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Ma C, Li S, Zeng Y, Lyu Y. DNA-Based Molecular Machines: Controlling Mechanisms and Biosensing Applications. BIOSENSORS 2024; 14:236. [PMID: 38785710 PMCID: PMC11117991 DOI: 10.3390/bios14050236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 04/26/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024]
Abstract
The rise of DNA nanotechnology has driven the development of DNA-based molecular machines, which are capable of performing specific operations and tasks at the nanoscale. Benefitting from the programmability of DNA molecules and the predictability of DNA hybridization and strand displacement, DNA-based molecular machines can be designed with various structures and dynamic behaviors and have been implemented for wide applications in the field of biosensing due to their unique advantages. This review summarizes the reported controlling mechanisms of DNA-based molecular machines and introduces biosensing applications of DNA-based molecular machines in amplified detection, multiplex detection, real-time monitoring, spatial recognition detection, and single-molecule detection of biomarkers. The challenges and future directions of DNA-based molecular machines in biosensing are also discussed.
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Affiliation(s)
- Chunran Ma
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (C.M.); (S.L.); (Y.Z.)
| | - Shiquan Li
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (C.M.); (S.L.); (Y.Z.)
| | - Yuqi Zeng
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (C.M.); (S.L.); (Y.Z.)
| | - Yifan Lyu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (C.M.); (S.L.); (Y.Z.)
- Furong Laboratory, Changsha 410082, China
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2
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Saura-Sanmartin A. Synthesis of 'Impossible' Rotaxanes. Chemistry 2024; 30:e202304025. [PMID: 38168751 DOI: 10.1002/chem.202304025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 12/31/2023] [Accepted: 01/03/2024] [Indexed: 01/05/2024]
Abstract
'Impossible' rotaxanes, which are constituted by interlocked components without obvious binding motifs, have attracted the interest of the mechanically interlocked molecules (MIMs) community. Within the synthetic efforts reported in the last decades towards the preparation of MIMs, some innovative protocols for accessing 'impossible' rotaxanes have been developed. This short review highlights different selected synthetic examples of 'impossible' rotaxanes, as well as suggests some future directions of this research area.
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Affiliation(s)
- Adrian Saura-Sanmartin
- Departamento de Química Orgánica, Facultad de Química, Universidad de Murcia, Campus de Espinardo, 30100, Murcia, Spain
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3
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Song Y, Kim JS. Structure and dynamics of double-stranded DNA rotaxanes. NANOSCALE 2024; 16:4317-4324. [PMID: 38353661 DOI: 10.1039/d3nr05846h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
A DNA rotaxane, with its unique mechanically interlocked architecture consisting of a circular DNA molecule threaded onto a linear DNA axle, holds promise as a fundamental component for nanoscale functional devices. Nevertheless, its structural and dynamic behaviors, essential for advancing molecular machinery, remain largely unexplored. Using extensive all-atom molecular dynamics simulations, we investigated the behaviors of double-stranded DNA (dsDNA) rotaxanes, concentrating on the effects of shape distortion induced by torsional stress in small circular dsDNA containing 70-90 base pairs. We analyzed structural characteristics, including shape, intermolecular distances, and tilt angles, while also exploring dynamic properties such as translational diffusion and toroidal rotation. Our results indicate that shape distortion brings the circular and linear dsDNA components into closer proximity and causes a slight increase in translational diffusion yet a minor decrease in toroidal rotation. Nevertheless, there is no apparent evidence of coupling between translation and rotation. Overall, the insights from this study indicate that such shape distortion does not significantly alter their structure and dynamics. This finding provides flexibility for the design of DNA rotaxanes in nanoscale applications.
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Affiliation(s)
- Yeonho Song
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea.
| | - Jun Soo Kim
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea.
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4
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Centola M, Poppleton E, Ray S, Centola M, Welty R, Valero J, Walter NG, Šulc P, Famulok M. A rhythmically pulsing leaf-spring DNA-origami nanoengine that drives a passive follower. NATURE NANOTECHNOLOGY 2024; 19:226-236. [PMID: 37857824 PMCID: PMC10873200 DOI: 10.1038/s41565-023-01516-x] [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: 02/27/2023] [Accepted: 08/31/2023] [Indexed: 10/21/2023]
Abstract
Molecular engineering seeks to create functional entities for modular use in the bottom-up design of nanoassemblies that can perform complex tasks. Such systems require fuel-consuming nanomotors that can actively drive downstream passive followers. Most artificial molecular motors are driven by Brownian motion, in which, with few exceptions, the generated forces are non-directed and insufficient for efficient transfer to passive second-level components. Consequently, efficient chemical-fuel-driven nanoscale driver-follower systems have not yet been realized. Here we present a DNA nanomachine (70 nm × 70 nm × 12 nm) driven by the chemical energy of DNA-templated RNA-transcription-consuming nucleoside triphosphates as fuel to generate a rhythmic pulsating motion of two rigid DNA-origami arms. Furthermore, we demonstrate actuation control and the simple coupling of the active nanomachine with a passive follower, to which it then transmits its motion, forming a true driver-follower pair.
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Affiliation(s)
- Mathias Centola
- LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institut für Organische Chemie und Biochemie, Universität Bonn, Bonn, Germany
- Max-Planck Institute for Neurobiology of Behaviour, Bonn, Germany
| | - Erik Poppleton
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
- Max-Planck-Institute for Medical Research, Heidelberg, Germany
| | - Sujay Ray
- Single Molecule Analysis Group, Department of Chemistry, Ann Arbor, MI, USA
| | | | - Robb Welty
- Single Molecule Analysis Group, Department of Chemistry, Ann Arbor, MI, USA
| | - Julián Valero
- LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institut für Organische Chemie und Biochemie, Universität Bonn, Bonn, Germany
- Max-Planck Institute for Neurobiology of Behaviour, Bonn, Germany
- Interdisciplinary Nanoscience Center - INANO-MBG, iNANO-huset, Århus, Denmark
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, Ann Arbor, MI, USA.
| | - Petr Šulc
- LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institut für Organische Chemie und Biochemie, Universität Bonn, Bonn, Germany.
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, USA.
| | - Michael Famulok
- LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institut für Organische Chemie und Biochemie, Universität Bonn, Bonn, Germany.
- Max-Planck Institute for Neurobiology of Behaviour, Bonn, Germany.
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Kuwahara K, Yajima S, Yamano Y, Nagatsugi F, Onizuka K. Formation of Direction-Controllable Pseudorotaxane and Catenane Using Chemically Cyclized Oligodeoxynucleotides and Their Noncovalent RNA Labeling. Bioconjug Chem 2023. [PMID: 36930464 DOI: 10.1021/acs.bioconjchem.3c00031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
The formation of interlocked structures, such as rotaxane and catenane, enables noncovalent conjugations. We previously confirmed that the chemically cyclized pseudorotaxane-forming oligodeoxynucleotides (prfODNs) with double-tailed parts formed a pseudorotaxane structure with the target DNA and RNA via the slipping process. Here, we report the one-step synthesis of cyclized prfODNs from alkyne-modified ODNs, after which we investigated the properties and mechanism of the slipping process and performed noncovalent RNA labeling with prfODNs. Additionally, the catenane structure was formed by the combination of pseudorotaxane formation with a 5'-end-phosphorylated RNA and enzymatic ligation. The newly synthesized prfODN represents a new tool for achieving the noncovalent conjugation of various functional moieties to RNAs.
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Affiliation(s)
- Kazuki Kuwahara
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Sayaka Yajima
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Yuuhei Yamano
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Kazumitsu Onizuka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai, Miyagi 980-8578, Japan.,Division for the Establishment of Frontier Sciences of Organization for Advanced Studies, Tohoku University, Aoba-ku, Sendai, Miyagi 980-8577, Japan
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6
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Xu C, Jiang Z, Zhong T, Chen C, Ren W, Sun T, Fu F. Multi-strand Fibers with Hierarchical Helical Structures Driven by Water or Moisture for Soft Actuators. ACS OMEGA 2023; 8:2243-2252. [PMID: 36687042 PMCID: PMC9850490 DOI: 10.1021/acsomega.2c06487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
Smart actuators that combine excellent mechanical properties and responsive actuating performance like biological muscles have attracted considerable attention. In this study, a water/humidity responsive actuator, consisting of multi-strand carboxyl methyl cellulose (CMC) fibers with helical structures, was prepared using wet-spinning and twisting methods. The results showed that owing to the multi-strand structure, the actuator consisted of one-, two-, three-, and four-strand helical fibers, thus achieving a combination of high strength (∼27 MPa), high toughness (>10.34 MJ/m3), and large load limit (>0.30 N), which enable the actuator to theoretically withstand a weight that is at least 20,000 times its weight. Meanwhile, owing to the excellent moisture-responsive ability of CMC, the actuator, with a 5 g load, could achieve untwisting motion. Additionally, its maximum speed was approximately 2158 ± 233 rpm/m under water stimulation, whereas the recovery speed could reach 804 ± 44 rpm/m. Moreover, this untwisting-recovery reversible process was cyclic, whereas the shape and the actuating speed of the actuator remained stable after more than 150 cycles. The actuator improved the load limit that the fiber could withstand when driving under stimulation, thereby enabling the actuator to lift or move heavy objects like human muscles when executing spontaneously under external stimuli. This result shows considerable potential applications in artificial muscles and biomimetic robots.
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Affiliation(s)
- Chenxue Xu
- College
of Chemistry and Chemical Engineering, Research Center for Advanced
Mirco- and Nano-Fabrication Materials, Shanghai
University of Engineering Science, Shanghai 201620, P. R. China
| | - Zhenlin Jiang
- College
of Chemistry and Chemical Engineering, Research Center for Advanced
Mirco- and Nano-Fabrication Materials, Shanghai
University of Engineering Science, Shanghai 201620, P. R. China
- Science and Technology on
Advanced Ceramic
Fibers and Composites Laboratory, National
University of Defense Technology, Changsha 410073, P. R.
China
| | - Tiantian Zhong
- College
of Chemistry and Chemical Engineering, Research Center for Advanced
Mirco- and Nano-Fabrication Materials, Shanghai
University of Engineering Science, Shanghai 201620, P. R. China
| | - Chen Chen
- College
of Chemistry and Chemical Engineering, Research Center for Advanced
Mirco- and Nano-Fabrication Materials, Shanghai
University of Engineering Science, Shanghai 201620, P. R. China
| | - Wanting Ren
- College
of Chemistry and Chemical Engineering, Research Center for Advanced
Mirco- and Nano-Fabrication Materials, Shanghai
University of Engineering Science, Shanghai 201620, P. R. China
| | - Tao Sun
- College
of Chemistry and Chemical Engineering, Research Center for Advanced
Mirco- and Nano-Fabrication Materials, Shanghai
University of Engineering Science, Shanghai 201620, P. R. China
| | - Fanfan Fu
- School
of Environmental and Biological Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Nanjing 210094, China
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Lim KT, Abd-Elsalam KA. Nanorobotics and Nanodiagnostics in Integrative Biology and Biomedicine: A Note from the Editors. NANOROBOTICS AND NANODIAGNOSTICS IN INTEGRATIVE BIOLOGY AND BIOMEDICINE 2023:1-13. [DOI: 10.1007/978-3-031-16084-4_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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8
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Onizuka K, Yamano Y, Abdelhady AM, Nagatsugi F. Hybridization-specific chemical reactions to create interstrand crosslinking and threaded structures of nucleic acids. Org Biomol Chem 2022; 20:4699-4708. [PMID: 35622064 DOI: 10.1039/d2ob00551d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The interstrand crosslinking and threaded structures of nucleic acids have high potential in oligonucleotide therapeutics, chemical biology, and nanotechnology. For example, properly designed crosslinking structures provide high activity and nuclease resistance for anti-miRNAs. The noncovalent labeling and modification by the threaded structures are useful as new chemical biology tools. Photoreversible crosslinking creates smart materials, such as reversible photoresponsive gels and DNA origami objects. This review introduces the creation of interstrand crosslinking and threaded structures, such as catenanes and rotaxanes, based on hybridization-specific chemical reactions and their functions and perspectives.
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Affiliation(s)
- Kazumitsu Onizuka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan. .,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan.,Division for the Establishment of Frontier Sciences of Organization for Advanced Studies, Tohoku University, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Yuuhei Yamano
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.
| | - Ahmed Mostafa Abdelhady
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan. .,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan.,Department of Chemistry, Faculty of Science, Al-Azhar University, Nasr City, 11884, Cairo, Egypt
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan. .,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
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9
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Design and simulation of DNA, RNA and hybrid protein-nucleic acid nanostructures with oxView. Nat Protoc 2022; 17:1762-1788. [PMID: 35668321 DOI: 10.1038/s41596-022-00688-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 01/18/2022] [Indexed: 11/08/2022]
Abstract
Molecular simulation has become an integral part of the DNA/RNA nanotechnology research pipeline. In particular, understanding the dynamics of structures and single-molecule events has improved the precision of nanoscaffolds and diagnostic tools. Here we present oxView, a design tool for visualization, design, editing and analysis of simulations of DNA, RNA and nucleic acid-protein nanostructures. oxView provides an accessible software platform for designing novel structures, tweaking existing designs, preparing them for simulation in the oxDNA/RNA molecular simulation engine and creating visualizations of simulation results. In several examples, we present procedures for using the tool, including its advanced features that couple the design capabilities with a coarse-grained simulation engine and scripting interface that can programmatically edit structures and facilitate design of complex structures from multiple substructures. These procedures provide a practical basis from which researchers, including experimentalists with limited computational experience, can integrate simulation and 3D visualization into their existing research programs.
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