1
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Gao MH, Yang XH, Tang JH, Zhou XM, Lei YM, Zhuo Y. Selective Activation of Cascade Assembly Amplification for DNA Methyltransferase Detection Using a Double-Loop Interlocked DNA Circuit. Anal Chem 2024. [PMID: 39024185 DOI: 10.1021/acs.analchem.4c02498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Precise and reliable monitoring of DNA adenine methyltransferase (Dam) activity is essential for disease diagnosis and biological analysis. However, existing techniques for detecting Dam activity often rely on specific DNA recognition probes that are susceptible to DNA degradation and exhibit limited target sensitivity and specificity. In this study, we designed and engineered a stable and dynamic DNA nanodevice called the double-loop interlocked DNA circuit (DOOR) that enables the sensitive and selective monitoring of Dam activity in complex biological environments. The DOOR incorporates two interlocked specialized sequences: a palindromic sequence for Dam identification and an initiator sequence for signal amplification. In the presence of Dam, the DOOR is cleaved by double-stranded DNA phosphodiesterase I endonuclease, generating massive double-stranded DNA (dsDNA) units. These units can self-assemble into a long dsDNA scaffold, thereby enhancing the subsequent reaction kinetics. The dsDNA scaffold further triggers a hyperbranched hybrid chain reaction to produce a fluorescent 3D DNA nanonet, enabling more precise monitoring of the Dam activity. The DOOR device exhibits excellent sensitivity, specificity, and stability, rendering it a powerful tool for studying DNA methylation in various biological processes and diseases.
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Affiliation(s)
- Mao-Hua Gao
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Xiao-Hong Yang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 266 Fangzheng Ave, Beibei, Chongqing 400714, China
| | - Jia-Hao Tang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Xue-Mei Zhou
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Yan-Mei Lei
- Institute of Developmental Biology and Regenerative Medicine, Southwest University, Chongqing 400715, P. R. China
| | - Ying Zhuo
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
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2
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Soni AK, Jha RK. Nanotechnology's Applications and Potential in Various Fields. Cureus 2024; 16:e59234. [PMID: 38813303 PMCID: PMC11134515 DOI: 10.7759/cureus.59234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 04/28/2024] [Indexed: 05/31/2024] Open
Abstract
Since ancient times, several sorts of nanoparticles have been employed in the quickly expanding field of nanotechnology. These features include size, shape, and chemical as well as physical properties. Because of their small size and huge surface area, carbon-based nanoparticles, including fullerenes, carbon nanotubes, graphene, graphene oxide, and carbon-based quantum dots, have attracted a lot of attention in a variety of sectors, including biomedical applications. Lipid bilayers form the spherical vesicles known as liposomes. Magnetic resonance imaging (MRI) contrast agents are iron oxide nanoparticles. These materials are perfect for drug and delivery of genes, bioimaging, and bone repair because of their remarkable mechanical, electrical, visual, and chemical properties. However, concerns about potential asbestos-related diseases have arisen due to their length-to-width aspect ratio. Ceramic nanoparticles, on the other hand, are a common material in daily life and play a crucial role in bone repair, multiscale hybridisation, and aerospace structures. These nanoparticles can enhance osseointegration and bone development by mimicking the nanocomposition and nanoscale characteristics of bone tissue and enhance osteoconductive and osteoinductive capacities. Ceramic nanoparticles, however, have the potential to generate oxidative stress, which can result in irritation of the reticuloendothelial system, cytotoxicity to the heart, liver, and lungs, as well as toxicity to the cells that are attached. Additionally, oxidative stress, cell damage, and genotoxicity might result from the generation of free radicals by ceramic nanoparticles. Metal nanoparticles exhibit linear optical properties similar to molecular systems but arise from a different physical process. Semiconductor nanocrystals (NCs) are made from various compounds, such as silicon and germanium. Polyandry nanoparticles are particles approximately 10 and 10000 nanometers (nm) in size that can contain active substances. They have applications in vaccine delivery, gene therapy, and polymer nanoparticles (nanomedicine) for therapeutic applications.
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Affiliation(s)
- Asmith K Soni
- Medical Education, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Roshan K Jha
- Biochemistry, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
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3
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López-Tena M, Farrera-Soler L, Barluenga S, Winssinger N. Pseudo-Complementary G:C Base Pair for Mixed Sequence dsDNA Invasion and Its Applications in Diagnostics (SARS-CoV-2 Detection). JACS AU 2023; 3:449-458. [PMID: 36873687 PMCID: PMC9975836 DOI: 10.1021/jacsau.2c00588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/18/2023] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Pseudo-complementary oligonucleotides contain artificial nucleobases designed to reduce duplex formation in the pseudo-complementary pair without compromising duplex formation to targeted (complementary) oligomers. The development of a pseudo-complementary A:T base pair, Us:D, was important in achieving dsDNA invasion. Herein, we report pseudo-complementary analogues of the G:C base pair leveraged on steric and electrostatic repulsion between the cationic phenoxazine analogue of cytosine (G-clamp, C+) and N-7 methyl guanine (G+), which is also cationic. We show that while complementary peptide nucleic acids (PNA) form a much more stable homoduplex than the PNA:DNA heteroduplex, oligomers based on pseudo-C:G complementary PNA favor PNA:DNA hybridization. We show that this enables dsDNA invasion at physiological salt concentration and that stable invasion complexes are obtained with low equivalents of PNAs (2-4 equiv). We harnessed the high yield of dsDNA invasion for the detection of RT-RPA amplicon using a lateral flow assay (LFA) and showed that two strains of SARS-CoV-2 can be discriminated owing to single nucleotide resolution.
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4
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Yan Y, Chang D, Xu Y, Chang Y, Zhang Q, Yuan Q, Salena BJ, Li Y, Liu M. Engineering a Ligase Binding DNA Aptamer into a Templating DNA Scaffold to Guide the Selective Synthesis of Circular DNAzymes and DNA Aptamers. J Am Chem Soc 2023; 145:2630-2637. [PMID: 36657012 PMCID: PMC9896561 DOI: 10.1021/jacs.2c12666] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Functional nucleic acids (FNAs), such as DNAzymes and DNA aptamers, can be engineered into circular forms for improved performance. Circular FNAs are promising candidates for bioanalytical and biomedical applications due to their intriguing properties of enhanced biological stability and compatibility with rolling circle amplification. They are typically made from linear single-stranded (ss) DNA molecules via ligase-mediated ligation. However, it remains a great challenge to synthesize circular ssDNA molecules in high yield due to inherent side reactions where two or more of the same ssDNA molecules are ligated. Herein, we present a strategy to overcome this issue by first using in vitro selection to search from a random-sequence DNA library a ligatable DNA aptamer that binds a DNA ligase and then by engineering this aptamer into a general-purpose templating DNA scaffold to guide the ligase to execute selective intramolecular circularization. We demonstrate the broad utility of this approach via the creation of several species of circular DNA molecules, including a circular DNAzyme sensor for a bacterium and a circular DNA aptamer sensor for a protein target with excellent detection sensitivity and specificity.
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Affiliation(s)
- Yu Yan
- School
of Environmental Science and Technology, Key Laboratory of Industrial
Ecology and Environmental Engineering (Ministry of Education), Dalian
POCT Laboratory, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Dingran Chang
- Department
of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S4K1, Canada
| | - Yongbin Xu
- Department
of Bioengineering, College of Life Science, Dalian Nationalities University, Dalian, Liaoning 116600, China
| | - Yangyang Chang
- School
of Environmental Science and Technology, Key Laboratory of Industrial
Ecology and Environmental Engineering (Ministry of Education), Dalian
POCT Laboratory, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Qiang Zhang
- School
of Bioengineering, Dalian University of
Technology, Dalian, Liaoning 116024, China
| | - Quan Yuan
- State
Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry
and Chemical Engineering, Institute of Chemical
Biology and Nanomedicine, Hunan University, Changsha 410082, China
| | - Bruno J. Salena
- Department
of Medicine, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S4K1, Canada
| | - Yingfu Li
- Department
of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S4K1, Canada,
| | - Meng Liu
- School
of Environmental Science and Technology, Key Laboratory of Industrial
Ecology and Environmental Engineering (Ministry of Education), Dalian
POCT Laboratory, Dalian University of Technology, Dalian, Liaoning 116024, China,
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5
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Li Q, Centola M, Keppner D, Valero J, Famulok M. Reconfigurable Nanopolygons Made of DNA Catenanes. Bioconjug Chem 2023; 34:105-110. [PMID: 36595299 DOI: 10.1021/acs.bioconjchem.2c00464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The development of new types of bonds and linkages that can reversibly tune the geometry and structural features of molecules is an elusive goal in chemistry. Herein, we report the use of catenated DNA structures as nanolinkages that can reversibly switch their angle and form different kinds of polygonal nanostructures. We designed a reconfigurable catenane that can self-assemble into a triangular or hexagonal structure upon addition of programmable DNA strands that function via toehold strand-displacement. The nanomechanical and structural features of these catenated nanojoints can be applied for the construction of dynamic systems such as molecular motors with switchable functionalities.
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Affiliation(s)
- Qi Li
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Xianlie Middle Road 100, 510070 Guangzhou, China.,LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institut für Organische Chemie und Biochemie, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Mathias Centola
- LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institut für Organische Chemie und Biochemie, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany.,Chemical Biology Max-Planck-Fellow Group, Max-Planck Institute for Neurobiology of Behavior - Caesar, Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Daniel Keppner
- LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institut für Organische Chemie und Biochemie, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Julián Valero
- LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institut für Organische Chemie und Biochemie, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Michael Famulok
- LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institut für Organische Chemie und Biochemie, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany.,Chemical Biology Max-Planck-Fellow Group, Max-Planck Institute for Neurobiology of Behavior - Caesar, Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
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6
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Yao S, Chang Y, Zhai Z, Sugiyama H, Endo M, Zhu W, Xu Y, Yang Y, Qian X. DNA-Based Daisy Chain Rotaxane Nanocomposite Hydrogels as Dual-Programmable Dynamic Scaffolds for Stem Cell Adhesion. ACS APPLIED MATERIALS & INTERFACES 2022; 14:20739-20748. [PMID: 35485950 DOI: 10.1021/acsami.2c03265] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Interlocked DNA nanostructures perform programmable movements in nanoscales such as sliding, contraction, and expansion. However, utilizing nanoscaled interlocked movements to regulate the functions of larger length scaled matrix and developing their applications has not yet been reported. Herein we describe the assembly of DNA-based daisy chain rotaxane nanostructure (DNA-DCR) composed of two hollow DNA nanostructures as macrocycles, two interlocked axles and two triangular prism-shaped DNA structures as stoppers, in which three mechanical states─fixed extended state (FES), sliding state (SS), and fixed contracted state (FCS)─are characterized by using toehold-mediated strand displacement reaction (SDR). The DNA-DCRs are further used as nanocomposites and introduced into hydrogel matrix to produce interlocked hydrogels, which shows modulable stiffness by elongating the interlocked axles to regulate the hydrogel swelling with hybridization chain reaction (HCR) treatment. Then the DCR-hydrogels are employed as dynamic biointerfaces for human mesenchymal stem cells (hMSCs) adhesion studies. First, hMSCs showed lower cell density on bare DCR-hydrogel treated with HCR-initiated swelling for stiffness decreasing. Second, the cell adhesion ligand (RGD) modified DNA-DCRs are constructed for hydrogel functionalization. DCR(RGD) hydrogel endows the mobility of RGDs by switching the mechanical states of DNA-DCR. HMSCs showed increased cell density on DCRSS(RGD) hydrogel than on DCRFCS(RGD) hydrogel. Therefore, our DNA-DCR nanocomposite hydrogel exhibit dual-programmable performances including swelling adjustment and offering sliding for incorporated ligands, which can be both utilized as dynamic scaffolds for regulating the stem cell adhesion. The dual-programmable cross-scale regulation from interlocked DNA nanostructures to hydrogel matrix was achieved, demonstrating a new pathway of DNA-based materials.
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Affiliation(s)
- Shengtao Yao
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai200237, China
| | - Yongyun Chang
- Shanghai Key Laboratory of Orthopaedic Implants, Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai200011, China
| | - Zanjing Zhai
- Shanghai Key Laboratory of Orthopaedic Implants, Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai200011, China
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto606-8502, Japan
| | - Masayuki Endo
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto606-8502, Japan
| | - Weiping Zhu
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai200237, China
| | - Yufang Xu
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai200237, China
| | - Yangyang Yang
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai200237, China
| | - Xuhong Qian
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai200237, China
- State Key Laboratory of Bioreactor, East China University of Science and Technology, Shanghai200237, China
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7
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Abstract
DNA walkers are molecular machines that can move with high precision onthe nanoscale due to their structural and functional programmability. Despite recent advances in the field that allow exploring different energy sources, stimuli, and mechanisms of action for these nanomachines, the continuous operation and reusability of DNA walkers remains challenging because in most cases the steps, once taken by the walker, cannot be taken again. Herein we report the path regeneration of a burnt-bridges DNA catenane walker using RNase A. This walker uses a T7RNA polymerase that produces long RNA transcripts to hybridize to the path and move forward while the RNA remains hybridized to the path and blocks it for an additional walking cycle. We show that RNA degradation triggered by RNase A restores the path and returns the walker to the initial position. RNase inhibition restarts the function of the walker.
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Affiliation(s)
- Julián Valero
- LIMES Chemical Biology UnitUniversität BonnGerhard-Domagk-Straße 153121BonnGermany
- Center of Advanced European Studies and ResearchLudwig-Erhard-Allee 253175BonnGermany
- Present address: Interdisciplinary Nanoscience Center—INANO-MBG, iNANO-husetGustav Wieds Vej 14, building 1592, 3288000Aarhus CDenmark
| | - Michael Famulok
- LIMES Chemical Biology UnitUniversität BonnGerhard-Domagk-Straße 153121BonnGermany
- Center of Advanced European Studies and ResearchLudwig-Erhard-Allee 253175BonnGermany
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8
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Valero J, Škugor M. Mechanisms, Methods of Tracking and Applications of DNA Walkers: A Review. Chemphyschem 2020; 21:1971-1988. [DOI: 10.1002/cphc.202000235] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 06/04/2020] [Indexed: 11/08/2022]
Affiliation(s)
- Julián Valero
- Interdisciplinary Nanoscience Center (iNANO) Aarhus University Gustav Wieds Vej 14 8000 Aarhus Denmark
- LIMES Chemical Biology Unit Universität Bonn Gerhard-Domagk-Straße 1 53121 Bonn Germany
| | - Marko Škugor
- LIMES Chemical Biology Unit Universität Bonn Gerhard-Domagk-Straße 1 53121 Bonn Germany
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9
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Valero J, Famulok M. Regeneration of Burnt Bridges on a DNA Catenane Walker. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Julián Valero
- LIMES Chemical Biology UnitUniversität Bonn Gerhard-Domagk-Straße 1 53121 Bonn Germany
- Center of Advanced European Studies and Research Ludwig-Erhard-Allee 2 53175 Bonn Germany
- Present address: Interdisciplinary Nanoscience Center—INANO-MBG, iNANO-huset Gustav Wieds Vej 14, building 1592, 328 8000 Aarhus C Denmark
| | - Michael Famulok
- LIMES Chemical Biology UnitUniversität Bonn Gerhard-Domagk-Straße 1 53121 Bonn Germany
- Center of Advanced European Studies and Research Ludwig-Erhard-Allee 2 53175 Bonn Germany
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10
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Hu Y, Wang Y, Yan J, Wen N, Xiong H, Cai S, He Q, Peng D, Liu Z, Liu Y. Dynamic DNA Assemblies in Biomedical Applications. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2000557. [PMID: 32714763 PMCID: PMC7375253 DOI: 10.1002/advs.202000557] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 04/07/2020] [Indexed: 05/13/2023]
Abstract
Deoxyribonucleic acid (DNA) has been widely used to construct homogeneous structures with increasing complexity for biological and biomedical applications due to their powerful functionalities. Especially, dynamic DNA assemblies (DDAs) have demonstrated the ability to simulate molecular motions and fluctuations in bionic systems. DDAs, including DNA robots, DNA probes, DNA nanochannels, DNA templates, etc., can perform structural transformations or predictable behaviors in response to corresponding stimuli and show potential in the fields of single molecule sensing, drug delivery, molecular assembly, etc. A wave of exploration of the principles in designing and usage of DDAs has occurred, however, knowledge on these concepts is still limited. Although some previous reviews have been reported, systematic and detailed reviews are rare. To achieve a better understanding of the mechanisms in DDAs, herein, the recent progress on the fundamental principles regarding DDAs and their applications are summarized. The relative assembly principles and computer-aided software for their designing are introduced. The advantages and disadvantages of each software are discussed. The motional mechanisms of the DDAs are classified into exogenous and endogenous stimuli-triggered responses. The special dynamic behaviors of DDAs in biomedical applications are also summarized. Moreover, the current challenges and future directions of DDAs are proposed.
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Affiliation(s)
- Yaqin Hu
- Department of Pharmaceutical EngineeringCollege of Chemistry and Chemical EngineeringCentral South UniversityChangshaHunan410083P. R. China
| | - Ying Wang
- Department of Pharmaceutical EngineeringCollege of Chemistry and Chemical EngineeringCentral South UniversityChangshaHunan410083P. R. China
| | - Jianhua Yan
- Xiangya School of Pharmaceutical SciencesCentral South UniversityChangshaHunan410013P. R. China
| | - Nachuan Wen
- Department of Pharmaceutical EngineeringCollege of Chemistry and Chemical EngineeringCentral South UniversityChangshaHunan410083P. R. China
| | - Hongjie Xiong
- Xiangya School of Pharmaceutical SciencesCentral South UniversityChangshaHunan410013P. R. China
| | - Shundong Cai
- Xiangya School of Pharmaceutical SciencesCentral South UniversityChangshaHunan410013P. R. China
| | - Qunye He
- Xiangya School of Pharmaceutical SciencesCentral South UniversityChangshaHunan410013P. R. China
| | - Dongming Peng
- Department of Medicinal ChemistrySchool of PharmacyHunan University of Chinese MedicineChangshaHunan410013P. R. China
| | - Zhenbao Liu
- Xiangya School of Pharmaceutical SciencesCentral South UniversityChangshaHunan410013P. R. China
- Molecular Imaging Research Center of Central South UniversityChangshaHunan410013P. R. China
| | - Yanfei Liu
- Department of Pharmaceutical EngineeringCollege of Chemistry and Chemical EngineeringCentral South UniversityChangshaHunan410083P. R. China
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11
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Liang X, Li L, Tang J, Komiyama M, Ariga K. Dynamism of Supramolecular DNA/RNA Nanoarchitectonics: From Interlocked Structures to Molecular Machines. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2020. [DOI: 10.1246/bcsj.20200012] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, P. R. China
| | - Lin Li
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Jiaxuan Tang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Katsuhiko Ariga
- WPI-MANA, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
- Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan
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12
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Acevedo-Jake A, Ball AT, Galli M, Kukwikila M, Denis M, Singleton DG, Tavassoli A, Goldup SM. AT-CuAAC Synthesis of Mechanically Interlocked Oligonucleotides. J Am Chem Soc 2020; 142:5985-5990. [PMID: 32155338 PMCID: PMC8016193 DOI: 10.1021/jacs.0c01670] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Indexed: 12/22/2022]
Abstract
We present a simple strategy for the synthesis of main chain oligonucleotide rotaxanes with precise control over the position of the macrocycle. The novel DNA-based rotaxanes were analyzed to assess the effect of the mechanical bond on their properties.
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Affiliation(s)
- Amanda Acevedo-Jake
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Andrew T. Ball
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Marzia Galli
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Mikiembo Kukwikila
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Mathieu Denis
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Daniel G. Singleton
- ATDBio
Ltd, School of Chemistry, University of
Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Ali Tavassoli
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Stephen M. Goldup
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
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13
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Xiong Q, Xie C, Zhang Z, Liu L, Powell JT, Shen Q, Lin C. DNA Origami Post-Processing by CRISPR-Cas12a. Angew Chem Int Ed Engl 2020; 59:3956-3960. [PMID: 31883145 PMCID: PMC7101258 DOI: 10.1002/anie.201915555] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Indexed: 12/26/2022]
Abstract
Customizable nanostructures built through the DNA-origami technique hold tremendous promise in nanomaterial fabrication and biotechnology. Despite the cutting-edge tools for DNA-origami design and preparation, it remains challenging to separate structural components of an architecture built from-thus held together by-a continuous scaffold strand, which in turn limits the modularity and function of the DNA-origami devices. To address this challenge, here we present an enzymatic method to clean up and reconfigure DNA-origami structures. We target single-stranded (ss) regions of DNA-origami structures and remove them with CRISPR-Cas12a, a hyper-active ssDNA endonuclease without sequence specificity. We demonstrate the utility of this facile, selective post-processing method on DNA structures with various geometrical and mechanical properties, realizing intricate structures and structural transformations that were previously difficult to engineer. Given the biocompatibility of Cas12a-like enzymes, this versatile tool may be programmed in the future to operate functional nanodevices in cells.
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Affiliation(s)
| | | | - Zhao Zhang
- Department of Cell Biology & Nanobiology Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516 (USA)
| | - Longfei Liu
- Department of Cell Biology & Nanobiology Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516 (USA)
| | - John T Powell
- Department of Cell Biology & Nanobiology Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516 (USA)
| | - Qi Shen
- Department of Cell Biology & Nanobiology Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516 (USA)
| | - Chenxiang Lin
- Department of Cell Biology & Nanobiology Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516 (USA)
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14
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Xiong Q, Xie C, Zhang Z, Liu L, Powell JT, Shen Q, Lin C. DNA Origami Post‐Processing by CRISPR‐Cas12a. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915555] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Qiancheng Xiong
- Department of Cell Biology & Nanobiology Institute Yale University 850 West Campus Drive West Haven CT 06516 USA
| | - Chun Xie
- Department of Cell Biology & Nanobiology Institute Yale University 850 West Campus Drive West Haven CT 06516 USA
| | - Zhao Zhang
- Department of Cell Biology & Nanobiology Institute Yale University 850 West Campus Drive West Haven CT 06516 USA
| | - Longfei Liu
- Department of Cell Biology & Nanobiology Institute Yale University 850 West Campus Drive West Haven CT 06516 USA
| | - John T Powell
- Department of Cell Biology & Nanobiology Institute Yale University 850 West Campus Drive West Haven CT 06516 USA
| | - Qi Shen
- Department of Cell Biology & Nanobiology Institute Yale University 850 West Campus Drive West Haven CT 06516 USA
| | - Chenxiang Lin
- Department of Cell Biology & Nanobiology Institute Yale University 850 West Campus Drive West Haven CT 06516 USA
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15
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Ali M, Afshan N, Jiang C, Zheng H, Xiao SJ. 2D DNA lattice arrays assembled from DNA dumbbell tiles using poly(A-T)-rich stems. NANOSCALE 2019; 11:22216-22221. [PMID: 31728476 DOI: 10.1039/c9nr07911d] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Poly(A-T)-rich sequences have been applied as stems of DNA dumbbell tiles for construction of single crystalline 2D DNA lattice arrays in slightly acidic solutions. These arrays show much higher stability and better organised crystalline lattice structures than those assembled from DNA dumbbell tiles with randomly sequenced stems in slightly alkaline environments. DNA nanotechnology probably provides a useful platform to study the mechanical properties of DNA duplexes with specific sequences.
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Affiliation(s)
- Mashooq Ali
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, Jiangsu, China.
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16
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Design, assembly, characterization, and operation of double-stranded interlocked DNA nanostructures. Nat Protoc 2019; 14:2818-2855. [DOI: 10.1038/s41596-019-0198-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 05/16/2019] [Indexed: 01/03/2023]
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17
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Simmel FC, Yurke B, Singh HR. Principles and Applications of Nucleic Acid Strand Displacement Reactions. Chem Rev 2019; 119:6326-6369. [PMID: 30714375 DOI: 10.1021/acs.chemrev.8b00580] [Citation(s) in RCA: 357] [Impact Index Per Article: 71.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Dynamic DNA nanotechnology, a subfield of DNA nanotechnology, is concerned with the study and application of nucleic acid strand-displacement reactions. Strand-displacement reactions generally proceed by three-way or four-way branch migration and initially were investigated for their relevance to genetic recombination. Through the use of toeholds, which are single-stranded segments of DNA to which an invader strand can bind to initiate branch migration, the rate with which strand displacement reactions proceed can be varied by more than 6 orders of magnitude. In addition, the use of toeholds enables the construction of enzyme-free DNA reaction networks exhibiting complex dynamical behavior. A demonstration of this was provided in the year 2000, in which strand displacement reactions were employed to drive a DNA-based nanomachine (Yurke, B.; et al. Nature 2000, 406, 605-608). Since then, toehold-mediated strand displacement reactions have been used with ever increasing sophistication and the field of dynamic DNA nanotechnology has grown exponentially. Besides molecular machines, the field has produced enzyme-free catalytic systems, all DNA chemical oscillators and the most complex molecular computers yet devised. Enzyme-free catalytic systems can function as chemical amplifiers and as such have received considerable attention for sensing and detection applications in chemistry and medical diagnostics. Strand-displacement reactions have been combined with other enzymatically driven processes and have also been employed within living cells (Groves, B.; et al. Nat. Nanotechnol. 2015, 11, 287-294). Strand-displacement principles have also been applied in synthetic biology to enable artificial gene regulation and computation in bacteria. Given the enormous progress of dynamic DNA nanotechnology over the past years, the field now seems poised for practical application.
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Affiliation(s)
| | - Bernard Yurke
- Micron School of Materials Science and Engineering , Boise State University , Boise , ID 83725 , United States
| | - Hari R Singh
- Physics Department , TU München , 85748 Garching , Germany
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18
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Singh J, Kim DH, Kim EH, Singh N, Kim H, Hadiputra R, Jung J, Chi KW. Selective and quantitative synthesis of a linear [3]catenane by two component coordination-driven self-assembly. Chem Commun (Camb) 2019; 55:6866-6869. [DOI: 10.1039/c9cc03336j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Coordination-driven self-assembly and synergistic non-covalent intercycler interactions (π–π, CH–π and CH–N) for the selective formation of a linear [3]catenane.
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Affiliation(s)
- Jatinder Singh
- Department of Chemistry
- University of Ulsan
- Ulsan 44610
- Republic of Korea
| | - Dong Hwan Kim
- Department of Chemistry
- University of Ulsan
- Ulsan 44610
- Republic of Korea
| | - Eun-Hee Kim
- Protein Structure Group
- Korea Basic Science Institute
- Ochang
- Chungbuk 28119
- Republic of Korea
| | - Nem Singh
- Department of Chemistry
- University of Ulsan
- Ulsan 44610
- Republic of Korea
| | - Hyunuk Kim
- Energy Materials Laboratory
- Korea Institute of Energy Research
- Daejeon 34129
- Republic of Korea
| | - Rizky Hadiputra
- Department of Chemistry
- University of Ulsan
- Ulsan 44610
- Republic of Korea
| | - Jaehoon Jung
- Department of Chemistry
- University of Ulsan
- Ulsan 44610
- Republic of Korea
| | - Ki-Whan Chi
- Department of Chemistry
- University of Ulsan
- Ulsan 44610
- Republic of Korea
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19
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Wang XW, Zhang WB. Chemical Topology and Complexity of Protein Architectures. Trends Biochem Sci 2018; 43:806-817. [DOI: 10.1016/j.tibs.2018.07.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 07/01/2018] [Accepted: 07/03/2018] [Indexed: 12/16/2022]
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