1
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Alarcón-Correa M, Kilwing L, Peter F, Liedl T, Fischer P. Platinum-DNA Origami Hybrid Structures in Concentrated Hydrogen Peroxide. Chemphyschem 2023; 24:e202300294. [PMID: 37640688 DOI: 10.1002/cphc.202300294] [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: 04/24/2023] [Revised: 08/21/2023] [Accepted: 08/22/2023] [Indexed: 08/31/2023]
Abstract
The DNA origami technique allows fast and large-scale production of DNA nanostructures that stand out with an accurate addressability of their anchor points. This enables the precise organization of guest molecules on the surfaces and results in diverse functionalities. However, the compatibility of DNA origami structures with catalytically active matter, a promising pathway to realize autonomous DNA machines, has so far been tested only in the context of bio-enzymatic activity, but not in chemically harsh reaction conditions. The latter are often required for catalytic processes involving high-energy fuels. Here, we provide proof-of-concept data showing that DNA origami structures are stable in 5 % hydrogen peroxide solutions over the course of at least three days. We report a protocol to couple these to platinum nanoparticles and show catalytic activity of the hybrid structures. We suggest that the presented hybrid structures are suitable to realize catalytic nanomachines combined with precisely engineered DNA nanostructures.
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Affiliation(s)
- Mariana Alarcón-Correa
- Max Planck Institute for Medical Research, Jahnstr. 29, 69120, Heidelberg, Germany
- Institute for Molecular Systems Engineering and Advanced Materials, Heidelberg University, INF 225, 69120, Heidelberg, Germany
| | - Luzia Kilwing
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Florian Peter
- Max Planck Institute for Medical Research, Jahnstr. 29, 69120, Heidelberg, Germany
- Institute for Molecular Systems Engineering and Advanced Materials, Heidelberg University, INF 225, 69120, Heidelberg, Germany
| | - Tim Liedl
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Peer Fischer
- Max Planck Institute for Medical Research, Jahnstr. 29, 69120, Heidelberg, Germany
- Institute for Molecular Systems Engineering and Advanced Materials, Heidelberg University, INF 225, 69120, Heidelberg, Germany
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2
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Sun LZ, Ying YJ. Moving dynamics of a nanorobot with three DNA legs on nanopore-based tracks. NANOSCALE 2023; 15:15794-15809. [PMID: 37740362 DOI: 10.1039/d3nr03747a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
DNA nanorobots have garnered increasing attention in recent years due to their unique advantages of modularity and algorithm simplicity. To accomplish specific tasks in complex environments, various walking strategies are required for the DNA legs of the nanorobot. In this paper, we employ computational simulations to investigate a well-designed DNA-legged nanorobot moving along a nanopore-based track on a planar membrane. The nanorobot consists of a large nanoparticle as the robot core and three single-stranded DNAs (ssDNAs) as the robot legs. The nanopores linearly embedded in the membrane serve as the toeholds for the robot legs. A charge gradient along the pore distribution mainly powers the activation of the nanorobot. The nanorobot can move in two modes: a walking mode, where the robot legs sequentially enter the nanopores, and a jumping mode, where the robot legs may skip a nanopore to reach the next one. Moreover, we observe that the moving dynamics of the nanorobot on the nanopore-based tracks depends on pore-pore distance, pore charge gradient, external voltage, and leg length.
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Affiliation(s)
- Li-Zhen Sun
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China.
| | - Yao-Jun Ying
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China.
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3
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Siti W, Too HL, Anderson T, Liu XR, Loh IY, Wang Z. Autonomous DNA molecular motor tailor-designed to navigate DNA origami surface for fast complex motion and advanced nanorobotics. SCIENCE ADVANCES 2023; 9:eadi8444. [PMID: 37738343 PMCID: PMC10516491 DOI: 10.1126/sciadv.adi8444] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 08/23/2023] [Indexed: 09/24/2023]
Abstract
Nanorobots powered by designed DNA molecular motors on DNA origami platforms are vigorously pursued but still short of fully autonomous and sustainable operation, as the reported systems rely on manually operated or autonomous but bridge-burning molecular motors. Expanding DNA nanorobotics requires origami-based autonomous non-bridge-burning motors, but such advanced artificial molecular motors are rare, and their integration with DNA origami remains a challenge. Here, we report an autonomous non-bridge-burning DNA motor tailor-designed for a triangle DNA origami substrate. This is a translational bipedal molecular motor but demonstrates effective translocation on both straight and curved segments of a self-closed circular track on the origami, including sharp ~90° turns by a single hand-over-hand step. The motor is highly directional and attains a record-high speed among the autonomous artificial molecular motors reported to date. The resultant DNA motor-origami system, with its complex translational-rotational motion and big nanorobotic capacity, potentially offers a self-contained "seed" nanorobotic platform to automate or scale up many applications.
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Affiliation(s)
- Winna Siti
- Department of Physics, National University of Singapore, Singapore 117542, Singapore
| | - Hon Lin Too
- Department of Physics, National University of Singapore, Singapore 117542, Singapore
- Integrated Science and Engineering Programme, NUS Graduate School, Singapore 119077, Singapore
| | - Tommy Anderson
- Department of Physics, National University of Singapore, Singapore 117542, Singapore
| | - Xiao Rui Liu
- Department of Physics, National University of Singapore, Singapore 117542, Singapore
| | - Iong Ying Loh
- Department of Physics, National University of Singapore, Singapore 117542, Singapore
| | - Zhisong Wang
- Department of Physics, National University of Singapore, Singapore 117542, Singapore
- Integrated Science and Engineering Programme, NUS Graduate School, Singapore 119077, Singapore
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4
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Ma H, Chen L, Lv J, Yan X, Li Y, Xu G. The rate-limiting procedure of 3D DNA walkers and their applications in tandem technology. Chem Commun (Camb) 2023; 59:10330-10342. [PMID: 37615403 DOI: 10.1039/d3cc02597g] [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: 08/25/2023]
Abstract
DNA walkers, artificial dynamic DNA nanomachines, can mimic actin to move rapidly along a predefined nucleic acid track. They can generally be classified as one- (1D), two- (2D), and three-dimensional (3D) DNA walkers. In particular, 3D DNA walkers demonstrate amazing sustainable walking ability, strong enrichment ability, and fantastic signal amplification ability. In light of these, 3D DNA walkers have been widely used in fields such as biosensors, bioanalysis and cell imaging. Most notably, the strong compatibility of 3D DNA walkers allows their integration with a range of amplification strategies, effectively enhancing signal transduction and amplifying biosensor sensing signals. Herein, we first systematically expound the walking principle of the 3D walkers in this review. Then, by presenting representative examples, the research direction of 3D walkers in recent years is discussed. Furthermore, we also categorize and evaluate diverse tandem signal amplification strategies in 3D walkers. Finally, the challenges and development trends of 3D DNA walkers in the emerging field of analysis are carefully discussed. It is believed that this work can provide new ideas for researchers to quickly understand 3D DNA walkers and their applications in diverse biosensors.
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Affiliation(s)
- Hongmin Ma
- Department of Clinical Laboratory, The Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang 215600, China.
| | - Long Chen
- Department of Clinical Laboratory, The Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang 215600, China.
| | - Jingnan Lv
- The Second Affiliated People's Hospital of Soochow University, Suzhou 215008, China
| | - Xiaoyu Yan
- Guang'an Vocational & Technical College, Sichuan 638000, China
| | - Yonghao Li
- Department of Clinical Laboratory, The Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang 215600, China.
| | - Guoxin Xu
- Department of Clinical Laboratory, The Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang 215600, China.
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5
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Liu XR, Loh IY, Siti W, Too HL, Anderson T, Wang Z. A light-operated integrated DNA walker-origami system beyond bridge burning. NANOSCALE HORIZONS 2023; 8:827-841. [PMID: 37038716 DOI: 10.1039/d2nh00565d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Integrating rationally designed DNA molecular walkers and DNA origami platforms is a promising route towards advanced nano-robotics of diverse functions. Unleashing the full potential in this direction requires DNA walker-origami systems beyond the present simplistic bridge-burning designs for automated repeatable operation and scalable nano-robotic functions. Here we report such a DNA walker-origami system integrating an advanced light-powered DNA bipedal walker and a ∼170 nm-long rod-like DNA origami platform. This light-powered walker is fully qualified as a genuine translational molecular motor, and relies entirely on pure mechanical effects that are complicated by the origami surface but must be preserved for the walker's proper operation. This is made possible by tailor-designing the origami for optimal match with the walker to best preserve its core mechanics. A new fluorescence method is combined with site-controlled motility experiments to yield distinct and reliable signals for the walker's self-directed and processive motion despite origami-complicated fluorophore emission. The resultant integrated DNA walker-origami system provides a 'seed' system for future development of advanced light-powered DNA nano-robots (e.g., for scalable walker-automated chemical synthesis), and also truly bio-mimicking nano-muscles powered by genuine artificial translational molecular motors.
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Affiliation(s)
- Xiao Rui Liu
- Department of Physics, National University of Singapore, 117542, Singapore.
| | - Iong Ying Loh
- Department of Physics, National University of Singapore, 117542, Singapore.
| | - Winna Siti
- Department of Physics, National University of Singapore, 117542, Singapore.
| | - Hon Lin Too
- Department of Physics, National University of Singapore, 117542, Singapore.
- Integrative Sciences and Engineering Programme, NUS Graduate School, National University of Singapore, 117542, Singapore
| | - Tommy Anderson
- Department of Physics, National University of Singapore, 117542, Singapore.
| | - Zhisong Wang
- Department of Physics, National University of Singapore, 117542, Singapore.
- Integrative Sciences and Engineering Programme, NUS Graduate School, National University of Singapore, 117542, Singapore
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6
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Hou R, Wang Z. Extract Motive Energy from Single-Molecule Trajectories. J Phys Chem B 2022; 126:10460-10470. [PMID: 36459483 DOI: 10.1021/acs.jpcb.2c06802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Single-molecule trajectories from nonequilibrium unfolding experiments are widely used to recover a biomolecule's intrinsic free-energy profile. Trajectories of molecular motors from similar single-molecule experiments may be mapped to biased diffusion over an inclined free-energy profile. Such an effective potential is not a static equilibrium property anymore, and how it can benefit molecular motor study is unclear. Here, we introduce a method to deduce this effective potential from motor trajectories with realistic temporal-spatial resolution and find that the potential yields a motor's stall force─a quantity that not only characterizes a motor's force-generating capacity but also largely determines its energy efficiency. Interestingly, this potential allows the extraction of a motor's stall force from trajectories recorded at a single resisting force or even zero force, as verified with trajectories from two molecular motor models and also experimental trajectories from a real artificial motor. This finding drastically reduces the difficulty of stall force measurement, making it accessible even to force-incapable optical tracking experiments (commonly regarded as irrelevant to stall force determination). This study further provides a method for experimentally measuring a second-law-decreed least energy price for submicroscopic directionality─a previously elusive but thermodynamically important quantity pertinent to efficient energy conversion of molecular motors.
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Affiliation(s)
- Ruizheng Hou
- Department of Applied Physics, School of Science, Xi'an University of Technology, Xi'an, Shaan Xi710048, China
| | - Zhisong Wang
- Department of Physics and NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore117542, Singapore
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7
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Unksov IN, Korosec CS, Surendiran P, Verardo D, Lyttleton R, Forde NR, Linke H. Through the Eyes of Creators: Observing Artificial Molecular Motors. ACS NANOSCIENCE AU 2022; 2:140-159. [PMID: 35726277 PMCID: PMC9204826 DOI: 10.1021/acsnanoscienceau.1c00041] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/20/2021] [Accepted: 12/20/2021] [Indexed: 11/28/2022]
Abstract
![]()
Inspired by molecular
motors in biology, there has been significant
progress in building artificial molecular motors, using a number of
quite distinct approaches. As the constructs become more sophisticated,
there is also an increasing need to directly observe the motion of
artificial motors at the nanoscale and to characterize their performance.
Here, we review the most used methods that tackle those tasks. We
aim to help experimentalists with an overview of the available tools
used for different types of synthetic motors and to choose the method
most suited for the size of a motor and the desired measurements,
such as the generated force or distances in the moving system. Furthermore,
for many envisioned applications of synthetic motors, it will be a
requirement to guide and control directed motions. We therefore also
provide a perspective on how motors can be observed on structures
that allow for directional guidance, such as nanowires and microchannels.
Thus, this Review facilitates the future research on synthetic molecular
motors, where observations at a single-motor level and a detailed
characterization of motion will promote applications.
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Affiliation(s)
- Ivan N. Unksov
- Solid State Physics and NanoLund, Lund University, Box 118, SE-221 00 Lund, Sweden
| | - Chapin S. Korosec
- Department of Physics, Simon Fraser University, V5A 1S6 Burnaby, British Columbia, Canada
| | | | - Damiano Verardo
- Solid State Physics and NanoLund, Lund University, Box 118, SE-221 00 Lund, Sweden
- AlignedBio AB, Medicon Village, Scheeletorget 1, 223 63 Lund, Sweden
| | - Roman Lyttleton
- Solid State Physics and NanoLund, Lund University, Box 118, SE-221 00 Lund, Sweden
| | - Nancy R. Forde
- Department of Physics, Simon Fraser University, V5A 1S6 Burnaby, British Columbia, Canada
| | - Heiner Linke
- Solid State Physics and NanoLund, Lund University, Box 118, SE-221 00 Lund, Sweden
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8
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Liu XR, Hu X, Loh IY, Wang Z. A high-fidelity light-powered nanomotor from a chemically fueled counterpart via site-specific optomechanical fuel control. NANOSCALE 2022; 14:5899-5914. [PMID: 35373800 DOI: 10.1039/d1nr07964f] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Optically powered nanomotors are advantageous for clean nanotechnology over chemically fuelled nanomotors. The two motor types are further bounded by different physical principles. Despite the gap, we show here that an optically powered DNA bipedal nanomotor is readily created from a high-performing chemically fuelled counterpart by subjecting its fuel to cyclic site-specific optomechanical control - as if the fuel is optically recharged. Optimizing azobenzene-based control of the original nucleotide fuel selects a light-responsive fuel analog that replicates the different binding affinity of the fuel and reaction products. The resultant motor largely retains high-performing features of the original chemical motor, and achieves the highest directional fidelity among reported light-driven DNA nanomotors. This study thus demonstrates a novel strategy for transforming chemical nanomotors to optical ones for clean nanotechnology. The strategy is potentially applicable to many chemical nanomotors with oligomeric fuels like nucleotides, peptides and synthetic polymers, leading to a new class of light-powered nanomotors that are akin to chemical nanomotors and benefit from their generally high efficiency mechanistically. The motor from this study also provides a rare model system for studying the subtle boundary between chemical and optical nanomotors - a topic pertinent to chemomechanical and optomechanical energy conversion at the single-molecule level.
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Affiliation(s)
- Xiao Rui Liu
- Department of Physics, National University of Singapore, Singapore 117542
| | - Xinpeng Hu
- Department of Physics, National University of Singapore, Singapore 117542
| | - Iong Ying Loh
- Department of Physics, National University of Singapore, Singapore 117542
| | - Zhisong Wang
- Department of Physics, National University of Singapore, Singapore 117542
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117542.
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9
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Gao Y, Wei F, Chao Y, Yao L. Bioinspired soft microrobots actuated by magnetic field. Biomed Microdevices 2021; 23:52. [PMID: 34599405 DOI: 10.1007/s10544-021-00590-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2021] [Indexed: 12/16/2022]
Abstract
In contrast to traditional large-scale robots, which require complicated mechanical joints and material rigidity, microrobots made of soft materials have exhibited amazing features and great potential for extensive applications, such as minimally invasive surgery. However, microrobots are faced with energy supply and control issues due to the miniaturization. Magnetic field actuation emerges as an appropriate approach to tackle with these issues. This review summarizes the latest progress of biomimetic soft microrobots actuated by magnetic field. Starting with an overview of the soft material and magnetic material adopted in the magnetic field actuated soft microrobots, the various fabrication methods and design structures of soft microrobots are summarized. Subsequently, practical and potential applications, such as targeted therapy, surgical operation, and the transportation of microscopic objects, in the fields of biomedicine and environmental remediation are presented. In the end, some current challenges, and the future development trends of magnetic soft microrobots are briefly discussed. This review is expected to offer a helpful guidance for the new researchers of biomimetic soft microrobots actuated by magnetic field.
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Affiliation(s)
- Yuwen Gao
- School of Mechanical Engineering and Automation, Fuzhou University, Fuzhou, China
| | - Fanan Wei
- School of Mechanical Engineering and Automation, Fuzhou University, Fuzhou, China.
| | - Yin Chao
- School of Mechanical Engineering and Automation, Fuzhou University, Fuzhou, China
| | - Ligang Yao
- School of Mechanical Engineering and Automation, Fuzhou University, Fuzhou, China
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10
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Hu X, Zhao X, Loh IY, Yan J, Wang Z. Single-molecule mechanical study of an autonomous artificial translational molecular motor beyond bridge-burning design. NANOSCALE 2021; 13:13195-13207. [PMID: 34477726 DOI: 10.1039/d1nr02296b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
A key capability of molecular motors is sustainable force generation by a single motor copy. Direct force characterization at the single-motor level is still missing for artificial molecular motors, though long reported for their biological counterparts. Here we report single-molecule detection of sustained force-generating motility for an artificial track-walking molecular motor capable of autonomous chemically fueled operation. A single motor plus its track (both made of deoxyribonucleic acids or DNA) is assembled, operated and detected under magnetic tweezers by a method designed to overcome difficulty from the motor's soft double-stranded track. The motor shows self-directed walking by ∼16 nm steps up to a distance of 120 nm (covering the entire track), yielding a stall force of ∼2-3 pN. These results imply a reasonably efficient chemomechanical conversion of the motor compared to a high-efficiency biomotor. The stall force is near the level of translational biomotors powering human muscles and allows similar force-demanding applications by their artificial counterparts. This single-motor study reveals fast subsecond steps, suggesting big room for improvement in the speed of DNA motors in general. Besides, the established single-molecule method is applicable to force measurements of many other DNA motors with soft tracks.
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Affiliation(s)
- Xinpeng Hu
- Department of Physics, National University of Singapore, 117542 Singapore
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11
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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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12
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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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13
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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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14
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Abbasi-Pérez D, Sang H, Pérez-García L, Floris A, Amabilino DB, Raval R, Recio JM, Kantorovich L. Controlling the preferential motion of chiral molecular walkers on a surface. Chem Sci 2019; 10:5864-5874. [PMID: 31360390 PMCID: PMC6582760 DOI: 10.1039/c9sc01135h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 05/08/2019] [Indexed: 12/13/2022] Open
Abstract
Molecular walkers standing on two or more "feet" on an anisotropic periodic potential of a crystal surface may perform a one-dimensional Brownian motion at the surface-vacuum interface along a particular direction in which their mobility is the largest. In thermal equilibrium the molecules move with equal probabilities both ways along this direction, as expected from the detailed balance principle, well-known in chemical reactivity and in the theory of molecular motors. For molecules that possess an asymmetric potential energy surface (PES), we propose a generic method based on the application of a time-periodic external stimulus that would enable the molecules to move preferentially in a single direction thereby acting as Brownian ratchets. To illustrate this method, we consider a prototypical synthetic chiral molecular walker, 1,3-bis(imidazol-1-ylmethyl)-5(1-phenylethyl)benzene, diffusing on the anisotropic Cu(110) surface along the Cu rows. As unveiled by our kinetic Monte Carlo simulations based on the rates calculated using ab initio density functional theory, this molecule moves to the nearest equivalent lattice site via the so-called inchworm mechanism in which it steps first with the rear foot and then with the front foot. As a result, the molecule diffuses via a two-step mechanism, and due to its inherent asymmetry, the corresponding PES is also spatially asymmetric. Taking advantage of this fact, we show how the external stimulus can be tuned to separate molecules of different chirality, orientation and conformation. The consequences of these findings for molecular machines and the separation of enantiomers are also discussed.
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Affiliation(s)
- David Abbasi-Pérez
- Department of Physics , King's College London , London , WC2R 2LS , UK . ;
| | - Hongqian Sang
- Department of Physics , King's College London , London , WC2R 2LS , UK . ;
- Institute for Interdisciplinary Research , Jianghan University , Wuhan 430056 , China
| | - Lluïsa Pérez-García
- School of Pharmacy , University of Nottingham , University Park , Nottingham , NG7 2RD , UK
| | - Andrea Floris
- School of Chemistry , University of Lincoln , Brayford Pool , Lincoln LN6 7TS , UK
| | - David B Amabilino
- School of Chemistry , GSK Carbon Neutral Lab. for Sustainable Chemistry , University of Nottingham , Triumph Road , NG7 2TU , UK
| | - Rasmita Raval
- Surface Science Research Centre , Department of Chemistry , University of Liverpool , Liverpool L69 3BX , UK
| | - J Manuel Recio
- MALTA-Consolider Team and Department of Analytical and Physical Chemistry , Universidad de Oviedo , Oviedo , 33006 , Spain
| | - Lev Kantorovich
- Department of Physics , King's College London , London , WC2R 2LS , UK . ;
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15
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Wang Z, Hou R, Loh IY. Track-walking molecular motors: a new generation beyond bridge-burning designs. NANOSCALE 2019; 11:9240-9263. [PMID: 31062798 DOI: 10.1039/c9nr00033j] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Track-walking molecular motors are the core bottom-up mechanism for nanometre-resolved translational movements - a fundamental technological capability at the root of numerous applications ranging from nanoscale assembly lines and chemical synthesis to molecular robots and shape-changing materials. Over the last 10 years, artificial molecular walkers (or nanowalkers) have evolved from the 1st generation of bridge-burning designs to the 2nd generation capable of truly sustainable movements. Invention of non-bridge-burning nanowalkers was slow at first, but has picked up speed since 2012, and is now close to breaking major barriers for wide-spread development. Here we review the 2nd generation of artificial nanowalkers, which are mostly made of DNA molecules and draw energy from light illumination or from chemical fuels for entirely autonomous operation. They are typically symmetric dimeric motors walking on entirely periodic tracks, yet the motors possess an inherent direction for large-scale amplification of the action of many motor copies. These translational motors encompass the function of rotational molecular motors on circular or linear tracks, and may involve molecular shuttles as 'engine' motifs. Some rules of thumb are provided to help readers design similar motors from DNA or other molecular building blocks. Opportunities and challenges for future development are discussed, especially in the areas of molecular robotics and active materials based on the advanced motors.
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Affiliation(s)
- Zhisong Wang
- Department of Physics, National University of Singapore, Singapore 117542, Singapore.
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16
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Hou R, Wang N, Bao W, Wang Z. Polymer-Based Accurate Positioning: An Exact Worm-like-Chain Study. ACS OMEGA 2018; 3:14318-14326. [PMID: 31458122 PMCID: PMC6644801 DOI: 10.1021/acsomega.8b01448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 10/18/2018] [Indexed: 06/10/2023]
Abstract
Precise positioning of molecular objects from one location to another is important for nanomanipulation and is also involved in molecular motors. Here, we study single-polymer-based positioning on the basis of the exact solution to the realistic three-dimensional worm-like-chain (WLC) model. The results suggest the possibility of a surprisingly accurate flyfishing-like positioning in which tilting one end of a flexible short polymer enables positioning of the other diffusing end to a distant location within an error of ∼1 nm. This offers a new mechanism for designing molecular positioning devices. The flyfishing effect (and reverse process) likely plays a role in biological molecular motors and may be used to improve speed of artificial counterparts. To facilitate these applications, a new force-extension formula is obtained from the exact WLC solution. This formula has an improved accuracy over the widely used Marko-Siggia formula for stretched polymers and is valid for compressed polymers too. The new formula is useful in analysis of single-molecule stretching experiments and in estimating intramolecular forces of molecular motors, especially those involving both stretched and compressed polymer components.
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Affiliation(s)
- Ruizheng Hou
- Department
of Applied Physics, School of Science, and Institute of Quantum Optics
and Quantum Information, Xi’an Jiaotong
University, Xi’an, Shaan Xi 710049, China
| | - Nan Wang
- Department of Mathematics and NUS Graduate
School for Integrative Sciences
and Engineering, National University of
Singapore, 119076, Singapore
| | - Weizhu Bao
- Department of Mathematics and NUS Graduate
School for Integrative Sciences
and Engineering, National University of
Singapore, 119076, Singapore
| | - Zhisong Wang
- Department of Mathematics and NUS Graduate
School for Integrative Sciences
and Engineering, National University of
Singapore, 119076, Singapore
- Department
of Physics, National University of Singapore, 117542, Singapore
| |
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