1
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Wang Y, Cao LP, Shuai XJ, Liu L, Huang CZ, Li CM. DNA Nanospheres Assisted Spatial Confinement Signal Amplification for MicroRNA Imaging in Live Cancer Cells. Anal Chem 2024; 96:4597-4604. [PMID: 38456210 DOI: 10.1021/acs.analchem.3c05554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
DNA assemblies are commonly used in biosensing, particularly for the detection and imaging of microRNAs (miRNAs), which are biomarkers associated with tumor progression. However, the difficulty lies in the exploration of high-sensitivity analytical techniques for miRNA due to its limited presence in living cells. In this study, we introduced a DNA nanosphere (DS) enhanced catalytic hairpin assembly (CHA) system for the detection and imaging of intracellular miR-21. The single-stranded DNA with four palindromic portions and extending sequences at the terminal was annealed for assembling DS, which avoided the complex sequence design and high cost of long DNA strands. Benefiting from the multiple modification sites of DS, functional hairpins H1 (modified with Cy3 and BHQ2) and H2 were grafted onto the surface of DS for assembling DS-H1-H2 using a hybridization reaction. The DS-H1-H2 system utilized spatial confinement and the CHA reaction to amplify fluorescence signals of Cy3. This enabled highly sensitive and rapid detection of miR-21 in the range from 0.05 to 3.5 nM. The system achieved a limit of determination (LOD) of 2.0 pM, which was 56 times lower than that of the control CHA circuit with freedom hairpins. Additionally, the sensitivity was improved by 8 times. Moreover, DS-H1-H2 also showed an excellent imaging capability for endogenous miR-21 in tumor cells. This was due to enhanced cell internalization efficiency, accelerated reaction kinetics, and improved biostability. The imaging strategy was shown to effectively monitor the dynamic content of miR-21 in live cancer cells and differentiate various cells. In general, the simple nanostructure DS not only enhanced the detection and imaging capability of the conventional probe but also could be easily integrated with the reported DNA-free probe, indicating a wide range of potential applications.
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Affiliation(s)
- Yao Wang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Li Ping Cao
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Xin Jia Shuai
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Lin Liu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Cheng Zhi Huang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Chun Mei Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
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2
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Xu D, Li Y, Yin S, Huang F. Strategies to address key challenges of metallacycle/metallacage-based supramolecular coordination complexes in biomedical applications. Chem Soc Rev 2024; 53:3167-3204. [PMID: 38385584 DOI: 10.1039/d3cs00926b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Owing to their capacity for dynamically linking two or more functional molecules, supramolecular coordination complexes (SCCs), exemplified by two-dimensional (2D) metallacycles and three-dimensional (3D) metallacages, have gained increasing significance in biomedical applications. However, their inherent hydrophobicity and self-assembly driven by heavy metal ions present common challenges in their applications. These challenges can be overcome by enhancing the aqueous solubility and in vivo circulation stability of SCCs, alongside minimizing their side effects during treatment. Addressing these challenges is crucial for advancing the fundamental research of SCCs and their subsequent clinical translation. In this review, drawing on extensive contemporary research, we offer a thorough and systematic analysis of the strategies employed by SCCs to surmount these prevalent yet pivotal obstacles. Additionally, we explore further potential challenges and prospects for the broader application of SCCs in the biomedical field.
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Affiliation(s)
- Dongdong Xu
- Key Laboratory of Organosilicon Chemistry and Materials Technology of Ministry of Education, College of Materials, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 311121, P. R. China.
| | - Yang Li
- Key Laboratory of Organosilicon Chemistry and Materials Technology of Ministry of Education, College of Materials, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 311121, P. R. China.
| | - Shouchun Yin
- Key Laboratory of Organosilicon Chemistry and Materials Technology of Ministry of Education, College of Materials, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 311121, P. R. China.
| | - Feihe Huang
- Stoddart Institute of Molecular Science, Department of Chemistry, Zhejiang University, Hangzhou 310058, P. R. China.
- Zhejiang-Israel Joint Laboratory of Self-Assembling Functional Materials, ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 311215, P. R. China
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3
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Narayanan RP, Prasad A, Buchberger A, Zou L, Bernal-Chanchavac J, MacCulloch T, Fahmi NE, Yan H, Zhang F, Webber MJ, Stephanopoulos N. High-Affinity Host-Guest Recognition for Efficient Assembly and Enzymatic Responsiveness of DNA Nanostructures. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2307585. [PMID: 37849034 PMCID: PMC10922742 DOI: 10.1002/smll.202307585] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Indexed: 10/19/2023]
Abstract
The combination of multiple orthogonal interactions enables hierarchical complexity in self-assembled nanoscale materials. Here, efficient supramolecular polymerization of DNA origami nanostructures is demonstrated using a multivalent display of small molecule host-guest interactions. Modification of DNA strands with cucurbit[7]uril (CB[7]) and its adamantane guest, yielding a supramolecular complex with an affinity of order 1010 m-1 , directs hierarchical assembly of origami monomers into 1D nanofibers. This affinity regime enables efficient polymerization; a lower-affinity β-cyclodextrin-adamantane complex does not promote extended structures at a similar valency. Finally, the utility of the high-affinity CB[7]-adamantane interactions is exploited to enable responsive enzymatic actuation of origami nanofibers assembled using peptide linkers. This work demonstrates the power of high-affinity CB[7]-guest recognition as an orthogonal axis to drive self-assembly in DNA nanotechnology.
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Affiliation(s)
- Raghu Pradeep Narayanan
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, AZ, 85287, USA
| | - Abhay Prasad
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, AZ, 85287, USA
| | - Alex Buchberger
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, AZ, 85287, USA
| | - Lei Zou
- Chemical & Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Julio Bernal-Chanchavac
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, AZ, 85287, USA
| | - Tara MacCulloch
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, AZ, 85287, USA
| | - Nour Eddine Fahmi
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, AZ, 85287, USA
| | - Hao Yan
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, AZ, 85287, USA
| | - Fei Zhang
- Department of Chemistry, Rutgers University-Newark, Newark, NJ, 07102, USA
| | - Matthew J Webber
- Chemical & Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Nicholas Stephanopoulos
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, AZ, 85287, USA
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4
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Berg WR, Berengut JF, Bai C, Wimberger L, Lee LK, Rizzuto FJ. Light-Activated Assembly of DNA Origami into Dissipative Fibrils. Angew Chem Int Ed Engl 2023; 62:e202314458. [PMID: 37903739 DOI: 10.1002/anie.202314458] [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: 09/26/2023] [Revised: 10/26/2023] [Accepted: 10/30/2023] [Indexed: 11/01/2023]
Abstract
Hierarchical DNA nanostructures offer programmable functions at scale, but making these structures dynamic, while keeping individual components intact, is challenging. Here we show that the DNA A-motif-protonated, self-complementary poly(adenine) sequences-can propagate DNA origami into one-dimensional, micron-length fibrils. When coupled to a small molecule pH regulator, visible light can activate the hierarchical assembly of our DNA origami into dissipative fibrils. This system is recyclable and does not require DNA modification. By employing a modular and waste-free strategy to assemble and disassemble hierarchical structures built from DNA origami, we offer a facile and accessible route to developing well-defined, dynamic, and large DNA assemblies with temporal control. As a general tool, we envision that coupling the A-motif to cycles of dissipative protonation will allow the transient construction of diverse DNA nanostructures, finding broad applications in dynamic and non-equilibrium nanotechnology.
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Affiliation(s)
- Willi R Berg
- School of Chemistry, University of New South Wales, Sydney, 2052, Australia
- Institut für Chemie und Biochemie, Freie Universität Berlin, Fabeckstraße 34-36, 14195, Berlin, Germany
| | - Jonathan F Berengut
- EMBL Australia Node for Single Molecule Science, School of Biomedical Sciences, University of New South Wales, Sydney, 2052, Australia
- ARC Centre of Excellence in Synthetic Biology, University of New South Wales, Sydney, 2052, Australia
| | - Changzhuang Bai
- School of Chemistry, University of New South Wales, Sydney, 2052, Australia
| | - Laura Wimberger
- School of Chemistry, University of New South Wales, Sydney, 2052, Australia
| | - Lawrence K Lee
- EMBL Australia Node for Single Molecule Science, School of Biomedical Sciences, University of New South Wales, Sydney, 2052, Australia
- ARC Centre of Excellence in Synthetic Biology, University of New South Wales, Sydney, 2052, Australia
| | - Felix J Rizzuto
- School of Chemistry, University of New South Wales, Sydney, 2052, Australia
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5
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Zhang Q, Lin C, Chen C, Zhang L, Shi F, Cheng M. Polyelectrolyte chain conformation matters in macroscopic supramolecular self-assembly. Chem Commun (Camb) 2023; 59:14114-14117. [PMID: 37929664 DOI: 10.1039/d3cc04140a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
We demonstrate molecular-conformation-dependent macroscopic supramolecular self-assembly (MSA) driven by electrostatic interactions. Evidence from single molecular force spectroscopy reveals that polyelectrolytes modified on MSA component surfaces make MSA possible with a loop conformation, while those with a flat conformation lead to no assembly, which is attributed to distinct molecular mobility. We believe that this finding is also applicable in fundamental phenomena such as surface adsorption and adhesion regarding polymers.
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Affiliation(s)
- Qian Zhang
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China.
| | - Cuiling Lin
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China.
| | - Chen Chen
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China.
| | - Liqun Zhang
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China.
| | - Feng Shi
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China.
| | - Mengjiao Cheng
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China.
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6
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Tan Y, Zhou J, Xing X, Wang J, Huang J, Liu H, Chen J, Dong M, Xiang Q, Dong H, Zhang X. DNA Assembly of Plasmonic Nanostructures Enables In Vivo SERS-Based MicroRNA Detection and Tumor Photoacoustic Imaging. Anal Chem 2023. [PMID: 37467354 DOI: 10.1021/acs.analchem.3c00775] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
Controllable self-assembly of the DNA-linked gold nanoparticle (AuNP) architecture for in vivo biomedical applications remains a key challenge. Here, we describe the use of the programmed DNA tetrahedral structure to control the assembly of three different types of AuNPs (∼20, 10, and 5 nm) by organizing them into defined positioning and arrangement. A DNA-assembled "core-satellite" architecture is built by DNA sequencing where satellite AuNPs (10 and 5 nm) surround a central core AuNP (20 nm). The density and arrangement of the AuNP satellites around the core AuNP were controlled by tuning the size and amount of the DNA tetrahedron functionalized on the core AuNPs, resulting in strong electromagnetic field enhancement derived from hybridized plasmonic coupling effects. By conjugating with the Raman molecule, strong surface-enhanced Raman scattering photoacoustic imaging signals could be generated, which were able to image microRNA-21 and tumor tissues in vivo. These results provided an efficient strategy to build precision plasmonic superstructures in plasmonic-based bioanalysis and imaging.
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Affiliation(s)
- Yan Tan
- Marshall Laboratory of Biomedical Engineering, Precision Medicine and Health Research Institute, Research Center for Biosensor and Nanotheranostic, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Jianxing Zhou
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronics Engineering, Shenzhen University, Shenzhen 518060, China
| | - Xiaotong Xing
- Marshall Laboratory of Biomedical Engineering, Precision Medicine and Health Research Institute, Research Center for Biosensor and Nanotheranostic, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Junren Wang
- Marshall Laboratory of Biomedical Engineering, Precision Medicine and Health Research Institute, Research Center for Biosensor and Nanotheranostic, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Jinkun Huang
- Marshall Laboratory of Biomedical Engineering, Precision Medicine and Health Research Institute, Research Center for Biosensor and Nanotheranostic, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Huiyu Liu
- Marshall Laboratory of Biomedical Engineering, Precision Medicine and Health Research Institute, Research Center for Biosensor and Nanotheranostic, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Jiajie Chen
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronics Engineering, Shenzhen University, Shenzhen 518060, China
| | - Mingjie Dong
- Marshall Laboratory of Biomedical Engineering, Precision Medicine and Health Research Institute, Research Center for Biosensor and Nanotheranostic, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Qin Xiang
- Marshall Laboratory of Biomedical Engineering, Precision Medicine and Health Research Institute, Research Center for Biosensor and Nanotheranostic, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Haifeng Dong
- Marshall Laboratory of Biomedical Engineering, Precision Medicine and Health Research Institute, Research Center for Biosensor and Nanotheranostic, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Xueji Zhang
- Marshall Laboratory of Biomedical Engineering, Precision Medicine and Health Research Institute, Research Center for Biosensor and Nanotheranostic, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518060, China
- Guangdong Laboratory of Artificial Intelligence and Digital Economy (SZ), Shenzhen 518060, China
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7
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Gao C, Tang M, Lee SMY, Wang R. Synthesis of Bacteria-mimetic Gold Nanoparticles for Phagocytosis by Immune Cells. Bio Protoc 2023; 13:e4695. [PMID: 37397790 PMCID: PMC10308183 DOI: 10.21769/bioprotoc.4695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 01/08/2023] [Accepted: 04/05/2023] [Indexed: 07/04/2023] Open
Abstract
Cell-based carrier exhibits inherent advantages as the next generation of drug delivery system, namely high biocompatibility and physiological function. Current cell-based carriers are constructed via direct payload internalization or conjugation between cell and payload. However, the cells involved in these strategies must be firstly extracted from the body and the cell-based carrier must be prepared in vitro. Herein, we synthesize bacteria-mimetic gold nanoparticles (GNPs) for the construction of cell-based carrier in mice. Both β-cyclodextrin (β-CD)-modified GNPs and adamantane (ADA)-modified GNPs are coated by E. coli outer membrane vesicles (OMVs). The E. coli OMVs induce the phagocytosis of GNPs by circulating immune cells, leading to intracellular degradation of OMVs and subsequent supramolecular self-assembly of GNPs driven by β-CD-ADA host-guest interactions. In vivo construction of cell-based carrier based on bacteria-mimetic GNPs avoids the immunogenicity induced by allogeneic cells and restriction by the number of separated cells. Due to the inflammatory tropism, endogenous immune cells carry the intracellular GNP aggregates to the tumor tissues in vivo. Graphical overview Collect the outer membrane vesicles (OMVs) of E. coli by gradient centrifugation (a) and coat on gold nanoparticles (GNP) surface (b) to prepare OMV-coated cyclodextrin (CD)-GNPs and OMV-coated adamantane (ADA)-GNPs (c) via ultrasonic method.
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Affiliation(s)
- Cheng Gao
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau, China
- MoE Frontiers Science Center for Precision Oncology, University of Macau, Taipa, Macau, China
| | - Mian Tang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau, China
- MoE Frontiers Science Center for Precision Oncology, University of Macau, Taipa, Macau, China
| | - Simon M. Y. Lee
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau, China
- MoE Frontiers Science Center for Precision Oncology, University of Macau, Taipa, Macau, China
| | - Ruibing Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau, China
- MoE Frontiers Science Center for Precision Oncology, University of Macau, Taipa, Macau, China
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8
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Liu Y, Wu Y, Luo Z, Li M. Designing supramolecular self-assembly nanomaterials as stimuli-responsive drug delivery platforms for cancer therapy. iScience 2023; 26:106279. [PMID: 36936787 PMCID: PMC10014307 DOI: 10.1016/j.isci.2023.106279] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
Stimuli-responsive nanomaterials have attracted substantial interest in cancer therapy, as they hold promise to deliver anticancer agents to tumor sites in a precise and on-demand manner. Interestingly, supramolecular chemistry is a burgeoning discipline that entails the reversible bonding between components at the molecular and nanoscale levels, and the recent advances in this area offer the possibility to design nanotherapeutics with improved controllability and functionality for cancer therapy. Herein, we provide a comprehensive summary of typical non-covalent interaction modes, which primarily include hydrophobic interaction, hydrogel bonding, host-guest interaction, π-π stacking, and electrostatic interaction. Special emphasis is placed on the implications of these interaction modes to design novel stimuli-responsive drug delivery principles and concepts, aiming to enhance the spatial, temporal, and dosage precision of drug delivery to cancer cells. Finally, future perspectives are discussed to highlight current challenges and future opportunities in self-assembly-based stimuli-responsive drug delivery nanotechnologies for cancer therapy.
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Affiliation(s)
- Yingqi Liu
- School of Life Science, Chongqing University, Chongqing 400044, P. R. China
| | - Yunyun Wu
- Chongqing Municipal Center for Disease Control and Prevention, Chongqing 400042, China
| | - Zhong Luo
- School of Life Science, Chongqing University, Chongqing 400044, P. R. China
| | - Menghuan Li
- School of Life Science, Chongqing University, Chongqing 400044, P. R. China
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9
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Abstract
Hierarchical assembly of programmable DNA frameworks─such as DNA origami─paves the way for versatile nanometer-precise parallel nanopatterning up to macroscopic scales. As of now, the rapid evolution of the DNA nanostructure design techniques and the accessibility of these methods provide a feasible platform for building highly ordered DNA-based assemblies for various purposes. So far, a plethora of different building blocks based on DNA tiles and DNA origami have been introduced, but the dynamics of the large-scale lattice assembly of such modules is still poorly understood. Here, we focus on the dynamics of two-dimensional surface-assisted DNA origami lattice assembly at mica and lipid substrates and the techniques for prospective three-dimensional assemblies, and finally, we summarize the potential applications of such systems.
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Affiliation(s)
- Sofia Julin
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
| | - Adrian Keller
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098 Paderborn, Germany
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
- LIBER Center of Excellence, Aalto University, 00076 Aalto, Finland
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10
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Zhang Q, Zhao B, Lin Z, Shi F, Cheng M. Macroscopic Supramolecular Assembly of Rigid Building Blocks Facilitated by Layer-By-Layer Assembled Microgel Film. ACS APPLIED MATERIALS & INTERFACES 2023; 15:2459-2467. [PMID: 36538496 DOI: 10.1021/acsami.2c19546] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Macroscopic supramolecular assembly (MSA) of building blocks larger than 1 μm provides new methodology for fabrication of functional supramolecular materials and a platform for mechanism investigation of interfacial phenomena. Most reports on MSA are restricted to soft hydrogels, and supramolecular groups can be directly integrated into a hydrogel matrix to generate sufficient attraction for maintaining macroscopic assemblies. For non-hydrogel stiff building blocks, two layer-by-layer modification processes consisting of flexible spacing coating and additional interacting groups are necessary to enable MSA, which is laborious and time-consuming. Approaches for highly efficient MSA based on flexible spacing coating are desired. In this work, MSA of polydimethylsiloxane (PDMS) building blocks is demonstrated by inducing microgel films that serve as both flexible spacing coating and surface functional groups, thus avoiding a two-step LbL modification process. By the varying bilayer number of microgel films, the MSA probability of modified PDMS increases from 54% at 3 bilayers to 100% at 6 bilayers. Control experiments and in situ force measurement strongly support the obtained MSA results and verify the dominant role of the microgel film as a flexible spacing coating and a supramolecularly interactive layer in achieving MSA. Moreover, the underlying mechanism is interpreted as low Young's modulus microgel films rendering surface groups highly mobile to enhance the multivalent interfacial binding. Taken together, this work has demonstrated the feasibility of MSA of rigid building blocks assisted by microgel films as flexible spacing coating and supramolecularly interactive layer simultaneously, which may extend the application fields of microgel materials to interfacial adhesion and advanced manufacturing with MSA methodology.
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Affiliation(s)
- Qian Zhang
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Bingkun Zhao
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Zhenxing Lin
- State Key Laboratory of Marine Coatings, Marine Chemical Research Institute Co., Ltd., Qingdao 266071, China
| | - Feng Shi
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Mengjiao Cheng
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
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11
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Zou J, Stammers AC, Taladriz-Sender A, Withers JM, Christie I, Santana Vega M, Aekbote BL, Peveler WJ, Rusling DA, Burley GA, Clark AW. Fluorous-Directed Assembly of DNA Origami Nanostructures. ACS NANO 2023; 17:752-759. [PMID: 36537902 PMCID: PMC9835977 DOI: 10.1021/acsnano.2c10727] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/15/2022] [Indexed: 05/27/2023]
Abstract
An orthogonal, noncovalent approach to direct the assembly of higher-order DNA origami nanostructures is described. By incorporating perfluorinated tags into the edges of DNA origami tiles we control their hierarchical assembly via fluorous-directed recognition. When we combine this approach with Watson-Crick base-pairing we form discrete dimeric constructs in significantly higher yield (8x) than when either molecular recognition method is used in isolation. This integrated "catch-and-latch" approach, which combines the strength and mobility of the fluorous effect with the specificity of base-pairing, provides an additional toolset for DNA nanotechnology, one that enables increased assembly efficiency while requiring significantly fewer DNA sequences. As a result, our integration of fluorous-directed assembly into origami systems represents a cheap, atom-efficient means to produce discrete superstructures.
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Affiliation(s)
- Jiajia Zou
- James
Watt School of Engineering, Advanced Research Centre, University of Glasgow, Glasgow G11 6EW, United
Kingdom
| | - Ashley C. Stammers
- James
Watt School of Engineering, Advanced Research Centre, University of Glasgow, Glasgow G11 6EW, United
Kingdom
| | - Andrea Taladriz-Sender
- Department
of Pure Applied Chemistry, Thomas Graham Building, 295 Cathedral Street, University of Strathclyde, Glasgow G1 1XL, United Kingdom
| | - Jamie M. Withers
- James
Watt School of Engineering, Advanced Research Centre, University of Glasgow, Glasgow G11 6EW, United
Kingdom
| | - Iain Christie
- James
Watt School of Engineering, Advanced Research Centre, University of Glasgow, Glasgow G11 6EW, United
Kingdom
| | - Marina Santana Vega
- James
Watt School of Engineering, Advanced Research Centre, University of Glasgow, Glasgow G11 6EW, United
Kingdom
| | - Badri L. Aekbote
- James
Watt School of Engineering, Advanced Research Centre, University of Glasgow, Glasgow G11 6EW, United
Kingdom
| | - William J. Peveler
- School
of Chemistry, Joseph Black Building, University
of Glasgow, Glasgow G12 8QQ, United
Kingdom
| | - David A. Rusling
- School
of Pharmacy and Biomedical Sciences, St. Michael’s Building, University of Portsmouth, Portsmouth PO1 2DT, United Kingdom
| | - Glenn A. Burley
- Department
of Pure Applied Chemistry, Thomas Graham Building, 295 Cathedral Street, University of Strathclyde, Glasgow G1 1XL, United Kingdom
| | - Alasdair W. Clark
- James
Watt School of Engineering, Advanced Research Centre, University of Glasgow, Glasgow G11 6EW, United
Kingdom
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12
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Kucinic A, Huang CM, Wang J, Su HJ, Castro CE. DNA origami tubes with reconfigurable cross-sections. NANOSCALE 2023; 15:562-572. [PMID: 36520453 DOI: 10.1039/d2nr05416g] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Structural DNA nanotechnology has enabled the design and construction of complex nanoscale structures with precise geometry and programmable dynamic and mechanical properties. Recent efforts have led to major advances in the capacity to actuate shape changes of DNA origami devices and incorporate DNA origami into larger assemblies, which open the prospect of using DNA to design shape-morphing assemblies as components of micro-scale reconfigurable or sensing materials. Indeed, a few studies have constructed higher order assemblies with reconfigurable devices; however, these demonstrations have utilized structures with relatively simple motion, primarily hinges that open and close. To advance the shape changing capabilities of DNA origami assemblies, we developed a multi-component DNA origami 6-bar mechanism that can be reconfigured into various shapes and can be incorporated into larger assemblies while maintaining capabilities for a variety of shape transformations. We demonstrate the folding of the 6-bar mechanism into four different shapes and demonstrate multiple transitions between these shapes. We also studied the shape preferences of the 6-bar mechanism in competitive folding reactions to gain insight into the relative free energies of the shapes. Furthermore, we polymerized the 6-bar mechanism into tubes with various cross-sections, defined by the shape of the individual mechanism, and we demonstrate the ability to change the shape of the tube cross-section. This expansion of current single-device reconfiguration to higher order scales provides a foundation for nano to micron scale DNA nanotechnology applications such as biosensing or materials with tunable properties.
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Affiliation(s)
- Anjelica Kucinic
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Chao-Min Huang
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA.
| | - Jingyuan Wang
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA.
| | - Hai-Jun Su
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA.
| | - Carlos E Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA.
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
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13
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Stenke LJ, Saccà B. Growth Rate and Thermal Properties of DNA Origami Filaments. NANO LETTERS 2022; 22:8818-8826. [PMID: 36327970 PMCID: PMC9706658 DOI: 10.1021/acs.nanolett.2c02255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 10/14/2022] [Indexed: 06/16/2023]
Abstract
Synthetic DNA filaments exploit the programmability of the individual units and their predictable self-association to mimic the structural and dynamic features of natural protein filaments. Among them, DNA origami filamentous structures are of particular interest, due to the versatility of morphologies, mechanical properties, and functionalities attainable. We here explore the thermodynamic and kinetic properties of linear structures grown from a ditopic DNA origami unit, i.e., a monomer with two distinct interfaces, and employ either base-hybridization or base-stacking interactions to trigger the dimerization and polymerization process. By observing the temporal evolution of the system toward equilibrium, we reveal kinetic aspects of filament growth that cannot be easily captured by postassembly studies. Our work thus provides insights into the thermodynamics and kinetics of hierarchical DNA origami assembly and shows how it can be mastered by the anisotropy of the building unit and its self-association mode.
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14
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Abstract
Over the past 40 years, structural and dynamic DNA nanotechnologies have undoubtedly demonstrated to be effective means for organizing matter at the nanoscale and reconfiguring equilibrium structures, in a predictable fashion and with an accuracy of a few nanometers. Recently, novel concepts and methodologies have been developed to integrate nonequilibrium dynamics into DNA nanostructures, opening the way to the construction of synthetic materials that can adapt to environmental changes and thus acquire new properties. In this Review, we summarize the strategies currently applied for the construction of synthetic DNA filaments and conclude by reporting some recent and most relevant examples of DNA filaments that can emulate typical structural and dynamic features of the cytoskeleton, such as compartmentalization in cell-like vesicles, support for active transport of cargos, sustained or transient growth, and responsiveness to external stimuli.
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15
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Cui H, Zhang T, Kong Y, Xing H, Wei B. Controllable assembly of synthetic constructs with programmable ternary DNA interaction. Nucleic Acids Res 2022; 50:7188-7196. [PMID: 35713533 PMCID: PMC9262601 DOI: 10.1093/nar/gkac478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/28/2022] [Accepted: 06/15/2022] [Indexed: 12/24/2022] Open
Abstract
Compared with the dual binding components in a binary interaction, the third component of a ternary interaction often serves as modulator or regulator in biochemical processes. Here, we presented a programmable ternary interaction strategy based on the natural DNA triplex structure. With the DNA triplex-based ternary interaction, we have successfully demonstrated controllable hierarchical assemblies from nanometer scale synthetic DNA nanostructure units to micrometer scale live bacteria. A selective signaling system responsive to orthogonal nucleic acid signals via ternary interaction was also demonstrated. This assembly method could further enrich the diversified design schemes of DNA nanotechnology.
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Affiliation(s)
- Huangchen Cui
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Tianqing Zhang
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Yuhan Kong
- Institute of Chemical Biology and Nanomedicine; State Key Laboratory of Chemo/Biosensing and Chemometrics; Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology; College of Chemistry and Chemical Engineering; Hunan University, Changsha 410082, China
| | - Hang Xing
- Institute of Chemical Biology and Nanomedicine; State Key Laboratory of Chemo/Biosensing and Chemometrics; Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology; College of Chemistry and Chemical Engineering; Hunan University, Changsha 410082, China
| | - 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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16
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Gao C, Wang Q, Li J, Kwong CHT, Wei J, Xie B, Lu S, Lee SMY, Wang R. In vivo hitchhiking of immune cells by intracellular self-assembly of bacteria-mimetic nanomedicine for targeted therapy of melanoma. SCIENCE ADVANCES 2022; 8:eabn1805. [PMID: 35544569 PMCID: PMC9094661 DOI: 10.1126/sciadv.abn1805] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 03/29/2022] [Indexed: 05/31/2023]
Abstract
Cell-based drug carriers are mostly prepared in vitro, which may negatively affect the physiological functions of cells, and induce possible immune rejections when applied to different individuals. In addition, the immunosuppressive tumor microenvironment limits immune cell-mediated delivery. Here, we report an in vivo strategy to construct cell-based nanomedicine carriers, where bacteria-mimetic gold nanoparticles (GNPs) are intravenously injected, selectively phagocytosed by phagocytic immune cells, and subsequently self-assemble into sizable intracellular aggregates via host-guest interactions. The intracellular aggregates minimize exocytosis of GNPs from immune cells and activate the photothermal property via plasmonic coupling effects. Phagocytic immune cells carry the intracellular GNP aggregates to melanoma tissue via inflammatory tropism. Moreover, an initial photothermal treatment (PTT) of the tumor induces tumor damage that subsequently provides positive feedback to recruit more immune cell-based carriers for enhanced targeting efficiency. The optimized secondary PTT notably improves antitumor immunotherapy, further strengthened by immune checkpoint blockade.
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Affiliation(s)
- Cheng Gao
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau 999078, China
- MoE Frontiers Science Center for Precision Oncology, University of Macau, Taipa, Macau 999078, China
| | - Qingfu Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau 999078, China
| | - Junyan Li
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau 999078, China
| | - Cheryl H. T. Kwong
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau 999078, China
| | - Jianwen Wei
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau 999078, China
| | - Beibei Xie
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau 999078, China
| | - Siyu Lu
- Green Catalysis Center, College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou, 450000, China
| | - Simon M. Y. Lee
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau 999078, China
- MoE Frontiers Science Center for Precision Oncology, University of Macau, Taipa, Macau 999078, China
| | - Ruibing Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau 999078, China
- MoE Frontiers Science Center for Precision Oncology, University of Macau, Taipa, Macau 999078, China
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17
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Fan X, Walther A. 1D Colloidal chains: recent progress from formation to emergent properties and applications. Chem Soc Rev 2022; 51:4023-4074. [PMID: 35502721 DOI: 10.1039/d2cs00112h] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Integrating nanoscale building blocks of low dimensionality (0D; i.e., spheres) into higher dimensional structures endows them and their corresponding materials with emergent properties non-existent or only weakly existent in the individual building blocks. Constructing 1D chains, 2D arrays and 3D superlattices using nanoparticles and colloids therefore continues to be one of the grand goals in colloid and nanomaterial science. Amongst these higher order structures, 1D colloidal chains are of particular interest, as they possess unique anisotropic properties. In recent years, the most relevant advances in 1D colloidal chain research have been made in novel synthetic methodologies and applications. In this review, we first address a comprehensive description of the research progress concerning various synthetic strategies developed to construct 1D colloidal chains. Following this, we highlight the amplified and emergent properties of the resulting materials, originating from the assembly of the individual building blocks and their collective behavior, and discuss relevant applications in advanced materials. In the discussion of synthetic strategies, properties, and applications, particular attention will be paid to overarching concepts, fresh trends, and potential areas of future research. We believe that this comprehensive review will be a driver to guide the interdisciplinary field of 1D colloidal chains, where nanomaterial synthesis, self-assembly, physical property studies, and material applications meet, to a higher level, and open up new research opportunities at the interface of classical disciplines.
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Affiliation(s)
- Xinlong Fan
- Institute for Macromolecular Chemistry, Albert-Ludwigs-University Freiburg, Stefan-Meier-Str. 31, 79104, Freiburg, Germany.
| | - Andreas Walther
- A3BMS Lab, Department of Chemistry, University of Mainz, Duesbergweg 10-14, 55128 Mainz, Germany.
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18
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Xiong Y, Lin Z, Mostarac D, Minevich B, Peng Q, Zhu G, Sánchez PA, Kantorovich S, Ke Y, Gang O. Divalent Multilinking Bonds Control Growth and Morphology of Nanopolymers. NANO LETTERS 2021; 21:10547-10554. [PMID: 34647751 PMCID: PMC8704199 DOI: 10.1021/acs.nanolett.1c03009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/24/2021] [Indexed: 05/22/2023]
Abstract
Assembly of nanoscale objects into linear architectures resembling molecular polymers is a basic organization resulting from divalent interactions. Such linear architectures occur for particles with two binding patches on opposite sides, known as Janus particles. However, unlike molecular systems where valence bonds can be envisioned as pointlike interactions nanoscale patches are often realized through multiple molecular linkages. The relationship between the characteristics of these linkages, the resulting interpatch connectivity, and assembly morphology is not well-explored. Here, we investigate assembly behavior of model divalent nanomonomers, DNA nanocuboid with tailorable multilinking bonds. Our study reveals that the characteristics of individual molecular linkages and their collective properties have a profound effect on nanomonomer reactivity and resulting morphologies. Beyond linear nanopolymers, a common signature of divalent nanomonomers, we observe an effective valence increase as linkages lengthened, leading to the nanopolymer bundling. The experimental findings are rationalized by molecular dynamics simulations.
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Affiliation(s)
- Yan Xiong
- Department
of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Zhiwei Lin
- Department
of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Deniz Mostarac
- Computational
and Soft Matter Physics, Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
- MMM
Mathematics-Magnetism-Materials, Research Platform, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
| | - Brian Minevich
- Department
of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Qiuyuan Peng
- Department
of Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027, United States
| | - Guolong Zhu
- Department
of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Pedro A. Sánchez
- Computational
and Soft Matter Physics, Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
| | - Sofia Kantorovich
- Computational
and Soft Matter Physics, Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
- Department
of Mathematical and Theoretical Physics, Institute of Mathematics
and Natural Sciences, Ural Federal University, Ekaterinburg, 620026, Russia
- MMM
Mathematics-Magnetism-Materials, Research Platform, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
| | - Yonggang Ke
- Wallace H.
Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Oleg Gang
- Department
of Chemical Engineering, Columbia University, New York, New York 10027, United States
- Department
of Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027, United States
- Center
for Functional Nanomaterials, Brookhaven
National Laboratory, Upton, New York 11973, United States
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19
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Li Y, Pei J, Lu X, Jiao Y, Liu F, Wu X, Liu J, Ding B. Hierarchical Assembly of Super-DNA Origami Based on a Flexible and Covalent-Bound Branched DNA Structure. J Am Chem Soc 2021; 143:19893-19900. [PMID: 34783532 DOI: 10.1021/jacs.1c09472] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
DNA origami technique provides a programmable way to construct nanostructures with arbitrary shapes. The dimension of assembled DNA origami, however, is usually limited by the length of the scaffold strand. Herein, we report a general strategy to efficiently organize multiple DNA origami tiles to form super-DNA origami using a flexible and covalent-bound branched DNA structure. In our design, the branched DNA structures (Bn: with a certain number of 2-6 branches) are synthesized by a copper-free click reaction. Equilateral triangular DNA origamis with different numbers of capture strands (Tn: T1, T2, and T3) are constructed as the coassembly tiles. After hybridization with the branched DNA structures, the super-DNA origami (up to 13 tiles) can be efficiently ordered in the predesigned patterns. Compared with traditional DNA junctions (Jn: J2-J6, as control groups) assembled by base pairing between several DNA strands, a higher yield and more compact structures are obtained using our strategy. The highly ordered and discrete DNA origamis can further precisely organize gold nanoparticles into different patterns. This rationally developed DNA origami ordering strategy based on the flexible and covalent-bound branched DNA structure presents a new avenue for the construction of sophisticated DNA architectures with larger molecular weights.
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Affiliation(s)
- Yan Li
- School of Pharmaceutical Sciences, Jilin University, Changchun, Jilin 130012, China.,CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Jin Pei
- School of Pharmaceutical Sciences, Jilin University, Changchun, Jilin 130012, China
| | - Xuehe Lu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Yunfei Jiao
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fengsong Liu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaohui Wu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianbing Liu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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20
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Rubio-Sánchez R, Fabrini G, Cicuta P, Di Michele L. Amphiphilic DNA nanostructures for bottom-up synthetic biology. Chem Commun (Camb) 2021; 57:12725-12740. [PMID: 34750602 PMCID: PMC8631003 DOI: 10.1039/d1cc04311k] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/28/2021] [Indexed: 12/28/2022]
Abstract
DNA nanotechnology enables the construction of sophisticated biomimetic nanomachines that are increasingly central to the growing efforts of creating complex cell-like entities from the bottom-up. DNA nanostructures have been proposed as both structural and functional elements of these artificial cells, and in many instances are decorated with hydrophobic moieties to enable interfacing with synthetic lipid bilayers or regulating bulk self-organisation. In this feature article we review recent efforts to design biomimetic membrane-anchored DNA nanostructures capable of imparting complex functionalities to cell-like objects, such as regulated adhesion, tissue formation, communication and transport. We then discuss the ability of hydrophobic modifications to enable the self-assembly of DNA-based nanostructured frameworks with prescribed morphology and functionality, and explore the relevance of these novel materials for artificial cell science and beyond. Finally, we comment on the yet mostly unexpressed potential of amphiphilic DNA-nanotechnology as a complete toolbox for bottom-up synthetic biology - a figurative and literal scaffold upon which the next generation of synthetic cells could be built.
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Affiliation(s)
- Roger Rubio-Sánchez
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK.
- fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Giacomo Fabrini
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
- fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Pietro Cicuta
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK.
| | - Lorenzo Di Michele
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK.
- fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
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21
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Groeer S, Schumann K, Loescher S, Walther A. Molecular communication relays for dynamic cross-regulation of self-sorting fibrillar self-assemblies. SCIENCE ADVANCES 2021; 7:eabj5827. [PMID: 34818037 PMCID: PMC8612681 DOI: 10.1126/sciadv.abj5827] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Structures in living systems cross-regulate via exchange of molecular information to assemble or disassemble on demand and in a coordinated, signal-triggered fashion. DNA strand displacement (DSD) reaction networks allow rational design of signaling and feedback loops, but combining DSD with structural nanotechnology to achieve self-reconfiguring hierarchical system states is still in its infancy. We introduce modular DSD networks with increasing amounts of regulatory functions, such as negative feedback, signal amplification, and signal thresholding, to cross-regulate the transient polymerization/depolymerization of two self-sorting DNA origami nanofibrils and nanotubes. This is achieved by concatenation of the DSD network with molecular information relays embedded on the origami tips. The two origamis exchange information and display programmable transient states observable by TEM and fluorescence spectroscopy. The programmability on the DSD and the origami level is a viable starting point toward more complex lifelike behavior of colloidal multicomponent systems featuring advanced signal processing functions.
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Affiliation(s)
- Saskia Groeer
- ABMS Lab–Active, Adaptive and Autonomous Bioinspired Materials, Institute for Macromolecular Chemistry, University of Freiburg, Stefan-Meier-Straße 31, 79104 Freiburg, Germany
- Freiburg Materials Research Center (FMF), University of Freiburg, Stefan-Meier-Str. 21, 79104 Freiburg, Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Katja Schumann
- ABMS Lab–Active, Adaptive and Autonomous Bioinspired Materials, Institute for Macromolecular Chemistry, University of Freiburg, Stefan-Meier-Straße 31, 79104 Freiburg, Germany
| | - Sebastian Loescher
- ABMS Lab–Active, Adaptive and Autonomous Bioinspired Materials, Institute for Macromolecular Chemistry, University of Freiburg, Stefan-Meier-Straße 31, 79104 Freiburg, Germany
- Freiburg Materials Research Center (FMF), University of Freiburg, Stefan-Meier-Str. 21, 79104 Freiburg, Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Andreas Walther
- ABMS Lab–Active, Adaptive and Autonomous Bioinspired Materials, Department of Chemistry, University of Mainz, Duesbergweg 10-14, 50447 Mainz, Germany
- Corresponding author.
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22
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Islam MS, Wilkens GD, Wolski K, Zapotoczny S, Heddle JG. Chiral 3D DNA origami structures for ordered heterologous arrays. NANOSCALE ADVANCES 2021; 3:4685-4691. [PMID: 36134307 PMCID: PMC9418780 DOI: 10.1039/d1na00385b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 07/04/2021] [Indexed: 06/16/2023]
Abstract
The DNA origami technique allows the facile design and production of three-dimensional shapes from single template strands of DNA. These can act as functional devices with multiple potential applications but are constrained by practical limitations on size. Multi-functionality could be achieved by connecting together distinct DNA origami modules in an ordered manner. Arraying of non-identical, three-dimensional DNA origamis in an ordered manner is challenging due for example, to a lack of compatible rotational symmetries. Here we show that we can design and build ordered DNA structures using non-identical 3D building blocks by using DNA origami snub-cubes in left-handed and right-handed forms. These can be modified such that one form only binds to the opposite-handed form allowing regular arrays wherein building blocks demonstrate alternating chirality.
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Affiliation(s)
- Md Sirajul Islam
- Malopolska Centre of Biotechnology, Jagiellonian University Gronostajowa 7A Kraków 30-387 Poland
| | - Gerrit David Wilkens
- Malopolska Centre of Biotechnology, Jagiellonian University Gronostajowa 7A Kraków 30-387 Poland
- School of Molecular Medicine, Medical University of Warsaw Warszawa 02-091 Poland
| | - Karol Wolski
- Faculty of Chemistry, Jagiellonian University Gronostajowa 2 Kraków 30-387 Poland
| | - Szczepan Zapotoczny
- Faculty of Chemistry, Jagiellonian University Gronostajowa 2 Kraków 30-387 Poland
| | - Jonathan Gardiner Heddle
- Malopolska Centre of Biotechnology, Jagiellonian University Gronostajowa 7A Kraków 30-387 Poland
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23
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Advances in the synthesis and application of self-assembling biomaterials. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 167:46-62. [PMID: 34329646 DOI: 10.1016/j.pbiomolbio.2021.07.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 07/14/2021] [Accepted: 07/20/2021] [Indexed: 02/08/2023]
Abstract
The present study scrutinized some of the crucial advancements in the synthesis and functionalisation of self-assembling biomaterials for application in biomedicine. The basic concept of self-organization was discussed along with the mechanisms and methods involved in its implementation with biomaterials. Further, several recent applications of this technology in the biological and medical domain, and the avenues for future research and development were presented. This study brought to focus the vast potential of basic and applied research involved, especially in the context of hybrids and composites, as well as the difference in pace of new developments for different types of biomolecular materials. As nanobiotechnology matures, the tools and techniques available for developing and controlling self-assembled biomaterials as well as studying their interaction with biological tissue, will grow exponentially. Presently, self-assembly remains a potent tool for the synthesis of functional biomaterials.
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24
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Ryzhkov NV, Nikolaev KG, Ivanov AS, Skorb EV. Infochemistry and the Future of Chemical Information Processing. Annu Rev Chem Biomol Eng 2021; 12:63-95. [PMID: 33909470 DOI: 10.1146/annurev-chembioeng-122120-023514] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Nowadays, information processing is based on semiconductor (e.g., silicon) devices. Unfortunately, the performance of such devices has natural limitations owing to the physics of semiconductors. Therefore, the problem of finding new strategies for storing and processing an ever-increasing amount of diverse data is very urgent. To solve this problem, scientists have found inspiration in nature, because living organisms have developed uniquely productive and efficient mechanisms for processing and storing information. We address several biological aspects of information and artificial models mimicking corresponding bioprocesses. For instance, we review the formation of synchronization patterns and the emergence of order out of chaos in model chemical systems. We also consider molecular logic and ion fluxes as information carriers. Finally, we consider recent progress in infochemistry, a new direction at the interface of chemistry, biology, and computer science, considering unconventional methods of information processing.
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Affiliation(s)
- Nikolay V Ryzhkov
- Infochemistry Scientific Center of ITMO University, 191002 Saint Petersburg, Russia; , , ,
| | - Konstantin G Nikolaev
- Infochemistry Scientific Center of ITMO University, 191002 Saint Petersburg, Russia; , , ,
| | - Artemii S Ivanov
- Infochemistry Scientific Center of ITMO University, 191002 Saint Petersburg, Russia; , , ,
| | - Ekaterina V Skorb
- Infochemistry Scientific Center of ITMO University, 191002 Saint Petersburg, Russia; , , ,
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25
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Wang D, Chen C, Liu Q, Zhao Q, Wu D, Yuan Y, Huang C, Sun X, Huang C, Leong DT, Wang G, Qian H. Functionalizing DNA nanostructures with natural cationic amino acids. Bioact Mater 2021; 6:2946-2955. [PMID: 33732965 PMCID: PMC7930363 DOI: 10.1016/j.bioactmat.2021.02.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 02/12/2021] [Accepted: 02/13/2021] [Indexed: 11/04/2022] Open
Abstract
Complexing self-assembled DNA nanostructures with various functional guest species is the key to unlocking new and exciting biomedical applications. Cationic guest species not only induce magnesium-free DNA to self-assemble into defined structures but also endow the final complex nanomaterials with new properties. Herein, we propose a novel strategy that employs naturally occurring cationic amino acids to induce DNA self-assembly into defined nanostructures. Natural l-arginine and l-lysine can readily induce the assembly of tile-based DNA nanotubes and DNA origami sheets in a magnesium-free manner. The self-assembly processes are demonstrated to be pH- and concentration-dependent and are achieved at constant temperatures. Moreover, the assembled DNA/amino acid complex nanomaterials are stable at a physiological temperature of 37 °C. Substituting l-arginine with its D form enhances its serum stability. Further preliminary examination of this complex nanomaterial platform for biomedical applications indicates that DNA/amino acids exhibit distinct cellular uptake behaviors compared with their magnesium-assembled counterparts. The nanomaterial mainly clusters around the cell membrane and might be utilized to manipulate molecular events on the membrane. Our study suggests that the properties of DNA nanostructures can be tuned by complexing them with customized guest molecules for a designed application. The strategy proposed herein might be promising to advance the biomedical applications of DNA nanostructures. A “noncanonical DNA self-assembly” strategy is proposed. Cationic amino acids can assemble DNA nanostructures in a magnesium-free system. The complex nanomaterial exhibited high structural and serum stability. DNA nanostructures can be engineered with customized guest molecules for multiple applications.
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Affiliation(s)
- Dong Wang
- Institute of Respiratory Diseases, Xinqiao Hospital, Third Military Medical University, 183 Xinqiao Street, Chongqing, 400037, China.,Department of Respiratory Medicine, Jinling Hospital, Nanjing, Jiangsu, 210002, China
| | - Chunfa Chen
- Institute of Respiratory Diseases, Xinqiao Hospital, Third Military Medical University, 183 Xinqiao Street, Chongqing, 400037, China
| | - Qian Liu
- Laboratory of Pharmacy and Chemistry, And Laboratory of Tissue and Cell Biology, Lab Teaching & Management Center, Chongqing Medical University, Chongqing, 400016, China
| | - Qianwen Zhao
- Institute of Respiratory Diseases, Xinqiao Hospital, Third Military Medical University, 183 Xinqiao Street, Chongqing, 400037, China
| | - Di Wu
- Institute of Respiratory Diseases, Xinqiao Hospital, Third Military Medical University, 183 Xinqiao Street, Chongqing, 400037, China
| | - Yue Yuan
- Institute of Respiratory Diseases, Xinqiao Hospital, Third Military Medical University, 183 Xinqiao Street, Chongqing, 400037, China
| | - Chaowang Huang
- Institute of Respiratory Diseases, Xinqiao Hospital, Third Military Medical University, 183 Xinqiao Street, Chongqing, 400037, China
| | - Xiaorong Sun
- Institute of Respiratory Diseases, Xinqiao Hospital, Third Military Medical University, 183 Xinqiao Street, Chongqing, 400037, China
| | - Chunji Huang
- Basic Medical College, Third Military Medical University, Chongqing, 400038, China
| | - David Tai Leong
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore
| | - Guansong Wang
- Institute of Respiratory Diseases, Xinqiao Hospital, Third Military Medical University, 183 Xinqiao Street, Chongqing, 400037, China
| | - Hang Qian
- Institute of Respiratory Diseases, Xinqiao Hospital, Third Military Medical University, 183 Xinqiao Street, Chongqing, 400037, China
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Loescher S, Walther A. Multivalency Pattern Recognition to Sort Colloidal Assemblies. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2005668. [PMID: 33448120 PMCID: PMC7612461 DOI: 10.1002/smll.202005668] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/15/2020] [Indexed: 05/03/2023]
Abstract
Multivalent interaction is an important principle for self-assembly and has been widely used to assemble colloids. However, surface binding partners are statistically distributed, which falls short of the interaction possibilities arising from geometrically controlled multivalency patterns as seen in viruses. Herein, the precision provided by 3D DNA origami is exploited to introduce multivalency pattern recognition via designing geometrically precise interaction patterns at patches of patchy nanocylinders. This gives rise to self-sorting of colloidal assemblies despite having the same type and number of supramolecular binding motifs-solely based on the pattern located on a 20 × 20 nm2 cross-section. The degree of sorting can be modulated by the geometric overlap of patterns and homo; mixed and alternating supracolloidal polymerizations are demonstrated. Multivalency patterns are able to provide an additional information layer to organize soft matter, important towards engineering of biological responses and functional materials design.
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27
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Li F, Li J, Dong B, Wang F, Fan C, Zuo X. DNA nanotechnology-empowered nanoscopic imaging of biomolecules. Chem Soc Rev 2021; 50:5650-5667. [DOI: 10.1039/d0cs01281e] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
DNA nanotechnology has led to the rise of DNA nanostructures, which possess programmable shapes and are capable of organizing different functional molecules and materials. A variety of DNA nanostructure-based imaging probes have been developed.
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Affiliation(s)
- Fan Li
- Institute of Molecular Medicine
- Department of Urology
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine
- Renji Hospital
- School of Medicine
| | - Jiang Li
- Bioimaging Center
- Shanghai Synchrotron Radiation Facility
- Zhangjiang Laboratory
- Shanghai Advanced Research Institute
- Chinese Academy of Sciences
| | - Baijun Dong
- Institute of Molecular Medicine
- Department of Urology
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine
- Renji Hospital
- School of Medicine
| | - Fei Wang
- Frontiers Science Center for Transformative Molecules
- School of Chemistry and Chemical Engineering
- Shanghai Jiao Tong University
- Shanghai 200240
- China
| | - Chunhai Fan
- Institute of Molecular Medicine
- Department of Urology
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine
- Renji Hospital
- School of Medicine
| | - Xiaolei Zuo
- Institute of Molecular Medicine
- Department of Urology
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine
- Renji Hospital
- School of Medicine
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28
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Jeevan AK, Krishnan SB, Gopidas KR. Structural Deformation to
β
‐Cyclodextrin Due to Strong π‐Stacking in the Self‐Assembly of Inclusion Complex. ChemistrySelect 2020. [DOI: 10.1002/slct.202004488] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Athira K. Jeevan
- Chemical Sciences and Technology Division CSIR-National Institute for Interdisciplinary Science and Technology Thiruvananthapuram 695 019 India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad - 200 002 India
| | - Sumesh B. Krishnan
- Chemical Sciences and Technology Division CSIR-National Institute for Interdisciplinary Science and Technology Thiruvananthapuram 695 019 India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad - 200 002 India
| | - Karical R. Gopidas
- Chemical Sciences and Technology Division CSIR-National Institute for Interdisciplinary Science and Technology Thiruvananthapuram 695 019 India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad - 200 002 India
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29
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Buddingh' BC, Llopis-Lorente A, Abdelmohsen LKEA, van Hest JCM. Dynamic spatial and structural organization in artificial cells regulates signal processing by protein scaffolding. Chem Sci 2020; 11:12829-12834. [PMID: 34094478 PMCID: PMC8163283 DOI: 10.1039/d0sc03933k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 11/04/2020] [Indexed: 01/25/2023] Open
Abstract
Structural and spatial organization are fundamental properties of biological systems that allow cells to regulate a wide range of biochemical processes. This organization is often transient and governed by external cues that initiate dynamic self-assembly processes. The construction of synthetic cell-like materials with similar properties requires the hierarchical and reversible organization of selected functional components on molecular scaffolds to dynamically regulate signaling pathways. The realization of such transient molecular programs in synthetic cells, however, remains underexplored due to the associated complexity of such hierarchical platforms. In this contribution, we effectuate dynamic spatial organization of effector protein subunits in a synthetic biomimetic compartment, a giant unilamellar vesicle (GUV), by associating in a reversible manner two fragments of a split luciferase to the membrane. This induces their structural dimerization, which consequently leads to the activation of enzymatic signaling. Importantly, such organization and activation are dynamic processes, and can be autonomously regulated - thus opening up avenues toward continuous spatiotemporal control over supramolecular organization and signaling in an artificial cell.
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Affiliation(s)
- Bastiaan C Buddingh'
- Department of Chemical Engineering and Chemistry, Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology PO Box 513 5600 MB Eindhoven The Netherlands
| | - Antoni Llopis-Lorente
- Department of Chemical Engineering and Chemistry, Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology PO Box 513 5600 MB Eindhoven The Netherlands
| | - Loai K E A Abdelmohsen
- Department of Chemical Engineering and Chemistry, Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology PO Box 513 5600 MB Eindhoven The Netherlands
| | - Jan C M van Hest
- Department of Chemical Engineering and Chemistry, Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology PO Box 513 5600 MB Eindhoven The Netherlands
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30
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Groeer S, Walther A. Switchable supracolloidal 3D DNA origami nanotubes mediated through fuel/antifuel reactions. NANOSCALE 2020; 12:16995-17004. [PMID: 32780076 PMCID: PMC7612458 DOI: 10.1039/d0nr04209a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
3D DNA origami provide access to the de novo design of monodisperse and functional bio(organic) nanoparticles, and complement structural protein engineering and inorganic and organic nanoparticle synthesis approaches for the design of self-assembling colloidal systems. We show small 3D DNA origami nanoparticles, which polymerize and depolymerize reversibly to nanotubes of micrometer lengths by applying fuel/antifuel switches. 3D DNA nanocylinders are engineered as a basic building block with different numbers of overhang strands at the open sides to allow for their assembly via fuel strands that bridge both overhangs, resulting in the supracolloidal polymerization. The influence of the multivalent interaction patterns and the length of the bridging fuel strand on efficient polymerization and nanotube length distribution is investigated. The polymerized multivalent nanotubes disassemble through toehold-mediated rehybridization by adding equimolar amounts of antifuel strands. Finally, Förster resonance energy transfer yields in situ insights into the kinetics and reversibility of the nanotube polymerization and depolymerization.
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Affiliation(s)
- Saskia Groeer
- A3BMS Lab - Active, Adaptive and Autonomous Bioinspired Material Systems, Institute for Macromolecular Chemistry, University of Freiburg, Stefan-Meier-Straße 31, 79104 Freiburg, Germany. and Freiburg Materials Research Center (FMF), University of Freiburg, Stefan-Meier-Str. 21, 79104 Freiburg, Germany and Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Andreas Walther
- A3BMS Lab - Active, Adaptive and Autonomous Bioinspired Material Systems, Institute for Macromolecular Chemistry, University of Freiburg, Stefan-Meier-Straße 31, 79104 Freiburg, Germany. and Freiburg Materials Research Center (FMF), University of Freiburg, Stefan-Meier-Str. 21, 79104 Freiburg, Germany and Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany and Cluster of Excellence livMatS @ FIT, 79110 Freiburg, Germany
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31
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32
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Loescher S, Walther A. Supracolloidal Self-Assembly of Divalent Janus 3D DNA Origami via Programmable Multivalent Host/Guest Interactions. Angew Chem Int Ed Engl 2020; 59:5515-5520. [PMID: 31814217 PMCID: PMC7154728 DOI: 10.1002/anie.201911795] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 11/26/2019] [Indexed: 01/17/2023]
Abstract
We introduce divalent 3D DNA origami cuboids as truly monodisperse colloids and harness their ability for precision functionalization with defined patches and defined numbers of supramolecular binding motifs. We demonstrate that even adamantane/β-cyclodextrin host/guest inclusion complexes of moderate association strength can induce efficient supracolloidal fibrillization at high dilution of the 3D DNA Origami as a result of cooperative multivalency. We show details on the assembly of Janus and non-Janus 3D DNA origami into supracolloidal homo- and heterofibrils with respect to multivalency effects, electrostatic screening, and stoichiometry. We believe that the merger of 3D DNA origami with colloidal self-assembly and supramolecular motifs provides new synergies at the interface of these disciplines to better understand multivalency effects, to promote structural complexity, and add non-DNA assembling and switching mechanisms to DNA nanoscience.
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Affiliation(s)
- Sebastian Loescher
- ABMS LabInstitute for Macromolecular ChemistryUniversity of FreiburgStefan-Meier-Strasse 3179104FreiburgGermany
- Freiburg Materials Research CenterUniversity of FreiburgStefan-Meier-Strasse 2179104FreiburgGermany
- Freiburg Center for Interactive Materials and Bioinspired TechnologiesUniversity of FreiburgGeorges-Kçhler-Allee 10579110FreiburgGermany
- Freiburg Institute for Advanced Studies (FRIAS)University of FreiburgAlbertstrasse 1979104FreiburgGermany
| | - Andreas Walther
- ABMS LabInstitute for Macromolecular ChemistryUniversity of FreiburgStefan-Meier-Strasse 3179104FreiburgGermany
- Freiburg Materials Research CenterUniversity of FreiburgStefan-Meier-Strasse 2179104FreiburgGermany
- Freiburg Center for Interactive Materials and Bioinspired TechnologiesUniversity of FreiburgGeorges-Kçhler-Allee 10579110FreiburgGermany
- Freiburg Institute for Advanced Studies (FRIAS)University of FreiburgAlbertstrasse 1979104FreiburgGermany
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