1
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Xu H, Zheng Y, Xie J, Duan W, Yu L, Lin R, Li CC, Jia L. Imaging mRNA in vitro and in vivo with nanofirecracker probes via intramolecular hybridization chain reaction. Biosens Bioelectron 2024; 248:115973. [PMID: 38150797 DOI: 10.1016/j.bios.2023.115973] [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: 10/20/2023] [Revised: 12/06/2023] [Accepted: 12/24/2023] [Indexed: 12/29/2023]
Abstract
Hybridization chain reaction (HCR) based enzyme-free amplification techniques have recently been developed for the visualization of intracellular messenger RNA (mRNA). However, the slow kinetics and potential interference with the intricate biological environments hinder its application in the clinic and in vivo. Herein, we designed a nanofirecracker probe-based strategy using intramolecular hybridization chain reaction (IHCR) amplifier for rapid, efficient, sensitive, specific detection and imaging of survivin mRNA both in vitro and vivo. Two probes, HP1 and HP2, in IHCR were simultaneously incorporated into a DNA nanowire scaffolds to bring HP1 and HP2 to close proximity on the assembled nanowire scaffolds. Empowered by the DNA nanowire scaffolds and spatial confinement effect, the nanofirecracker probe-based IHCR sensing system exhibited improved biostability, accelerated reaction kinetics, and enhanced signal amplification. This new strategy has been successfully applied to imaging mRNA in both cultured cells and in mice. Importantly, this novel sensing method was capable of detecting survivin mRNA in clinical blood samples from subjects with colorectal cancer. Thus, this novel nanofirecracker probe-based IHCR strategy holds great potential in advancing both biomedical research and in molecular diagnostics.
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Affiliation(s)
- Huo Xu
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou, 350108, Fujian, China.
| | - Yanhui Zheng
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou, 350108, Fujian, China
| | - Jingjing Xie
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen, 361102, Fujian, China
| | - Wei Duan
- School of Medicine, Faculty of Health, Deakin University, Waurn Ponds, Victoria, 3216, Australia
| | - Lixue Yu
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen, 361102, Fujian, China
| | - Ruimiao Lin
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen, 361102, Fujian, China
| | - Chen-Chen Li
- Shandong Key Laboratory of Biochemical Analysis, Qingdao University of Science and Technology, Qingdao, Shangdong, 266042, China
| | - Lee Jia
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou, 350108, Fujian, China
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2
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Feng F, Xiao SJ. Structural Description of Chiral E-Tiling DNA Nanotubes with the Chiral Indices (n,m) and Handedness Defined by Microscopic Imaging. Chembiochem 2023; 24:e202300460. [PMID: 37675822 DOI: 10.1002/cbic.202300460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/22/2023] [Indexed: 09/08/2023]
Abstract
In structural DNA nanotechnology, E-tiling DNA nanotubes are evidenced to be homogeneous in diameter and thus have great potential in biomedical applications such as cellular transport and communication, transmembrane ion/molecule channeling, and drug delivery. However, a precise structural description of chiral DNA nanotubes with chiral parameters was lacking, thus greatly hindering their application breadth and depth, until we recently raised and partly solved this problem. In this perspective, we summarize recent progress in defining the chiral indices and handedness of E-tiling DNA nanotubes by microscopic imaging, especially atomic force microscopy (AFM) imaging. Such a detailed understanding of the chiral structures of E-tiling DNA nanotubes will be very helpful in the future, on the one hand for engineering DNA nanostructures precisely, and, on the other, for realizing specific physicochemical properties and biological functions successfully.
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Affiliation(s)
- Feiyang Feng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, P.R. China
| | - Shou-Jun Xiao
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, P.R. China
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3
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Luo X, Saliba D, Yang T, Gentile S, Mori K, Islas P, Das T, Bagheri N, Porchetta A, Guarne A, Cosa G, Sleiman HF. Minimalist Design of Wireframe DNA Nanotubes: Tunable Geometry, Size, Chirality, and Dynamics. Angew Chem Int Ed Engl 2023; 62:e202309869. [PMID: 37610293 DOI: 10.1002/anie.202309869] [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: 07/11/2023] [Revised: 08/07/2023] [Accepted: 08/18/2023] [Indexed: 08/24/2023]
Abstract
DNA nanotubes (NTs) have attracted extensive interest as artificial cytoskeletons for biomedical, synthetic biology, and materials applications. Here, we report the modular design and assembly of a minimalist yet robust DNA wireframe nanotube with tunable cross-sectional geometry, cavity size, chirality, and length, while using only four DNA strands. We introduce an h-motif structure incorporating double-crossover (DX) tile-like DNA edges to achieve structural rigidity and provide efficient self-assembly of h-motif-based DNA nanotube (H-NT) units, thus producing programmable, micrometer-long nanotubes. We demonstrate control of the H-NT nanotube length via short DNA modulators. Finally, we use an enzyme, RNase H, to take these structures out of equilibrium and trigger nanotube assembly at a physiologically relevant temperature, underlining future cellular applications. The minimalist H-NTs can assemble at near-physiological salt conditions and will serve as an easily synthesized, DNA-economical modular template for biosensors, plasmonics, or other functional materials and as cost-efficient drug-delivery vehicles for biomedical applications.
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Affiliation(s)
- Xin Luo
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal QC, H3A 0B8, Canada
| | - Daniel Saliba
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal QC, H3A 0B8, Canada
| | - Tianxiao Yang
- Department of Biochemistry and Centre de Recherche en Biologie Structurale, McGill University, Montreal QC, Canada
| | - Serena Gentile
- Department of Chemistry, University of Rome Tor Vergata, Rome, Italy
| | - Keita Mori
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal QC, H3A 0B8, Canada
| | - Patricia Islas
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal QC, H3A 0B8, Canada
| | - Trishalina Das
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal QC, H3A 0B8, Canada
| | - Neda Bagheri
- Department of Chemistry, University of Rome Tor Vergata, Rome, Italy
| | | | - Alba Guarne
- Department of Biochemistry and Centre de Recherche en Biologie Structurale, McGill University, Montreal QC, Canada
| | - Gonzalo Cosa
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal QC, H3A 0B8, Canada
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal QC, H3A 0B8, Canada
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4
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Torkan E, Salmani-Tehrani M. Conformational dynamics and mechanical properties of biomimetic RNA, DNA, and RNA-DNA hybrid nanotubes: an atomistic molecular dynamics study. Phys Chem Chem Phys 2023. [PMID: 37309220 DOI: 10.1039/d3cp01028g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
With the nanotechnology boom, artificially designed nucleic acid nanotubes have aroused interest due to their practical applications in nanorobotics, vaccine design, membrane channels, drug delivery, and force sensing. In this paper, computational study was performed to investigate the structural dynamics and mechanical properties of RNA nanotubes (RNTs), DNA nanotubes (DNTs), and RNA-DNA hybrid nanotubes (RDHNTs). So far, the structural and mechanical properties of RDHNTs have not been examined in experiments or theoretical calculations, and there is limited knowledge regarding these properties for RNTs. Here, the simulations were carried out using the equilibrium molecular dynamics (MD) and steered molecular dynamics (SMD) approaches. Using in-house scripting, we modeled hexagonal nanotubes composed of six double-stranded molecules connected by four-way Holliday junctions. Classical MD analyses were performed on the collected trajectory data to investigate structural properties. Analyses of the microscopic structural parameters of RDHNT indicated a structural transition from the A-form to a conformation between the A- and B-forms, which may be attributable to the increased rigidity of RNA scaffolds compared to DNA staples. Comprehensive research on the elastic mechanical properties was also conducted based on spontaneous thermal fluctuations of nanotubes and employing the equipartition theorem. The Young's modulus of RDHNT (E = 165 MPa) and RNT (E = 144 MPa) was found to be almost the same and nearly half of that found for DNT (E = 325 MPa). Furthermore, the results showed that RNT was more resistant to bending, torsional, and volumetric deformations than DNT and RDHNT. We also used non-equilibrium SMD simulations to acquire comprehensive knowledge of the mechanical response of nanotubes to tensile stress.
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Affiliation(s)
- Ehsan Torkan
- Department of Mechanical Engineering, Isfahan University of Technology, Isfahan, 84156-83111, Iran.
| | - Mehdi Salmani-Tehrani
- Department of Mechanical Engineering, Isfahan University of Technology, Isfahan, 84156-83111, Iran.
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5
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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.
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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
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6
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Saliba D, Luo X, Rizzuto FJ, Sleiman HF. Programming rigidity into size-defined wireframe DNA nanotubes. NANOSCALE 2023; 15:5403-5413. [PMID: 36826342 DOI: 10.1039/d2nr06185f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Nanotubes built from DNA hold promise for several biological and materials applications, due to their high aspect ratio and encapsulation potential. A particularly appealing goal is to control the size, shape, and dynamic behaviour of DNA nanotubes with minimal design alteration, as nanostructures of varying morphologies and lengths have been shown to exhibit distinct cellular uptake, encapsulation behaviour, and in vivo biodistribution. Herein, we report a systematic investigation, combining experimental and computational design, to modulate the length, flexibility, and longitudinal patterns of wireframe DNA nanotubes. Subtle design changes govern the structure and properties of our nanotubes, which are built from a custom-made, long, and size-defined template strand to which DNA rungs and linkers are attached. Unlike DNA origami, these custom-made strands possess regions with repeating sequences at strategic locations, thereby reducing the number of strands necessary for assembly. Through strand displacement, the nanotubes can be reversibly altered between extended and collapsed morphologies. These design concepts enable fine-tuning of the nanotube stiffness and may pave the way for the development of designer nanotubes for a variety of applications, including the study of cellular internalization, biodistribution, and uptake mechanisms for structures of varied shapes and sizes.
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Affiliation(s)
- Daniel Saliba
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC, H3A 0B8, Canada.
| | - Xin Luo
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC, H3A 0B8, Canada.
| | - Felix J Rizzuto
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC, H3A 0B8, Canada.
- School of Chemistry, University of New South Wales, Sydney, 2052, Australia
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC, H3A 0B8, Canada.
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7
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Wang X, Jun H, Bathe M. Programming 2D Supramolecular Assemblies with Wireframe DNA Origami. J Am Chem Soc 2022; 144:4403-4409. [PMID: 35230115 DOI: 10.1021/jacs.1c11332] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Wireframe DNA origami offers the ability to program nearly arbitrary 2D and 3D nanoscale geometries, with six-helix bundle (6HB) edge designs providing both geometric versatility and fidelity with respect to the target origami shape. Because individual DNA origami objects are limited in size by the length of the DNA scaffold, here, we introduce a hierarchical self-assembly strategy to overcome this limitation by programming supramolecular assemblies and periodic arrays using wireframe DNA origami objects as building blocks. Parallel half-crossovers are used together with lateral cohesive interactions between staples and the scaffold to introduce symmetry into supramolecular assemblies constructed from single DNA origami units that cannot be self-assembled directly using base-stacking or conventional antiparallel crossover designs. This hierarchical design approach can be applied readily to 2D wireframe DNA origami designed using the top-down sequence design strategy METIS without any prerequisites on scaffold and staple routing. We demonstrate the utility of our strategy by fabricating dimers and self-limiting hexameric superstructures using both triangular and hexagonal wireframe origami building blocks. We generalize our self-assembly approach to fabricate close-packed and non-close-packed periodic 2D arrays. Visualization using atomic force microscopy and transmission electron microscopy demonstrates that superstructures exhibit similar structural integrity to that of the individual origami building blocks designed using METIS. Our results offer a general platform for the design and fabrication of 2D materials for a variety of applications.
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Affiliation(s)
- Xiao Wang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Hyungmin Jun
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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8
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Gao D, Ma N, Yan X, Ji M, Zhu JJ, Min Q, Tian Y. Low-entropy lattices engineered through bridged DNA origami frames. Chem Sci 2021; 13:283-289. [PMID: 35059178 PMCID: PMC8694312 DOI: 10.1039/d1sc05060e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/30/2021] [Indexed: 11/21/2022] Open
Abstract
The transformation from disorder to order in self-assembly is an autonomous entropy-decreasing process. The spatial organization of nanoscale anisotropic building blocks involves the intrinsic heterogeneity in three dimensions and requires sufficiently precise control to coordinate intricate interactions. Only a few approaches have been shown to achieve the anisotropic extension from components to assemblies. Here, we demonstrate the ability to engineer three-dimensional low-entropy lattices at the nucleotide level from modular DNA origami frames. Through the programmable DNA bridging strategy, DNA domains of the same composition are periodically arranged in the crystal growth directions. We combine the site-specific positioning of guest nanoparticles to reflect the anisotropy control, which is validated by small-angle X-ray scattering and electron microscopy. We expect that our DNA origami-mediated crystallization method will facilitate both the exploration of refined self-assembly platforms and the creation of anisotropic metamaterials. Through the bridging principle, DNA origami building blocks are integrated into ordered self-assembled structures. Periodically arranged DNA domains can locate the nanoparticles in a uniform site to achieve precise control of the contents.![]()
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Affiliation(s)
- Di Gao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, College of Engineering and Applied Sciences, Nanjing University Nanjing 210023 China
| | - Ningning Ma
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, College of Engineering and Applied Sciences, Nanjing University Nanjing 210023 China
| | - Xuehui Yan
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, College of Engineering and Applied Sciences, Nanjing University Nanjing 210023 China
| | - Min Ji
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, College of Engineering and Applied Sciences, Nanjing University Nanjing 210023 China
| | - Jun-Jie Zhu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, College of Engineering and Applied Sciences, Nanjing University Nanjing 210023 China
| | - Qianhao Min
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, College of Engineering and Applied Sciences, Nanjing University Nanjing 210023 China
| | - Ye Tian
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, College of Engineering and Applied Sciences, Nanjing University Nanjing 210023 China .,Shenzhen Research Institute of Nanjing University Shenzhen 518000 China
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9
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Shen L, Wang P, Ke Y. DNA Nanotechnology-Based Biosensors and Therapeutics. Adv Healthc Mater 2021; 10:e2002205. [PMID: 34085411 DOI: 10.1002/adhm.202002205] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/19/2021] [Indexed: 12/19/2022]
Abstract
Over the past few decades, DNA nanotechnology engenders a vast variety of programmable nanostructures utilizing Watson-Crick base pairing. Due to their precise engineering, unprecedented programmability, and intrinsic biocompatibility, DNA nanostructures cannot only interact with small molecules, nucleic acids, proteins, viruses, and cancer cells, but also can serve as nanocarriers to deliver different therapeutic agents. Such addressability innate to DNA nanostructures enables their use in various fields of biomedical applications such as biosensors and cancer therapy. This review is begun with a brief introduction of the development of DNA nanotechnology, followed by a summary of recent applications of DNA nanostructures in biosensors and therapeutics. Finally, challenges and opportunities for practical applications of DNA nanotechnology are discussed.
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Affiliation(s)
- Luyao Shen
- Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University Atlanta GA 30322 USA
- Institute of Molecular Medicine Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Pengfei Wang
- Institute of Molecular Medicine Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University Atlanta GA 30322 USA
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10
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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.
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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.
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11
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Wu JT, Liu R, Chen YR, Zheng XQ, Wu ZS. The hierarchical assembly of a multi-level DNA ring-based nanostructure in a precise order and its application for screening tumor cells. Biomater Sci 2021; 9:2262-2270. [PMID: 33533777 DOI: 10.1039/d0bm00085j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA nanotechnology can be used to precisely construct nanostructures of different shapes, sizes and surface chemistry, which is appreciated in a variety of areas such as biomaterials, nanodevices, disease diagnosis, imaging, and drug delivery. Enzymatic degradation resistance and cell-targeting capability are indispensable for the applications of DNA nanostructures in biological and biomedical fields, and is challenging to rationally design the desirable nanoscale DNA materials suitable for the clinical translation by the existing assembly methodologies. Herein, we present a simple and efficient method for the hierarchical assembly of a three-level DNA ring-based nanostructure (DNA h-Nanoring) in a precise order, where DNA compositions at the primary level, the second level and the third level are a single DNA ring, two-ring-hybridized duplex and uniform complex macro-cycle, respectively. Most as-assembled DNA h-Nanorings exhibit the regular two-dimensional cycle-shaped structure characterized by atomic force microscopy (AFM). The Nanoring exhibits a significantly enhanced resistance to enzymatic attack, such that it can remain intact in 10% fetal bovine serum (FBS) for 24 h, and even stably exist in the presence of nuclease at a high concentration. More importantly, it is very easy to modify the DNA h-Nanoring with functional moieties (e.g., targeting ligand aptamer) because there are many single-stranded fragments available for further hybridization. By combining with receptor-targeted Sgc8, the nanoring can be used to accomplish the cell imaging and criminate target CEM cells from control cells, demonstrating a potential platform for in vivo tumor imaging and targeted chemotherapeutics delivery.
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Affiliation(s)
- Jing-Ting Wu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China.
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12
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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.
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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.
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13
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Mogheiseh M, Hasanzadeh Ghasemi R, Soheilifard R. The effect of crossovers on the stability of DNA origami type nanocarriers. ACTA ACUST UNITED AC 2020. [DOI: 10.1108/mmms-05-2020-0094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
PurposeThe purpose of this paper is to compare the stability of the three nanocarriers created by DNA origami method with different positions and numbers of crossoversDesign/methodology/approachNanocarriers are attractive components among a variety of nanostructures created by DNA origami and can have numerous applications in mechanical and medical engineering. For this reason, the current study compares three nanotubes with different positions and numbers of crossovers created by DNA origami method that can be utilized as nanocarriers. To investigate the structures, the DNA nanocarriers are studied at the human body temperature 310 K. Molecular dynamics simulations are used for this study. For a quantitative analysis of DNA nanocarriers, the areas of three hexagons at three different sites in each of the nanotubes are investigated. The results indicate that the number and position of crossovers are among the significant factors in the structure stability of nanocarriers. The analyses also revealed that although adding crossovers in locations with fewer crossovers increase structural stability, the position of crossovers can have different effects on the stability. DNA origami-based nanocarriers can be implemented in drug delivery, allow the nanocargoes to pass various surfaces and act as filters for passing cargoes of different dimensions and chemical structures.FindingsThe results indicate that the number and position of crossovers are among the significant factors in the structure stability of nanocarriersOriginality/valueIn this paper, the stability of DNA origami nanocarriers with different positions and numbers of crossovers was investigated.
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14
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Badu S, Melnik R, Singh S. Mathematical and computational models of RNA nanoclusters and their applications in data-driven environments. MOLECULAR SIMULATION 2020. [DOI: 10.1080/08927022.2020.1804564] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Shyam Badu
- MS2Discovery Interdisciplinary Research Institute, Wilfrid Laurier University, Waterloo, Ontario, Canada
| | - Roderick Melnik
- MS2Discovery Interdisciplinary Research Institute, Wilfrid Laurier University, Waterloo, Ontario, Canada
- BCAM-Basque Center for Applied Mathematics, Bilbao, Spain
| | - Sundeep Singh
- MS2Discovery Interdisciplinary Research Institute, Wilfrid Laurier University, Waterloo, Ontario, Canada
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15
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Ouyang X, Wang M, Guo L, Cui C, Liu T, Ren Y, Zhao Y, Ge Z, Guo X, Xie G, Li J, Fan C, Wang L. DNA Nanoribbon-Templated Self-Assembly of Ultrasmall Fluorescent Copper Nanoclusters with Enhanced Luminescence. Angew Chem Int Ed Engl 2020; 59:11836-11844. [PMID: 32267600 DOI: 10.1002/anie.202003905] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Indexed: 01/23/2023]
Abstract
Fluorescent copper nanoclusters (CuNCs) have been widely used in chemical sensors, biological imaging, and light-emitting devices. However, individual fluorescent CuNCs have limitations in their capabilities arising from poor photostability and weak emission intensities. As one kind of aggregation-induced emission luminogen (AIEgen), the formation of aggregates with high compactness and good order can efficiently improve the emission intensity, stability, and tunability of CuNCs. Here, DNA nanoribbons, containing multiple specific binding sites, serve as a template for in situ synthesis and assembly of ultrasmall CuNCs (0.6 nm). These CuNC self-assemblies exhibit enhanced luminescence and excellent fluorescence stability because of tight and ordered arrangement through DNA nanoribbons templating. Furthermore, the stable and bright CuNC assemblies are demonstrated in the high-sensitivity detection and intracellular fluorescence imaging of biothiols.
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Affiliation(s)
- Xiangyuan Ouyang
- Key Laboratory of Synthetic and Natural Functional Molecule of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, Shaanxi, 710127, P. R. China
| | - Meifang Wang
- Key Laboratory of Synthetic and Natural Functional Molecule of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, Shaanxi, 710127, P. R. China
| | - Linjie Guo
- Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China.,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
| | - Chengjun Cui
- Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China.,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
| | - Ting Liu
- Key Laboratory of Synthetic and Natural Functional Molecule of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, Shaanxi, 710127, P. R. China
| | - Yongan Ren
- Key Laboratory of Synthetic and Natural Functional Molecule of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, Shaanxi, 710127, P. R. China
| | - Yan Zhao
- Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China.,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
| | - Zhilei Ge
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Xiniu Guo
- Instrumental Analysis Center, Shanghai Jiao Tong University, Shanghai, China
| | - Gang Xie
- Key Laboratory of Synthetic and Natural Functional Molecule of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, Shaanxi, 710127, P. R. China
| | - Jiang Li
- Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China.,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
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Lihua Wang
- Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China.,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
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16
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Ouyang X, Wang M, Guo L, Cui C, Liu T, Ren Y, Zhao Y, Ge Z, Guo X, Xie G, Li J, Fan C, Wang L. DNA Nanoribbon‐Templated Self‐Assembly of Ultrasmall Fluorescent Copper Nanoclusters with Enhanced Luminescence. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003905] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Xiangyuan Ouyang
- Key Laboratory of Synthetic and Natural Functional Molecule of Ministry of Education College of Chemistry & Materials Science Northwest University Xi'an Shaanxi 710127 P. R. China
| | - Meifang Wang
- Key Laboratory of Synthetic and Natural Functional Molecule of Ministry of Education College of Chemistry & Materials Science Northwest University Xi'an Shaanxi 710127 P. R. China
| | - Linjie Guo
- Shanghai Synchrotron Radiation Facility Zhangjiang Laboratory Shanghai Advanced Research Institute Chinese Academy of Sciences Shanghai 201210 China
- 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
| | - Chengjun Cui
- Shanghai Synchrotron Radiation Facility Zhangjiang Laboratory Shanghai Advanced Research Institute Chinese Academy of Sciences Shanghai 201210 China
- 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
| | - Ting Liu
- Key Laboratory of Synthetic and Natural Functional Molecule of Ministry of Education College of Chemistry & Materials Science Northwest University Xi'an Shaanxi 710127 P. R. China
| | - Yongan Ren
- Key Laboratory of Synthetic and Natural Functional Molecule of Ministry of Education College of Chemistry & Materials Science Northwest University Xi'an Shaanxi 710127 P. R. China
| | - Yan Zhao
- Shanghai Synchrotron Radiation Facility Zhangjiang Laboratory Shanghai Advanced Research Institute Chinese Academy of Sciences Shanghai 201210 China
- 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
| | - Zhilei Ge
- School of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai 200127 China
| | - Xiniu Guo
- Instrumental Analysis Center Shanghai Jiao Tong University Shanghai China
| | - Gang Xie
- Key Laboratory of Synthetic and Natural Functional Molecule of Ministry of Education College of Chemistry & Materials Science Northwest University Xi'an Shaanxi 710127 P. R. China
| | - Jiang Li
- Shanghai Synchrotron Radiation Facility Zhangjiang Laboratory Shanghai Advanced Research Institute Chinese Academy of Sciences Shanghai 201210 China
- 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
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai 200127 China
| | - Lihua Wang
- Shanghai Synchrotron Radiation Facility Zhangjiang Laboratory Shanghai Advanced Research Institute Chinese Academy of Sciences Shanghai 201210 China
- 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
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17
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Ma N, Minevich B, Liu J, Ji M, Tian Y, Gang O. Directional Assembly of Nanoparticles by DNA Shapes: Towards Designed Architectures and Functionality. Top Curr Chem (Cham) 2020; 378:36. [DOI: 10.1007/s41061-020-0301-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 03/11/2020] [Indexed: 10/24/2022]
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19
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Abstract
Nucleic acids hold great promise for bottom-up construction of nanostructures via programmable self-assembly. Especially, the emerging of advanced sequence design principles and the maturation of chemical synthesis of nucleic acids together have led to the rapid development of structural DNA/RNA nanotechnology. Diverse nucleic acids-based nano objects and patterns have been constructed with near-atomic resolutions and with controllable sizes and geometries. The monodispersed distribution of objects, the up-to-submillimeter scalability of patterns, and the excellent feasibility of carrying other materials with spatial and temporal resolutions have made DNA/RNA assemblies extremely unique in molecular engineering. In this review, we summarize recent advances in nucleic acids-based (mainly DNA-based) near-atomic fabrication by focusing on state-of-the-art design techniques, toolkits for DNA/RNA nanoengineering, and related applications in a range of areas.
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Affiliation(s)
- Kai Xia
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences , Fudan University , Shanghai 200032 , China
| | - Jianlei Shen
- School of Chemistry and Chemical Engineering , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Qian Li
- School of Chemistry and Chemical Engineering , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Hongzhou Gu
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences , Fudan University , Shanghai 200032 , China
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20
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Zhang Y, Chen X, Kang G, Peng R, Pan V, Sundaresan R, Wang P, Ke Y. Programming DNA Tube Circumference by Tile Offset Connection. J Am Chem Soc 2019; 141:19529-19532. [PMID: 31793775 DOI: 10.1021/jacs.9b08921] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
DNA tubes with prescribed circumferences are appealing for numerous multidisciplinary applications. The DNA single-stranded tiles (SSTs) assembly method has demonstrated an unprecedented capability for programming the circumferences of DNA tubes in a modular fashion. Nevertheless, a distinct set of SSTs is typically required to assemble DNA tube of a specific circumference, with wider tubes requiring higher numbers of tiles of unique sequences, which not only increases the expense and design complexity but also hampers the assembly yield. Herein, we introduce "offset connection" to circumvent such challenges in conventional SST tube assembly. In this new connection scheme, the boundary SST tiles in an SST array are designed to connect in an offset manner. To compensate for the offset, the SST array has to grow wider until the array can close to form a wide tube with a tolerable degree of twist. Using this strategy, we have successfully assembled DNA tubes with prescribed circumferences consisting of 8, 12, 14, 16, 20, 24, 28, 32, 36, 42, 56, or 70 helices from two distinct sets of SSTs composed of 19×4 or 19×14 tiles.
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Affiliation(s)
- Yingwei Zhang
- State Key Laboratory of Chemical Resource Engineering, College of Materials Science and Engineering , Beijing University of Chemical Technology , Beijing 100082 , China
| | - Xianhui Chen
- State Key Laboratory of Chemical Resource Engineering, College of Materials Science and Engineering , Beijing University of Chemical Technology , Beijing 100082 , China
| | - Guangjie Kang
- State Key Laboratory of Chemical Resource Engineering, College of Materials Science and Engineering , Beijing University of Chemical Technology , Beijing 100082 , China
| | - Ruizi Peng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province , Hunan University , Changsha , Hunan 410082 , China.,Wallace H. Coulter Department of Biomedical Engineering , Georgia Institute of Technology and Emory University , Atlanta , Georgia 30322 , United States
| | - Victor Pan
- Wallace H. Coulter Department of Biomedical Engineering , Georgia Institute of Technology and Emory University , Atlanta , Georgia 30322 , United States
| | - Ranjani Sundaresan
- Wallace H. Coulter Department of Biomedical Engineering , Georgia Institute of Technology and Emory University , Atlanta , Georgia 30322 , United States
| | - Pengfei Wang
- Institute of Molecular Medicine, Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai 200127 , China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering , Georgia Institute of Technology and Emory University , Atlanta , Georgia 30322 , United States.,Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
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21
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Naskar S, Joshi H, Chakraborty B, Seeman NC, Maiti PK. Atomic structures of RNA nanotubes and their comparison with DNA nanotubes. NANOSCALE 2019; 11:14863-14878. [PMID: 31355845 DOI: 10.1039/c9nr00786e] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We present a computational framework to model RNA based nanostructures and study their microscopic structures. We model hexagonal nanotubes made of 6 dsRNA (RNTs) connected by double crossover (DX) at different positions. Using several hundred nano-second (ns) long all-atom molecular dynamics simulations, we study the atomic structure, conformational change and elastic properties of RNTs in the presence of explicit water and ions. Based on several structural quantities such as root mean square deviation (RMSD) and root mean square fluctuation (RMSF), we find that the RNTs are almost as stable as DNA nanotubes (DNTs). Although the central portion of the RNTs maintain its cylindrical shape, both the terminal regions open up to give rise to a gating like behavior which can play a crucial role in drug delivery. From the bending angle distribution, we observe that the RNTs are more flexible than DNTs. The calculated persistence length of the RNTs is in the micron range which is an order of magnitude higher than that of a single dsRNA. The stretch modulus of the RNTs from the contour length distribution is in the range of 4-7 nN depending on the sequence. The calculated persistence length and stretch modulus are in the same range of values as in the case of DNTs. To understand the structural properties of RNTs at the individual base-pair level we have also calculated all the helicoidal parameters and analyzed the relative flexibility and rigidity of RNTs having a different sequence. These findings emphasized the fascinating properties of RNTs which will expedite further theoretical and experimental studies in this field.
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Affiliation(s)
- Supriyo Naskar
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
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22
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Han S, Liu W, Yang S, Wang R. Facile and Label-Free Electrochemical Biosensors for MicroRNA Detection Based on DNA Origami Nanostructures. ACS OMEGA 2019; 4:11025-11031. [PMID: 31460200 PMCID: PMC6649092 DOI: 10.1021/acsomega.9b01166] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 06/13/2019] [Indexed: 05/25/2023]
Abstract
MicroRNAs (miRNAs) have emerged as the promising molecular biomarkers for early diagnosis and enhanced understanding of the molecular pathogenesis of cancers as well as certain diseases. Here, a facile, label-free, and amplification-free electrochemical biosensor was developed to detect miRNA by using DNA origami nanostructure-supported DNA probes, with methylene blue (MB) serving as the hybridization redox indicator, for the first time. Specifically, the use of cross-shaped DNA origami nanostructures containing multiple single-stranded DNA probes at preselected locations on each DNA nanostructure could increase the accessibility and the recognition efficiency of the probes (due to the rational controlled density of DNA probes). The successful immobilization of DNA origami probes and their hybridization with targeted miRNA-21 molecules was confirmed by electrochemical impedance spectroscopy and cyclic voltammetry methods. A differential pulse voltammetry technique was employed to record the oxidation peak current of MB before and after target hybridization. The linear detection range of this biosensor was from 0.1 pM to 10.0 nM, with a lower detection limit of 79.8 fM. The selectivity of the miRNA biosensor was also studied by observing the discrimination ability of single-base mismatched sequences. Because of the larger surface area and unprecedented customizability of DNA origami nanostructures, this strategy demonstrated great potential for sensitive, selective, and label-free determination of miRNA for translational biomedical research and clinical applications.
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Affiliation(s)
- Shuo Han
- Department
of Chemistry and Center for Research in Energy and Environment, Missouri University of Science and Technology, Rolla, Missouri 65409, United States
| | - Wenyan Liu
- Department
of Chemistry and Center for Research in Energy and Environment, Missouri University of Science and Technology, Rolla, Missouri 65409, United States
| | - Shuo Yang
- Department
of Chemistry and Center for Research in Energy and Environment, Missouri University of Science and Technology, Rolla, Missouri 65409, United States
| | - Risheng Wang
- Department
of Chemistry and Center for Research in Energy and Environment, Missouri University of Science and Technology, Rolla, Missouri 65409, United States
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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
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24
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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.
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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
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Bayrak T, Jagtap NS, Erbe A. Review of the Electrical Characterization of Metallic Nanowires on DNA Templates. Int J Mol Sci 2018; 19:E3019. [PMID: 30282940 PMCID: PMC6213931 DOI: 10.3390/ijms19103019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 09/24/2018] [Accepted: 09/26/2018] [Indexed: 01/29/2023] Open
Abstract
The use of self-assembly techniques may open new possibilities in scaling down electronic circuits to their ultimate limits. Deoxyribonucleic acid (DNA) nanotechnology has already demonstrated that it can provide valuable tools for the creation of nanostructures of arbitrary shape, therefore presenting an ideal platform for the development of nanoelectronic circuits. So far, however, the electronic properties of DNA nanostructures are mostly insulating, thus limiting the use of the nanostructures in electronic circuits. Therefore, methods have been investigated that use the DNA nanostructures as templates for the deposition of electrically conducting materials along the DNA strands. The most simple such structure is given by metallic nanowires formed by deposition of metals along the DNA nanostructures. Here, we review the fabrication and the characterization of the electronic properties of nanowires, which were created using these methods.
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Affiliation(s)
- Türkan Bayrak
- Institute of Ion Beam Physics and Materials Research, Helmholtz-Zentrum Dresden-Rossendorf, 01328 Dresden, Germany.
- Cluster of Excellence Center for Advancing Electronics Dresden (cfaed), TU Dresden, 01062 Dresden, Germany.
| | - Nagesh S Jagtap
- Institute of Ion Beam Physics and Materials Research, Helmholtz-Zentrum Dresden-Rossendorf, 01328 Dresden, Germany.
| | - Artur Erbe
- Institute of Ion Beam Physics and Materials Research, Helmholtz-Zentrum Dresden-Rossendorf, 01328 Dresden, Germany.
- Cluster of Excellence Center for Advancing Electronics Dresden (cfaed), TU Dresden, 01062 Dresden, Germany.
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Hu Q, Wang S, Wang L, Gu H, Fan C. DNA Nanostructure-Based Systems for Intelligent Delivery of Therapeutic Oligonucleotides. Adv Healthc Mater 2018; 7:e1701153. [PMID: 29356400 DOI: 10.1002/adhm.201701153] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 11/27/2017] [Indexed: 12/15/2022]
Abstract
In the beginning of the 21st century, therapeutic oligonucleotides have shown great potential for the treatment of many life-threatening diseases. However, effective delivery of therapeutic oligonucleotides to the targeted location in vivo remains a major issue. As an emerging field, DNA nanotechnology is applied in many aspects including bioimaging, biosensing, and drug delivery. With sequence programming and optimization, a series of DNA nanostructures can be precisely engineered with defined size, shape, surface chemistry, and function. Simply with hybridization, therapeutic oligonucleotides including unmethylated cytosine-phosphate-guanine dinucleotide oligos, small interfering RNA (siRNA) or antisense RNA, single guide RNA of the regularly interspaced short palindromic repeat-Cas9 system, and aptamers, are successfully loaded on DNA nanostructures for delivery. In this progress report, the development history of DNA nanotechnology is first introduced, and then the mechanisms and means for cellular uptake of DNA nanostructures are discussed. Next, current approaches to deliver therapeutic oligonucleotides with DNA nanovehicles are summarized. In the end, the challenges and opportunities for DNA nanostructure-based systems for the delivery of therapeutic oligonucleotides are discussed.
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Affiliation(s)
- Qinqin Hu
- Fudan University Shanghai Cancer Center, and Institutes of Biomedical Sciences; Shanghai Medical College of Fudan University; Fudan University; Shanghai 200032 China
| | - Sheng Wang
- Fudan University Shanghai Cancer Center, and Institutes of Biomedical Sciences; Shanghai Medical College of Fudan University; Fudan University; Shanghai 200032 China
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center; Shanghai Synchrotron Radiation Facility Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
| | - Hongzhou Gu
- Fudan University Shanghai Cancer Center, and Institutes of Biomedical Sciences; Shanghai Medical College of Fudan University; Fudan University; Shanghai 200032 China
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center; Shanghai Synchrotron Radiation Facility Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
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27
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Ren YA, Gao H, Ouyang X. Advances in DNA Origami Nanopores: Fabrication, Characterization and Applications. CHINESE J CHEM 2018. [DOI: 10.1002/cjoc.201800173] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Yong-An Ren
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education of China, Key Laboratory of Modern Separation Science in Shaanxi Province, College of Chemistry & Material Science; Northwest University; Xi'an Shaanxi 710127 China
| | - Han Gao
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education of China, Key Laboratory of Modern Separation Science in Shaanxi Province, College of Chemistry & Material Science; Northwest University; Xi'an Shaanxi 710127 China
| | - Xiangyuan Ouyang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education of China, Key Laboratory of Modern Separation Science in Shaanxi Province, College of Chemistry & Material Science; Northwest University; Xi'an Shaanxi 710127 China
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28
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Zhang Y, Tu J, Wang D, Zhu H, Maity SK, Qu X, Bogaert B, Pei H, Zhang H. Programmable and Multifunctional DNA-Based Materials for Biomedical Applications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1703658. [PMID: 29389041 DOI: 10.1002/adma.201703658] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 09/09/2017] [Indexed: 06/07/2023]
Abstract
DNA encodes the genetic information; recently, it has also become a key player in material science. Given the specific Watson-Crick base-pairing interactions between only four types of nucleotides, well-designed DNA self-assembly can be programmable and predictable. Stem-loops, sticky ends, Holliday junctions, DNA tiles, and lattices are typical motifs for forming DNA-based structures. The oligonucleotides experience thermal annealing in a near-neutral buffer containing a divalent cation (usually Mg2+ ) to produce a variety of DNA nanostructures. These structures not only show beautiful landscape, but can also be endowed with multifaceted functionalities. This Review begins with the fundamental characterization and evolutionary trajectory of DNA-based artificial structures, but concentrates on their biomedical applications. The coverage spans from controlled drug delivery to high therapeutic profile and accurate diagnosis. A variety of DNA-based materials, including aptamers, hydrogels, origamis, and tetrahedrons, are widely utilized in different biomedical fields. In addition, to achieve better performance and functionality, material hybridization is widely witnessed, and DNA nanostructure modification is also discussed. Although there are impressive advances and high expectations, the development of DNA-based structures/technologies is still hindered by several commonly recognized challenges, such as nuclease instability, lack of pharmacokinetics data, and relatively high synthesis cost.
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Affiliation(s)
- Yuezhou Zhang
- Department of Pharmaceutical Science Laboratory, Åbo Akademi University, 20520, Turku, Finland
| | - Jing Tu
- Department of Pharmaceutical Science Laboratory, Åbo Akademi University, 20520, Turku, Finland
| | - Dongqing Wang
- Department of Radiology, Affiliated Hospital of Jiangsu University Jiangsu University, 212001, Zhenjiang, P. R. China
| | - Haitao Zhu
- Department of Radiology, Affiliated Hospital of Jiangsu University Jiangsu University, 212001, Zhenjiang, P. R. China
| | | | - Xiangmeng Qu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 200241, Shanghai, P. R. China
| | - Bram Bogaert
- Department of Pharmaceutical Science Laboratory, Åbo Akademi University, 20520, Turku, Finland
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 200241, Shanghai, P. R. China
| | - Hongbo Zhang
- Department of Pharmaceutical Science Laboratory, Åbo Akademi University, 20520, Turku, Finland
- Department of Radiology, Affiliated Hospital of Jiangsu University Jiangsu University, 212001, Zhenjiang, P. R. China
- Turku Center for Biotechnology, Åbo Akademi University, 20520, Turku, Finland
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29
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Pfeifer W, Saccà B. Synthetic DNA filaments: from design to applications. Biol Chem 2018; 399:773-785. [DOI: 10.1515/hsz-2018-0110] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 03/25/2018] [Indexed: 01/06/2023]
Abstract
Abstract
Natural filaments, such as microtubules and actin filaments, are fundamental components of the cell. Despite their relatively simple linear structure, filaments play a number of crucial roles in living organisms, from scaffolding to cellular adhesion and motility. The mechanical properties of natural filaments mostly rely on the structural features of the component units and on the way they are connected together, thus providing an ideal molecular model for emulation purposes. In this review, we describe the progresses done in this field using DNA for the rational design of synthetic filamentous-like materials with tailored structural and physical characteristics. We firstly survey the strategies that have been adopted until now for the construction of individual DNA building components and their programmable self-assembly into linear oligomeric structures. We then describe the theoretical models of polymer elasticity applied to calculate the bending strength of DNA filaments, expressed in terms of persistence length. Finally, we report some of the most exciting examples of truly biomimetic DNA filaments, which are capable of mimicking not only the sophisticated structural features of their natural counterparts but also their responsiveness to external stimuli, thus resulting in active motion and growing networks between distant loci.
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Affiliation(s)
- Wolfgang Pfeifer
- Centre for Medical Biotechnology (ZMB) and Centre for Nano Integration Duisburg-Essen (CENIDE) , University of Duisburg-Essen, Universitätstraße 2 , D-45117 Essen , Germany
| | - Barbara Saccà
- Centre for Medical Biotechnology (ZMB) and Centre for Nano Integration Duisburg-Essen (CENIDE) , University of Duisburg-Essen, Universitätstraße 2 , D-45117 Essen , Germany
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30
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Joshi H, Maiti PK. Structure and electrical properties of DNA nanotubes embedded in lipid bilayer membranes. Nucleic Acids Res 2018; 46:2234-2242. [PMID: 29136243 PMCID: PMC5861442 DOI: 10.1093/nar/gkx1078] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 09/25/2017] [Accepted: 11/03/2017] [Indexed: 01/18/2023] Open
Abstract
Engineering the synthetic nanopores through lipid bilayer membrane to access the interior of a cell is a long persisting challenge in biotechnology. Here, we demonstrate the stability and dynamics of a tile-based 6-helix DNA nanotube (DNT) embedded in POPC lipid bilayer using the analysis of 0.2 μs long equilibrium MD simulation trajectories. We observe that the head groups of the lipid molecules close to the lumen cooperatively tilt towards the hydrophilic sugar-phosphate backbone of DNA and form a toroidal structure around the patch of DNT protruding in the membrane. Further, we explore the effect of ionic concentrations to the in-solution structure and stability of the lipid-DNT complex. Transmembrane ionic current measurements for the constant electric field MD simulation provide the I-V characteristics of the water filled DNT lumen in lipid membrane. With increasing salt concentrations, the measured values of transmembrane ionic conductance of the porous DNT lumen vary from 4.3 to 20.6 nS. Simulations of the DNTs with ssDNA and dsDNA overhangs at the mouth of the pore show gating effect with remarkable difference in the transmembrane ionic conductivities for open and close state nanopores.
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Affiliation(s)
- Himanshu Joshi
- 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
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31
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Ouyang X, Chang YN, Yang KW, Wang WM, Bai JJ, Wang JW, Zhang YJ, Wang SY, Xie BB, Wang LL. A DNA nanoribbon as a potent inhibitor of metallo-β-lactamases. Chem Commun (Camb) 2018; 53:8878-8881. [PMID: 28737795 DOI: 10.1039/c7cc04483f] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We discovered a promising metallo-β-lactamase inhibitor, a DNA nanoribbon, by enzymatic kinetics and isothermal titration calorimetry evaluations. Atomic force microscopy, gel electrophoresis, competitive binding experiments, circular dichroic and thermal denaturation studies suggested that the DNA nanoribbon could bind to the enzyme through a minor groove.
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Affiliation(s)
- Xiangyuan Ouyang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education of China, Key Laboratory of Modern Separation Science in Shaanxi Province, College of Chemistry & Material Science, Northwest University, Xi'an, 710127, China.
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32
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Hu Q, Li H, Wang L, Gu H, Fan C. DNA Nanotechnology-Enabled Drug Delivery Systems. Chem Rev 2018; 119:6459-6506. [PMID: 29465222 DOI: 10.1021/acs.chemrev.7b00663] [Citation(s) in RCA: 532] [Impact Index Per Article: 88.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Over the past decade, we have seen rapid advances in applying nanotechnology in biomedical areas including bioimaging, biodetection, and drug delivery. As an emerging field, DNA nanotechnology offers simple yet powerful design techniques for self-assembly of nanostructures with unique advantages and high potential in enhancing drug targeting and reducing drug toxicity. Various sequence programming and optimization approaches have been developed to design DNA nanostructures with precisely engineered, controllable size, shape, surface chemistry, and function. Potent anticancer drug molecules, including Doxorubicin and CpG oligonucleotides, have been successfully loaded on DNA nanostructures to increase their cell uptake efficiency. These advances have implicated the bright future of DNA nanotechnology-enabled nanomedicine. In this review, we begin with the origin of DNA nanotechnology, followed by summarizing state-of-the-art strategies for the construction of DNA nanostructures and drug payloads delivered by DNA nanovehicles. Further, we discuss the cellular fates of DNA nanostructures as well as challenges and opportunities for DNA nanostructure-based drug delivery.
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Affiliation(s)
- Qinqin Hu
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University , Shanghai 200032 , China.,Department of Systems Biology for Medicine , School of Basic Medical Sciences, Fudan University , Shanghai 200032 , China
| | - Hua Li
- Shanghai Institute of Cardiovascular Diseases , Zhongshan Hospital, Fudan University , Shanghai 200032 , China.,Research & Development Center, Shandong Buchang Pharmaceutical Company, Limited, Heze 274000 , China
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility Shanghai Institute of Applied Physics , Chinese Academy of Sciences , Shanghai 201800 , China.,School of Life Science and Technology , ShanghaiTech University , Shanghai 201210 , China
| | - Hongzhou Gu
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University , Shanghai 200032 , China.,Department of Systems Biology for Medicine , School of Basic Medical Sciences, Fudan University , Shanghai 200032 , China.,Shanghai Institute of Cardiovascular Diseases , Zhongshan Hospital, Fudan University , Shanghai 200032 , China
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility Shanghai Institute of Applied Physics , Chinese Academy of Sciences , Shanghai 201800 , China.,School of Life Science and Technology , ShanghaiTech University , Shanghai 201210 , China
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33
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Chandrasekaran AR, Rusling DA. Triplex-forming oligonucleotides: a third strand for DNA nanotechnology. Nucleic Acids Res 2018; 46:1021-1037. [PMID: 29228337 PMCID: PMC5814803 DOI: 10.1093/nar/gkx1230] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 11/21/2017] [Accepted: 11/30/2017] [Indexed: 11/14/2022] Open
Abstract
DNA self-assembly has proved to be a useful bottom-up strategy for the construction of user-defined nanoscale objects, lattices and devices. The design of these structures has largely relied on exploiting simple base pairing rules and the formation of double-helical domains as secondary structural elements. However, other helical forms involving specific non-canonical base-base interactions have introduced a novel paradigm into the process of engineering with DNA. The most notable of these is a three-stranded complex generated by the binding of a third strand within the duplex major groove, generating a triple-helical ('triplex') structure. The sequence, structural and assembly requirements that differentiate triplexes from their duplex counterparts has allowed the design of nanostructures for both dynamic and/or structural purposes, as well as a means to target non-nucleic acid components to precise locations within a nanostructure scaffold. Here, we review the properties of triplexes that have proved useful in the engineering of DNA nanostructures, with an emphasis on applications that hitherto have not been possible by duplex formation alone.
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Affiliation(s)
| | - David A Rusling
- Biological Sciences, Institute for Life Sciences, University of Southampton, Southampton, Hampshire SO17 1BJ, UK
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34
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Yang D, Tan Z, Mi Y, Wei B. DNA nanostructures constructed with multi-stranded motifs. Nucleic Acids Res 2017; 45:3606-3611. [PMID: 28334880 PMCID: PMC5389474 DOI: 10.1093/nar/gkx121] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Accepted: 02/09/2017] [Indexed: 11/25/2022] Open
Abstract
Earlier studies in DNA self-assembly have foretold the feasibility of building addressable nanostructures with multi-stranded motifs, which is fully validated in this study. In realizing this feasibility in DNA nanotechnology, a diversified set of motifs of modified domain lengths is extended from a classic type. The length of sticky ends can be adjusted to form different dihedral angles between the matching motifs, which corresponds to different connecting patterns. Moreover, the length of rigidity core can also be tuned to result in different dihedral angles between the component helices of a certain motif therefore different numbers of component helices. The extended set of motifs is used for self-assembly of complex one dimensional, two dimensional and three dimensional structures.
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Affiliation(s)
- Donglei Yang
- School of Chemical Science and Engineering, Tongji University, Shanghai 200092, China
| | - Zhenyu Tan
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Yongli Mi
- School of Chemical Science and Engineering, Tongji University, Shanghai 200092, China.,Department of Chemical and Biomolecular Engineering, the Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Bryan Wei
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
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35
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Zhao M, Wang X, Ren S, Xing Y, Wang J, Teng N, Zhao D, Liu W, Zhu D, Su S, Shi J, Song S, Wang L, Chao J, Wang L. Cavity-Type DNA Origami-Based Plasmonic Nanostructures for Raman Enhancement. ACS APPLIED MATERIALS & INTERFACES 2017; 9:21942-21948. [PMID: 28618781 DOI: 10.1021/acsami.7b05959] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
DNA origami has been established as addressable templates for site-specific anchoring of gold nanoparticles (AuNPs). Given that AuNPs are assembled by charged DNA oligonucleotides, it is important to reduce the charge repulsion between AuNPs-DNA and the template to realize high yields. Herein, we developed a cavity-type DNA origami as templates to organize 30 nm AuNPs, which formed dimer and tetramer plasmonic nanostructures. Transmission electron microscopy images showed that high yields of dimer and tetramer plasmonic nanostructures were obtained by using the cavity-type DNA origami as the template. More importantly, we observed significant Raman signal enhancement from molecules covalently attached to the plasmonic nanostructures, which provides a new way to high-sensitivity Raman sensing.
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Affiliation(s)
- Mengzhen Zhao
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Institute of Advanced Materials (IAM), National Syngerstic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications , 9 Wenyuan Road, Nanjing 210023, China
| | - Xu Wang
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Institute of Advanced Materials (IAM), National Syngerstic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications , 9 Wenyuan Road, Nanjing 210023, China
| | - Shaokang Ren
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Institute of Advanced Materials (IAM), National Syngerstic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications , 9 Wenyuan Road, Nanjing 210023, China
| | - Yikang Xing
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Institute of Advanced Materials (IAM), National Syngerstic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications , 9 Wenyuan Road, Nanjing 210023, China
| | - Jun Wang
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Institute of Advanced Materials (IAM), National Syngerstic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications , 9 Wenyuan Road, Nanjing 210023, China
| | - Nan Teng
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Institute of Advanced Materials (IAM), National Syngerstic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications , 9 Wenyuan Road, Nanjing 210023, China
| | - Dongxia Zhao
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Institute of Advanced Materials (IAM), National Syngerstic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications , 9 Wenyuan Road, Nanjing 210023, China
| | - Wei Liu
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Institute of Advanced Materials (IAM), National Syngerstic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications , 9 Wenyuan Road, Nanjing 210023, China
| | - Dan Zhu
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Institute of Advanced Materials (IAM), National Syngerstic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications , 9 Wenyuan Road, Nanjing 210023, China
| | - Shao Su
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Institute of Advanced Materials (IAM), National Syngerstic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications , 9 Wenyuan Road, Nanjing 210023, China
| | - Jiye Shi
- UCB Pharma , 208 Bath Road, Slough SL1 3WE, U.K
| | - Shiping Song
- 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
| | - 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
| | - Jie Chao
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Institute of Advanced Materials (IAM), National Syngerstic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications , 9 Wenyuan Road, Nanjing 210023, China
| | - Lianhui Wang
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Institute of Advanced Materials (IAM), National Syngerstic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications , 9 Wenyuan Road, Nanjing 210023, China
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36
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Liu W, Mahynski NA, Gang O, Panagiotopoulos AZ, Kumar SK. Directionally Interacting Spheres and Rods Form Ordered Phases. ACS NANO 2017; 11:4950-4959. [PMID: 28488848 DOI: 10.1021/acsnano.7b01592] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The structures formed by mixtures of dissimilarly shaped nanoscale objects can significantly enhance our ability to produce nanoscale architectures. However, understanding their formation is a complex problem due to the interplay of geometric effects (entropy) and energetic interactions at the nanoscale. Spheres and rods are perhaps the most basic geometrical shapes and serve as convenient models of such dissimilar objects. The ordered phases formed by each of these individual shapes have already been explored, however, when mixed, spheres and rods have demonstrated only limited structural organization to date. Here, we show using experiments and theory that the introduction of directional attractions between rod ends and isotropically interacting spherical nanoparticles (NPs) through DNA base pairing leads to the formation of ordered three-dimensional lattices. The spheres and rods arrange themselves in a complex alternating manner, where the spheres can form either a face-centered cubic (FCC) or hexagonal close-packed (HCP) lattice, or a disordered phase, as observed by in situ X-ray scattering. Increasing NP diameter at fixed rod length yields an initial transition from a disordered phase to the HCP crystal, energetically stabilized by rod-rod attraction across alternating crystal layers, as revealed by theory. In the limit of large NPs, the FCC structure is instead stabilized over the HCP by rod entropy. We, therefore, propose that directionally specific attractions in mixtures of anisotropic and isotropic objects offer insight into unexplored self-assembly behavior of noncomplementary shaped particles.
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Affiliation(s)
- Wenyan Liu
- Center for Functional Nanomaterials, Brookhaven National Laboratories , Upton, New York 11973, United States
| | - Nathan A Mahynski
- Department of Chemical and Biological Engineering, Princeton University , Princeton, New Jersey 08544, United States
| | - Oleg Gang
- Center for Functional Nanomaterials, Brookhaven National Laboratories , Upton, New York 11973, United States
| | - Athanassios Z Panagiotopoulos
- Department of Chemical and Biological Engineering, Princeton University , Princeton, New Jersey 08544, United States
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37
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Maier AM, Bae W, Schiffels D, Emmerig JF, Schiff M, Liedl T. Self-Assembled DNA Tubes Forming Helices of Controlled Diameter and Chirality. ACS NANO 2017; 11:1301-1306. [PMID: 28125777 PMCID: PMC6544521 DOI: 10.1021/acsnano.6b05602] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Multihelical DNA bundles could enhance the functionality of nanomaterials and serve as model architectures to mimic protein filaments on the molecular and cellular level. We report the self-assembly of micrometer-sized helical DNA nanotubes with widely controllable helical diameters ranging from tens of nanometers to a few micrometers. Nanoscale helical shapes of DNA tile tubes (4-, 6-, 8-, 10-, and 12-helix tile tubes) are achieved by introducing discrete amounts of bending and twist through base pair insertions and/or deletions. Microscale helical diameters, which require smaller amounts of twist and bending, are achieved by controlling the intrinsic "supertwist" present in tile tubes with uneven number of helices (11-, 13-, and 15-helix tile tubes). Supertwist fine-tuning also allows us to produce helical nanotubes of defined chirality.
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Affiliation(s)
- Alexander Mario Maier
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität (LMU) , Geschwister-Scholl-Platz 1, 80539 München, Germany
| | - Wooli Bae
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität (LMU) , Geschwister-Scholl-Platz 1, 80539 München, Germany
| | - Daniel Schiffels
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität (LMU) , Geschwister-Scholl-Platz 1, 80539 München, Germany
| | - Johannes Friedrich Emmerig
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität (LMU) , Geschwister-Scholl-Platz 1, 80539 München, Germany
| | - Maximilian Schiff
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität (LMU) , Geschwister-Scholl-Platz 1, 80539 München, Germany
| | - Tim Liedl
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität (LMU) , Geschwister-Scholl-Platz 1, 80539 München, Germany
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38
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Joshi H, Kaushik A, Seeman NC, Maiti PK. Nanoscale Structure and Elasticity of Pillared DNA Nanotubes. ACS NANO 2016; 10:7780-91. [PMID: 27400249 DOI: 10.1021/acsnano.6b03360] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We present an atomistic model of pillared DNA nanotubes (DNTs) and their elastic properties which will facilitate further studies of these nanotubes in several important nanotechnological and biological applications. In particular, we introduce a computational design to create an atomistic model of a 6-helix DNT (6HB) along with its two variants, 6HB flanked symmetrically with two double helical DNA pillars (6HB+2) and 6HB flanked symmetrically by three double helical DNA pillars (6HB+3). Analysis of 200 ns all-atom simulation trajectories in the presence of explicit water and ions shows that these structures are stable and well behaved in all three geometries. Hydrogen bonding is well maintained for all variants of 6HB DNTs. From the equilibrium bending angle distribution, we calculate the persistence lengths of these tubes. The measured persistence lengths of these nanotubes are ∼10 μm, which is 2 orders of magnitude larger than that of dsDNA. We also find a gradual increase of persistence length with an increasing number of pillars, in quantitative agreement with previous experimental findings. To have a quantitative understanding of the stretch modulus of these tubes, we carried out nonequilibrium steered molecular dynamics (SMD). The linear part of the force-extension plot gives a stretch modulus in the range 6500 pN for 6HB without pillars, which increases to 11 000 pN for tubes with three pillars. The values of the stretch modulus calculated using contour length distribution obtained from equilibrium MD simulations are similar to those obtained from nonequilibrium SMD simulations. The addition of pillars makes these DNTs very rigid.
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Affiliation(s)
- Himanshu Joshi
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science , Bangalore 560012, India
| | - Atul Kaushik
- Department of Biotechnology, Indian Institute of Technology Madras , Chennai 600 036, India
| | - Nadrian C Seeman
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science , Bangalore 560012, India
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39
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Wang W, Lin T, Zhang S, Bai T, Mi Y, Wei B. Self-assembly of fully addressable DNA nanostructures from double crossover tiles. Nucleic Acids Res 2016; 44:7989-96. [PMID: 27484479 PMCID: PMC5027514 DOI: 10.1093/nar/gkw670] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 07/20/2016] [Indexed: 11/23/2022] Open
Abstract
DNA origami and single-stranded tile (SST) are two proven approaches to self-assemble finite-size complex DNA nanostructures. The construction elements appeared in structures from these two methods can also be found in multi-stranded DNA tiles such as double crossover tiles. Here we report the design and observation of four types of finite-size lattices with four different double crossover tiles, respectively, which, we believe, in terms of both complexity and robustness, will be rival to DNA origami and SST structures.
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Affiliation(s)
- Wen Wang
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China Bioengineering Graduate Program, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Depatment of Chemistry, Tongji University, Shanghai 200092, China
| | - Tong Lin
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Suoyu Zhang
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Tanxi Bai
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Yongli Mi
- Bioengineering Graduate Program, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Depatment of Chemistry, Tongji University, Shanghai 200092, China Department of Chemical and Biomolecular Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Bryan Wei
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
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40
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Wang P, Gaitanaros S, Lee S, Bathe M, Shih WM, Ke Y. Programming Self-Assembly of DNA Origami Honeycomb Two-Dimensional Lattices and Plasmonic Metamaterials. J Am Chem Soc 2016; 138:7733-40. [DOI: 10.1021/jacs.6b03966] [Citation(s) in RCA: 144] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Pengfei Wang
- Wallance
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Stavros Gaitanaros
- Department
of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Seungwoo Lee
- SKKU
Advanced Institute of Nanotechnology & School of Chemical Engineering, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
| | - Mark Bathe
- Department
of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - William M. Shih
- Wyss
Institute for Biologically Inspired Engineering and Department of Cancer Biology, Dana-Farber Cancer Institute, and Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical
School, Harvard University, Boston, Massachusetts 02115, United States
| | - Yonggang Ke
- Wallance
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
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41
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Liang L, Zhang Z, Kong Z, Liu Y, Shen JW, Li D, Wang Q. Charge-tunable insertion process of carbon nanotubes into DNA nanotubes. J Mol Graph Model 2016; 66:20-5. [PMID: 27017425 DOI: 10.1016/j.jmgm.2016.03.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 03/20/2016] [Accepted: 03/22/2016] [Indexed: 12/16/2022]
Abstract
Control over interactions with biomolecules holds the key of the applications of carbon nanotubes (CNTs) in biotechnology. Here we report a molecule dynamics study on the encapsulation process of different charged CNTs into DNA nanotubes. Our results demonstrated that insertion process of CNTs into DNA nanotubes are charge-tunable. The positive charged CNTs could spontaneously encapsulate and confined in the hollow of DNA nanotubes under the combination of electrostatic and vdW interaction in our ns scale simulation. The conformation of DNA nanotubes is very stable even after the insertion of CNTs. For pristine CNTs, it could not entirely encapsulated by DNA nanotubes in simulation scale in this study. The encapsulation time of pristine CNTs into DNA nanotubes was estimated about 21.9s based on the potential of mean force along the reaction coordination of encapsulation process of CNTs into DNA nanotubes. In addition, the encapsulation process was also affected by the diameter of CNTs. These findings highlight the charge-tunable self-assembly process of nanomaterials and biomolecules. Our study suggests that the encapsulated CNTs-DNA nanotubes could be used as building blocks for constructing organic-inorganic hybrid materials and has the potential applications in the field of biosensor, drug delivery system and biomaterials etc.
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Affiliation(s)
- Lijun Liang
- College of Life Information Science and Instrument Engineering, Hangzhou Dianzi University, Hangzhou, People's Republic of China; Department of Chemistry, Zhejiang University, Hangzhou 310027, People's Republic of China
| | - Zhisen Zhang
- Research Institute for Soft Matter and Biomimetics, Department of Physics, Xiamen University, Xiamen 361005, People's Republic of China
| | - Zhe Kong
- College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou 310018, People's Republic of China
| | - Yong Liu
- School of Medicine, Hangzhou Normal University, Hangzhou 310016, People's Republic of China
| | - Jia-Wei Shen
- School of Medicine, Hangzhou Normal University, Hangzhou 310016, People's Republic of China.
| | - Debing Li
- College of Life Information Science and Instrument Engineering, Hangzhou Dianzi University, Hangzhou, People's Republic of China
| | - Qi Wang
- Department of Chemistry, Zhejiang University, Hangzhou 310027, People's Republic of China.
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42
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Rahbani JF, Hariri AA, Cosa G, Sleiman HF. Dynamic DNA Nanotubes: Reversible Switching between Single and Double-Stranded Forms, and Effect of Base Deletions. ACS NANO 2015; 9:11898-11908. [PMID: 26556531 DOI: 10.1021/acsnano.5b04387] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
DNA nanotubes hold great potential as drug delivery vehicles and as programmable templates for the organization of materials and biomolecules. Existing methods for their construction produce assemblies that are entirely double-stranded and rigid, and thus have limited intrinsic dynamic character, or they rely on chemically modified and ligated DNA structures. Here, we report a simple and efficient synthesis of DNA nanotubes from 11 short unmodified strands, and the study of their dynamic behavior by atomic force microscopy and in situ single molecule fluorescence microscopy. This method allows the programmable introduction of DNA structural changes within the repeat units of the tubes. We generate and study fully double-stranded nanotubes, and convert them to nanotubes with one, two and three single-stranded sides, using strand displacement strategies. The nanotubes can be reversibly switched between these forms without compromising their stability and micron-scale lengths. We then site-specifically introduce DNA strands that shorten two sides of the nanotubes, while keeping the length of the third side. The nanotubes undergo bending with increased length mismatch between their sides, until the distortion is significant enough to shorten them, as measured by AFM and single-molecule fluorescence photobleaching experiments. The method presented here produces dynamic and robust nanotubes that can potentially behave as actuators, and allows their site-specific addressability while using a minimal number of component strands.
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Affiliation(s)
- Janane F Rahbani
- Department of Chemistry and Centre for Self-Assembled Chemical Structures, McGill University , 801 Sherbrooke Street West, Montreal, H3A 0B8, Canada
| | - Amani A Hariri
- Department of Chemistry and Centre for Self-Assembled Chemical Structures, McGill University , 801 Sherbrooke Street West, Montreal, H3A 0B8, Canada
| | - Gonzalo Cosa
- Department of Chemistry and Centre for Self-Assembled Chemical Structures, McGill University , 801 Sherbrooke Street West, Montreal, H3A 0B8, Canada
| | - Hanadi F Sleiman
- Department of Chemistry and Centre for Self-Assembled Chemical Structures, McGill University , 801 Sherbrooke Street West, Montreal, H3A 0B8, Canada
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43
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Rafati A, Gill P. Ultrastructural characterizations of DNA nanotubes using scanning tunneling and atomic force microscopes. J Microsc Ultrastruct 2015; 4:1-5. [PMID: 30023203 PMCID: PMC6014237 DOI: 10.1016/j.jmau.2015.08.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Revised: 08/13/2015] [Accepted: 08/20/2015] [Indexed: 11/28/2022] Open
Abstract
The potential applications of scanning tunneling microscopy and atomic force microscopy for the characterizations of DNA nanotubes in nanoscale have been described here. The nanotubes were designed using the Cadnano software according to M13 mp18 DNA as a scaffold. DNA nanotubes were fabricated using the origami technique assisted with ligase treatment subsequently. Transmission electron microscopy confirmed the morphology of DNA nanotubes. For the topographic characterization of DNA nanotubes, an atomic force microscope was used in comparison to a scanning tunneling microscope. The scanning tunneling microscopy results revealed a high-resolution topography of DNA nanotubes in the constant-current mode; however, more details of the self-assembly in DNA strands in nanotubes were explored by atomic force microscopy with contact mode (or constant height). Our findings suggested that those two microscopes could be candidates for ultrastructural characterizations of DNA nanotubes for obtaining two- and three-dimensional micrographs
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Affiliation(s)
- Adele Rafati
- Department of Medical Biotechnology, Faculty of Advanced Medical Technologies, Golestan University of Medical Sciences, Gorgan, Iran.,Department of Nanobiomedicine, Faculty of Medicine, Mazandaran University of Medical Sciences, Mazandaran, Iran.,Department of Nanobiotechnology, Faculty of New Sciences and Technologies, University of Isfahan, Isfahan, Iran
| | - Pooria Gill
- Department of Nanobiomedicine, Faculty of Medicine, Mazandaran University of Medical Sciences, Mazandaran, Iran.,Nanomedicine Group, Immunogenetics Research Center, Mazandaran University of Medical Sciences, Sari, Iran
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44
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Abstract
Biosensors employ biological molecules to recognize the target and utilize output elements which can translate the biorecognition event into electrical, optical or mass-sensitive signals to determine the quantities of the target. DNA-based biosensors, as a sub-field to biosensor, utilize DNA strands with short oligonucleotides as probes for target recognition. Although DNA-based biosensors have offered a promising alternative for fast, simple and cheap detection of target molecules, there still exist key challenges including poor stability and reproducibility that hinder their competition with the current gold standard for DNA assays. By exploiting the self-recognition properties of DNA molecules, researchers have dedicated to make versatile DNA nanostructures in a highly rigid, controllable and functionalized manner, which offers unprecedented opportunities for developing DNA-based biosensors. In this review, we will briefly introduce the recent advances on design and fabrication of static and dynamic DNA nanostructures, and summarize their applications for fabrication and functionalization of DNA-based biosensors.
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Affiliation(s)
- Jie Chao
- Key Laboratory for Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China; 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, Shanghai 201800, China
| | - Dan 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, Shanghai 201800, China
| | - Yinan Zhang
- 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, Shanghai 201800, China
| | - Lianhui Wang
- Key Laboratory for Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Chunhai Fan
- 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, Shanghai 201800, China
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45
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Chao J, Ouyang X, Peng H, Su S, Wang L. Self-assembly of Micrometer-long DNA Nanoribbons with Four Oligonucleotides. CHINESE J CHEM 2015. [DOI: 10.1002/cjoc.201500211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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46
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Agostinelli E, Vianello F, Magliulo G, Thomas T, Thomas TJ. Nanoparticle strategies for cancer therapeutics: Nucleic acids, polyamines, bovine serum amine oxidase and iron oxide nanoparticles (Review). Int J Oncol 2015; 46:5-16. [PMID: 25333509 DOI: 10.3892/ijo.2014.2706] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 09/01/2014] [Indexed: 11/06/2022] Open
Abstract
Nanotechnology for cancer gene therapy is an emerging field. Nucleic acids, polyamine analogues and cytotoxic products of polyamine oxidation, generated in situ by an enzyme-catalyzed reaction, can be developed for nanotechnology-based cancer therapeutics with reduced systemic toxicity and improved therapeutic efficacy. Nucleic acid-based gene therapy approaches depend on the compaction of DNA/RNA to nanoparticles and polyamine analogues are excellent agents for the condensation of nucleic acids to nanoparticles. Polyamines and amine oxidases are found in higher levels in tumours compared to that of normal tissues. Therefore, the metabolism of polyamines spermidine and spermine, and their diamine precursor, putrescine, can be targets for antineoplastic therapy since these naturally occurring alkylamines are essential for normal mammalian cell growth. Intracellular polyamine concentrations are maintained at a cell type-specific set point through the coordinated and highly regulated interplay between biosynthesis, transport, and catabolism. In particular, polyamine catabolism involves copper-containing amine oxidases. Several studies showed an important role of these enzymes in developmental and disease-related processes in animals through the control of polyamine homeostasis in response to normal cellular signals, drug treatment, and environmental and/or cellular stress. The production of toxic aldehydes and reactive oxygen species (ROS), H2O2 in particular, by these oxidases suggests a mechanism by which amine oxidases can be exploited as antineoplastic drug targets. The combination of bovine serum amine oxidase (BSAO) and polyamines prevents tumour growth, particularly well if the enzyme has been conjugated with a biocompatible hydrogel polymer. The findings described herein suggest that enzymatically formed cytotoxic agents activate stress signal transduction pathways, leading to apoptotic cell death. Consequently, superparamagnetic nanoparticles or other advanced nanosystem based on directed nucleic acid assemblies, polyamine-induced DNA condensation, and bovine serum amine oxidase may be proposed for futuristic anticancer therapy utilizing nucleic acids, polyamines and BSAO. BSAO based nanoparticles can be employed for the generation of cytotoxic polyamine metabolites.
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Affiliation(s)
- Enzo Agostinelli
- Istituto Pasteur-Fondazione Cenci Bolognetti Department of Biochemical Sciences 'A. Rossi Fanelli', Sapienza University of Rome and CNR, Institute of Biology and Molecular Pathology, 00185 Rome, Italy
| | - Fabio Vianello
- Department of Comparative Biomedicine and Food Science, University of Padua, 35020 Legnaro, Italy and Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacky University in Olomouc, Olomouc 77146, Czech Republic
| | - Giuseppe Magliulo
- Department Organi di Senso, Sapienza University of Rome, 00185 Rome, Italy
| | - Thresia Thomas
- Formerly Department of Environmental and Occupational Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers the State University of New Jersey, Piscataway, NJ 08854, USA
| | - T J Thomas
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers the State University of New Jersey, New Brunswick, NJ 08901, USA
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47
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Joshi H, Dwaraknath A, Maiti PK. Structure, stability and elasticity of DNA nanotubes. Phys Chem Chem Phys 2015; 17:1424-34. [DOI: 10.1039/c4cp04547e] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA nanotubes: an extension to DNA crossover molecules.
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Affiliation(s)
- Himanshu Joshi
- Centre for Condensed Matter Theory
- Department of Physics
- Indian Institute of Science
- Bangalore
- India
| | - Anjan Dwaraknath
- Centre for Condensed Matter Theory
- Department of Physics
- Indian Institute of Science
- Bangalore
- India
| | - Prabal K. Maiti
- Centre for Condensed Matter Theory
- Department of Physics
- Indian Institute of Science
- Bangalore
- India
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48
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Hernández-Ainsa S, Keyser UF. DNA origami nanopores: developments, challenges and perspectives. NANOSCALE 2014; 6:14121-32. [PMID: 25325422 DOI: 10.1039/c4nr04094e] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
DNA nanotechnology has enabled the construction of DNA origami nanopores; synthetic nanopores that present improved capabilities for the area of single molecule detection. Their extraordinary versatility makes them a new and powerful tool in nanobiotechnology for a wide range of important applications beyond molecular sensing. In this review, we briefly present the recent developments in this emerging field of research. We discuss the current challenges and possible solutions that would enhance the sensing capabilities of DNA origami nanopores. Finally, we anticipate novel avenues for future research and highlight a range of exciting ideas and applications that could be explored in the near future.
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49
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Chao J, Liu H, Su S, Wang L, Huang W, Fan C. Structural DNA nanotechnology for intelligent drug delivery. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:4626-4635. [PMID: 24955859 DOI: 10.1002/smll.201401309] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 06/02/2014] [Indexed: 06/03/2023]
Abstract
Drug delivery carriers have been popularly employed to improve solubility, stability, and efficacy of chemical and biomolecular drugs. Despite the rapid progress in this field, it remains a great challenge to develop an ideal carrier with minimal cytotoxicity, high biocompatibility and intelligence for targeted controlled release. The emergence of DNA nanotechnology offers unprecedented opportunities in this regard. Due to the unparalleled self-recognition properties of DNA molecules, it is possible to create numerous artificial DNA nanostructures with well-defined structures and DNA nanodevices with precisely controlled motions. More importantly, recent studies have proven that DNA nanostructures possess greater permeability to the membrane barrier of cells, which pave the way to developing new drug delivery carriers with nucleic acids, are summarized. In this Concept, recent advances on the design and fabrication of both static and dynamic DNA nanostructures, and the use of these nanostructures for the delivery of various types of drugs, are highlighted. It is also demonstrated that dynamic DNA nanostructures provide the required intelligence to realize logically controlled drug release.
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Affiliation(s)
- Jie Chao
- 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, Shanghai, 201800, China; Key Laboratory for Organic Electronics & Information Displays (KLOEID), Institute of Advanced Materials (IAM) and School of Materials Science and Engineering, Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing, 210046, China
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50
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Liu H, Shen X, Wang ZG, Kuzyk A, Ding B. Helical nanostructures based on DNA self-assembly. NANOSCALE 2014; 6:9331-9338. [PMID: 24740255 DOI: 10.1039/c3nr06913c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Recent advances in design and fabrication of helical nanostructures based on DNA self-assembly are reviewed. These helical nanostructures are either constructed entirely by DNA or based on DNA guided metal nanoparticles self-assembly. Biophysical properties and optical responses of corresponding helical nanostructures are also discussed.
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Affiliation(s)
- Huan Liu
- National Center for NanoScience and Technology, 11 BeiYiTiao, ZhongGuanCun, Beijing, 100190, China.
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