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Piranej S, Zhang L, Bazrafshan A, Marin M, Melikian GB, Salaita K. Rolosense: Mechanical Detection of SARS-CoV-2 Using a DNA-Based Motor. ACS CENTRAL SCIENCE 2024; 10:1332-1347. [PMID: 39071064 PMCID: PMC11273449 DOI: 10.1021/acscentsci.4c00312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/29/2024] [Accepted: 05/01/2024] [Indexed: 07/30/2024]
Abstract
Assays that detect viral infections play a significant role in limiting the spread of diseases such as SARS-CoV-2. Here, we present Rolosense, a virus sensing platform that leverages the motion of 5 μm DNA-based motors on RNA fuel chips to transduce the presence of viruses. Motors and chips are modified with aptamers, which are designed for multivalent binding to viral targets and lead to stalling of motion. Therefore, the motors perform a "mechanical test" of the viral target and stall in the presence of whole virions, which represents a unique mechanism of transduction distinct from conventional assays. Rolosense can detect SARS-CoV-2 spiked in artificial saliva and exhaled breath condensate with a sensitivity of 103 copies/mL and discriminates among other respiratory viruses. The assay is modular and amenable to multiplexing, as demonstrated by our one-pot detection of influenza A and SARS-CoV-2. As a proof of concept, we show that readout can be achieved using a smartphone camera with a microscopic attachment in as little as 15 min without amplification reactions. Taken together, these results show that mechanical detection using Rolosense can be broadly applied to any viral target and has the potential to enable rapid, low-cost point-of-care screening of circulating viruses.
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Affiliation(s)
- Selma Piranej
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Luona Zhang
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Alisina Bazrafshan
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Mariana Marin
- Department
of Pediatrics, Emory University School of
Medicine, Atlanta, Georgia 30322, United States
- Children’s
Healthcare of Atlanta, Atlanta, Georgia 30322, United States
| | - Gregory B. Melikian
- Department
of Pediatrics, Emory University School of
Medicine, Atlanta, Georgia 30322, United States
- Children’s
Healthcare of Atlanta, Atlanta, Georgia 30322, United States
| | - Khalid Salaita
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
- Wallace
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
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2
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Zhang L, Piranej S, Namazi A, Narum S, Salaita K. "Turbo-Charged" DNA Motors with Optimized Sequence Enable Single-Molecule Nucleic Acid Sensing. Angew Chem Int Ed Engl 2024; 63:e202316851. [PMID: 38214887 PMCID: PMC10947818 DOI: 10.1002/anie.202316851] [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: 11/06/2023] [Revised: 12/22/2023] [Accepted: 01/10/2024] [Indexed: 01/13/2024]
Abstract
DNA motors that consume chemical energy to generate processive mechanical motion mimic natural motor proteins and have garnered interest due to their potential applications in dynamic nanotechnology, biosensing, and drug delivery. Such motors translocate by a catalytic cycle of binding, cleavage, and rebinding between DNA "legs" on the motor body and RNA "footholds" on a track. Herein, we address the well-documented trade-off between motor speed and processivity and investigate how these parameters are controlled by the affinity between DNA legs and their complementary footholds. Specifically, we explore the role of DNA leg length and GC content in tuning motor performance by dictating the rate of leg-foothold dissociation. Our investigations reveal that motors with 0 % GC content exhibit increased instantaneous velocities of up to 150 nm/sec, three-fold greater than previously reported DNA motors and comparable to the speeds of biological motor proteins. We also demonstrate that the faster speed and weaker forces generated by 0 % GC motors can be leveraged for enhanced capabilities in sensing. We observe single-molecule sensitivity when programming the motors to stall in response to the binding of nucleic acid targets. These findings offer insights for the design of high-performance DNA motors with promising real-world biosensing applications.
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Affiliation(s)
- Luona Zhang
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Selma Piranej
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Arshiya Namazi
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Steven Narum
- Wallace H. Coulter Department of Biomedical Engineering, Georgia, Institute of Technology and Emory University, Atlanta, GA 30322, USA
| | - Khalid Salaita
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
- Wallace H. Coulter Department of Biomedical Engineering, Georgia, Institute of Technology and Emory University, Atlanta, GA 30322, USA
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3
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Korosec CS, Unksov IN, Surendiran P, Lyttleton R, Curmi PMG, Angstmann CN, Eichhorn R, Linke H, Forde NR. Motility of an autonomous protein-based artificial motor that operates via a burnt-bridge principle. Nat Commun 2024; 15:1511. [PMID: 38396042 PMCID: PMC10891099 DOI: 10.1038/s41467-024-45570-y] [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: 02/20/2023] [Accepted: 01/25/2024] [Indexed: 02/25/2024] Open
Abstract
Inspired by biology, great progress has been made in creating artificial molecular motors. However, the dream of harnessing proteins - the building blocks selected by nature - to design autonomous motors has so far remained elusive. Here we report the synthesis and characterization of the Lawnmower, an autonomous, protein-based artificial molecular motor comprised of a spherical hub decorated with proteases. Its "burnt-bridge" motion is directed by cleavage of a peptide lawn, promoting motion towards unvisited substrate. We find that Lawnmowers exhibit directional motion with average speeds of up to 80 nm/s, comparable to biological motors. By selectively patterning the peptide lawn on microfabricated tracks, we furthermore show that the Lawnmower is capable of track-guided motion. Our work opens an avenue towards nanotechnology applications of artificial protein motors.
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Affiliation(s)
- Chapin S Korosec
- Department of Physics, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.
- Department of Mathematics and Statistics, York University, Toronto, ON, M3J 1P3, Canada.
| | - Ivan N Unksov
- NanoLund and Solid State Physics, Lund University, Box 118, SE - 22100, Lund, Sweden
| | - Pradheebha Surendiran
- NanoLund and Solid State Physics, Lund University, Box 118, SE - 22100, Lund, Sweden
| | - Roman Lyttleton
- NanoLund and Solid State Physics, Lund University, Box 118, SE - 22100, Lund, Sweden
| | - Paul M G Curmi
- School of Physics, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Christopher N Angstmann
- School of Mathematics and Statistics, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Ralf Eichhorn
- Nordita, Royal Institute of Technology and Stockholm University, 106 91, Stockholm, Sweden
| | - Heiner Linke
- NanoLund and Solid State Physics, Lund University, Box 118, SE - 22100, Lund, Sweden.
| | - Nancy R Forde
- Department of Physics, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.
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4
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Shrivastava A, Du Y, Adepu HK, Li R, Madhvacharyula AS, Swett AA, Choi JH. Motility of Synthetic Cells from Engineered Lipids. ACS Synth Biol 2023; 12:2789-2801. [PMID: 37729546 DOI: 10.1021/acssynbio.3c00271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Synthetic cells are artificial systems that resemble natural cells. Significant efforts have been made over the years to construct synthetic protocells that can mimic biological mechanisms and perform various complex processes. These include compartmentalization, metabolism, energy supply, communication, and gene reproduction. Cell motility is also of great importance, as nature uses elegant mechanisms for intracellular trafficking, immune response, and embryogenesis. In this review, we discuss the motility of synthetic cells made from lipid vesicles and relevant molecular mechanisms. Synthetic cell motion may be classified into surface-based or solution-based depending on whether it involves interactions with surfaces or movement in fluids. Collective migration behaviors have also been demonstrated. The swarm motion requires additional mechanisms for intercellular signaling and directional motility that enable communication and coordination among the synthetic vesicles. In addition, intracellular trafficking for molecular transport has been reconstituted in minimal cells with the help of DNA nanotechnology. These efforts demonstrate synthetic cells that can move, detect, respond, and interact. We envision that new developments in protocell motility will enhance our understanding of biological processes and be instrumental in bioengineering and therapeutic applications.
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Affiliation(s)
- Aishwary Shrivastava
- School of Mechanical Engineering, Purdue University, 585 Purdue Mall, West Lafayette, Indiana 47907, United States
| | - Yancheng Du
- School of Mechanical Engineering, Purdue University, 585 Purdue Mall, West Lafayette, Indiana 47907, United States
| | - Harshith K Adepu
- School of Mechanical Engineering, Purdue University, 585 Purdue Mall, West Lafayette, Indiana 47907, United States
| | - Ruixin Li
- School of Mechanical Engineering, Purdue University, 585 Purdue Mall, West Lafayette, Indiana 47907, United States
| | - Anirudh S Madhvacharyula
- School of Mechanical Engineering, Purdue University, 585 Purdue Mall, West Lafayette, Indiana 47907, United States
| | - Alexander A Swett
- School of Mechanical Engineering, Purdue University, Neil Armstrong Hall of Engineering, 701 W. Stadium Avenue, West Lafayette, Indiana 47907, United States
| | - Jong Hyun Choi
- School of Mechanical Engineering, Purdue University, 585 Purdue Mall, West Lafayette, Indiana 47907, United States
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5
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Zhan P, Peil A, Jiang Q, Wang D, Mousavi S, Xiong Q, Shen Q, Shang Y, Ding B, Lin C, Ke Y, Liu N. Recent Advances in DNA Origami-Engineered Nanomaterials and Applications. Chem Rev 2023; 123:3976-4050. [PMID: 36990451 PMCID: PMC10103138 DOI: 10.1021/acs.chemrev.3c00028] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Indexed: 03/31/2023]
Abstract
DNA nanotechnology is a unique field, where physics, chemistry, biology, mathematics, engineering, and materials science can elegantly converge. Since the original proposal of Nadrian Seeman, significant advances have been achieved in the past four decades. During this glory time, the DNA origami technique developed by Paul Rothemund further pushed the field forward with a vigorous momentum, fostering a plethora of concepts, models, methodologies, and applications that were not thought of before. This review focuses on the recent progress in DNA origami-engineered nanomaterials in the past five years, outlining the exciting achievements as well as the unexplored research avenues. We believe that the spirit and assets that Seeman left for scientists will continue to bring interdisciplinary innovations and useful applications to this field in the next decade.
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Affiliation(s)
- Pengfei Zhan
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Andreas Peil
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Qiao Jiang
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Dongfang Wang
- School
of Biomedical Engineering and Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou 215123, China
| | - Shikufa Mousavi
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Qiancheng Xiong
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
| | - Qi Shen
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
- Department
of Molecular Biophysics and Biochemistry, Yale University, 266
Whitney Avenue, New Haven, Connecticut 06511, United States
| | - Yingxu Shang
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Baoquan Ding
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Chenxiang Lin
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
- Department
of Biomedical Engineering, Yale University, 17 Hillhouse Avenue, New Haven, Connecticut 06511, United States
| | - Yonggang Ke
- Wallace
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Na Liu
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
- Max Planck
Institute for Solid State Research, Heisenbergstrasse 1, 70569 Stuttgart, Germany
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6
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Maffeo C, Quednau L, Wilson J, Aksimentiev A. DNA double helix, a tiny electromotor. NATURE NANOTECHNOLOGY 2023; 18:238-242. [PMID: 36564521 DOI: 10.1038/s41565-022-01285-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 11/04/2022] [Indexed: 06/17/2023]
Abstract
Flowing fluid past chiral objects has been used for centuries to power rotary motion in man-made machines. By contrast, rotary motion in nanoscale biological or chemical systems is produced by biasing Brownian motion through cyclic chemical reactions. Here we show that a chiral biological molecule, a DNA or RNA duplex rotates unidirectionally at billions of revolutions per minute when an electric field is applied along the duplex, with the rotation direction being determined by the chirality of the duplex. The rotation is found to be powered by the drag force of the electro-osmotic flow, realizing the operating principle of a macroscopic turbine at the nanoscale. The resulting torques are sufficient to power rotation of nanoscale beads and rods, offering an engineering principle for constructing nanoscale systems powered by electric field.
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Affiliation(s)
- Christopher Maffeo
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Lauren Quednau
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - James Wilson
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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7
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Wang J, Fu X, Liu S, Liu R, Li J, Wang K, Huang J. Catalyst-Accelerated Circular Cascaded DNA Circuits: Simpler Design, Faster Speed, Higher Gain. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2205903. [PMID: 36638250 DOI: 10.1002/smll.202205903] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/28/2022] [Indexed: 06/17/2023]
Abstract
DNA cascaded circuits have great potential in detecting low abundance molecules in complex biological environment due to their powerful signal amplification capability and nonenzymatic feature. However, the problem of the cascaded circuits is that the design is relatively complex and the kinetics is slow. Herein, a new design paradigm called catalyst-accelerated circular cascaded circuits is proposed, where the catalyst inlet is implanted and the reaction speed can be adjusted by the catalyst concentration. This new design is very simple and only requires three hairpin probes. Meanwhile, the results of a series of studies demonstrate that the reaction speed can be accelerated and the sensitivity can be also improved. Moreover, endogenous mRNA can also be used as a catalyst to drive the circuits to amplify the detection of target miRNA in live cells and in mice. These catalyst-accelerated circular cascaded circuits can substantially expand the toolbox for intracellular low abundance molecular detection.
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Affiliation(s)
- Jiaoli Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, P. R. China
| | - Xiaoxiao Fu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, P. R. China
| | - Shiyuan Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, P. R. China
| | - Ruiting Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, P. R. China
| | - Jing Li
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, 225012, P. R. China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, P. R. China
| | - Jin Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, P. R. China
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8
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Kilwing L, Lill P, Nathwani B, Singh JKD, Liedl T, Shih WM. Three-phase DNA-origami stepper mechanism based on multi-leg interactions. Biophys J 2022; 121:4860-4866. [PMID: 36045576 PMCID: PMC9808544 DOI: 10.1016/j.bpj.2022.08.040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/17/2022] [Accepted: 08/25/2022] [Indexed: 01/07/2023] Open
Abstract
Nanoscale stepper motors such as kinesin and dynein play a key role in numerous natural processes such as mitotic spindle formation during cell division or intracellular organelle transport. Their high efficacy in terms of operational speed and processivity has inspired the investigation of biomimetic technologies based on the use of programmable molecules. In particular, several designs of molecular walkers have been explored using DNA nanotechnology. Here, we study the actuation of a DNA-origami walker on a DNA-origami track based on three principles: 1) octapedal instead of bipedal walking for greater redundancy; 2) three pairs of orthogonal sequences, each of which fuels one repeatable stepping phase for cyclically driven motion with controlled directionality based on strain-based step selection; 3) designed size of only 3.5 nm per step on an origami track. All three principles are innovative in the sense that earlier demonstrations of steppers relied on a maximum of four legs on at least four orthogonal sequences to drive cyclic stepping, and took steps much larger than 3.4 nm in size. Using gel electrophoresis and negative-stain electron microscopy, we demonstrate cyclic actuation of DNA-origami structures through states defined by three sets of specific sequences of anchor points. However, this mechanism was not able to provide the intended control over directionality of movement. DNA-origami-based stepper motors will offer a future platform for investigating how increasing numbers of legs can be exploited to achieve robust stepping with relatively small step sizes.
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Affiliation(s)
- Luzia Kilwing
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Munich, Germany; Department of Cancer Biology, Dana-Farber Cancer Institute and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts; Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts
| | - Pascal Lill
- Department of Cancer Biology, Dana-Farber Cancer Institute and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts; Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts
| | - Bhavik Nathwani
- Department of Cancer Biology, Dana-Farber Cancer Institute and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts; Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts
| | - Jasleen Kaur Daljit Singh
- School of Chemistry, School of Chemical and Biomolecular Engineering, The University of Sydney Nano Institute, The University of Sydney, Sydney, New South Wales, Australia
| | - Tim Liedl
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Munich, Germany.
| | - William M Shih
- Department of Cancer Biology, Dana-Farber Cancer Institute and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts; Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts.
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9
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Blanchard AT, Piranej S, Pan V, Salaita K. Adhesive Dynamics Simulations of Highly Polyvalent DNA Motors. J Phys Chem B 2022; 126:7495-7509. [PMID: 36137248 DOI: 10.1021/acs.jpcb.2c01897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular motors, such as myosin and kinesin, perform diverse tasks ranging from vesical transport to bulk muscle contraction. Synthetic molecular motors may eventually be harnessed to perform similar tasks in versatile synthetic systems. The most promising type of synthetic molecular motor, the DNA walker, can undergo processive motion but generally exhibits low speeds and virtually no capacity for force generation. However, we recently showed that highly polyvalent DNA motors (HPDMs) can rival biological motors by translocating at micrometer per minute speeds and generating 100+ pN of force. Accordingly, DNA nanotechnology-based designs may hold promise for the creation of synthetic, force-generating nanomotors. However, the dependencies of HPDM speed and force on tunable design parameters are poorly understood and difficult to characterize experimentally. To overcome this challenge, we present RoloSim, an adhesive dynamics software package for fine-grained simulations of HPDM translocation. RoloSim uses biophysical models for DNA duplex formation and dissociation kinetics to explicitly model tens of thousands of molecular scale interactions. These molecular interactions are then used to calculate the nano- and microscale motions of the motor. We use RoloSim to uncover how motor force and speed scale with several tunable motor properties such as motor size and DNA duplex length. Our results support our previously defined hypothesis that force scales linearly with polyvalency. We also demonstrate that HPDMs can be steered with external force, and we provide design parameters for novel HPDM-based molecular sensor and nanomachine designs.
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Affiliation(s)
- Aaron T Blanchard
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Selma Piranej
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Victor Pan
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Khalid Salaita
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States.,Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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10
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Gupta A, Soni S, Chauhan N, Khanuja M, Jain U. Nanobots-based advancement in targeted drug delivery and imaging: An update. J Control Release 2022; 349:97-108. [PMID: 35718213 DOI: 10.1016/j.jconrel.2022.06.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 06/11/2022] [Accepted: 06/12/2022] [Indexed: 10/17/2022]
Abstract
Manipulation and targeted navigation of nanobots in complex biological conditions can be achieved by chemical reactions, by applying external forces, and via motile cells. Several studies have applied fuel-based and fuel-free propulsion mechanisms for nanobots movements in environmental sciences and robotics. However, their applications in biomedical sciences are still in the budding phase. Therefore, the current review introduces the fundamentals of different propulsion strategies based on the advantageous features of applied nanomaterials or cellular components. Furthermore, the recent developments reported in various literatures on next-generation nanobots, such as Xenobots with applications of in-vitro and in-vivo drug delivery and imaging were also explored in detail. The challenges and the future prospects are also highlighted with corresponding advantages and limitations of nanobots in biomedical applications. This review concludes that with ever booming research enthusiasm in this field and increasing multidisciplinary cooperation, micro-/nanorobots with intelligence and multifunctions will emerge in the near future, which would have a profound impact on the treatment of diseases.
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Affiliation(s)
- Abhinandan Gupta
- Amity Institute of Nanotechnology (AINT), Amity University Uttar Pradesh (AUUP), Sector-125, Noida 201313, India
| | - Shringika Soni
- Amity Institute of Nanotechnology (AINT), Amity University Uttar Pradesh (AUUP), Sector-125, Noida 201313, India
| | - Nidhi Chauhan
- Amity Institute of Nanotechnology (AINT), Amity University Uttar Pradesh (AUUP), Sector-125, Noida 201313, India
| | - Manika Khanuja
- Centre for Nanoscience & Nanotechnology, Jamia Millia Islamia (A Central University), New Delhi 110025, India
| | - Utkarsh Jain
- Amity Institute of Nanotechnology (AINT), Amity University Uttar Pradesh (AUUP), Sector-125, Noida 201313, India.
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11
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Abstract
The cytoskeleton is an essential component of a cell. It controls the cell shape, establishes the internal organization, and performs vital biological functions. Building synthetic cytoskeletons that mimic key features of their natural counterparts delineates a crucial step towards synthetic cells assembled from the bottom up. To this end, DNA nanotechnology represents one of the most promising routes, given the inherent sequence specificity, addressability and programmability of DNA. Here we demonstrate functional DNA-based cytoskeletons operating in microfluidic cell-sized compartments. The synthetic cytoskeletons consist of DNA tiles self-assembled into filament networks. These filaments can be rationally designed and controlled to imitate features of natural cytoskeletons, including reversible assembly and ATP-triggered polymerization, and we also explore their potential for guided vesicle transport in cell-sized confinement. Also, they possess engineerable characteristics, including assembly and disassembly powered by DNA hybridization or aptamer–target interactions and autonomous transport of gold nanoparticles. This work underpins DNA nanotechnology as a key player in building synthetic cells. ![]()
Cytoskeletons are essential components of cells that perform a variety of tasks, and artificial cytoskeletons that perform these functions are required for the bottom-up assembly of synthetic cells. Now, a multi-functional cytoskeleton mimic has been engineered from DNA, consisting of confined DNA filaments that are capable of reversible self-assembly and transport of gold nanoparticles and vesicular cargo.
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12
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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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13
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Song L, Zhuge Y, Zuo X, Li M, Wang F. DNA Walkers for Biosensing Development. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2200327. [PMID: 35460209 PMCID: PMC9366574 DOI: 10.1002/advs.202200327] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/07/2022] [Indexed: 05/07/2023]
Abstract
The ability to design nanostructures with arbitrary shapes and controllable motions has made DNA nanomaterials used widely to construct diverse nanomachines with various structures and functions. The DNA nanostructures exhibit excellent properties, including programmability, stability, biocompatibility, and can be modified with different functional groups. Among these nanoscale architectures, DNA walker is one of the most popular nanodevices with ingenious design and flexible function. In the past several years, DNA walkers have made amazing progress ranging from structural design to biological applications including constructing biosensors for the detection of cancer-associated biomarkers. In this review, the key driving forces of DNA walkers are first summarized. Then, the DNA walkers with different numbers of legs are introduced. Furthermore, the biosensing applications of DNA walkers including the detection- of nucleic acids, proteins, ions, and bacteria are summarized. Finally, the new frontiers and opportunities for developing DNA walker-based biosensors are discussed.
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Affiliation(s)
- Lu Song
- Department of CardiologyShanghai General HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200800China
- Institute of Molecular MedicineShanghai Key Laboratory for Nucleic Acid Chemistry and NanomedicineSchool of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Ying Zhuge
- Department of CardiologyShanghai General HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200800China
| | - Xiaolei Zuo
- Institute of Molecular MedicineShanghai Key Laboratory for Nucleic Acid Chemistry and NanomedicineSchool of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Min Li
- Institute of Molecular MedicineShanghai Key Laboratory for Nucleic Acid Chemistry and NanomedicineSchool of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Fang Wang
- Department of CardiologyShanghai General HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200800China
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14
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Piranej S, Bazrafshan A, Salaita K. Chemical-to-mechanical molecular computation using DNA-based motors with onboard logic. NATURE NANOTECHNOLOGY 2022; 17:514-523. [PMID: 35347272 PMCID: PMC9119907 DOI: 10.1038/s41565-022-01080-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 01/13/2022] [Indexed: 05/15/2023]
Abstract
DNA has become the biomolecule of choice for molecular computation that may one day complement conventional silicon-based processors. In general, DNA computation is conducted in individual tubes, is slow in generating chemical outputs in response to chemical inputs and requires fluorescence readout. Here, we introduce a new paradigm for DNA computation where the chemical input is processed and transduced into a mechanical output using dynamic DNA-based motors operating far from equilibrium. We show that DNA-based motors with onboard logic (DMOLs) can perform Boolean functions (NOT, YES, AND and OR) with 15 min readout times. Because DMOLs are micrometre-sized, massive arrays of DMOLs that are identical or uniquely encoded by size and refractive index can be multiplexed and perform motor-to-motor communication on the same chip. Finally, DMOL computational outputs can be detected using a conventional smartphone camera, thus transducing chemical information into the electronic domain in a facile manner, suggesting potential applications.
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Affiliation(s)
- Selma Piranej
- Department of Chemistry, Emory University, Atlanta, GA, USA
| | | | - Khalid Salaita
- Department of Chemistry, Emory University, Atlanta, GA, USA.
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA.
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15
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Ibusuki R, Morishita T, Furuta A, Nakayama S, Yoshio M, Kojima H, Oiwa K, Furuta K. Programmable molecular transport achieved by engineering protein motors to move on DNA nanotubes. Science 2022; 375:1159-1164. [PMID: 35271337 DOI: 10.1126/science.abj5170] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Intracellular transport is the basis of microscale logistics within cells and is powered by biomolecular motors. Mimicking transport for in vitro applications has been widely studied; however, the inflexibility in track design and control has hindered practical applications. Here, we developed protein-based motors that move on DNA nanotubes by combining a biomolecular motor dynein and DNA binding proteins. The new motors and DNA-based nanoarchitectures enabled us to arrange the binding sites on the track, locally control the direction of movement, and achieve multiplexed cargo transport by different motors. The integration of these technologies realized microscale cargo sorters and integrators that automatically transport molecules as programmed in DNA sequences on a branched DNA nanotube. Our system should provide a versatile, controllable platform for future applications.
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Affiliation(s)
- Ryota Ibusuki
- Graduate School of Life Science, University of Hyogo, Harima Science Park City, Hyogo 678-1297, Japan
| | - Tatsuya Morishita
- Graduate School of Life Science, University of Hyogo, Harima Science Park City, Hyogo 678-1297, Japan
| | - Akane Furuta
- Japan Society for the Promotion of Science, Chiyoda-ku, Tokyo 102-0083, Japan.,Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe, Hyogo 651-2492, Japan
| | - Shintaro Nakayama
- Graduate School of Life Science, University of Hyogo, Harima Science Park City, Hyogo 678-1297, Japan
| | - Maki Yoshio
- Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe, Hyogo 651-2492, Japan
| | - Hiroaki Kojima
- Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe, Hyogo 651-2492, Japan
| | - Kazuhiro Oiwa
- Graduate School of Life Science, University of Hyogo, Harima Science Park City, Hyogo 678-1297, Japan.,Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe, Hyogo 651-2492, Japan
| | - Ken'ya Furuta
- Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe, Hyogo 651-2492, Japan
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16
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Staufer O, De Lora JA, Bailoni E, Bazrafshan A, Benk AS, Jahnke K, Manzer ZA, Otrin L, Díez Pérez T, Sharon J, Steinkühler J, Adamala KP, Jacobson B, Dogterom M, Göpfrich K, Stefanovic D, Atlas SR, Grunze M, Lakin MR, Shreve AP, Spatz JP, López GP. Building a community to engineer synthetic cells and organelles from the bottom-up. eLife 2021; 10:e73556. [PMID: 34927583 PMCID: PMC8716100 DOI: 10.7554/elife.73556] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 12/17/2021] [Indexed: 12/19/2022] Open
Abstract
Employing concepts from physics, chemistry and bioengineering, 'learning-by-building' approaches are becoming increasingly popular in the life sciences, especially with researchers who are attempting to engineer cellular life from scratch. The SynCell2020/21 conference brought together researchers from different disciplines to highlight progress in this field, including areas where synthetic cells are having socioeconomic and technological impact. Conference participants also identified the challenges involved in designing, manipulating and creating synthetic cells with hierarchical organization and function. A key conclusion is the need to build an international and interdisciplinary research community through enhanced communication, resource-sharing, and educational initiatives.
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Affiliation(s)
- Oskar Staufer
- Max Planck Institute for Medical ResearchHeidelbergGermany
- Max Planck School Matter to LifeHeidelbergGermany
- Max Planck Bristol Center for Minimal Biology, University of BristolBristolUnited Kingdom
| | | | | | | | - Amelie S Benk
- Max Planck Institute for Medical ResearchHeidelbergGermany
| | - Kevin Jahnke
- Max Planck Institute for Medical ResearchHeidelbergGermany
| | | | - Lado Otrin
- Max Planck Institute for Dynamics of Complex Technical SystemsMagdeburgGermany
| | | | | | | | | | | | | | - Kerstin Göpfrich
- Max Planck Institute for Medical ResearchHeidelbergGermany
- Max Planck School Matter to LifeHeidelbergGermany
| | | | | | - Michael Grunze
- Max Planck Institute for Medical ResearchHeidelbergGermany
- Max Planck School Matter to LifeHeidelbergGermany
| | | | | | - Joachim P Spatz
- Max Planck Institute for Medical ResearchHeidelbergGermany
- Max Planck School Matter to LifeHeidelbergGermany
- Max Planck Bristol Center for Minimal Biology, University of BristolBristolUnited Kingdom
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17
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Su H, Brockman JM, Duan Y, Sen N, Chhabra H, Bazrafshan A, Blanchard AT, Meyer T, Andrews B, Doye JPK, Ke Y, Dyer RB, Salaita K. Massively Parallelized Molecular Force Manipulation with On-Demand Thermal and Optical Control. J Am Chem Soc 2021; 143:19466-19473. [PMID: 34762807 DOI: 10.1021/jacs.1c08796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In single-molecule force spectroscopy (SMFS), a tethered molecule is stretched using a specialized instrument to study how macromolecules extend under force. One problem in SMFS is the serial and slow nature of the measurements, performed one molecule at a time. To address this long-standing challenge, we report on the origami polymer force clamp (OPFC) which enables parallelized manipulation of the mechanical forces experienced by molecules without the need for dedicated SMFS instruments or surface tethering. The OPFC positions target molecules between a rigid nanoscale DNA origami beam and a responsive polymer particle that shrinks on demand. As a proof-of-concept, we record the steady state and time-resolved mechanical unfolding dynamics of DNA hairpins using the fluorescence signal from ensembles of molecules and confirm our conclusion using modeling.
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Affiliation(s)
- Hanquan Su
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Joshua M Brockman
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Yuxin Duan
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Navoneel Sen
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Hemani Chhabra
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Alisina Bazrafshan
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Aaron T Blanchard
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Travis Meyer
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Brooke Andrews
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Yonggang Ke
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States.,Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - R Brian Dyer
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Khalid Salaita
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States.,Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
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18
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Saper G, Tsitkov S, Katira P, Hess H. Robotic end-to-end fusion of microtubules powered by kinesin. Sci Robot 2021; 6:eabj7200. [PMID: 34731025 DOI: 10.1126/scirobotics.abj7200] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The active assembly of molecules by nanorobots has advanced greatly since “molecular manufacturing”—that is, the use of nanoscale tools to build molecular structures—was proposed. In contrast to a catalyst, which accelerates a reaction by smoothing the potential energy surface along the reaction coordinate, molecular machines expend energy to accelerate a reaction relative to the baseline provided by thermal motion and forces. Here, we design a nanorobotics system to accelerate end-to-end microtubule assembly by using kinesin motors and a circular confining chamber. We show that the mechanical interaction of kinesin-propelled microtubules gliding on a surface with the walls of the confining chamber results in a nonequilibrium distribution of microtubules, which increases the number of end-to-end microtubule fusion events 20-fold compared with microtubules gliding on a plane. In contrast to earlier nanorobots, where a nonequilibrium distribution was built into the initial state and drove the process, our nanorobotic system creates and actively maintains the building blocks in the concentrated state responsible for accelerated assembly through the adenosine triphosphate–fueled generation of force by kinesin-1 motor proteins. This approach can be used in the future to develop biohybrid or bioinspired nanorobots that use molecular machines to access nonequilibrium states and accelerate nanoscale assembly.
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Affiliation(s)
- Gadiel Saper
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Stanislav Tsitkov
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Parag Katira
- Department of Mechanical Engineering, San Diego State University, San Diego, CA, USA
| | - Henry Hess
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
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19
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Pitikultham P, Wang Z, Wang Y, Shang Y, Jiang Q, Ding B. Stimuli-Responsive DNA Origami Nanodevices and Their Biological Applications. ChemMedChem 2021; 17:e202100635. [PMID: 34729948 DOI: 10.1002/cmdc.202100635] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/29/2021] [Indexed: 02/05/2023]
Abstract
DNA origami nanotechnology has provided predictable static nanoarchitectures and dynamic nanodevices with rationally designed geometries, precise spatial addressability, and marked biocompatibility. Multiple functional elements, such as peptides, aptamers, nanoparticles, fluorescence probes, and proteins, etc. can be easily integrated into DNA origami templates with nanoscale precision, leading to a variety of promising applications. Triggered by chemical/physical stimuli, dynamic DNA origami nanodevices can switch between defined conformations or translocate autonomously, providing powerful tools for intelligent biosensing and drug delivery. In this minireview, we summarize the recent progress of dynamic DNA origami nanodevices with desired reconfigurability and feasibility to perform multiple biological tasks. We introduce varieties of DNA nanodevices that can be controlled by different molecular triggers and external stimuli. Subsequently, we highlight the recent advances in employing DNA nanodevices as biosensors and drug delivery vehicles. At last, future possibilities and perspectives are also discussed.
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Affiliation(s)
- Piyawat Pitikultham
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, 11 BeiYiTiao ZhongGuanCun, Beijing, 100190, China.,School of Nanoscience and Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhaoran Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, 11 BeiYiTiao ZhongGuanCun, Beijing, 100190, China
| | - Yiming Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, 11 BeiYiTiao ZhongGuanCun, Beijing, 100190, China.,School of Nanoscience and Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yingxu Shang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, 11 BeiYiTiao ZhongGuanCun, Beijing, 100190, China
| | - Qiao Jiang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, 11 BeiYiTiao ZhongGuanCun, Beijing, 100190, China.,School of Nanoscience and Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, 11 BeiYiTiao ZhongGuanCun, Beijing, 100190, China.,School of Nanoscience and Technology, University of Chinese Academy of Sciences, Beijing, 100049, China.,School of Materials Science and Engineering, Zhengzhou University, Zhengzhou, 450001, China
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20
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He Q, Liu Y, Li K, Wu Y, Wang T, Tan Y, Jiang T, Liu X, Liu Z. Deoxyribonucleic acid anchored on cell membranes for biomedical application. Biomater Sci 2021; 9:6691-6717. [PMID: 34494042 DOI: 10.1039/d1bm01057c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Engineering cellular membranes with functional molecules provides an attractive strategy to manipulate cellular behaviors and functionalities. Currently, synthetic deoxyribonucleic acid (DNA) has emerged as a promising molecular tool to engineer cellular membranes for biomedical applications due to its molecular recognition and programmable properties. In this review, we summarized the recent advances in anchoring DNA on the cellular membranes and their applications. The strategies for anchoring DNA on cell membranes were summarized. Then their applications, such as immune response activation, receptor oligomerization regulation, membrane structure mimicking, cell-surface biosensing, and construction of cell clusters, were listed. The DNA-enabled intelligent systems which were able to sense stimuli such as DNA strands, light, and metal ions were highlighted. Finally, insights regarding the remaining challenges and possible future directions were provided.
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Affiliation(s)
- Qunye He
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, P. R. China.
| | - Yanfei Liu
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, Hunan Province, P. R. China
| | - Ke Li
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, P. R. China.
| | - Yuwei Wu
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, P. R. China.
| | - Ting Wang
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, P. R. China.
| | - Yifu Tan
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, Hunan Province, P. R. China
| | - Ting Jiang
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, Hunan Province, P. R. China
| | - Xiaoqin Liu
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, Hunan Province, P. R. China
| | - Zhenbao Liu
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, P. R. China. .,Molecular Imaging Research Center of Central South University, Changsha 410008, Hunan, P. R. China
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21
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Wei W, Lin H, Hao T, Wang S, Hu Y, Guo Z, Luo X. DNA walker-mediated biosensor for target-triggered triple-mode detection of Vibrio parahaemolyticus. Biosens Bioelectron 2021; 186:113305. [PMID: 33990037 DOI: 10.1016/j.bios.2021.113305] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 04/27/2021] [Accepted: 05/02/2021] [Indexed: 01/04/2023]
Abstract
Herein, we have constructed a target-triggered and DNA walker-mediated biosensor with triple signal (BTS) outputs mode for sensitive and reliable detection of pathogenic bacteria. Vibrio parahaemolyticus (VP) being the detection target model, the aptamer conformational changes induced by VP have been designed to activate the DNA walk on the modifiable and conductive surface of Fe3O4 nanoparticles to generate triple signal outputs, including electrochemiluminescence (ECL), fast scan cyclic voltammetry (FSCV) and fluorescent pixel counting (FLPC). Limits of quantification (LOQ) of VP were as low as 1 CFU⋅mL-1 by ECL with a linear range of 1-106 CFU⋅mL-1, 1 CFU⋅mL-1 by FSCV with a linear range of 1-106 CFU⋅mL-1, and 10 CFU⋅mL-1 by FLPC with a linear range of 10-107 CFU⋅mL-1 respectively, all squared correlation coefficients R2 being > 0.99. In addition, optical and electrochemical results, signal-on and signal-off results, electrode phase and solution phase results could be mutually verified by integrating of multiple detection techniques in one biosensor, greatly improving the accuracy and reliability. Therefore, the designed BTS has provided a powerful strategy for pathogenic bacteria detection considering its high detection sensitivity and accuracy, exhibiting great potential in food safety, water quality and biological contamination.
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Affiliation(s)
- Wenting Wei
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, State Key Laboratory Base of Novel Functional Materials and Preparation Science, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, PR China
| | - Han Lin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, State Key Laboratory Base of Novel Functional Materials and Preparation Science, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, PR China.
| | - Tingting Hao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, State Key Laboratory Base of Novel Functional Materials and Preparation Science, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, PR China
| | - Sui Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, State Key Laboratory Base of Novel Functional Materials and Preparation Science, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, PR China
| | - Yufang Hu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, State Key Laboratory Base of Novel Functional Materials and Preparation Science, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, PR China
| | - Zhiyong Guo
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, State Key Laboratory Base of Novel Functional Materials and Preparation Science, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, PR China.
| | - Xingyu Luo
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, State Key Laboratory Base of Novel Functional Materials and Preparation Science, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, PR China
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22
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Abstract
Creating artificial macromolecular transport systems that can support the movement of molecules along defined routes is a key goal of nanotechnology. Here, we report the bottom-up construction of a macromolecular transport system in which molecular pistons diffusively move through micrometer-long, hollow filaments. The pistons can cover micrometer distances in fractions of seconds. We build the system using multi-layer DNA origami and analyze the structures of the components using transmission electron microscopy. We study the motion of the pistons along the tubes using single-molecule fluorescence microscopy and perform Langevin simulations to reveal details of the free energy surface that directs the motions of the pistons. The tubular transport system achieves diffusivities and displacement ranges known from natural molecular motors and realizes mobility improvements over five orders of magnitude compared to previous artificial random walker designs. Electric fields can also be employed to actively pull the pistons along the filaments, thereby realizing a nanoscale electric rail system. Our system presents a platform for artificial motors that move autonomously driven by chemical fuels and for performing nanotribology studies, and it could form a basis for future molecular transportation networks. DNA origami can be used to control the movement of nanoscale assemblies. Here the authors construct multiple-micrometer-long hollow DNA filaments through which DNA pistons move with micrometer-per-second speeds.
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23
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Blanchard AT. Burnt bridge ratchet motor force scales linearly with polyvalency: a computational study. SOFT MATTER 2021; 17:6056-6062. [PMID: 34151336 DOI: 10.1039/d1sm00676b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Nano- and micro-scale burnt bridge ratchet motors, which translocate via "guide" molecules that bind to and degrade a field of "fuel" molecules, have recently emerged in several biological and engineering contexts. The capacity of these motors to generate mechanical forces remains an open question. Here, chemomechanical modeling suggests that BBR force scales linearly with the steady-state number of guide-fuel bonds.
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Affiliation(s)
- Aaron T Blanchard
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA and Michigan Society of Fellows, University of Michigan, Ann Arbor, Michigan 48109, USA.
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24
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Abstract
We present here a model for multivalent diffusive transport whereby a central point-like hub is coupled to multiple feet, which bind to complementary sites on a two-dimensional landscape. The available number of binding interactions is dependent on the number of feet (multivalency) and on their allowed distance from the central hub (span). Using Monte Carlo simulations that implement the Gillespie algorithm, we simulate multivalent diffusive transport processes for 100 distinct walker designs. Informed by our simulation results, we derive an analytical expression for the diffusion coefficient of a general multivalent diffusive process as a function of multivalency, span, and dissociation constant Kd. Our findings can be used to guide the experimental design of multivalent transporters, in particular, providing insight into how to overcome trade-offs between diffusivity and processivity.
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Affiliation(s)
- Antonia Kowalewski
- Department of Physics, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Nancy R Forde
- Department of Physics, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Chapin S Korosec
- Department of Physics, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
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25
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Bazrafshan A, Kyriazi ME, Holt BA, Deng W, Piranej S, Su H, Hu Y, El-Sagheer AH, Brown T, Kwong GA, Kanaras AG, Salaita K. DNA Gold Nanoparticle Motors Demonstrate Processive Motion with Bursts of Speed Up to 50 nm Per Second. ACS NANO 2021; 15:8427-8438. [PMID: 33956424 DOI: 10.1021/acsnano.0c10658] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Synthetic motors that consume chemical energy to produce mechanical work offer potential applications in many fields that span from computing to drug delivery and diagnostics. Among the various synthetic motors studied thus far, DNA-based machines offer the greatest programmability and have shown the ability to translocate micrometer-distances in an autonomous manner. DNA motors move by employing a burnt-bridge Brownian ratchet mechanism, where the DNA "legs" hybridize and then destroy complementary nucleic acids immobilized on a surface. We have previously shown that highly multivalent DNA motors that roll offer improved performance compared to bipedal walkers. Here, we use DNA-gold nanoparticle conjugates to investigate and enhance DNA nanomotor performance. Specifically, we tune structural parameters such as DNA leg density, leg span, and nanoparticle anisotropy as well as buffer conditions to enhance motor performance. Both modeling and experiments demonstrate that increasing DNA leg density boosts the speed and processivity of motors, whereas DNA leg span increases processivity and directionality. By taking advantage of label-free imaging of nanomotors, we also uncover Lévy-type motion where motors exhibit bursts of translocation that are punctuated with transient stalling. Dimerized particles also demonstrate more ballistic trajectories confirming a rolling mechanism. Our work shows the fundamental properties that control DNA motor performance and demonstrates optimized motors that can travel multiple micrometers within minutes with speeds of up to 50 nm/s. The performance of these nanoscale motors approaches that of motor proteins that travel at speeds of 100-1000 nm/s, and hence this work can be important in developing protocellular systems as well next generation sensors and diagnostics.
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Affiliation(s)
- Alisina Bazrafshan
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322 United States
| | - Maria-Eleni Kyriazi
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO171BJ, U.K
| | - Brandon Alexander Holt
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322 United States
| | - Wenxiao Deng
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322 United States
| | - Selma Piranej
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322 United States
| | - Hanquan Su
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322 United States
| | - Yuesong Hu
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322 United States
| | - Afaf H El-Sagheer
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, U.K
- Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez, 43721, Egypt
| | - Tom Brown
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, U.K
| | - Gabriel A Kwong
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322 United States
| | - Antonios G Kanaras
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO171BJ, U.K
- Institute for Life Sciences, University of Southampton, Southampton, SO171BJ, U.K
| | - Khalid Salaita
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322 United States
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322 United States
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26
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Xu M, Tang D. Recent advances in DNA walker machines and their applications coupled with signal amplification strategies: A critical review. Anal Chim Acta 2021; 1171:338523. [PMID: 34112433 DOI: 10.1016/j.aca.2021.338523] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 04/13/2021] [Accepted: 04/13/2021] [Indexed: 02/08/2023]
Abstract
DNA walkers, a type of dynamic nanomachines, have become the subject of burgeoning research in the field of biology. These walkers are powered by driving forces based on strand displacement reactions, protein enzyme/DNAzyme reactions and conformational transitions. With the unique properties of high directionality, flexibility and efficiency, DNA walkers move progressively and autonomously along multiple dimensional tracks, offering abundant and promising applications in biosensing, material assembly and synthesis, and early cancer diagnosis. Notably, DNA walkers identified as signal amplifiers can be combined with various amplification approaches to enhance signal transduction and amplify biosensor sensing signals. Herein, we systematically and comprehensively review the walking principles of various DNA walkers and the recent progress on multiple dimensional tracks by presenting representative examples and an insightful discussion. We also summarized and categorized the diverse signal amplification strategies with which DNA walkers have coupled. Finally, we outline the challenges and future trends of DNA walker machines in emerging analytical fields.
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Affiliation(s)
- Mingdi Xu
- College of Ecological Environment and Urban Construction, Fujian University of Technology, Fuzhou 350108, People's Republic of China; Key Laboratory of Analytical Science for Food Safety and Biology (MOE & Fujian Province), Department of Chemistry, Fuzhou University, Fuzhou 350108, People's Republic of China.
| | - Dianping Tang
- Key Laboratory of Analytical Science for Food Safety and Biology (MOE & Fujian Province), Department of Chemistry, Fuzhou University, Fuzhou 350108, People's Republic of China.
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27
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Blanchard AT, Salaita K. Multivalent molecular tension probes as anisotropic mechanosensors: concept and simulation. Phys Biol 2021; 18:034001. [PMID: 33316784 DOI: 10.1088/1478-3975/abd333] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Cells use protein-based mechanosensors to measure the physical properties of their surroundings. Synthetic tension sensors made of proteins, DNA, and other molecular building blocks have recently emerged as tools to visualize and perturb the mechanics of these mechanosensors. While almost all synthetic tension sensors are designed to exhibit orientation-independent force responses, recent work has shown that biological mechanosensors often function in a manner that is highly dependent on force orientation. Accordingly, the design of synthetic mechanosensors with orientation-dependent force responses can provide a means to study the role of orientation in mechanosensation. Furthermore, the process of designing anisotropic force responses may yield insight into the physical basis for orientation-dependence in biological mechanosensors. Here, we propose a DNA-based molecular tension sensor design wherein multivalency is used to create an orientation-dependent force response. We apply chemomechanical modeling to show that multivalency can be used to create synthetic mechanosensors with force response thresholds that vary by tens of pN with respect to force orientation.
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Affiliation(s)
- Aaron T Blanchard
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30322, United States of America
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28
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Zhou B, Dong Y, Liu D. Recent Progress in DNA Motor-Based Functional Systems. ACS APPLIED BIO MATERIALS 2021; 4:2251-2261. [PMID: 35014349 DOI: 10.1021/acsabm.0c01540] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The designability, functionalization, and diverse secondary structures of DNA enable the construction of DNA motors with stimuli-responsiveness. Therefore, it has been widely used to fabricate functional systems or generate mechanical power under external stimuli, such as pH, light, heat, electrical, and chemical molecular signals. Furthermore, the DNA motor has also been demonstrated to promote the applications of smart devices and materials, particularly in controllable drug delivery and reversible molecular switching. In this review, we have summarized and discussed recent progress of the construction and applications of DNA motor-based functional systems, such as responsive nanodevices, modified surfaces, and hydrogels.
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Affiliation(s)
- Bini Zhou
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, 100084, PR China
| | - Yuanchen Dong
- Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Dongsheng Liu
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, 100084, PR China
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29
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Korosec CS, Jindal L, Schneider M, Calderon de la Barca I, Zuckermann MJ, Forde NR, Emberly E. Substrate stiffness tunes the dynamics of polyvalent rolling motors. SOFT MATTER 2021; 17:1468-1479. [PMID: 33347523 DOI: 10.1039/d0sm01811b] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Nature has evolved many mechanisms for achieving directed motion on the subcellular level. The burnt-bridges ratchet (BBR) is one mechanism used to achieve superdiffusive molecular motion over long distances through the successive cleavage of surface-bound energy-rich substrate sites. This mechanism has been associated with both nanoscale and microscale movement, with the latter accomplished through polyvalent interactions between a large hub (e.g. influenza virus) and substrate (e.g. cell surface receptors). Experimental successes in achieving superdiffusive motion by synthetic polyvalent BBRs have raised questions about the dynamics of their motility, including whether rolling or translation is better able to direct motion of microscale spherical hubs. Here we simulate the three-dimensional dynamics of a polyvalent sphere moving on and cleaving an elastic substrate. We find that substrate stiffness plays an important role in controlling both the motor's mode of motility and its directional persistence. As we tune lateral substrate stiffness from soft to stiff we find there exists an intermediate value that optimizes rolling behaviour. We also find that there is an optimal substrate stiffness for maximizing persistence length, while stiffness does not influence as strongly the superdiffusive dynamics of the particle. Lastly, we examine the effect of substrate density, and show that softer landscapes are better able to buffer against decreases in substrate occupancy, with the spherical motor maintaining superdiffusive motion more on softer landscapes than on stiff landscapes as occupancy drops. Our results highlight the importance of surface in controlling the motion of polyvalent BBRs.
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Affiliation(s)
- Chapin S Korosec
- Department of Physics, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada.
| | - Lavisha Jindal
- Department of Physics, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada.
| | - Mathew Schneider
- Department of Physics, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada.
| | - Ignacio Calderon de la Barca
- Department of Physics, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada.
| | - Martin J Zuckermann
- Department of Physics, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada.
| | - Nancy R Forde
- Department of Physics, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada.
| | - Eldon Emberly
- Department of Physics, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada.
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30
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31
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Du Y, Pan J, Qiu H, Mao C, Choi JH. Mechanistic Understanding of Surface Migration Dynamics with DNA Walkers. J Phys Chem B 2021; 125:507-517. [PMID: 33428424 DOI: 10.1021/acs.jpcb.0c09048] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yancheng Du
- School of Mechanical Engineering, Purdue University, 610 Purdue Mall, West Lafayette, Indiana 47907, United States
| | - Jing Pan
- Department of Mechanical and Aerospace Engineering, University of Florida, Gainesville, Florida 32611, United States
| | - Hengming Qiu
- School of Mechanical Engineering, Purdue University, 610 Purdue Mall, West Lafayette, Indiana 47907, United States
| | - Chengde Mao
- Department of Chemistry, Purdue University, 610 Purdue Mall, West Lafayette, Indiana 47907, United States
| | - Jong Hyun Choi
- School of Mechanical Engineering, Purdue University, 610 Purdue Mall, West Lafayette, Indiana 47907, United States
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32
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Lv H, Chen A, Cheng W, Kong L, Zhao M, Ding S, Ju H, Cheng W. Efficient DNA Walker Guided with Well-Regulated Interfacial Tracks for Ultrasensitive Electrochemiluminescence Biosensing. Anal Chem 2020; 92:15624-15631. [DOI: 10.1021/acs.analchem.0c03893] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Heye Lv
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Anyi Chen
- School of Public Health and Management, Chongqing Medical University, Chongqing 400016, China
| | - Wenqian Cheng
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Liangsheng Kong
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Min Zhao
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Wei Cheng
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
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33
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Wei TY, Ruder WC. Engineering control circuits for molecular robots using synthetic biology. APL MATERIALS 2020; 8:101104. [PMID: 33101786 PMCID: PMC7560983 DOI: 10.1063/5.0020429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/24/2020] [Indexed: 06/11/2023]
Abstract
The integration of molecular robots and synthetic biology allows for the creation of sophisticated behaviors at the molecular level. Similar to the synergy between bioelectronics and soft robotics, synthetic biology provides control circuitry for molecular robots. By encoding perception-action modules within synthetic circuits, molecular machines can advance beyond repeating tasks to the incorporation of complex behaviors. In particular, cell-free synthetic biology provides biomolecular circuitry independent of living cells. This research update reviews the current progress in using synthetic biology as perception-action control modules in robots from molecular robots to macroscale robots. Additionally, it highlights recent developments in molecular robotics and cell-free synthetic biology and suggests their combined use as a necessity for future molecular robot development.
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Affiliation(s)
- Ting-Yen Wei
- Department of Bioengineering, University of
Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
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34
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Brockman JM, Su H, Blanchard AT, Duan Y, Meyer T, Quach ME, Glazier R, Bazrafshan A, Bender RL, Kellner AV, Ogasawara H, Ma R, Schueder F, Petrich BG, Jungmann R, Li R, Mattheyses AL, Ke Y, Salaita K. Live-cell super-resolved PAINT imaging of piconewton cellular traction forces. Nat Methods 2020; 17:1018-1024. [PMID: 32929270 PMCID: PMC7574592 DOI: 10.1038/s41592-020-0929-2] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 07/20/2020] [Indexed: 11/09/2022]
Abstract
Despite the vital role of mechanical forces in biology, it still remains a challenge to image cellular force with sub-100-nm resolution. Here, we present tension points accumulation for imaging in nanoscale topography (tPAINT), integrating molecular tension probes with the DNA points accumulation for imaging in nanoscale topography (DNA-PAINT) technique to map piconewton mechanical events with ~25-nm resolution. To perform live-cell dynamic tension imaging, we engineered reversible probes with a cryptic docking site revealed only when the probe experiences forces exceeding a defined mechanical threshold (~7-21 pN). Additionally, we report a second type of irreversible tPAINT probe that exposes its cryptic docking site permanently and thus integrates force history over time, offering improved spatial resolution in exchange for temporal dynamics. We applied both types of tPAINT probes to map integrin receptor forces in live human platelets and mouse embryonic fibroblasts. Importantly, tPAINT revealed a link between platelet forces at the leading edge of cells and the dynamic actin-rich ring nucleated by the Arp2/3 complex.
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Affiliation(s)
- Joshua M Brockman
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Hanquan Su
- Department of Chemistry, Emory University, Atlanta, GA, USA
| | - Aaron T Blanchard
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Yuxin Duan
- Department of Chemistry, Emory University, Atlanta, GA, USA
| | - Travis Meyer
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - M Edward Quach
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Department of Pediatrics, Emory University, Atlanta, GA, USA
| | - Roxanne Glazier
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | | | | | - Anna V Kellner
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | | | - Rong Ma
- Department of Chemistry, Emory University, Atlanta, GA, USA
| | - Florian Schueder
- Faculty of Physics and Center for Nanoscience, Ludwig Maximilian University, Munich, Germany
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Brian G Petrich
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Department of Pediatrics, Emory University, Atlanta, GA, USA
| | - Ralf Jungmann
- Faculty of Physics and Center for Nanoscience, Ludwig Maximilian University, Munich, Germany
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Renhao Li
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Department of Pediatrics, Emory University, Atlanta, GA, USA
| | - Alexa L Mattheyses
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Department of Chemistry, Emory University, Atlanta, GA, USA
| | - Khalid Salaita
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA.
- Department of Chemistry, Emory University, Atlanta, GA, USA.
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35
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Linke H, Höcker B, Furuta K, Forde NR, Curmi PMG. Synthetic biology approaches to dissecting linear motor protein function: towards the design and synthesis of artificial autonomous protein walkers. Biophys Rev 2020; 12:1041-1054. [PMID: 32651904 PMCID: PMC7429643 DOI: 10.1007/s12551-020-00717-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 07/02/2020] [Indexed: 12/20/2022] Open
Abstract
Molecular motors and machines are essential for all cellular processes that together enable life. Built from proteins with a wide range of properties, functionalities and performance characteristics, biological motors perform complex tasks and can transduce chemical energy into mechanical work more efficiently than human-made combustion engines. Sophisticated studies of biological protein motors have provided many structural and biophysical insights and enabled the development of models for motor function. However, from the study of highly evolved, biological motors, it remains difficult to discern detailed mechanisms, for example, about the relative role of different force generation mechanisms, or how information is communicated across a protein to achieve the necessary coordination. A promising, complementary approach to answering these questions is to build synthetic protein motors from the bottom up. Indeed, much effort has been invested in functional protein design, but so far, the "holy grail" of designing and building a functional synthetic protein motor has not been realized. Here, we review the progress made to date, and we put forward a roadmap for achieving the aim of constructing the first artificial, autonomously running protein motor. Specifically, we propose to break down the task into (i) enzymatic control of track binding, (ii) the engineering of asymmetry and (iii) the engineering of allosteric control for internal communication. We also propose specific approaches for solving each of these challenges.
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Affiliation(s)
- Heiner Linke
- NanoLund and Solid State Physics, Lund University, Box 118, SE 22100, Lund, Sweden
| | - Birte Höcker
- Department of Biochemistry, University of Bayreuth, 95447, Bayreuth, Germany
| | - Ken'ya Furuta
- Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe, Hyogo, 651-2492, Japan
| | - Nancy R Forde
- Department of Physics, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Paul M G Curmi
- School of Physics, University of New South Wales, Sydney, NSW, 2052, Australia.
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36
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Deal BR, Ma R, Ma VPY, Su H, Kindt JT, Salaita K. Engineering DNA-Functionalized Nanostructures to Bind Nucleic Acid Targets Heteromultivalently with Enhanced Avidity. J Am Chem Soc 2020; 142:9653-9660. [PMID: 32338896 PMCID: PMC7340273 DOI: 10.1021/jacs.0c01568] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Improving the affinity of nucleic acids to their complements is an important goal for many fields spanning from genomics to antisense therapy and diagnostics. One potential approach to achieving this goal is to use multivalent binding, which often boosts the affinity between ligands and receptors, as exemplified by virus-cell binding and antibody-antigen interactions. Herein, we investigate the binding of heteromultivalent DNA-nanoparticle conjugates, where multiple unique oligonucleotides displayed on a nanoparticle form a multivalent complex with a long DNA target containing the complementary sequences. By developing a strategy to spatially pattern oligonucleotides on a nanoparticle, we demonstrate that the molecular organization of heteromultivalent nanostructures is critical for effective binding; patterned particles have a ∼23 order-of-magnitude improvement in affinity compared to chemically identical particles patterned incorrectly. We envision that nanostructures presenting spatially patterned heteromultivalent DNA will offer important biomedical applications given the utility of DNA-functionalized nanostructures in diagnostics and therapeutics.
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37
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Davey SG. Roll this way. Nat Rev Chem 2020; 4:169. [PMID: 37128045 DOI: 10.1038/s41570-020-0179-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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