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Amiri A, Abedanzadeh S, Davaeil B, Shaabani A, Moosavi-Movahedi AA. Protein click chemistry and its potential for medical applications. Q Rev Biophys 2024; 57:e6. [PMID: 38619322 DOI: 10.1017/s0033583524000027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
A revolution in chemical biology occurred with the introduction of click chemistry. Click chemistry plays an important role in protein chemistry modifications, providing specific, sensitive, rapid, and easy-to-handle methods. Under physiological conditions, click chemistry often overlaps with bioorthogonal chemistry, defined as reactions that occur rapidly and selectively without interfering with biological processes. Click chemistry is used for the posttranslational modification of proteins based on covalent bond formations. With the contribution of click reactions, selective modification of proteins would be developed, representing an alternative to other technologies in preparing new proteins or enzymes for studying specific protein functions in different biological processes. Click-modified proteins have potential in diverse applications such as imaging, labeling, sensing, drug design, and enzyme technology. Due to the promising role of proteins in disease diagnosis and therapy, this review aims to highlight the growing applications of click strategies in protein chemistry over the last two decades, with a special emphasis on medicinal applications.
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Affiliation(s)
- Ahmad Amiri
- Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | | | - Bagher Davaeil
- Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Ahmad Shaabani
- Department of Chemistry, Shahid Beheshti University, Tehran, Iran
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2
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Heber S, McClintock MA, Simon B, Mehtab E, Lapouge K, Hennig J, Bullock SL, Ephrussi A. Tropomyosin 1-I/C coordinates kinesin-1 and dynein motors during oskar mRNA transport. Nat Struct Mol Biol 2024; 31:476-488. [PMID: 38297086 PMCID: PMC10948360 DOI: 10.1038/s41594-024-01212-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 01/02/2024] [Indexed: 02/02/2024]
Abstract
Dynein and kinesin motors mediate long-range intracellular transport, translocating towards microtubule minus and plus ends, respectively. Cargoes often undergo bidirectional transport by binding to both motors simultaneously. However, it is not known how motor activities are coordinated in such circumstances. In the Drosophila female germline, sequential activities of the dynein-dynactin-BicD-Egalitarian (DDBE) complex and of kinesin-1 deliver oskar messenger RNA from nurse cells to the oocyte, and within the oocyte to the posterior pole. We show through in vitro reconstitution that Tm1-I/C, a tropomyosin-1 isoform, links kinesin-1 in a strongly inhibited state to DDBE-associated oskar mRNA. Nuclear magnetic resonance spectroscopy, small-angle X-ray scattering and structural modeling indicate that Tm1-I/C suppresses kinesin-1 activity by stabilizing its autoinhibited conformation, thus preventing competition with dynein until kinesin-1 is activated in the oocyte. Our work reveals a new strategy for ensuring sequential activity of microtubule motors.
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Affiliation(s)
- Simone Heber
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Mark A McClintock
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Bernd Simon
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, USA
| | - Eve Mehtab
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Karine Lapouge
- Protein Expression and Purification Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Janosch Hennig
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Biochemistry IV, Biophysical Chemistry, University of Bayreuth, Bayreuth, Germany
| | - Simon L Bullock
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, UK.
| | - Anne Ephrussi
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
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3
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Yadav SA, Khatri D, Soni A, Khetan N, Athale CA. Wave-like oscillations of clamped microtubules driven by collective dynein transport. Biophys J 2024; 123:509-524. [PMID: 38258292 PMCID: PMC10912927 DOI: 10.1016/j.bpj.2024.01.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 12/05/2023] [Accepted: 01/17/2024] [Indexed: 01/24/2024] Open
Abstract
Microtubules (MTs) are observed to move and buckle driven by ATP-dependent molecular motors in both mitotic and interphasic eukaryotic cells as well as in specialized structures such as flagella and cilia with a stereotypical geometry. In previous work, clamped MTs driven by a few kinesin motors were seen to buckle and occasionally flap in what was referred to as flagella-like motion. Theoretical models of active-filament dynamics and a following force have predicted that, with sufficient force and binding-unbinding, such clamped filaments should spontaneously undergo periodic buckling oscillations. However, a systematic experimental test of the theory and reconciliation to a model was lacking. Here, we have engineered a minimal system of MTs clamped at their plus ends and transported by a sheet of dynein motors that demonstrate the emergence of spontaneous traveling-wave oscillations along single filaments. The frequencies of tip oscillations are in the millihertz range and are statistically indistinguishable in the onset and recovery phases. We develop a 2D computational model of clamped MTs binding and unbinding stochastically to motors in a "gliding-assay" geometry. The simulated MTs oscillate with a frequency comparable to experiment. The model predicts the effect of MT length and motor density on qualitative transitions between distinct phases of flapping, regular oscillations, and looping. We develop an effective "order parameter" based on the relative deflection along the filament and orthogonal to it. The transitions predicted in simulations are validated by experimental data. These results demonstrate a role for geometry, MT buckling, and collective molecular motor activity in the emergence of oscillatory dynamics.
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Affiliation(s)
| | | | - Aman Soni
- Division of Biology, IISER Pune, Pune, India
| | - Neha Khetan
- Division of Biology, IISER Pune, Pune, India
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4
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Spratt J, Dias JM, Kolonelou C, Kiriako G, Engström E, Petrova E, Karampelias C, Cervenka I, Papanicolaou N, Lentini A, Reinius B, Andersson O, Ambrosetti E, Ruas JL, Teixeira AI. Multivalent insulin receptor activation using insulin-DNA origami nanostructures. Nat Nanotechnol 2024; 19:237-245. [PMID: 37813939 PMCID: PMC10873203 DOI: 10.1038/s41565-023-01507-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 08/15/2023] [Indexed: 10/11/2023]
Abstract
Insulin binds the insulin receptor (IR) and regulates anabolic processes in target tissues. Impaired IR signalling is associated with multiple diseases, including diabetes, cancer and neurodegenerative disorders. IRs have been reported to form nanoclusters at the cell membrane in several cell types, even in the absence of insulin binding. Here we exploit the nanoscale spatial organization of the IR to achieve controlled multivalent receptor activation. To control insulin nanoscale spatial organization and valency, we developed rod-like insulin-DNA origami nanostructures carrying different numbers of insulin molecules with defined spacings. Increasing the insulin valency per nanostructure markedly extended the residence time of insulin-DNA origami nanostructures at the receptors. Both insulin valency and spacing affected the levels of IR activation in adipocytes. Moreover, the multivalent insulin design associated with the highest levels of IR activation also induced insulin-mediated transcriptional responses more effectively than the corresponding monovalent insulin nanostructures. In an in vivo zebrafish model of diabetes, treatment with multivalent-but not monovalent-insulin nanostructures elicited a reduction in glucose levels. Our results show that the control of insulin multivalency and spatial organization with nanoscale precision modulates the IR responses, independent of the insulin concentration. Therefore, we propose insulin nanoscale organization as a design parameter in developing new insulin therapies.
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Affiliation(s)
- Joel Spratt
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - José M Dias
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Christina Kolonelou
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Georges Kiriako
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Enya Engström
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ekaterina Petrova
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Christos Karampelias
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Igor Cervenka
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Natali Papanicolaou
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Antonio Lentini
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Björn Reinius
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Olov Andersson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Elena Ambrosetti
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Center for Life Nano- and Neuro-Science, Istituto Italiano di Tecnologia, Rome, Italy
| | - Jorge L Ruas
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Ana I Teixeira
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.
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5
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Bauer J, Reichl A, Tinnefeld P. Kinetic Referencing Allows Identification of Epigenetic Cytosine Modifications by Single-Molecule Hybridization Kinetics and Superresolution DNA-PAINT Microscopy. ACS Nano 2024; 18:1496-1503. [PMID: 38157484 DOI: 10.1021/acsnano.3c08451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
We develop a DNA origami-based internal kinetic referencing system with a colocalized reference and target molecule to provide increased sensitivity and robustness for transient binding kinetics. To showcase this, we investigate the subtle changes in binding strength of DNA oligonucleotide hybrids induced by cytosine modifications. These cytosine modifications, especially 5-methylcytosine but also its oxidized derivatives, have been increasingly studied in the context of epigenetics. Recently revealed correlations of epigenetic modifications and disease also render them interesting biomarkers for early diagnosis. Internal kinetic referencing allows us to probe and compare the influence of the different epigenetic cytosine modifications on the strengths of 7-nucleotide long DNA hybrids with one or two modified nucleotides by single-molecule imaging of their transient binding, revealing subtle differences in binding times. Interestingly, the influence of epigenetic modifications depends on their position in the DNA strand, and in the case of two modifications, effects are additive. The sensitivity of the assay indicates its potential for the direct detection of epigenetic disease markers.
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Affiliation(s)
- Julian Bauer
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
| | - Andreas Reichl
- Department of Chemistry, Ludwig-Maximilians-Universität München, Würmtalstraße 201, 81377 München, Germany
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
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6
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Zhang Q, Wang W, Zhou S, Zhang R, Bischofberger I. Flow-induced periodic chiral structures in an achiral nematic liquid crystal. Nat Commun 2024; 15:7. [PMID: 38191525 PMCID: PMC10774319 DOI: 10.1038/s41467-023-43978-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 11/26/2023] [Indexed: 01/10/2024] Open
Abstract
Supramolecular chirality typically originates from either chiral molecular building blocks or external chiral stimuli. Generating chirality in achiral systems in the absence of a chiral input, however, is non-trivial and necessitates spontaneous mirror symmetry breaking. Achiral nematic lyotropic chromonic liquid crystals have been reported to break mirror symmetry under strong surface or geometric constraints. Here we describe a previously unrecognised mechanism for creating chiral structures by subjecting the material to a pressure-driven flow in a microfluidic cell. The chirality arises from a periodic double-twist configuration of the liquid crystal and manifests as a striking stripe pattern. We show that the mirror symmetry breaking is triggered at regions of flow-induced biaxial-splay configurations of the director field, which are unstable to small perturbations and evolve into lower energy structures. The simplicity of this unique pathway to mirror symmetry breaking can shed light on the requirements for forming macroscopic chiral structures.
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Affiliation(s)
- Qing Zhang
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Weiqiang Wang
- Department of Physics, Hong Kong University of Science and Technology, Hong Kong, China
| | - Shuang Zhou
- Department of Physics, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Rui Zhang
- Department of Physics, Hong Kong University of Science and Technology, Hong Kong, China.
| | - Irmgard Bischofberger
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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7
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Bensel BM, Previs S, Bookwalter C, Trybus KM, Walcott S, Warshaw DM. "Spatial Relationships Matter: Kinesin-1 Molecular Motors Transport Liposome Cargo Through 3D Microtubule Intersections In Vitro". bioRxiv 2023:2023.12.01.569616. [PMID: 38076816 PMCID: PMC10705568 DOI: 10.1101/2023.12.01.569616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Kinesin-1 ensembles maneuver vesicular cargoes through intersections in the 3-dimensional (3D) intracellular microtubule (MT) network. To characterize directional outcomes (straight, turn, terminate) at MT intersections, we challenge 350 nm fluid-like liposomes transported by ~10 constitutively active, truncated kinesin-1 KIF5B (K543) with perpendicular 2-dimensional (2D) and 3D intersections in vitro. Liposomes frequently pause at 2D and 3D intersections (~2s), suggesting that motor teams can simultaneously engage each MT and undergo a tug-of-war. Once resolved, the directional outcomes at 2D MT intersections have a straight to turn ratio of 1.1; whereas at 3D MT intersections, liposomes more frequently go straight (straight to turn ratio of 1.8), highlighting that spatial relationships at intersections bias directional outcomes. Using 3D super-resolution microscopy (STORM), we define the gap between intersecting MTs and the liposome azimuthal approach angle heading into the intersection. We develop an in silico model in which kinesin-1 motors diffuse on the liposome surface, simultaneously engage the intersecting MTs, generate forces and detach from MTs governed by the motors' mechanochemical cycle, and undergo a tug-of-war with the winning team determining the directional outcome in 3D. The model predicts that 1-3 motors typically engage the MT, consistent with optical trapping measurements. Modeled liposomes also predominantly go straight through 3D intersections over a range of intersection gaps and liposome approach angles, even when obstructed by the crossing MT. Our observations and modeling offer mechanistic insights into how cells might tune the MT cytoskeleton, cargo, and motors to modulate cargo transport.
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Affiliation(s)
- Brandon M Bensel
- Department of Molecular Physiology and Biophysics, University of Vermont Larner College of Medicine, Burlington, VT 05405
| | - Samantha Previs
- Department of Molecular Physiology and Biophysics, University of Vermont Larner College of Medicine, Burlington, VT 05405
| | - Carol Bookwalter
- Department of Molecular Physiology and Biophysics, University of Vermont Larner College of Medicine, Burlington, VT 05405
| | - Kathleen M Trybus
- Department of Molecular Physiology and Biophysics, University of Vermont Larner College of Medicine, Burlington, VT 05405
| | - Sam Walcott
- Department of Mathematical Sciences, Worcester Polytechnic Institute, Worcester, MA 01609
| | - David M Warshaw
- Department of Molecular Physiology and Biophysics, University of Vermont Larner College of Medicine, Burlington, VT 05405
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8
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D'Souza AI, Grover R, Monzon GA, Santen L, Diez S. Vesicles driven by dynein and kinesin exhibit directional reversals without regulators. Nat Commun 2023; 14:7532. [PMID: 37985763 PMCID: PMC10662051 DOI: 10.1038/s41467-023-42605-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 10/16/2023] [Indexed: 11/22/2023] Open
Abstract
Intracellular vesicular transport along cytoskeletal filaments ensures targeted cargo delivery. Such transport is rarely unidirectional but rather bidirectional, with frequent directional reversals owing to the simultaneous presence of opposite-polarity motors. So far, it has been unclear whether such complex motility pattern results from the sole mechanical interplay between opposite-polarity motors or requires regulators. Here, we demonstrate that a minimal system, comprising purified Dynein-Dynactin-BICD2 (DDB) and kinesin-3 (KIF16B) attached to large unilamellar vesicles, faithfully reproduces in vivo cargo motility, including runs, pauses, and reversals. Remarkably, opposing motors do not affect vesicle velocity during runs. Our computational model reveals that the engagement of a small number of motors is pivotal for transitioning between runs and pauses. Taken together, our results suggest that motors bound to vesicular cargo transiently engage in a tug-of-war during pauses. Subsequently, stochastic motor attachment and detachment events can lead to directional reversals without the need for regulators.
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Affiliation(s)
- Ashwin I D'Souza
- B CUBE - Center for Molecular Bioengineering, TU Dresden, Dresden, Germany
| | - Rahul Grover
- B CUBE - Center for Molecular Bioengineering, TU Dresden, Dresden, Germany
| | - Gina A Monzon
- B CUBE - Center for Molecular Bioengineering, TU Dresden, Dresden, Germany
- Center for Biophysics, Department of Physics, Saarland University, Saarbrücken, Germany
| | - Ludger Santen
- Center for Biophysics, Department of Physics, Saarland University, Saarbrücken, Germany.
| | - Stefan Diez
- B CUBE - Center for Molecular Bioengineering, TU Dresden, Dresden, Germany.
- Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany.
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
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9
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Tayar AM, Caballero F, Anderberg T, Saleh OA, Cristina Marchetti M, Dogic Z. Controlling liquid-liquid phase behaviour with an active fluid. Nat Mater 2023; 22:1401-1408. [PMID: 37679525 DOI: 10.1038/s41563-023-01660-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 08/02/2023] [Indexed: 09/09/2023]
Abstract
Demixing binary liquids is a ubiquitous transition explained using a well-established thermodynamic formalism that requires the equality of intensive thermodynamics parameters across phase boundaries. Demixing transitions also occur when binary fluid mixtures are driven away from equilibrium, but predicting and designing such out-of-equilibrium transitions remains a challenge. Here we study the liquid-liquid phase separation of attractive DNA nanostars driven away from equilibrium using a microtubule-based active fluid. We find that activity lowers the critical temperature and narrows the range of coexistence concentrations, but only in the presence of mechanical bonds between the liquid droplets and reconfiguring active fluid. Similar behaviours are observed in numerical simulations, suggesting that the activity suppression of the critical point is a generic feature of active liquid-liquid phase separation. Our work describes a versatile platform for building soft active materials with feedback control and providing an insight into self-organization in cell biology.
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Affiliation(s)
- Alexandra M Tayar
- Department of Physics, University of California, Santa Barbara, CA, USA.
| | | | - Trevor Anderberg
- Department of Physics, University of California, Santa Barbara, CA, USA
| | - Omar A Saleh
- Department of Physics, University of California, Santa Barbara, CA, USA
- Materials Department, University of California, Santa Barbara, CA, USA
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA, USA
| | - M Cristina Marchetti
- Department of Physics, University of California, Santa Barbara, CA, USA
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA, USA
| | - Zvonimir Dogic
- Department of Physics, University of California, Santa Barbara, CA, USA.
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA, USA.
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10
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Chang C, Zheng T, Nettesheim G, Song H, Cho C, Crespi S, Shubeita G. On the use of thermal forces to probe kinesin's response to force. Front Mol Biosci 2023; 10:1260914. [PMID: 38028555 PMCID: PMC10644364 DOI: 10.3389/fmolb.2023.1260914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 09/14/2023] [Indexed: 12/01/2023] Open
Abstract
The stepping dynamics of cytoskeletal motor proteins determines the dynamics of cargo transport. In its native cellular environment, a molecular motor is subject to forces from several sources including thermal forces and forces ensuing from the interaction with other motors bound to the same cargo. Understanding how the individual motors respond to these forces can allow us to predict how they move their cargo when part of a team. Here, using simulation, we show that details of how the kinesin motor responds to small assisting forces-which, at the moment, are not experimentally constrained-can lead to significant changes in cargo dynamics. Using different models of the force-dependent detachment probability of the kinesin motor leads to different predictions on the run-length of the cargo they carry. These differences emerge from the thermal forces acting on the cargo and transmitted to the motor through the motor tail that tethers the motor head to the microtubule. We show that these differences appear for cargo carried by individual motors or motor teams, and use our findings to propose the use of thermal forces as a probe of kinesin's response to force in this otherwise inaccessible force regime.
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Affiliation(s)
- Chuan Chang
- Physics Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Tiantian Zheng
- Physics Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Guilherme Nettesheim
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, United Kingdom
| | - Hayoung Song
- Physics Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Changhyun Cho
- Physics Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Samuele Crespi
- Physics Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - George Shubeita
- Physics Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
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11
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Ma TC, Gicking AM, Feng Q, Hancock WO. Simulations suggest robust microtubule attachment of kinesin and dynein in antagonistic pairs. Biophys J 2023; 122:3299-3313. [PMID: 37464742 PMCID: PMC10465704 DOI: 10.1016/j.bpj.2023.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 05/04/2023] [Accepted: 07/10/2023] [Indexed: 07/20/2023] Open
Abstract
Intracellular transport is propelled by kinesin and cytoplasmic dynein motors that carry membrane-bound vesicles and organelles bidirectionally along microtubule tracks. Much is known about these motors at the molecular scale, but many questions remain regarding how kinesin and dynein cooperate and compete during bidirectional cargo transport at the cellular level. The goal of the present study was to use a stochastic stepping model constructed by using published load-dependent properties of kinesin-1 and dynein-dynactin-BicD2 (DDB) to identify specific motor properties that determine the speed, directionality, and transport dynamics of a cargo carried by one kinesin and one dynein motor. Model performance was evaluated by comparing simulations to recently published experiments of kinesin-DDB pairs connected by complementary oligonucleotide linkers. Plotting the instantaneous velocity distributions from kinesin-DDB experiments revealed a single peak centered around zero velocity. In contrast, velocity distributions from simulations displayed a central peak around 100 nm/s, along with two side peaks corresponding to the unloaded kinesin and DDB velocities. We hypothesized that frequent motor detachment events and relatively slow motor reattachment rates resulted in periods in which only one motor is attached. To investigate this hypothesis, we varied specific model parameters and compared the resulting instantaneous velocity distributions, and we confirmed this systematic investigation using a machine-learning approach that minimized the residual sum of squares between the experimental and simulation velocity distributions. The experimental data were best recapitulated by a model in which the kinesin and dynein stall forces are matched, the motor detachment rates are independent of load, and the kinesin-1 reattachment rate is 50 s-1. These results provide new insights into motor dynamics during bidirectional transport and put forth hypotheses that can be tested by future experiments.
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Affiliation(s)
- Tzu-Chen Ma
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania
| | - Allison M Gicking
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania
| | - Qingzhou Feng
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania
| | - William O Hancock
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania; Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania.
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12
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Levin JT, Pan A, Barrett MT, Alushin GM. A platform for dissecting force sensitivity and multivalency in actin networks. bioRxiv 2023:2023.08.15.553463. [PMID: 37645911 PMCID: PMC10462062 DOI: 10.1101/2023.08.15.553463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
The physical structure and dynamics of cells are supported by micron-scale actin networks with diverse geometries, protein compositions, and mechanical properties. These networks are composed of actin filaments and numerous actin binding proteins (ABPs), many of which engage multiple filaments simultaneously to crosslink them into specific functional architectures. Mechanical force has been shown to modulate the interactions between several ABPs and individual actin filaments, but it is unclear how this phenomenon contributes to the emergent force-responsive functional dynamics of actin networks. Here, we engineer filament linker complexes and combine them with photo-micropatterning of myosin motor proteins to produce an in vitro reconstitution platform for examining how force impacts the behavior of ABPs within multi-filament assemblies. Our system enables the monitoring of dozens of actin networks with varying architectures simultaneously using total internal reflection fluorescence microscopy, facilitating detailed dissection of the interplay between force-modulated ABP binding and network geometry. We apply our system to study a dimeric form of the critical cell-cell adhesion protein α-catenin, a model force-sensitive ABP. We find that myosin forces increase α-catenin's engagement of small filament bundles embedded within networks. This activity is absent in a force-sensing deficient mutant, whose binding scales linearly with bundle size in both the presence and absence of force. These data are consistent with filaments in smaller bundles bearing greater per-filament loads that enhance α-catenin binding, a mechanism that could equalize α-catenin's distribution across actin-myosin networks of varying sizes in cells to regularize their stability and composition.
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Affiliation(s)
- Joseph T. Levin
- Laboratory of Structural Biophysics and Mechanobiology, The Rockefeller University, New York, New York, USA
| | - Ariel Pan
- Laboratory of Structural Biophysics and Mechanobiology, The Rockefeller University, New York, New York, USA
| | - Michael T. Barrett
- Laboratory of Structural Biophysics and Mechanobiology, The Rockefeller University, New York, New York, USA
| | - Gregory M. Alushin
- Laboratory of Structural Biophysics and Mechanobiology, The Rockefeller University, New York, New York, USA
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13
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Ahmad K, Javed A, Lanphere C, Coveney PV, Orlova EV, Howorka S. Structure and dynamics of an archetypal DNA nanoarchitecture revealed via cryo-EM and molecular dynamics simulations. Nat Commun 2023; 14:3630. [PMID: 37336895 DOI: 10.1038/s41467-023-38681-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 05/11/2023] [Indexed: 06/21/2023] Open
Abstract
DNA can be folded into rationally designed, unique, and functional materials. To fully realise the potential of these DNA materials, a fundamental understanding of their structure and dynamics is necessary, both in simple solvents as well as more complex and diverse anisotropic environments. Here we analyse an archetypal six-duplex DNA nanoarchitecture with single-particle cryo-electron microscopy and molecular dynamics simulations in solvents of tunable ionic strength and within the anisotropic environment of biological membranes. Outside lipid bilayers, the six-duplex bundle lacks the designed symmetrical barrel-type architecture. Rather, duplexes are arranged in non-hexagonal fashion and are disorted to form a wider, less elongated structure. Insertion into lipid membranes, however, restores the anticipated barrel shape due to lateral duplex compression by the bilayer. The salt concentration has a drastic impact on the stability of the inserted barrel-shaped DNA nanopore given the tunable electrostatic repulsion between the negatively charged duplexes. By synergistically combining experiments and simulations, we increase fundamental understanding into the environment-dependent structural dynamics of a widely used nanoarchitecture. This insight will pave the way for future engineering and biosensing applications.
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Affiliation(s)
- Katya Ahmad
- Centre for Computational Science, University College London, London, WC1H 0AJ, UK
| | - Abid Javed
- Department of Biological Sciences, Birkbeck, University of London, London, WC1E 7HX, UK
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Conor Lanphere
- Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London, WC1H0AJ, UK
| | - Peter V Coveney
- Centre for Computational Science, University College London, London, WC1H 0AJ, UK.
- Advanced Research Computing Centre, University College London, London, WC1H 0AJ, UK.
- Informatics Institute, University of Amsterdam, Amsterdam, 1090 GH, The Netherlands.
| | - Elena V Orlova
- Department of Biological Sciences, Birkbeck, University of London, London, WC1E 7HX, UK.
| | - Stefan Howorka
- Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London, WC1H0AJ, UK.
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14
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Zhang Y, Yang D, Wang P, Ke Y. Building Large DNA Bundles via Controlled Hierarchical Assembly of DNA Tubes. ACS Nano 2023. [PMID: 37207344 DOI: 10.1021/acsnano.3c01342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Structural DNA nanotechnology is capable of fabricating designer nanoscale artificial architectures. Developing simple and yet versatile assembly methods to construct large DNA structures of defined spatial features and dynamic capabilities has remained challenging. Herein, we designed a molecular assembly system where DNA tiles can assemble into tubes and then into large one-dimensional DNA bundles following a hierarchical pathway. A cohesive link was incorporated into the tile to induce intertube binding for the formation of DNA bundles. DNA bundles with length of dozens of micrometers and width of hundreds of nanometers were produced, whose assembly was revealed to be collectively determined by cationic strength and linker designs (binding strength, spacer length, linker position, etc.). Furthermore, multicomponent DNA bundles with programmable spatial features and compositions were realized by using various distinct tile designs. Lastly, we implemented dynamic capability into large DNA bundles to realize reversible reconfigurations among tile, tube, and bundles following specific molecular stimulations. We envision this assembly strategy can enrich the toolbox of DNA nanotechnology for rational design of large-size DNA materials of defined features and properties that may be applied to a variety of fields in materials science, synthetic biology, biomedical science, and beyond.
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Affiliation(s)
- Yunlong Zhang
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Donglei Yang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Pengfei Wang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - 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
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15
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Fukumoto K, Miyazono Y, Ueda T, Harada Y, Tadakuma H. Evaluating the effect of two-dimensional molecular layout on DNA origami-based transporters. Nanoscale Adv 2023; 5:2590-2601. [PMID: 37143804 PMCID: PMC10153088 DOI: 10.1039/d3na00088e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/09/2023] [Indexed: 05/06/2023]
Abstract
Cellular transport systems are sophisticated and efficient. Hence, one of the ultimate goals of nanotechnology is to design artificial transport systems rationally. However, the design principle has been elusive, because how motor layout affects motile activity has not been established, partially owing to the difficulty in achieving a precise layout of the motile elements. Here, we employed a DNA origami platform to evaluate the two-dimensional (2D) layout effect of kinesin motor proteins on transporter motility. We succeeded in accelerating the integration speed of the protein of interest (POI) to the DNA origami transporter by up to 700 times by introducing a positively charged poly-lysine tag (Lys-tag) into the POI (kinesin motor protein). This Lys-tag approach allowed us to construct and purify a transporter with high motor density, allowing a precise evaluation on the 2D layout effect. Our single-molecule imaging showed that the densely packed layout of kinesin decreased the run length of the transporter, although its velocity was moderately affected. These results indicate that steric hindrance is a critical parameter to be considered in the design of transport systems.
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Affiliation(s)
- Kodai Fukumoto
- Institute for Protein Research, Osaka University Osaka 565-0871 Japan
- Department of Biological Sciences, Graduate School of Science, Osaka University Osaka 560-0043 Japan
| | - Yuya Miyazono
- Graduate School of Frontier Science, The University of Tokyo Chiba 277-8562 Japan
| | - Takuya Ueda
- Graduate School of Frontier Science, The University of Tokyo Chiba 277-8562 Japan
- Graduate School of Science and Engineering, Waseda University Tokyo 162-8480 Japan
| | - Yoshie Harada
- Institute for Protein Research, Osaka University Osaka 565-0871 Japan
- Center for Quantum Information and Quantum Biology, Osaka University Osaka 560-0043 Japan
- Premium Research Institute for Human Metaverse Medicine (WPI-PRIMe), Osaka University Osaka 565-0871 Japan
| | - Hisashi Tadakuma
- Institute for Protein Research, Osaka University Osaka 565-0871 Japan
- Graduate School of Frontier Science, The University of Tokyo Chiba 277-8562 Japan
- School of Life Science and Technology, ShanghaiTech University Shanghai 201210 People's Republic of China
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University Shanghai 201210 People's Republic of China
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16
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Geyer VF, Diez S. Horizontal Magnetic Tweezers to Directly Measure the Force-Velocity Relationship for Multiple Kinesin Motors. Small 2023:e2300558. [PMID: 37035988 DOI: 10.1002/smll.202300558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/11/2023] [Indexed: 06/19/2023]
Abstract
Transport of intracellular cargo along cytoskeletal filaments is often achieved by the concerted action of multiple motor molecules. While single-molecule studies have provided profound insight into the mechano-chemical principles and force generation of individual motors, studies on multi-motor systems are less advanced. Here, a horizontal magnetic-tweezers setup is applied, capable of producing up to 150 pN of horizontal force onto 2.8 µm superparamagnetic beads, to motor-propelled cytoskeletal filaments. It is found that kinesin-1 driven microtubules decorated with individual beads display frequent transitions in their gliding velocities which we attribute to dynamic changes in the number of engaged motors. Applying defined temporal force-ramps the force-velocity relationship is directly measured for multi-motor transport. It is found that the stall forces of individual motors are approximately additive and collective backward motion of the transport system under super-stall forces is observed. The magnetic-tweezers apparatus is expected to be readily applicable to a wide range of molecular and cellular motility assays.
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Affiliation(s)
- Veikko F Geyer
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Tatzberg 41, 01307, Dresden, Germany
| | - Stefan Diez
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Tatzberg 41, 01307, Dresden, Germany
- Cluster of Excellence Physics of Life, Technische Universität Dresden, Arnoldstraße 18, 01307, Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307, Dresden, Germany
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17
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Canty JT, Hensley A, Aslan M, Jack A, Yildiz A. TRAK adaptors regulate the recruitment and activation of dynein and kinesin in mitochondrial transport. Nat Commun 2023; 14:1376. [PMID: 36914620 PMCID: PMC10011603 DOI: 10.1038/s41467-023-36945-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 02/23/2023] [Indexed: 03/16/2023] Open
Abstract
Mitochondrial transport along microtubules is mediated by Miro1 and TRAK adaptors that recruit kinesin-1 and dynein-dynactin. To understand how these opposing motors are regulated during mitochondrial transport, we reconstitute the bidirectional transport of Miro1/TRAK along microtubules in vitro. We show that the coiled-coil domain of TRAK activates dynein-dynactin and enhances the motility of kinesin-1 activated by its cofactor MAP7. We find that TRAK adaptors that recruit both motors move towards kinesin-1's direction, whereas kinesin-1 is excluded from binding TRAK transported by dynein-dynactin, avoiding motor tug-of-war. We also test the predictions of the models that explain how mitochondrial transport stalls in regions with elevated Ca2+. Transport of Miro1/TRAK by kinesin-1 is not affected by Ca2+. Instead, we demonstrate that the microtubule docking protein syntaphilin induces resistive forces that stall kinesin-1 and dynein-driven motility. Our results suggest that mitochondrial transport stalls by Ca2+-mediated recruitment of syntaphilin to the mitochondrial membrane, not by disruption of the transport machinery.
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Affiliation(s)
- John T Canty
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA, 94720, USA.
- Department of Cancer Immunology, Genentech Inc., 1 DNA Way, 94080, South San Francisco, CA, USA.
| | - Andrew Hensley
- Physics Department, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Merve Aslan
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Amanda Jack
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Ahmet Yildiz
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA, 94720, USA.
- Physics Department, University of California at Berkeley, Berkeley, CA, 94720, USA.
- Department of Molecular and Cellular Biology, University of California at Berkeley, Berkeley, CA, 94720, USA.
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18
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Mills A, Aissaoui N, Finkel J, Elezgaray J, Bellot G. Mechanical DNA Origami to Investigate Biological Systems. Adv Biol (Weinh) 2023; 7:e2200224. [PMID: 36509679 DOI: 10.1002/adbi.202200224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 10/25/2022] [Indexed: 12/15/2022]
Abstract
The ability to self-assemble DNA nanodevices with programmed structural dynamics that can sense and respond to the local environment can enable transformative applications in fields including mechanobiology and nanomedicine. The responsive function of biomolecules is often driven by alterations in conformational distributions mediated by highly sensitive interactions with the local environment. In this review, the current state-of-the-art in constructing complex DNA geometries with dynamic and mechanical properties to enable a molecular scale force measurement is first summarized. Next, an overview of engineering modular DNA devices that interact with cell surfaces is highlighted detailing examples of mechanosensitive proteins and the force-induced dynamic molecular interaction on the downstream biochemical signaling. Finally, the challenges and an outlook on this promising class of DNA devices acting as nanomachines to operate at a low piconewton range suitable for a majority of biological effects or as hybrid materials to achieve higher tension exertion required for other biological investigations, are discussed.
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Affiliation(s)
- Allan Mills
- Centre de Biologie Structurale, INSERM, CNRS, Université de Montpellier, Montpellier, 34090, France
| | - Nesrine Aissaoui
- Laboratoire CiTCoM, Faculté de Santé, Université Paris Cité, CNRS, Paris, 75006, France
| | - Julie Finkel
- Centre de Biologie Structurale, INSERM, CNRS, Université de Montpellier, Montpellier, 34090, France
| | - Juan Elezgaray
- CRPP, CNRS, UMR 5031, Université de Bordeaux, Pessac, 33600, France
| | - Gaëtan Bellot
- Centre de Biologie Structurale, INSERM, CNRS, Université de Montpellier, Montpellier, 34090, France
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19
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Karan C, Chaudhuri D. Cooperation and competition in the collective drive by motor proteins: mean active force, fluctuations, and self-load. Soft Matter 2023; 19:1834-1843. [PMID: 36789956 DOI: 10.1039/d2sm01183b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
We consider the dynamics of a bio-filament under the collective drive of motor proteins. They are attached irreversibly to a substrate and undergo stochastic attachment-detachment with the filament to produce a directed force on it. We establish the dependence of the mean directed force and force correlations on the parameters describing the individual motor proteins using analytical theory and direct numerical simulations. The effective Langevin description for the filament motion gives mean-squared displacement, asymptotic diffusion constant, and mobility leading to an effective temperature. Finally, we show how competition between motor protein extensions generates a self-load, describable in terms of the effective temperature, affecting the filament motion.
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Affiliation(s)
- Chitrak Karan
- Institute of Physics, Sachivalaya Marg, Sainik School, Bhubaneswar, 751005, India.
- Homi Bhaba National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| | - Debasish Chaudhuri
- Institute of Physics, Sachivalaya Marg, Sainik School, Bhubaneswar, 751005, India.
- Homi Bhaba National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
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20
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Wintersinger CM, Minev D, Ershova A, Sasaki HM, Gowri G, Berengut JF, Corea-Dilbert FE, Yin P, Shih WM. Multi-micron crisscross structures grown from DNA-origami slats. Nat Nanotechnol 2023; 18:281-289. [PMID: 36543881 PMCID: PMC10818227 DOI: 10.1038/s41565-022-01283-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 10/27/2022] [Indexed: 06/17/2023]
Abstract
Living systems achieve robust self-assembly across a wide range of length scales. In the synthetic realm, nanofabrication strategies such as DNA origami have enabled robust self-assembly of submicron-scale shapes from a multitude of single-stranded components. To achieve greater complexity, subsequent hierarchical joining of origami can be pursued. However, erroneous and missing linkages restrict the number of unique origami that can be practically combined into a single design. Here we extend crisscross polymerization, a strategy previously demonstrated with single-stranded components, to DNA-origami 'slats' for fabrication of custom multi-micron shapes with user-defined nanoscale surface patterning. Using a library of ~2,000 strands that are combinatorially arranged to create unique DNA-origami slats, we realize finite structures composed of >1,000 uniquely addressable slats, with a mass exceeding 5 GDa, lateral dimensions of roughly 2 µm and a multitude of periodic structures. Robust production of target crisscross structures is enabled through strict control over initiation, rapid growth and minimal premature termination, and highly orthogonal binding specificities. Thus crisscross growth provides a route for prototyping and scalable production of structures integrating thousands of unique components (that is, origami slats) that each is sophisticated and molecularly precise.
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Affiliation(s)
- Christopher M Wintersinger
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Dionis Minev
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Anastasia Ershova
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Hiroshi M Sasaki
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- 10x Genomics, Inc., Pleasanton, CA, USA
| | - Gokul Gowri
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Jonathan F Berengut
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - F Eduardo Corea-Dilbert
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - William M Shih
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
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21
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Chiba K, Kita T, Anazawa Y, Niwa S. Insight into the regulation of axonal transport from the study of KIF1A-associated neurological disorder. J Cell Sci 2023; 136:286709. [PMID: 36655764 DOI: 10.1242/jcs.260742] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Neuronal function depends on axonal transport by kinesin superfamily proteins (KIFs). KIF1A is the molecular motor that transports synaptic vesicle precursors, synaptic vesicles, dense core vesicles and active zone precursors. KIF1A is regulated by an autoinhibitory mechanism; many studies, as well as the crystal structure of KIF1A paralogs, support a model whereby autoinhibited KIF1A is monomeric in solution, whereas activated KIF1A is dimeric on microtubules. KIF1A-associated neurological disorder (KAND) is a broad-spectrum neuropathy that is caused by mutations in KIF1A. More than 100 point mutations have been identified in KAND. In vitro assays show that most mutations are loss-of-function mutations that disrupt the motor activity of KIF1A, whereas some mutations disrupt its autoinhibition and abnormally hyperactivate KIF1A. Studies on disease model worms suggests that both loss-of-function and gain-of-function mutations cause KAND by affecting the axonal transport and localization of synaptic vesicles. In this Review, we discuss how the analysis of these mutations by molecular genetics, single-molecule assays and force measurements have helped to reveal the physiological significance of KIF1A function and regulation, and what physical parameters of KIF1A are fundamental to axonal transport.
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Affiliation(s)
- Kyoko Chiba
- Frontier Research Institute for Interdisciplinary Sciences (FRIS), Tohoku University, 6-3 Aramaki-Aoba, Aoba-ku, Sendai, Miyagi 980-0845, Japan
| | - Tomoki Kita
- Department of Applied Physics, Graduate School of Engineering, Tohoku University, 2-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Yuzu Anazawa
- Graduate School of Life Sciences, Tohoku University, 2-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Shinsuke Niwa
- Frontier Research Institute for Interdisciplinary Sciences (FRIS), Tohoku University, 6-3 Aramaki-Aoba, Aoba-ku, Sendai, Miyagi 980-0845, Japan.,Department of Applied Physics, Graduate School of Engineering, Tohoku University, 2-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8578, Japan.,Graduate School of Life Sciences, Tohoku University, 2-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8578, Japan
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22
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Büber E, Schröder T, Scheckenbach M, Dass M, Franquelim HG, Tinnefeld P. DNA Origami Curvature Sensors for Nanoparticle and Vesicle Size Determination with Single-Molecule FRET Readout. ACS Nano 2023; 17:3088-3097. [PMID: 36735241 DOI: 10.1021/acsnano.2c11981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Particle size is an important characteristic of materials with a direct effect on their physicochemical features. Besides nanoparticles, particle size and surface curvature are particularly important in the world of lipids and cellular membranes as the cell membrane undergoes conformational changes in many biological processes which leads to diverging local curvature values. On account of that, it is important to develop cost-effective, rapid and sufficiently precise systems that can measure the surface curvature on the nanoscale that can be translated to size for spherical particles. As an alternative approach for particle characterization, we present flexible DNA nanodevices that can adapt to the curvature of the structure they are bound to. The curvature sensors use Fluorescence Resonance Energy Transfer (FRET) as the transduction mechanism on the single-molecule level. The curvature sensors consist of segmented DNA origami structures connected via flexible DNA linkers incorporating a FRET pair. The activity of the sensors was first demonstrated with defined binding to different DNA origami geometries used as templates. Then the DNA origami curvature sensors were applied to measure spherical silica beads having different size, and subsequently on lipid vesicles. With the designed sensors, we could reliably distinguish different sized nanoparticles within a size range of 50-300 nm as well as the bending angle range of 50-180°. This study helps with the development of more advanced modular-curvature sensing devices that are capable of determining the sizes of nanoparticles and biological complexes.
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Affiliation(s)
- Ece Büber
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-University, Butenandtstraße 5-13, 81377Munich, Germany
| | - Tim Schröder
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-University, Butenandtstraße 5-13, 81377Munich, Germany
| | - Michael Scheckenbach
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-University, Butenandtstraße 5-13, 81377Munich, Germany
| | - Mihir Dass
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-University, 80539Munich, Germany
| | - Henri G Franquelim
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152Martinsried, Germany
- Interfaculty Centre for Bioactive Matter, Leipzig University, c/o Deutscher Platz 5 (BBZ), 04109Leipzig, Germany
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-University, Butenandtstraße 5-13, 81377Munich, Germany
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23
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Knappe GA, Wamhoff EC, Bathe M. Functionalizing DNA origami to investigate and interact with biological systems. Nat Rev Mater 2023; 8:123-138. [PMID: 37206669 PMCID: PMC10191391 DOI: 10.1038/s41578-022-00517-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/11/2022] [Indexed: 05/21/2023]
Abstract
DNA origami has emerged as a powerful method to generate DNA nanostructures with dynamic properties and nanoscale control. These nanostructures enable complex biophysical studies and the fabrication of next-generation therapeutic devices. For these applications, DNA origami typically needs to be functionalized with bioactive ligands and biomacromolecular cargos. Here, we review methods developed to functionalize, purify, and characterize DNA origami nanostructures. We identify remaining challenges, such as limitations in functionalization efficiency and characterization. We then discuss where researchers can contribute to further advance the fabrication of functionalized DNA origami.
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Affiliation(s)
- Grant A. Knappe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Address correspondence to or
| | - Eike-Christian Wamhoff
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Address correspondence to or
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24
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Nair A, Greeny A, Rajendran R, Abdelgawad MA, Ghoneim MM, Raghavan RP, Sudevan ST, Mathew B, Kim H. KIF1A-Associated Neurological Disorder: An Overview of a Rare Mutational Disease. Pharmaceuticals (Basel) 2023; 16:147. [PMID: 37259299 PMCID: PMC9962247 DOI: 10.3390/ph16020147] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/12/2023] [Accepted: 01/17/2023] [Indexed: 10/03/2023] Open
Abstract
KIF1A-associated neurological diseases (KANDs) are a group of inherited conditions caused by changes in the microtubule (MT) motor protein KIF1A as a result of KIF1A gene mutations. Anterograde transport of membrane organelles is facilitated by the kinesin family protein encoded by the MT-based motor gene KIF1A. Variations in the KIF1A gene, which primarily affect the motor domain, disrupt its ability to transport synaptic vesicles containing synaptophysin and synaptotagmin leading to various neurological pathologies such as hereditary sensory neuropathy, autosomal dominant and recessive forms of spastic paraplegia, and different neurological conditions. These mutations are frequently misdiagnosed because they result from spontaneous, non-inherited genomic alterations. Whole-exome sequencing (WES), a cutting-edge method, assists neurologists in diagnosing the illness and in planning and choosing the best course of action. These conditions are simple to be identified in pediatric and have a life expectancy of 5-7 years. There is presently no permanent treatment for these illnesses, and researchers have not yet discovered a medicine to treat them. Scientists have more hope in gene therapy since it can be used to cure diseases brought on by mutations. In this review article, we discussed some of the experimental gene therapy methods, including gene replacement, gene knockdown, symptomatic gene therapy, and cell suicide gene therapy. It also covered its clinical symptoms, pathogenesis, current diagnostics, therapy, and research advances currently occurring in the field of KAND-related disorders. This review also explained the impact that gene therapy can be designed in this direction and afford the remarkable benefits to the patients and society.
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Affiliation(s)
- Ayushi Nair
- Department of Pharmacy Practice, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, Amrita Health Science Campus, Kochi 682041, India
| | - Alosh Greeny
- Department of Pharmacy Practice, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, Amrita Health Science Campus, Kochi 682041, India
| | - Rajalakshmi Rajendran
- Department of Pharmacy Practice, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, Amrita Health Science Campus, Kochi 682041, India
| | - Mohamed A. Abdelgawad
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka, Al Jouf 72341, Saudi Arabia
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62514, Egypt
| | - Mohammed M. Ghoneim
- Department of Pharmacy Practice, College of Pharmacy, AlMaarefa University, Ad Diriyah 13713, Saudi Arabia
| | - Roshni Pushpa Raghavan
- Department of Pharmacy Practice, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, Amrita Health Science Campus, Kochi 682041, India
| | - Sachithra Thazhathuveedu Sudevan
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi 682 041, India
| | - Bijo Mathew
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi 682 041, India
| | - Hoon Kim
- Department of Pharmacy, and Research Institute of Life Pharmaceutical Sciences, Sunchon National University, Suncheon 57922, Republic of Korea
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25
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Li Q, Ferrare JT, Silver J, Wilson JO, Arteaga-Castaneda L, Qiu W, Vershinin M, King SJ, Neuman KC, Xu J. Cholesterol in the cargo membrane amplifies tau inhibition of kinesin-1-based transport. Proc Natl Acad Sci U S A 2023; 120:e2212507120. [PMID: 36626558 PMCID: PMC9934065 DOI: 10.1073/pnas.2212507120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 12/08/2022] [Indexed: 01/11/2023] Open
Abstract
Intracellular cargos are often membrane-enclosed and transported by microtubule-based motors in the presence of microtubule-associated proteins (MAPs). Whereas increasing evidence reveals how MAPs impact the interactions between motors and microtubules, critical questions remain about the impact of the cargo membrane on transport. Here we combined in vitro optical trapping with theoretical approaches to determine the effect of a lipid cargo membrane on kinesin-based transport in the presence of MAP tau. Our results demonstrate that attaching kinesin to a fluid lipid membrane reduces the inhibitory effect of tau on kinesin. Moreover, adding cholesterol, which reduces kinesin diffusion in the cargo membrane, amplifies the inhibitory effect of tau on kinesin binding in a dosage-dependent manner. We propose that reduction of kinesin diffusion in the cargo membrane underlies the effect of cholesterol on kinesin binding in the presence of tau, and we provide a simple model for this proposed mechanism. Our study establishes a direct link between cargo membrane cholesterol and MAP-based regulation of kinesin-1. The cholesterol effects uncovered here may more broadly extend to other lipid alterations that impact motor diffusion in the cargo membrane, including those associated with aging and neurological diseases.
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Affiliation(s)
- Qiaochu Li
- Department of Physics, University of California, Merced, CA95343
| | - James T. Ferrare
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, NIH, Bethesda, MD20892
| | - Jonathan Silver
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, NIH, Bethesda, MD20892
| | - John O. Wilson
- Department of Physics, University of California, Merced, CA95343
| | | | - Weihong Qiu
- Department of Physics, Oregon State University, Corvallis, OR97331
| | - Michael Vershinin
- Department of Physics and Astronomy, University of Utah, Salt Lake City, UT84112
| | - Stephen J. King
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL32827
| | - Keir C. Neuman
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, NIH, Bethesda, MD20892
| | - Jing Xu
- Department of Physics, University of California, Merced, CA95343
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26
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Mao X, Liu M, Li Q, Fan C, Zuo X. DNA-Based Molecular Machines. JACS Au 2022; 2:2381-2399. [PMID: 36465542 PMCID: PMC9709946 DOI: 10.1021/jacsau.2c00292] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/02/2022] [Accepted: 07/08/2022] [Indexed: 05/17/2023]
Abstract
Artificial molecular machines have found widespread applications ranging from fundamental studies to biomedicine. More recent advances in exploiting unique physical and chemical properties of DNA have led to the development of DNA-based artificial molecular machines. The unprecedented programmability of DNA provides a powerful means to design complex and sophisticated DNA-based molecular machines that can exert mechanical force or motion to realize complex tasks in a controllable, modular fashion. This Perspective highlights the potential and strategies to construct artificial molecular machines using double-stranded DNA, functional nucleic acids, and DNA frameworks, which enable improved control over reaction pathways and motion behaviors. We also outline the challenges and opportunities of using DNA-based molecular machines for biophysics, biosensing, and biocomputing.
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Affiliation(s)
- Xiuhai Mao
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Mengmeng Liu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200127, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
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27
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Xu A, Basant A, Schleich S, Newsome TP, Way M. Kinesin-1 transports morphologically distinct intracellular virions during vaccinia infection. J Cell Sci 2022; 136:276598. [PMID: 36093836 DOI: 10.1242/jcs.260175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 08/31/2022] [Indexed: 11/20/2022] Open
Abstract
Intracellular mature virus (IMV) are the first and most abundant infectious form of vaccinia virus to assemble during its replication cycle. IMV can undergo microtubule-based motility, but their directionality and the motor involved in their transport remain unknown. Here, we demonstrate that IMV, like intracellular enveloped virus (IEV), the second form of vaccinia that is wrapped in Golgi-derived membrane, recruit kinesin-1 and undergo anterograde transport. In vitro reconstitution of virion transport in infected cell extracts reveals that IMV and IEV move toward microtubule plus-ends with respective velocities of 0.66 and 0.56 µm/s. Quantitative imaging establishes that IMV and IEV recruit an average of 139 and 320 kinesin-1 motor complexes respectively. In the absence of kinesin-1 there is a near-complete loss of in vitro motility and reduction in the intracellular spread of both types of virion. Our observations demonstrate that kinesin-1 transports two morphologically distinct forms of vaccinia. Reconstitution of vaccinia-based microtubule motility in vitro provides a new model to elucidate how motor number and regulation impacts transport of a bona fide kinesin-1 cargo.
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Affiliation(s)
- Amadeus Xu
- Cellular signalling and cytoskeletal function laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Angika Basant
- Cellular signalling and cytoskeletal function laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Sibylle Schleich
- London Research Institute, Cancer Research UK, 44 Lincoln's Inn Fields, London, WC2A 3PX, UK
| | - Timothy P Newsome
- London Research Institute, Cancer Research UK, 44 Lincoln's Inn Fields, London, WC2A 3PX, UK
| | - Michael Way
- Cellular signalling and cytoskeletal function laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,London Research Institute, Cancer Research UK, 44 Lincoln's Inn Fields, London, WC2A 3PX, UK.,Department of Infectious Disease, Imperial College, London W2 1PG, UK
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28
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Wijeratne SS, Fiorenza SA, Neary AE, Subramanian R, Betterton MD. Motor guidance by long-range communication on the microtubule highway. Proc Natl Acad Sci U S A 2022; 119:e2120193119. [PMID: 35867749 DOI: 10.1073/pnas.2120193119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Coupling of motor proteins within arrays drives muscle contraction, flagellar beating, chromosome segregation, and other biological processes. Current models of motor coupling invoke either direct mechanical linkage or protein crowding, which rely on short-range motor-motor interactions. In contrast, coupling mechanisms that act at longer length scales remain largely unexplored. Here we report that microtubules can physically couple motor movement in the absence of detectable short-range interactions. The human kinesin-4 Kif4A changes the run length and velocity of other motors on the same microtubule in the dilute binding limit, when approximately 10-nm-sized motors are much farther apart than the motor size. This effect does not depend on specific motor-motor interactions because similar changes in Kif4A motility are induced by kinesin-1 motors. A micrometer-scale attractive interaction potential between motors is sufficient to recreate the experimental results in a biophysical model. Unexpectedly, our theory suggests that long-range microtubule-mediated coupling affects not only binding kinetics but also motor mechanochemistry. Therefore, the model predicts that motors can sense and respond to motors bound several micrometers away on a microtubule. Our results are consistent with a paradigm in which long-range motor interactions along the microtubule enable additional forms of collective motor behavior, possibly due to changes in the microtubule lattice.
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29
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Behler KL, Honemann MN, Rita Silva‐Santos A, Dietz H, Weuster‐Botz D. Phage‐free production of artificial ssDNA with
Escherichia coli. Biotechnol Bioeng 2022; 119:2878-2889. [DOI: 10.1002/bit.28171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 05/09/2022] [Accepted: 06/19/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Karl L. Behler
- Technical University of Munich, School of Engineering and Design, Chair of Biochemical EngineeringGarching nearMunichGermany
| | - Maximilian N. Honemann
- Technical University of MunichDepartment of PhysicsGarching nearMunichGermany
- Technical University of MunichMunich Institute of Biomedical EngineeringGarching nearMunichGermany
| | | | - Hendrik Dietz
- Technical University of MunichDepartment of PhysicsGarching nearMunichGermany
- Technical University of MunichMunich Institute of Biomedical EngineeringGarching nearMunichGermany
| | - Dirk Weuster‐Botz
- Technical University of Munich, School of Engineering and Design, Chair of Biochemical EngineeringGarching nearMunichGermany
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30
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Abdellatef SA, Tadakuma H, Yan K, Fujiwara T, Fukumoto K, Kondo Y, Takazaki H, Boudria R, Yasunaga T, Higuchi H, Hirose K. Oscillatory movement of a dynein-microtubule complex crosslinked with DNA origami. eLife 2022; 11:76357. [PMID: 35749159 PMCID: PMC9232216 DOI: 10.7554/elife.76357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 06/13/2022] [Indexed: 11/13/2022] Open
Abstract
Bending of cilia and flagella occurs when axonemal dynein molecules on one side of the axoneme produce force and move toward the microtubule (MT) minus end. These dyneins are then pulled back when the axoneme bends in the other direction, meaning oscillatory back and forth movement of dynein during repetitive bending of cilia/flagella. There are various factors that may regulate the dynein activity, e.g. the nexin-dynein regulatory complex, radial spokes, and central apparatus. In order to understand the basic mechanism of dynein’s oscillatory movement, we constructed a simple model system composed of MTs, outer-arm dyneins, and crosslinks between the MTs made of DNA origami. Electron microscopy (EM) showed pairs of parallel MTs crossbridged by patches of regularly arranged dynein molecules bound in two different orientations, depending on which of the MTs their tails bind to. The oppositely oriented dyneins are expected to produce opposing forces when the pair of MTs have the same polarity. Optical trapping experiments showed that the dynein-MT-DNA-origami complex actually oscillates back and forth after photolysis of caged ATP. Intriguingly, the complex, when held at one end, showed repetitive bending motions. The results show that a simple system composed of ensembles of oppositely oriented dyneins, MTs, and inter-MT crosslinkers, without any additional regulatory structures, has an intrinsic ability to cause oscillation and repetitive bending motions.
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Affiliation(s)
- Shimaa A Abdellatef
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan.,Research Center for Functional Materials, National Institute for Materials Science, Tsukuba, Japan
| | - Hisashi Tadakuma
- Institute for Protein Research, Osaka University, Osaka, Japan.,SLST and Gene Editing Center, ShanghaiTech University, Shanghai, China
| | - Kangmin Yan
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Takashi Fujiwara
- Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Kodai Fukumoto
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Yuichi Kondo
- Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Hiroko Takazaki
- Institute for Protein Research, Osaka University, Osaka, Japan.,Kyushu Institute of Technology, Fukuoka, Japan
| | - Rofia Boudria
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan.,Institut Pasteur, Paris, France
| | | | - Hideo Higuchi
- Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Keiko Hirose
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
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31
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Moya-Alvarado G, Guerra MV, Tiburcio R, Bravo E, Bronfman FC. The Rab11-regulated endocytic pathway and BDNF/TrkB signaling: Roles in plasticity changes and neurodegenerative diseases. Neurobiol Dis 2022; 171:105796. [PMID: 35728773 DOI: 10.1016/j.nbd.2022.105796] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 05/10/2022] [Accepted: 06/14/2022] [Indexed: 02/08/2023] Open
Abstract
Neurons are highly polarized cells that rely on the intracellular transport of organelles. This process is regulated by molecular motors such as dynein and kinesins and the Rab family of monomeric GTPases that together help move cargo along microtubules in dendrites, somas, and axons. Rab5-Rab11 GTPases regulate receptor trafficking along early-recycling endosomes, which is a process that determines the intracellular signaling output of different signaling pathways, including those triggered by BDNF binding to its tyrosine kinase receptor TrkB. BDNF is a well-recognized neurotrophic factor that regulates experience-dependent plasticity in different circuits in the brain. The internalization of the BDNF/TrkB complex results in signaling endosomes that allow local signaling in dendrites and presynaptic terminals, nuclear signaling in somas and dynein-mediated long-distance signaling from axons to cell bodies. In this review, we briefly discuss the organization of the endocytic pathway and how Rab11-recycling endosomes interact with other endomembrane systems. We further expand upon the roles of the Rab11-recycling pathway in neuronal plasticity. Then, we discuss the BDNF/TrkB signaling pathways and their functional relationships with the postendocytic trafficking of BDNF, including axonal transport, emphasizing the role of BDNF signaling endosomes, particularly Rab5-Rab11 endosomes, in neuronal plasticity. Finally, we discuss the evidence indicating that the dysfunction of the early-recycling pathway impairs BDNF signaling, contributing to several neurodegenerative diseases.
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32
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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: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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33
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Abstract
Natural dynein protein motors are reengineered to walk on specific artificial DNA tracks.
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Affiliation(s)
| | - Rizal F Hariadi
- Biodesign Institute, Arizona State University, Tempe, AZ, USA.,Department of Physics, Arizona State University, Tempe, AZ, USA
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34
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Chandrakar P, Berezney J, Lemma B, Hishamunda B, Berry A, Wu KT, Subramanian R, Chung J, Needleman D, Gelles J, Dogic Z. Engineering stability, longevity, and miscibility of microtubule-based active fluids. Soft Matter 2022; 18:1825-1835. [PMID: 35167642 DOI: 10.1039/d1sm01289d] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Microtubule-based active matter provides insight into the self-organization of motile interacting constituents. We describe several formulations of microtubule-based 3D active isotropic fluids. Dynamics of these fluids is powered by three types of kinesin motors: a processive motor, a non-processive motor, and a motor which is permanently linked to a microtubule backbone. Another modification uses a specific microtubule crosslinker to induce bundle formation instead of a non-specific polymer depletant. In comparison to the already established system, each formulation exhibits distinct properties. These developments reveal the temporal stability of microtubule-based active fluids while extending their reach and the applicability.
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Affiliation(s)
- Pooja Chandrakar
- The Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454, USA
- Department of Physics, University of California, Santa Barbara, California 93106, USA.
| | - John Berezney
- The Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454, USA
| | - Bezia Lemma
- The Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454, USA
- Department of Physics, University of California, Santa Barbara, California 93106, USA.
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Bernard Hishamunda
- The Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454, USA
| | - Angela Berry
- Hampton University School of Pharmacy, 121 William R. Harvey Way, Hampton, VA 23668, USA
- The Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454, USA
| | - Kun-Ta Wu
- The Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454, USA
- Department of Physics, Worcester Polytechnic Institute, 100 Institute Road, Worcester, Massachusetts 01609, USA
| | - Radhika Subramanian
- Department of Genetics, HMS and Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Johnson Chung
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02454, USA
| | - Daniel Needleman
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
- Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA
| | - Jeff Gelles
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02454, USA
| | - Zvonimir Dogic
- The Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454, USA
- Department of Physics, University of California, Santa Barbara, California 93106, USA.
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35
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Gibson JM, Cui H, Ali MY, Zhao X, Debler EW, Zhao J, Trybus KM, Solmaz SR, Wang C. Coil-to-α-helix transition at the Nup358-BicD2 interface activates BicD2 for dynein recruitment. eLife 2022; 11:74714. [PMID: 35229716 PMCID: PMC8956292 DOI: 10.7554/elife.74714] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 02/28/2022] [Indexed: 11/13/2022] Open
Abstract
Nup358, a protein of the nuclear pore complex, facilitates a nuclear positioning pathway that is essential for many biological processes, including neuromuscular and brain development. Nup358 interacts with the dynein adaptor Bicaudal D2 (BicD2), which in turn recruits the dynein machinery to position the nucleus. However, the molecular mechanisms of the Nup358/BicD2 interaction and the activation of transport remain poorly understood. Here for the first time, we show that a minimal Nup358 domain activates dynein/dynactin/BicD2 for processive motility on microtubules. Using nuclear magnetic resonance titration and chemical exchange saturation transfer, mutagenesis, and circular dichroism spectroscopy, a Nup358 α-helix encompassing residues 2162–2184 was identified, which transitioned from a random coil to an α-helical conformation upon BicD2 binding and formed the core of the Nup358-BicD2 interface. Mutations in this region of Nup358 decreased the Nup358/BicD2 interaction, resulting in decreased dynein recruitment and impaired motility. BicD2 thus recognizes Nup358 through a ‘cargo recognition α-helix,’ a structural feature that may stabilize BicD2 in its activated state and promote processive dynein motility.
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Affiliation(s)
- James M Gibson
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, United States
| | - Heying Cui
- Department of Chemistry, Binghamton University, Binghamton, United States
| | - M Yusuf Ali
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, United States
| | - Xioaxin Zhao
- Department of Biological Sciences, Binghamton University, Binghamton, United States
| | - Erik W Debler
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, United States
| | - Jing Zhao
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, United States
| | - Kathleen M Trybus
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, United States
| | - Sozanne R Solmaz
- Department of Chemistry, Binghamton University, Binghamton, United States
| | - Chunyu Wang
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, United States
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36
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Liu F, Liu X, Huang Q, Arai T. Recent Progress of Magnetically Actuated DNA Micro/Nanorobots. Cyborg and Bionic Systems 2022; 2022:9758460. [PMID: 36285315 PMCID: PMC9494703 DOI: 10.34133/2022/9758460] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/22/2021] [Indexed: 01/12/2023] Open
Abstract
In the past few decades, the field of DNA origami-based micro/nanotechnology has developed dramatically and spawned attention increasingly, as its high integrality, rigid structure, and excellent resistance ability to enzyme digestion. Many two-dimensional and three-dimensional DNA nanostructures coordinated with optical, chemical, or magnetic triggers have been designed and assembled, extensively used as versatile templates for molecular robots, nanosensors, and intracellular drug delivery. The magnetic field has been widely regarded as an ideal driving and operating system for micro/nanomaterials, as it does not require high-intensity lasers like light control, nor does it need to change the chemical composition similar to chemical activation. Herein, we review the recent achievements in the induction and actuation of DNA origami-based nanodevices that respond to magnetic fields. These magnetic actuation-based DNA nanodevices were regularly combined with magnetic beads or gold nanoparticles and applied to generate single-stranded scaffolds, assemble various DNA nanostructures, and purify specific DNA nanostructures. Moreover, they also produced artificial magnetism or moved regularly driven by external magnetic fields to explain deeper scientific issues.
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Affiliation(s)
- Fengyu Liu
- Key Laboratory of Biomimetic Robots and Systems, Ministry of Education, State Key Laboratory of Intelligent Control and Decision of Complex System, Beijing Advanced Innovation Center for Intelligent Robots and Systems and School of Mechatronical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Xiaoming Liu
- Key Laboratory of Biomimetic Robots and Systems, Ministry of Education, State Key Laboratory of Intelligent Control and Decision of Complex System, Beijing Advanced Innovation Center for Intelligent Robots and Systems and School of Mechatronical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Qiang Huang
- Key Laboratory of Biomimetic Robots and Systems, Ministry of Education, State Key Laboratory of Intelligent Control and Decision of Complex System, Beijing Advanced Innovation Center for Intelligent Robots and Systems and School of Mechatronical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Tatsuo Arai
- Key Laboratory of Biomimetic Robots and Systems, Ministry of Education, State Key Laboratory of Intelligent Control and Decision of Complex System, Beijing Advanced Innovation Center for Intelligent Robots and Systems and School of Mechatronical Engineering, Beijing Institute of Technology, Beijing 100081, China
- Center for Neuroscience and Biomedical Engineering, The University of Electro-Communications, Tokyo 182-8585, Japan
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37
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Keya JJ, Akter M, Kabir AMR, Ishii S, Kakugo A. Fabrication of Artificial Muscle from Microtubules, Kinesins, and DNA Origami Nanostructures. Methods Mol Biol 2022; 2430:231-240. [PMID: 35476336 DOI: 10.1007/978-1-0716-1983-4_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Fabrication of molecular devices using biomolecules through biomimetic approaches has witnessed a surge in interest in recent years. DNA a versatile programmable material offers an opportunity to realize complicated operations through the designing of various nanostructures such as DNA origami. Here we describe the methods to use DNA origami for the self-assembly of the biomolecular motor system, microtubule (MT)-kinesin. A rodlike DNA origami motif facilitates the self-assembly of MTs into asters. A smooth muscle like molecular contraction system could be realized following the method where DNA mediated self-assembly of MTs permits dynamic contraction in the presence of kinesins through an energy dissipative process.
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Affiliation(s)
| | - Mousumi Akter
- Faculty of Science, Hokkaido University, Sapporo, Japan
| | | | - Satsuki Ishii
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan
| | - Akira Kakugo
- Faculty of Science, Hokkaido University, Sapporo, Japan.
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan.
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Rubio-Sánchez R, Fabrini G, Cicuta P, Di Michele L. Amphiphilic DNA nanostructures for bottom-up synthetic biology. Chem Commun (Camb) 2021; 57:12725-12740. [PMID: 34750602 PMCID: PMC8631003 DOI: 10.1039/d1cc04311k] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/28/2021] [Indexed: 12/28/2022]
Abstract
DNA nanotechnology enables the construction of sophisticated biomimetic nanomachines that are increasingly central to the growing efforts of creating complex cell-like entities from the bottom-up. DNA nanostructures have been proposed as both structural and functional elements of these artificial cells, and in many instances are decorated with hydrophobic moieties to enable interfacing with synthetic lipid bilayers or regulating bulk self-organisation. In this feature article we review recent efforts to design biomimetic membrane-anchored DNA nanostructures capable of imparting complex functionalities to cell-like objects, such as regulated adhesion, tissue formation, communication and transport. We then discuss the ability of hydrophobic modifications to enable the self-assembly of DNA-based nanostructured frameworks with prescribed morphology and functionality, and explore the relevance of these novel materials for artificial cell science and beyond. Finally, we comment on the yet mostly unexpressed potential of amphiphilic DNA-nanotechnology as a complete toolbox for bottom-up synthetic biology - a figurative and literal scaffold upon which the next generation of synthetic cells could be built.
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Affiliation(s)
- Roger Rubio-Sánchez
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK.
- fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Giacomo Fabrini
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
- fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Pietro Cicuta
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK.
| | - Lorenzo Di Michele
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK.
- fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
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Liu W, Duan H, Zhang D, Zhang X, Luo Q, Xie T, Yan H, Peng L, Hu Y, Liang L, Zhao G, Xie Z, Hu J. Concepts and Application of DNA Origami and DNA Self-Assembly: A Systematic Review. Appl Bionics Biomech 2021; 2021:9112407. [PMID: 34824603 PMCID: PMC8610680 DOI: 10.1155/2021/9112407] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 10/20/2021] [Indexed: 01/02/2023] Open
Abstract
With the arrival of the post-Moore Era, the development of traditional silicon-based computers has reached the limit, and it is urgent to develop new computing technology to meet the needs of science and life. DNA computing has become an essential branch and research hotspot of new computer technology because of its powerful parallel computing capability and excellent data storage capability. Due to good biocompatibility and programmability properties, DNA molecules have been widely used to construct novel self-assembled structures. In this review, DNA origami is briefly introduced firstly. Then, the applications of DNA self-assembly in material physics, biogenetics, medicine, and other fields are described in detail, which will aid the development of DNA computational model in the future.
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Affiliation(s)
- Wei Liu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu 610106, China
| | - Huaichuan Duan
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu 610106, China
| | - Derong Zhang
- School of Marxism, Chengdu Vocational & Technical College of Industry, Chengdu 610081, China
| | - Xun Zhang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu 610106, China
| | - Qing Luo
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu 610106, China
| | - Tao Xie
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu 610106, China
| | - Hailian Yan
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu 610106, China
| | - Lianxin Peng
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu 610106, China
| | - Yichen Hu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu 610106, China
| | - Li Liang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu 610106, China
| | - Gang Zhao
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu 610106, China
| | - Zhenjian Xie
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu 610106, China
| | - Jianping Hu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu 610106, China
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Jensen MA, Feng Q, Hancock WO, McKinley SA. A change point analysis protocol for comparing intracellular transport by different molecular motor combinations. Math Biosci Eng 2021; 18:8962-8996. [PMID: 34814331 PMCID: PMC9817212 DOI: 10.3934/mbe.2021442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Intracellular transport by microtubule-based molecular motors is marked by qualitatively different behaviors. It is a long-standing and still-open challenge to accurately quantify the various individual-cargo behaviors and how they are affected by the presence or absence of particular motor families. In this work we introduce a protocol for analyzing change points in cargo trajectories that can be faithfully projected along the length of a (mostly) straight microtubule. Our protocol consists of automated identification of velocity change points, estimation of velocities during the behavior segments, and extrapolation to motor-specific velocity distributions. Using simulated data we show that our method compares favorably with existing methods. We then apply the technique to data sets in which quantum dots are transported by Kinesin-1, by Dynein-Dynactin-BicD2 (DDB), and by Kinesin-1/DDB pairs. In the end, we identify pausing behavior that is consistent with some tug-of-war model predictions, but also demonstrate that the simultaneous presence of antagonistic motors can lead to long processive runs that could contribute favorably to population-wide transport.
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Affiliation(s)
- Melanie A. Jensen
- Department of Mathematics, Tulane University, New Orleans, LA 70118, USA
- Schlumberger, 1 Hampshire St Ste 1, Cambridge, MA, 02319 USA
| | - Qingzhou Feng
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802
- Molecular Cellular and Integrative Biological Sciences Program, Huck Institute of Life Sciences, Pennsylvania State University, University Park, PA 16802
- Department of Cell Biology, Yale School of Medicine, Yale University, New Haven, CT 06520
| | - William O. Hancock
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802
- Molecular Cellular and Integrative Biological Sciences Program, Huck Institute of Life Sciences, Pennsylvania State University, University Park, PA 16802
| | - Scott A. McKinley
- Department of Mathematics, Tulane University, New Orleans, LA 70118, USA
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41
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Halbi G, Fayer I, Aranovich D, Gat S, Bar S, Erukhimovitch V, Granek R, Bernheim-Groswasser A. Nano-Particles Carried by Multiple Dynein Motors Self-Regulate Their Number of Actively Participating Motors. Int J Mol Sci 2021; 22:ijms22168893. [PMID: 34445598 PMCID: PMC8396316 DOI: 10.3390/ijms22168893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/28/2021] [Accepted: 08/04/2021] [Indexed: 12/13/2022] Open
Abstract
Intra-cellular active transport by native cargos is ubiquitous. We investigate the motion of spherical nano-particles (NPs) grafted with flexible polymers that end with a nuclear localization signal peptide. This peptide allows the recruitment of several mammalian dynein motors from cytoplasmic extracts. To determine how motor–motor interactions influenced motility on the single microtubule level, we conducted bead-motility assays incorporating surface adsorbed microtubules and combined them with model simulations that were based on the properties of a single dynein. The experimental and simulation results revealed long time trajectories: when the number of NP-ligated motors Nm increased, run-times and run-lengths were enhanced and mean velocities were somewhat decreased. Moreover, the dependence of the velocity on run-time followed a universal curve, regardless of the system composition. Model simulations also demonstrated left- and right-handed helical motion and revealed self-regulation of the number of microtubule-bound, actively transporting dynein motors. This number was stochastic along trajectories and was distributed mainly between one, two, and three motors, regardless of Nm. We propose that this self-regulation allows our synthetic NPs to achieve persistent motion that is associated with major helicity. Such a helical motion might affect obstacle bypassing, which can influence active transport efficiency when facing the crowded environment of the cell.
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Affiliation(s)
- Gal Halbi
- The Department of Chemical Engineering, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel; (G.H.); (D.A.); (S.G.); (S.B.); (V.E.)
| | - Itay Fayer
- The Stella and Avram Goren-Goldstein Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel;
| | - Dina Aranovich
- The Department of Chemical Engineering, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel; (G.H.); (D.A.); (S.G.); (S.B.); (V.E.)
| | - Shachar Gat
- The Department of Chemical Engineering, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel; (G.H.); (D.A.); (S.G.); (S.B.); (V.E.)
| | - Shay Bar
- The Department of Chemical Engineering, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel; (G.H.); (D.A.); (S.G.); (S.B.); (V.E.)
| | - Vitaly Erukhimovitch
- The Department of Chemical Engineering, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel; (G.H.); (D.A.); (S.G.); (S.B.); (V.E.)
| | - Rony Granek
- The Stella and Avram Goren-Goldstein Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel;
- The Ilse Katz Institute for Meso and Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
- Correspondence: (R.G.); (A.B.-G.)
| | - Anne Bernheim-Groswasser
- The Department of Chemical Engineering, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel; (G.H.); (D.A.); (S.G.); (S.B.); (V.E.)
- The Ilse Katz Institute for Meso and Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
- Correspondence: (R.G.); (A.B.-G.)
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42
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Abstract
At the nanoscale, pushing, pulling, and shearing forces drive biochemical processes in development and remodeling as well as in wound healing and disease progression. Research in the field of mechanobiology investigates not only how these loads affect biochemical signaling pathways but also how signaling pathways respond to local loading by triggering mechanical changes such as regional stiffening of a tissue. This feedback between mechanical and biochemical signaling is increasingly recognized as fundamental in embryonic development, tissue morphogenesis, cell signaling, and disease pathogenesis. Historically, the interdisciplinary field of mechanobiology has been driven by the development of technologies for measuring and manipulating cellular and molecular forces, with each new tool enabling vast new lines of inquiry. In this review, we discuss recent advances in the manufacturing and capabilities of molecular-scale force and strain sensors. We also demonstrate how DNA nanotechnology has been critical to the enhancement of existing techniques and to the development of unique capabilities for future mechanosensor assembly. DNA is a responsive and programmable building material for sensor fabrication. It enables the systematic interrogation of molecular biomechanics with forces at the 1- to 200-pN scale that are needed to elucidate the fundamental means by which cells and proteins transduce mechanical signals.
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Affiliation(s)
- Susana M Beltrán
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Marvin J Slepian
- Department of Medicine and Sarver Heart Center, University of Arizona, Tucson; Department of Biomedical Engineering, University of Arizona, Tucson; Department of Materials Science and Engineering, University of Arizona, Tucson
| | - Rebecca E Taylor
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania; Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania; Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania
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43
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Abstract
Cytoskeletal active nematics exhibit striking nonequilibrium dynamics that are powered by energy-consuming molecular motors. To gain insight into the structure and mechanics of these materials, we design programmable clusters in which kinesin motors are linked by a double-stranded DNA linker. The efficiency by which DNA-based clusters power active nematics depends on both the stepping dynamics of the kinesin motors and the chemical structure of the polymeric linker. Fluorescence anisotropy measurements reveal that the motor clusters, like filamentous microtubules, exhibit local nematic order. The properties of the DNA linker enable the design of force-sensing clusters. When the load across the linker exceeds a critical threshold, the clusters fall apart, ceasing to generate active stresses and slowing the system dynamics. Fluorescence readout reveals the fraction of bound clusters that generate interfilament sliding. In turn, this yields the average load experienced by the kinesin motors as they step along the microtubules. DNA-motor clusters provide a foundation for understanding the molecular mechanism by which nanoscale molecular motors collectively generate mesoscopic active stresses, which in turn power macroscale nonequilibrium dynamics of active nematics.
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Wang Y, Baars I, Fördös F, Högberg B. Clustering of Death Receptor for Apoptosis Using Nanoscale Patterns of Peptides. ACS Nano 2021; 15:9614-9626. [PMID: 34019379 PMCID: PMC8223489 DOI: 10.1021/acsnano.0c10104] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 05/18/2021] [Indexed: 05/20/2023]
Abstract
The nanoscale spatial organization of transmembrane tumor necrosis factor (TNF) receptors has been implicated in the regulation of cellular fate. Accordingly, molecular tools that can induce specific arrangements of these receptors on cell surfaces would give us an opportunity to study these effects in detail. To achieve this, we introduce DNA origami nanostructures that precisely scaffold the patterning of TNF-related apoptosis-inducing ligand-mimicking peptides at nanoscale level. Stimulating human breast cancer cells with these patterns, we find that around 5 nm is the critical interligand distance of hexagonally patterned peptides to induce death receptor clustering and a resulting apoptosis. We thus offer a strategy to reverse the non-efficacy of current ligand- and antibody-based methods for TNF superfamily activation.
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Affiliation(s)
- Yang Wang
- Department of Medical Biochemistry
and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Igor Baars
- Department of Medical Biochemistry
and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Ferenc Fördös
- Department of Medical Biochemistry
and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Björn Högberg
- Department of Medical Biochemistry
and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
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45
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Bertosin E, Stömmer P, Feigl E, Wenig M, Honemann MN, Dietz H. Cryo-Electron Microscopy and Mass Analysis of Oligolysine-Coated DNA Nanostructures. ACS Nano 2021; 15:9391-9403. [PMID: 33724780 PMCID: PMC8223477 DOI: 10.1021/acsnano.0c10137] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Cationic coatings can enhance the stability of synthetic DNA objects in low ionic strength environments such as physiological fluids. Here, we used single-particle cryo-electron microscopy (cryo-EM), pseudoatomic model fitting, and single-molecule mass photometry to study oligolysine and polyethylene glycol (PEG)-oligolysine-coated multilayer DNA origami objects. The coatings preserve coarse structural features well on a resolution of multiple nanometers but can also induce deformations such as twisting and bending. Higher-density coatings also led to internal structural deformations in the DNA origami test objects, in which a designed honeycomb-type helical lattice was deformed into a more square-lattice-like pattern. Under physiological ionic strength, where the uncoated objects disassembled, the coated objects remained intact but they shrunk in the helical direction and expanded in the direction perpendicular to the helical axis. Helical details like major/minor grooves and crossover locations were not discernible in cryo-EM maps that we determined of DNA origami coated with oligolysine and PEG-oligolysine, whereas these features were visible in cryo-EM maps determined from the uncoated reference objects. Blunt-ended double-helical interfaces remained accessible underneath the coating and may be used for the formation of multimeric DNA origami assemblies that rely on stacking interactions between blunt-ended helices. The ionic strength requirements for forming multimers from coated DNA origami differed from those needed for uncoated objects. Using single-molecule mass photometry, we found that the mass of coated DNA origami objects prior to and after incubation in low ionic strength physiological conditions remained unchanged. This finding indicated that the coating effectively prevented strand dissociation but also that the coating itself remained stable in place. Our results validate oligolysine coatings as a powerful stabilization method for DNA origami but also reveal several potential points of failure that experimenters should watch to avoid working with false premises.
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Kong G, Xiong M, Liu L, Hu L, Meng HM, Ke G, Zhang XB, Tan W. DNA origami-based protein networks: from basic construction to emerging applications. Chem Soc Rev 2021; 50:1846-1873. [PMID: 33306073 DOI: 10.1039/d0cs00255k] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Natural living systems are driven by delicate protein networks whose functions are precisely controlled by many parameters, such as number, distance, orientation, and position. Focusing on regulation rather than just imitation, the construction of artificial protein networks is important in many research areas, including biomedicine, synthetic biology and chemical biology. DNA origami, sophisticated nanostructures with rational design, can offer predictable, programmable, and addressable scaffolds for protein assembly with nanometer precision. Recently, many interdisciplinary efforts have achieved the precise construction of DNA origami-based protein networks, and their emerging application in many areas. To inspire more fantastic research and applications, herein we highlight the applicability and potentiality of DNA origami-based protein networks. After a brief introduction to the development and features of DNA origami, some important factors for the precise construction of DNA origami-based protein networks are discussed, including protein-DNA conjugation methods, networks with different patterns and the controllable parameters in the networks. The discussion then focuses on the emerging application of DNA origami-based protein networks in several areas, including enzymatic reaction regulation, sensing, bionics, biophysics, and biomedicine. Finally, current challenges and opportunities in this research field are discussed.
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Affiliation(s)
- Gezhi Kong
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Mengyi Xiong
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Lu Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Ling Hu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Hong-Min Meng
- College of Chemistry, Green Catalysis Center, Zhengzhou University, Zhengzhou 450001, China
| | - Guoliang Ke
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Xiao-Bing Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
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47
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Abstract
Dyneins make up a family of AAA+ motors that move toward the minus end of microtubules. Cytoplasmic dynein is responsible for transporting intracellular cargos in interphase cells and mediating spindle assembly and chromosome positioning during cell division. Other dynein isoforms transport cargos in cilia and power ciliary beating. Dyneins were the least studied of the cytoskeletal motors due to challenges in the reconstitution of active dynein complexes in vitro and the scarcity of high-resolution methods for in-depth structural and biophysical characterization of these motors. These challenges have been recently addressed, and there have been major advances in our understanding of the activation, mechanism, and regulation of dyneins. This review synthesizes the results of structural and biophysical studies for each class of dynein motors. We highlight several outstanding questions about the regulation of bidirectional transport along microtubules and the mechanisms that sustain self-coordinated oscillations within motile cilia.
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Affiliation(s)
- John T Canty
- Biophysics Graduate Group, University of California, Berkeley, California 94720, USA;
| | - Ruensern Tan
- Department of Molecular and Cellular Biology, University of California, Berkeley, California 94720, USA
| | - Emre Kusakci
- Biophysics Graduate Group, University of California, Berkeley, California 94720, USA;
| | - Jonathan Fernandes
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Ahmet Yildiz
- Biophysics Graduate Group, University of California, Berkeley, California 94720, USA; .,Department of Molecular and Cellular Biology, University of California, Berkeley, California 94720, USA.,Physics Department, University of California, Berkeley, California 94720, USA
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48
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Abstract
Nucleic acid-based nanodevices have been widely used in the fields of biosensing and nanomedicine. Traditionally, the majority of these nanodevices were first constructed in vitro using synthetic DNA or RNA oligonucleotides and then delivered into cells. Nowadays, the emergence of genetically encoded RNA nanodevices has provided a promising alternative approach for intracellular analysis and regulation. These genetically encoded RNA-based nanodevices can be directly transcribed and continuously produced inside living cells. A variety of highly precise and programmable nanodevices have been constructed in this way during the last decade. In this review, we will summarize the recent advances in the design and function of these artificial genetically encoded RNA nanodevices. In particular, we will focus on their applications in regulating cellular gene expression, imaging, logic operation, structural biology, and optogenetics. We believe these versatile RNA-based nanodevices will be broadly used in the near future to probe and program cells and other biological systems.
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Affiliation(s)
- Qikun Yu
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA.
| | - Kewei Ren
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA.
| | - Mingxu You
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA.
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Benson E, Carrascosa Marzo R, Bath J, Turberfield AJ. Strategies for Constructing and Operating DNA Origami Linear Actuators. Small 2021; 17:e2007704. [PMID: 33942502 DOI: 10.1002/smll.202007704] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/22/2021] [Indexed: 06/12/2023]
Abstract
Linear actuators are ubiquitous components at all scales of engineering. DNA nanotechnology offers a unique opportunity for bottom-up assembly at the molecular scale, providing nanoscale precision with multiple methods for constructing and operating devices. In this paper, DNA origami linear actuators with up to 200 nm travel, based on a rail threading a topologically locked slider, are demonstrated. Two strategies, one- and two-pot assembly, are demonstrated whereby the two components are folded from one or two DNA scaffold strands, respectively. In order to control the position of the slider on the rail, the rail and the inside of the slider are decorated with single-stranded oligonucleotides with distinct sequences. Two positioning strategies, based on diffusion and capture of signaling strands, are used to link the slider reversibly to determined positions on the rail with high yield and precision. These machine components provide a basis for applications in molecular machinery and nanoscale manufacture including programmed chemical synthesis.
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Affiliation(s)
- Erik Benson
- Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PU, UK
| | | | - Jonathan Bath
- Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PU, UK
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Urbanska M, Lüdecke A, Walter WJ, van Oijen AM, Duderstadt KE, Diez S. Highly-Parallel Microfluidics-Based Force Spectroscopy on Single Cytoskeletal Motors. Small 2021; 17:e2007388. [PMID: 33759372 DOI: 10.1002/smll.202007388] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/22/2021] [Indexed: 06/12/2023]
Abstract
Cytoskeletal motors transform chemical energy into mechanical work to drive essential cellular functions. Optical trapping experiments have provided crucial insights into the operation of these molecular machines under load. However, the throughput of such force spectroscopy experiments is typically limited to one measurement at a time. Here, a highly-parallel, microfluidics-based method that allows for rapid collection of force-dependent motility parameters of cytoskeletal motors with two orders of magnitude improvement in throughput compared to currently available methods is introduced. Tunable hydrodynamic forces to stepping kinesin-1 motors via DNA-tethered beads and utilize a large field of view to simultaneously track the velocities, run lengths, and interaction times of hundreds of individual kinesin-1 molecules under varying resisting and assisting loads are applied. Importantly, the 16 µm long DNA tethers between the motors and the beads significantly reduces the vertical component of the applied force pulling the motors away from the microtubule. The approach is readily applicable to other molecular systems and constitutes a new methodology for parallelized single-molecule force studies on cytoskeletal motors.
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Affiliation(s)
- Marta Urbanska
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, 01069, Dresden, Germany
| | - Annemarie Lüdecke
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, 01069, Dresden, Germany
| | - Wilhelm J Walter
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, 01069, Dresden, Germany
| | - Antoine M van Oijen
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, AE, 9700, Netherlands
- Molecular Horizons, University of Wollongong, Illawarra Health and Medical Research Institute, Wollongong, NSW, 2522, Australia
| | - Karl E Duderstadt
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, AE, 9700, Netherlands
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
- Physics Department, Technische Universität München, 85748, Garching, Germany
| | - Stefan Diez
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, 01069, Dresden, Germany
- Cluster of Excellence Physics of Life, Technische Universität Dresden, 01062, Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
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