Fundamental Research Center, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Zeyu Xiao
- Department of Pharmacology and Chemical Biology, & Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Clinical and Fundamental Research Center, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| |
Collapse
|
14
|
Liu X, Jing X, Liu P, Pan M, Liu Z, Dai X, Lin J, Li Q, Wang F, Yang S, Wang L, Fan C. DNA Framework-Encoded Mineralization of Calcium Phosphate. Chem 2020. [DOI: 10.1016/j.chempr.2019.12.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
|
15
|
Zhu B, Guo J, Zhang L, Pan M, Jing X, Wang L, Liu X, Zuo X. In-Situ Configuration Studies on Segmented DNA Origami Nanotubes. Chembiochem 2019; 20:1508-1513. [PMID: 30702811 DOI: 10.1002/cbic.201800727] [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: 11/27/2018] [Revised: 01/31/2019] [Indexed: 11/09/2022]
Abstract
One-dimensional nanotubes are of considerable interest in materials and biochemical sciences. A particular desire is to create DNA nanotubes with user-defined structural features and biological relevance, which will facilitate the application of these nanotubes in the controlled release of drugs, templating of other materials into linear arrays and the construction of artificial membrane channels. However, little is known about the structures of assembled DNA nanotubes in solution. Here we report an in situ exploration of segmented DNA nanotubes, composed of multiple units with set length distributions, by using synchrotron small-angle X-ray scattering (SAXS). Through joint experimental and theoretical studies, we show that the SAXS data are highly informative in the context of heterogeneous mixtures of DNA nanotubes. The structural parameters obtained by SAXS are in good agreement with those determined by atomic force microscopy (AFM), transmission electron microscopy (TEM), and dynamic light scattering (DLS). In particular, the SAXS data revealed important structural information on these DNA nanotubes, such as the in-solution diameters (≈25 nm), which could be obtained only with difficulty by use of other methods. Our results establish SAXS as a reliable structural analysis method for long DNA nanotubes and could assist in the rational design of these structures.
Collapse
Affiliation(s)
- Bowen Zhu
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Shanghai, 201800, China
| | - Jingyang Guo
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Shanghai, 201800, China
| | - Lixia Zhang
- Jiading District Central Hospital, Shanghai, 201800, China
| | - Muchen Pan
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Shanghai, 201800, China
| | - Xinxin Jing
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Shanghai, 201800, China
| | - Lihua Wang
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Shanghai, 201800, China
| | - Xiaoguo Liu
- School of Chemistry and Chemical Engineering and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaolei Zuo
- School of Chemistry and Chemical Engineering and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| |
Collapse
|
16
|
Fu J, Oh SW, Monckton K, Arbuckle-Keil G, Ke Y, Zhang T. Biomimetic Compartments Scaffolded by Nucleic Acid Nanostructures. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1900256. [PMID: 30884139 DOI: 10.1002/smll.201900256] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 02/19/2019] [Indexed: 05/28/2023]
Abstract
The behaviors of living cells are governed by a series of regulated and confined biochemical reactions. The design and successful construction of synthetic cellular reactors can be useful in a broad range of applications that will bring significant scientific and economic impact. Over the past few decades, DNA self-assembly has enabled the design and fabrication of sophisticated 1D, 2D, and 3D nanostructures, and is applied to organizing a variety of biomolecular components into prescribed 2D and 3D patterns. In this Concept, the recent and exciting progress in DNA-scaffolded compartmentalizations and their applications in enzyme encapsulation, lipid membrane assembly, artificial transmembrane nanopores, and smart drug delivery are in focus. Taking advantage of these features promises to deliver breakthroughs toward the attainment of new synthetic and biomimetic reactors.
Collapse
Affiliation(s)
- Jinglin Fu
- Department of Chemistry and Center for Computational and Integrative Biology, Rutgers University-Camden, 315 Penn Street, Camden, NJ, 08102, USA
| | - Sung Won Oh
- Department of Chemistry and Center for Computational and Integrative Biology, Rutgers University-Camden, 315 Penn Street, Camden, NJ, 08102, USA
| | - Kristin Monckton
- Department of Chemistry and Center for Computational and Integrative Biology, Rutgers University-Camden, 315 Penn Street, Camden, NJ, 08102, USA
| | - Georgia Arbuckle-Keil
- Department of Chemistry and Center for Computational and Integrative Biology, Rutgers University-Camden, 315 Penn Street, Camden, NJ, 08102, USA
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, 30322, USA
| | - Ting Zhang
- Department of Chemistry and Center for Computational and Integrative Biology, Rutgers University-Camden, 315 Penn Street, Camden, NJ, 08102, USA
| |
Collapse
|
17
|
Liu X, Zhao Y, Liu P, Wang L, Lin J, Fan C. Biomimetische DNA‐Nanoröhren: Gezielte Synthese und Anwendung nanoskopischer Kanäle. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201807779] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Xiaoguo Liu
- School of Chemistry and Chemical Engineering, and Institute of Molecular MedicineRenji HospitalSchool of MedicineShanghai Jiao Tong University Shanghai 201240 China
- Division of Physical Biology & Bioimaging CenterShanghai Synchrotron Radiation FacilityCAS Key Laboratory of Interfacial Physics and TechnologyShanghai Institute of Applied PhysicsChinese Academy of Sciences Shanghai 201800 China
| | - Yan Zhao
- Division of Physical Biology & Bioimaging CenterShanghai Synchrotron Radiation FacilityCAS Key Laboratory of Interfacial Physics and TechnologyShanghai Institute of Applied PhysicsChinese Academy of Sciences Shanghai 201800 China
| | - Pi Liu
- State Key Laboratory of Medicinal Chemical BiologyCollege of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research Nankai University Tianjin 300353 China
- Biodesign CenterTianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
| | - Lihua Wang
- Division of Physical Biology & Bioimaging CenterShanghai Synchrotron Radiation FacilityCAS Key Laboratory of Interfacial Physics and TechnologyShanghai Institute of Applied PhysicsChinese Academy of Sciences Shanghai 201800 China
| | - Jianping Lin
- State Key Laboratory of Medicinal Chemical BiologyCollege of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research Nankai University Tianjin 300353 China
- Biodesign CenterTianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, and Institute of Molecular MedicineRenji HospitalSchool of MedicineShanghai Jiao Tong University Shanghai 201240 China
- Division of Physical Biology & Bioimaging CenterShanghai Synchrotron Radiation FacilityCAS Key Laboratory of Interfacial Physics and TechnologyShanghai Institute of Applied PhysicsChinese Academy of Sciences Shanghai 201800 China
| |
Collapse
|
18
|
Liu X, Zhao Y, Liu P, Wang L, Lin J, Fan C. Biomimetic DNA Nanotubes: Nanoscale Channel Design and Applications. Angew Chem Int Ed Engl 2019; 58:8996-9011. [PMID: 30290046 DOI: 10.1002/anie.201807779] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 08/25/2018] [Indexed: 01/04/2023]
Abstract
Biomacromolecular nanotubes play important physiological roles in transmembrane ion/molecule channeling, intracellular transport, and inter-cellular communications. While genetically encoded protein nanotubes are prevalent in vivo, the in vitro construction of biomimetic DNA nanotubes has attracted intense interest with the rise of structural DNA nanotechnology. The abiotic use of DNA assembly provides a powerful bottom-up approach for the rational construction of complex materials with arbitrary size and shape at the nanoscale. More specifically, a typical DNA nanotube can be assembled either with parallel-aligned DNA duplexes or by closing DNA tile lattices. These artificial DNA nanotubes can be tailored and site-specifically modified to realize biomimetic functions including ionic or molecular channeling, bioreactors, drug delivery, and biomolecular sensing. In this Minireview, we aim to summarize recent advances in design strategies, including the characterization and applications of biomimetic DNA nanotubes.
Collapse
Affiliation(s)
- Xiaoguo Liu
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 201240, China.,Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Yan Zhao
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Pi Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research Nankai University, Tianjin, 300353, China.,Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Jianping Lin
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research Nankai University, Tianjin, 300353, China.,Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 201240, China.,Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| |
Collapse
|
19
|
Guilbaud S, Salomé L, Destainville N, Manghi M, Tardin C. Dependence of DNA Persistence Length on Ionic Strength and Ion Type. PHYSICAL REVIEW LETTERS 2019; 122:028102. [PMID: 30720315 DOI: 10.1103/physrevlett.122.028102] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Indexed: 06/09/2023]
Abstract
Even though the persistence length L_{P} of double-stranded DNA plays a pivotal role in cell biology and nanotechnologies, its dependence on ionic strength I lacks a consensual description. Using a high-throughput single-molecule technique and statistical physics modeling, we measure L_{P} in the presence of monovalent (Li^{+}, Na^{+}, K^{+}) and divalent (Mg^{2+}, Ca^{2+}) metallic and alkyl ammonium ions, over a large range 0.5 mM≤I≤5 M. We show that linear Debye-Hückel-type theories do not describe even part of these data. By contrast, the Netz-Orland and Trizac-Shen formulas, two approximate theories including nonlinear electrostatic effects and the finite DNA radius, fit our data with divalent and monovalent ions, respectively, over the whole I range. Furthermore, the metallic ion type does not influence L_{P}(I), in contrast to alkyl ammonium monovalent ions at high I.
Collapse
Affiliation(s)
- Sébastien Guilbaud
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31 077 Toulouse, France
| | - Laurence Salomé
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31 077 Toulouse, France
| | - Nicolas Destainville
- Laboratoire de Physique Théorique (IRSAMC), Université de Toulouse, CNRS, UPS, 31 062 Toulouse, France
| | - Manoel Manghi
- Laboratoire de Physique Théorique (IRSAMC), Université de Toulouse, CNRS, UPS, 31 062 Toulouse, France
| | - Catherine Tardin
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31 077 Toulouse, France
| |
Collapse
|
20
|
Wu N, Chen F, Zhao Y, Yu X, Wei J, Zhao Y. Functional and Biomimetic DNA Nanostructures on Lipid Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14721-14730. [PMID: 30044097 DOI: 10.1021/acs.langmuir.8b01818] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Sophisticated and dynamic membrane-anchored DNA nanostructures were developed to mimic a variety of membrane proteins, which play crucial roles in cellular functions. DNA biomimetic constructions bound on membranes are capable of modulating the morphologies, physical properties, and functions of lipid membranes, via mobility on membranes and/or inherent architectural features. This inspired young field of DNA-lipid-based nanobiomimetic systems is on the foundation of DNA nanotechnology. In this review, we highlight key successes in the development of structural DNA nanotechnology and demonstrate some typical static and dynamic complex DNA nanostructures first. Then, we discuss the biophysical properties of lipid membranes. Primary approaches are shown to attach hydrophilic DNA to hydrophobic lipid membranes. With appropriate designs, membrane-floating DNA nanostructures assemble and disassemble on membranes, modulated by external stimuluses. The aggregation of DNA nanostructures could influence the physical properties of lipid membranes. We also summarize artificial nanochannels made of DNA, analogous to transmembrane proteins. Transformations of DNA nanopores might be achieved under certain conditions and realize the transport of small molecules across membranes. Next, we focus on membrane-shaping functions of membrane-anchored DNA nanostructures. Curvature of the membrane is closely related to the rich diversity of cellular functions. Mimicking membrane-sculpting proteins, such as BAR family domains and SNARE proteins etc., DNA biomimetic nanostructures induce the transformations of lipid membranes and modulate membrane adhesion and membrane fusion processes. Although recent studies in DNA nanostructure-lipid membrane biomimetic nanosystems have made great progress, this field is still facing many challenges. In the future, the designs of more elaborated DNA architectures will be explored. Sophisticated dynamic DNA nanostructures inspired by natural membrane machines will be driven by the synergistic effect of multiple interactions, including hydrophobic force, electrostatic force, and ligand-receptor interactions by chemical modifications on bases, to expand their applications in vivo from model membrane to cell membrane to karyotheca.
Collapse
Affiliation(s)
- Na Wu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xi'an 710049 , People's Republic of China
| | - Feng Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xi'an 710049 , People's Republic of China
| | - Yue Zhao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xi'an 710049 , People's Republic of China
| | - Xu Yu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xi'an 710049 , People's Republic of China
| | - Jing Wei
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xi'an 710049 , People's Republic of China
| | - Yongxi Zhao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xi'an 710049 , People's Republic of China
| |
Collapse
|
21
|
Zhang Y, Ma W, Zhu Y, Shi S, Li Q, Mao C, Zhao D, Zhan Y, Shi J, Li W, Wang L, Fan C, Lin Y. Inhibiting Methicillin-Resistant Staphylococcus aureus by Tetrahedral DNA Nanostructure-Enabled Antisense Peptide Nucleic Acid Delivery. NANO LETTERS 2018; 18:5652-5659. [PMID: 30088771 DOI: 10.1021/acs.nanolett.8b02166] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
One of the biggest obstacles for the use of antisense oligonucleotides as antibacterial therapeutics is their limited uptake by bacterial cells without a suitable carrier, especially in multi-drug-resistant bacteria with a drug efflux mechanism. Existing vectors, such as cell-penetrating peptides, are inefficient and nontargeting, and accordingly are not ideal carriers. A noncytotoxic tetrahedral DNA nanostructure (TDN) with a controllable conformation has been developed as a delivery vehicle for antisense oligonucleotides. In this study, antisense peptide nucleic acids (asPNAs) targeting a specific gene ( ftsZ) were efficiently transported into methicillin-resistant Staphylococcus aureus cells by TDNs, and the expression of ftsZ was successfully inhibited in an asPNA-concentration-dependent manner. The delivery system specifically targeted the intended gene. This novel delivery system provides a better platform for future applications of antisense antibacterial therapeutics and provides a basis for the development of a new type of antibacterial drug for multi-drug-resistant bacterial infections.
Collapse
Affiliation(s)
- Yuxin Zhang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology , Sichuan University , Chengdu 610041 , P. R. China
| | - Wenjuan Ma
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology , Sichuan University , Chengdu 610041 , P. R. China
| | - Ying Zhu
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics , Chinese Academy of Sciences , Shanghai 201800 , P. R. China
| | - Sirong Shi
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology , Sichuan University , Chengdu 610041 , P. R. China
| | - Qianshun Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology , Sichuan University , Chengdu 610041 , P. R. China
| | - Chenchen Mao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology , Sichuan University , Chengdu 610041 , P. R. China
| | - Dan Zhao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology , Sichuan University , Chengdu 610041 , P. R. China
| | - Yuxi Zhan
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology , Sichuan University , Chengdu 610041 , P. R. China
| | - Jiye Shi
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics , Chinese Academy of Sciences , Shanghai 201800 , P. R. China
| | - Wei Li
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics , Chinese Academy of Sciences , Shanghai 201800 , P. R. China
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics , Chinese Academy of Sciences , Shanghai 201800 , P. R. China
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics , Chinese Academy of Sciences , Shanghai 201800 , P. R. China
| | - Yunfeng Lin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology , Sichuan University , Chengdu 610041 , P. R. China
| |
Collapse
|