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Meinecke CR, Heldt G, Blaudeck T, Lindberg FW, van Delft FCMJM, Rahman MA, Salhotra A, Månsson A, Linke H, Korten T, Diez S, Reuter D, Schulz SE. Nanolithographic Fabrication Technologies for Network-Based Biocomputation Devices. MATERIALS (BASEL, SWITZERLAND) 2023; 16:1046. [PMID: 36770052 PMCID: PMC9920894 DOI: 10.3390/ma16031046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/13/2023] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Network-based biocomputation (NBC) relies on accurate guiding of biological agents through nanofabricated channels produced by lithographic patterning techniques. Here, we report on the large-scale, wafer-level fabrication of optimized microfluidic channel networks (NBC networks) using electron-beam lithography as the central method. To confirm the functionality of these NBC networks, we solve an instance of a classical non-deterministic-polynomial-time complete ("NP-complete") problem, the subset-sum problem. The propagation of cytoskeletal filaments, e.g., molecular motor-propelled microtubules or actin filaments, relies on a combination of physical and chemical guiding along the channels of an NBC network. Therefore, the nanofabricated channels have to fulfill specific requirements with respect to the biochemical treatment as well as the geometrical confienement, with walls surrounding the floors where functional molecular motors attach. We show how the material stack used for the NBC network can be optimized so that the motor-proteins attach themselves in functional form only to the floor of the channels. Further optimizations in the nanolithographic fabrication processes greatly improve the smoothness of the channel walls and floors, while optimizations in motor-protein expression and purification improve the activity of the motor proteins, and therefore, the motility of the filaments. Together, these optimizations provide us with the opportunity to increase the reliability of our NBC devices. In the future, we expect that these nanolithographic fabrication technologies will enable production of large-scale NBC networks intended to solve substantially larger combinatorial problems that are currently outside the capabilities of conventional software-based solvers.
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Affiliation(s)
- Christoph R. Meinecke
- Center for Microtechnologies, Chemnitz University of Technology, 09107 Chemnitz, Germany
- Department Nano Device Technologies, Fraunhofer Institute for Electronic Nano Systems (ENAS), 09126 Chemnitz, Germany
| | - Georg Heldt
- Department Nano Device Technologies, Fraunhofer Institute for Electronic Nano Systems (ENAS), 09126 Chemnitz, Germany
| | - Thomas Blaudeck
- Center for Microtechnologies, Chemnitz University of Technology, 09107 Chemnitz, Germany
- Department Nano Device Technologies, Fraunhofer Institute for Electronic Nano Systems (ENAS), 09126 Chemnitz, Germany
- Research Center for Materials, Architectures and Integration of Nanomembranes (MAIN), Chemnitz University of Technology, 09126 Chemnitz, Germany
| | - Frida W. Lindberg
- NanoLund and Solid State Physics, Lund University, 22100 Lund, Sweden
| | | | | | - Aseem Salhotra
- Department of Chemistry and Biomedical Sciences, Linnaeus University, 39182 Kalmar, Sweden
| | - Alf Månsson
- Department of Chemistry and Biomedical Sciences, Linnaeus University, 39182 Kalmar, Sweden
| | - Heiner Linke
- NanoLund and Solid State Physics, Lund University, 22100 Lund, Sweden
| | - Till Korten
- B CUBE—Center for Molecular Bioengineering and Cluster of Excellence Physics of Life, Technische Universität Dresden, 01307 Dresden, Germany
| | - Stefan Diez
- B CUBE—Center for Molecular Bioengineering and Cluster of Excellence Physics of Life, Technische Universität Dresden, 01307 Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Danny Reuter
- Center for Microtechnologies, Chemnitz University of Technology, 09107 Chemnitz, Germany
- Department Nano Device Technologies, Fraunhofer Institute for Electronic Nano Systems (ENAS), 09126 Chemnitz, Germany
| | - Stefan E. Schulz
- Center for Microtechnologies, Chemnitz University of Technology, 09107 Chemnitz, Germany
- Department Nano Device Technologies, Fraunhofer Institute for Electronic Nano Systems (ENAS), 09126 Chemnitz, Germany
- Research Center for Materials, Architectures and Integration of Nanomembranes (MAIN), Chemnitz University of Technology, 09126 Chemnitz, Germany
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Zhang Y, Hess H. Enhanced Diffusion of Catalytically Active Enzymes. ACS CENTRAL SCIENCE 2019; 5:939-948. [PMID: 31263753 PMCID: PMC6598160 DOI: 10.1021/acscentsci.9b00228] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Indexed: 05/03/2023]
Abstract
The past decade has seen an increasing number of investigations into enhanced diffusion of catalytically active enzymes. These studies suggested that enzymes are actively propelled as they catalyze reactions or bind with ligands (e.g., substrates or inhibitors). In this Outlook, we chronologically summarize and discuss the experimental observations and theoretical interpretations and emphasize the potential contradictions in these efforts. We point out that the existing multimeric forms of enzymes or isozymes may cause artifacts in measurements and that the conformational changes upon substrate binding are usually not sufficient to give rise to a diffusion enhancement greater than 30%. Therefore, more rigorous experiments and a more comprehensive theory are urgently needed to quantitatively validate and describe the enhanced enzyme diffusion.
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Affiliation(s)
- Yifei Zhang
- Department of Biomedical Engineering, Columbia University, 351L Engineering Terrace, 1210 Amsterdam Avenue, New York, New York 10027, United States
| | - Henry Hess
- Department of Biomedical Engineering, Columbia University, 351L Engineering Terrace, 1210 Amsterdam Avenue, New York, New York 10027, United States
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3
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Rahman MA, Salhotra A, Månsson A. Comparative analysis of widely used methods to remove nonfunctional myosin heads for the in vitro motility assay. J Muscle Res Cell Motil 2019; 39:175-187. [PMID: 30850933 PMCID: PMC6494787 DOI: 10.1007/s10974-019-09505-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 02/27/2019] [Indexed: 11/28/2022]
Abstract
The in vitro motility assay allows studies of muscle contraction through observation of actin filament propulsion by surface-adsorbed myosin motors or motor fragments isolated from muscle. A possible problem is that motility may be compromised by nonfunctional, “dead”, motors, obtained in the isolation process. Here we investigate the effects on motile function of two approaches designed to eliminate the effects of these dead motors. We first tested the removal of heavy meromyosin (HMM) molecules with ATP-insensitive “dead” heads by pelleting them with actin filaments, using ultracentrifugation in the presence of 1 mM MgATP (“affinity purification”). Alternatively we incubated motility assay flow cells, after HMM surface adsorption, with non-fluorescent “blocking actin” (1 µM) to block the dead heads. Both affinity purification and use of blocking actin increased the fraction of motile filaments compared to control conditions. However, affinity purification significantly reduced the actin sliding speed in five out of seven experiments on silanized surfaces and in one out of four experiments on nitrocellulose surfaces. Similar effects on velocity were not observed with the use of blocking actin. However, a reduced speed was also seen (without affinity purification) if HMM or myosin subfragment 1 was mixed with 1 mM MgATP before and during surface adsorption. We conclude that affinity purification can produce unexpected effects that may complicate the interpretation of in vitro motility assays and other experiments with surface adsorbed HMM, e.g. single molecule mechanics experiments. The presence of MgATP during incubation with myosin motor fragments is critical for the complicating effects.
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Affiliation(s)
- Mohammad A Rahman
- Department of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar, 391 82, Sweden
| | - Aseem Salhotra
- Department of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar, 391 82, Sweden
| | - Alf Månsson
- Department of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar, 391 82, Sweden.
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4
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Hess H, Ross JL. Non-equilibrium assembly of microtubules: from molecules to autonomous chemical robots. Chem Soc Rev 2017; 46:5570-5587. [PMID: 28329028 PMCID: PMC5603359 DOI: 10.1039/c7cs00030h] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Biological systems have evolved to harness non-equilibrium processes from the molecular to the macro scale. It is currently a grand challenge of chemistry, materials science, and engineering to understand and mimic biological systems that have the ability to autonomously sense stimuli, process these inputs, and respond by performing mechanical work. New chemical systems are responding to the challenge and form the basis for future responsive, adaptive, and active materials. In this article, we describe a particular biochemical-biomechanical network based on the microtubule cytoskeletal filament - itself a non-equilibrium chemical system. We trace the non-equilibrium aspects of the system from molecules to networks and describe how the cell uses this system to perform active work in essential processes. Finally, we discuss how microtubule-based engineered systems can serve as testbeds for autonomous chemical robots composed of biological and synthetic components.
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Affiliation(s)
- H Hess
- Department of Biomedical Engineering, Columbia University, USA.
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5
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Kumar S, Mansson A. Covalent and non-covalent chemical engineering of actin for biotechnological applications. Biotechnol Adv 2017; 35:867-888. [PMID: 28830772 DOI: 10.1016/j.biotechadv.2017.08.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 08/09/2017] [Accepted: 08/16/2017] [Indexed: 12/26/2022]
Abstract
The cytoskeletal filaments are self-assembled protein polymers with 8-25nm diameters and up to several tens of micrometres length. They have a range of pivotal roles in eukaryotic cells, including transportation of intracellular cargoes (primarily microtubules with dynein and kinesin motors) and cell motility (primarily actin and myosin) where muscle contraction is one example. For two decades, the cytoskeletal filaments and their associated motor systems have been explored for nanotechnological applications including miniaturized sensor systems and lab-on-a-chip devices. Several developments have also revolved around possible exploitation of the filaments alone without their motor partners. Efforts to use the cytoskeletal filaments for applications often require chemical or genetic engineering of the filaments such as specific conjugation with fluorophores, antibodies, oligonucleotides or various macromolecular complexes e.g. nanoparticles. Similar conjugation methods are also instrumental for a range of fundamental biophysical studies. Here we review methods for non-covalent and covalent chemical modifications of actin filaments with focus on critical advantages and challenges of different methods as well as critical steps in the conjugation procedures. We also review potential uses of the engineered actin filaments in nanotechnological applications and in some key fundamental studies of actin and myosin function. Finally, we consider possible future lines of investigation that may be addressed by applying chemical conjugation of actin in new ways.
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Affiliation(s)
- Saroj Kumar
- Department of Biotechnology, Delhi Technological University, Delhi 110042, India; Department of Chemistry and Biomedical Sciences, Faculty of Health and Life Sciences, Linnaeus University, SE-391 82 Kalmar, Sweden.
| | - Alf Mansson
- Department of Chemistry and Biomedical Sciences, Faculty of Health and Life Sciences, Linnaeus University, SE-391 82 Kalmar, Sweden.
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Parallel computation with molecular-motor-propelled agents in nanofabricated networks. Proc Natl Acad Sci U S A 2016; 113:2591-6. [PMID: 26903637 DOI: 10.1073/pnas.1510825113] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The combinatorial nature of many important mathematical problems, including nondeterministic-polynomial-time (NP)-complete problems, places a severe limitation on the problem size that can be solved with conventional, sequentially operating electronic computers. There have been significant efforts in conceiving parallel-computation approaches in the past, for example: DNA computation, quantum computation, and microfluidics-based computation. However, these approaches have not proven, so far, to be scalable and practical from a fabrication and operational perspective. Here, we report the foundations of an alternative parallel-computation system in which a given combinatorial problem is encoded into a graphical, modular network that is embedded in a nanofabricated planar device. Exploring the network in a parallel fashion using a large number of independent, molecular-motor-propelled agents then solves the mathematical problem. This approach uses orders of magnitude less energy than conventional computers, thus addressing issues related to power consumption and heat dissipation. We provide a proof-of-concept demonstration of such a device by solving, in a parallel fashion, the small instance {2, 5, 9} of the subset sum problem, which is a benchmark NP-complete problem. Finally, we discuss the technical advances necessary to make our system scalable with presently available technology.
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Affiliation(s)
- Sundus Erbas-Cakmak
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - David A. Leigh
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Charlie T. McTernan
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Alina
L. Nussbaumer
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
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8
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Sitt A, Hess H. Directed transport by surface chemical potential gradients for enhancing analyte collection in nanoscale sensors. NANO LETTERS 2015; 15:3341-50. [PMID: 25817944 DOI: 10.1021/acs.nanolett.5b00595] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Nanoscale detectors hold great promise for single molecule detection and the analysis of small volumes of dilute samples. However, the probability of an analyte reaching the nanosensor in a dilute solution is extremely low due to the sensor's small size. Here, we examine the use of a chemical potential gradient along a surface to accelerate analyte capture by nanoscale sensors. Utilizing a simple model for transport induced by surface binding energy gradients, we study the effect of the gradient on the efficiency of collecting nanoparticles and single and double stranded DNA. The results indicate that chemical potential gradients along a surface can lead to an acceleration of analyte capture by several orders of magnitude compared to direct collection from the solution. The improvement in collection is limited to a relatively narrow window of gradient slopes, and its extent strongly depends on the size of the gradient patch. Our model allows the optimization of gradient layouts and sheds light on the fundamental characteristics of chemical potential gradient induced transport.
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Affiliation(s)
- Amit Sitt
- Department of Biomedical Engineering, Columbia University, New York, New York 10027, United States
| | - Henry Hess
- Department of Biomedical Engineering, Columbia University, New York, New York 10027, United States
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Bengtsson E, Persson M, Månsson A. Analysis of flexural rigidity of actin filaments propelled by surface adsorbed myosin motors. Cytoskeleton (Hoboken) 2013; 70:718-28. [PMID: 24039103 PMCID: PMC4230416 DOI: 10.1002/cm.21138] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 08/08/2013] [Accepted: 08/22/2013] [Indexed: 11/09/2022]
Abstract
Actin filaments are central components of the cytoskeleton and the contractile machinery of muscle. The filaments are known to exist in a range of conformational states presumably with different flexural rigidity and thereby different persistence lengths. Our results analyze the approaches proposed previously to measure the persistence length from the statistics of the winding paths of actin filaments that are propelled by surface-adsorbed myosin motor fragments in the in vitro motility assay. Our results suggest that the persistence length of heavy meromyosin propelled actin filaments can be estimated with high accuracy and reproducibility using this approach provided that: (1) the in vitro motility assay experiments are designed to prevent bias in filament sliding directions, (2) at least 200 independent filament paths are studied, (3) the ratio between the sliding distance between measurements and the camera pixel-size is between 4 and 12, (4) the sliding distances between measurements is less than 50% of the expected persistence length, and (5) an appropriate cut-off value is chosen to exclude abrupt large angular changes in sliding direction that are complications, e.g., due to the presence of rigor heads. If the above precautions are taken the described method should be a useful routine part of in vitro motility assays thus expanding the amount of information to be gained from these.
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Affiliation(s)
- Elina Bengtsson
- Faculty of Health and Life Sciences, Linnaeus University, Kalmar, Sweden
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Lard M, Ten Siethoff L, Kumar S, Persson M, Te Kronnie G, Linke H, Månsson A. Ultrafast molecular motor driven nanoseparation and biosensing. Biosens Bioelectron 2013; 48:145-52. [PMID: 23672875 DOI: 10.1016/j.bios.2013.03.071] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 03/27/2013] [Accepted: 03/28/2013] [Indexed: 11/29/2022]
Abstract
Portable biosensor systems would benefit from reduced dependency on external power supplies as well as from further miniaturization and increased detection rate. Systems built around self-propelled biological molecular motors and cytoskeletal filaments hold significant promise in these regards as they are built from nanoscale components that enable nanoseparation independent of fluidic pumping. Previously reported microtubule-kinesin based devices are slow, however, compared to several existing biosensor systems. Here we demonstrate that this speed limitation can be overcome by using the faster actomyosin motor system. Moreover, due to lower flexural rigidity of the actin filaments, smaller features can be achieved compared to microtubule-based systems, enabling further miniaturization. Using a device designed through optimization by Monte Carlo simulations, we demonstrate extensive myosin driven enrichment of actin filaments on a detector area of less than 10 μm², with a concentration half-time of approximately 40 s. We also show accumulation of model analyte (streptavidin at nanomolar concentration in nanoliter effective volume) detecting increased fluorescence intensity within seconds after initiation of motor-driven transportation from capture regions. We discuss further optimizations of the system and incorporation into a complete biosensing workflow.
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Affiliation(s)
- Mercy Lard
- The Nanometer Structure Consortium (nmC@LU), Division of Solid State Physics, Lund University, SE-22100 Lund, Sweden
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Persson M, Gullberg M, Tolf C, Lindberg AM, Månsson A, Kocer A. Transportation of nanoscale cargoes by myosin propelled actin filaments. PLoS One 2013; 8:e55931. [PMID: 23437074 PMCID: PMC3578877 DOI: 10.1371/journal.pone.0055931] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 01/03/2013] [Indexed: 02/04/2023] Open
Abstract
Myosin II propelled actin filaments move ten times faster than kinesin driven microtubules and are thus attractive candidates as cargo-transporting shuttles in motor driven lab-on-a-chip devices. In addition, actomyosin-based transportation of nanoparticles is useful in various fundamental studies. However, it is poorly understood how actomyosin function is affected by different number of nanoscale cargoes, by cargo size, and by the mode of cargo-attachment to the actin filament. This is studied here using biotin/fluorophores, streptavidin, streptavidin-coated quantum dots, and liposomes as model cargoes attached to monomers along the actin filaments (“side-attached”) or to the trailing filament end via the plus end capping protein CapZ. Long-distance transportation (>100 µm) could be seen for all cargoes independently of attachment mode but the fraction of motile filaments decreased with increasing number of side-attached cargoes, a reduction that occurred within a range of 10–50 streptavidin molecules, 1–10 quantum dots or with just 1 liposome. However, as observed by monitoring these motile filaments with the attached cargo, the velocity was little affected. This also applied for end-attached cargoes where the attachment was mediated by CapZ. The results with side-attached cargoes argue against certain models for chemomechanical energy transduction in actomyosin and give important insights of relevance for effective exploitation of actomyosin-based cargo-transportation in molecular diagnostics and other nanotechnological applications. The attachment of quantum dots via CapZ, without appreciable modulation of actomyosin function, is useful in fundamental studies as exemplified here by tracking with nanometer accuracy.
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Affiliation(s)
- Malin Persson
- School of Natural Sciences, Linnaeus University, Kalmar, Sweden
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12
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Effect of Path Persistence Length of Molecular Shuttles on Two-stage Analyte Capture in Biosensors. Cell Mol Bioeng 2012. [DOI: 10.1007/s12195-012-0262-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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13
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Kumar S, ten Siethoff L, Persson M, Lard M, te Kronnie G, Linke H, Månsson A. Antibodies covalently immobilized on actin filaments for fast myosin driven analyte transport. PLoS One 2012; 7:e46298. [PMID: 23056279 PMCID: PMC3463588 DOI: 10.1371/journal.pone.0046298] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 08/29/2012] [Indexed: 01/09/2023] Open
Abstract
Biosensors would benefit from further miniaturization, increased detection rate and independence from external pumps and other bulky equipment. Whereas transportation systems built around molecular motors and cytoskeletal filaments hold significant promise in the latter regard, recent proof-of-principle devices based on the microtubule-kinesin motor system have not matched the speed of existing methods. An attractive solution to overcome this limitation would be the use of myosin driven propulsion of actin filaments which offers motility one order of magnitude faster than the kinesin-microtubule system. Here, we realized a necessary requirement for the use of the actomyosin system in biosensing devices, namely covalent attachment of antibodies to actin filaments using heterobifunctional cross-linkers. We also demonstrated consistent and rapid myosin II driven transport where velocity and the fraction of motile actin filaments was negligibly affected by the presence of antibody-antigen complexes at rather high density (>20 µm(-1)). The results, however, also demonstrated that it was challenging to consistently achieve high density of functional antibodies along the actin filament, and optimization of the covalent coupling procedure to increase labeling density should be a major focus for future work. Despite the remaining challenges, the reported advances are important steps towards considerably faster nanoseparation than shown for previous molecular motor based devices, and enhanced miniaturization because of high bending flexibility of actin filaments.
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Affiliation(s)
- Saroj Kumar
- School of Natural Sciences, Linnaeus University, Kalmar, Sweden
| | | | - Malin Persson
- School of Natural Sciences, Linnaeus University, Kalmar, Sweden
| | - Mercy Lard
- The Nanometer Structure Consortium and Division of Solid State Physics, Lund University, Lund, Sweden
| | - Geertruy te Kronnie
- Department of Women’s and Children’s Health, University of Padua, Padova, Italy
| | - Heiner Linke
- The Nanometer Structure Consortium and Division of Solid State Physics, Lund University, Lund, Sweden
| | - Alf Månsson
- School of Natural Sciences, Linnaeus University, Kalmar, Sweden
- * E-mail:
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Translational actomyosin research: fundamental insights and applications hand in hand. J Muscle Res Cell Motil 2012; 33:219-33. [PMID: 22638606 PMCID: PMC3413815 DOI: 10.1007/s10974-012-9298-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 05/01/2012] [Indexed: 12/24/2022]
Abstract
This review describes the development towards actomyosin based nanodevices taking a starting point in pioneering studies in the 1990s based on conventional in vitro motility assays. References are given to parallel developments using the kinesin–microtubule motor system. The early developments focused on achieving cargo-transportation using actin filaments as cargo-loaded shuttles propelled by surface-adsorbed heavy meromyosin along micro- and nanofabricated channels. These efforts prompted extensive studies of surface–motor interactions contributing with new insights of general relevance in surface and colloid chemistry. As a result of these early efforts, a range of complex devices have now emerged, spanning applications in medical diagnostics, biocomputation and formation of complex nanostructures by self-organization. In addition to giving a comprehensive account of the developments towards real-world applications an important goal of the present review is to demonstrate important connections between the applied studies and fundamental biophysical studies of actomyosin and muscle function. Thus the manipulation of the motor proteins towards applications has resulted in new insights into methodological aspects of the in vitro motiliy assay. Other developments have advanced the understanding of the dynamic materials properties of actin filaments.
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15
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Self-organization of motor-propelled cytoskeletal filaments at topographically defined borders. J Biomed Biotechnol 2012; 2012:647265. [PMID: 22536023 PMCID: PMC3321463 DOI: 10.1155/2012/647265] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 01/07/2012] [Indexed: 11/29/2022] Open
Abstract
Self-organization phenomena are of critical importance in living organisms and of great interest to exploit in nanotechnology. Here we describe in vitro self-organization of molecular motor-propelled actin filaments, manifested as a tendency of the filaments to accumulate in high density close to topographically defined edges on nano- and microstructured surfaces. We hypothesized that this “edge-tracing” effect either (1) results from increased motor density along the guiding edges or (2) is a direct consequence of the asymmetric constraints on stochastic changes in filament sliding direction imposed by the edges. The latter hypothesis is well captured by a model explicitly defining the constraints of motility on structured surfaces in combination with Monte-Carlo simulations [cf. Nitta et al. (2006)] of filament sliding. In support of hypothesis 2 we found that the model reproduced the edge tracing effect without the need to assume increased motor density at the edges. We then used model simulations to elucidate mechanistic details. The results are discussed in relation to nanotechnological applications and future experiments to test model predictions.
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16
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Idan O, Lam A, Kamcev J, Gonzales J, Agarwal A, Hess H. Nanoscale transport enables active self-assembly of millimeter-scale wires. NANO LETTERS 2012; 12:240-245. [PMID: 22111572 DOI: 10.1021/nl203450h] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Active self-assembly processes exploit an energy source to accelerate the movement of building blocks and intermediate structures and modify their interactions. A model system is the assembly of biotinylated microtubules partially coated with streptavidin into linear bundles as they glide on a surface coated with kinesin motor proteins. By tuning the assembly conditions, microtubule bundles with near millimeter length are created, demonstrating that active self-assembly is beneficial if components are too large for diffusive self-assembly but too small for robotic assembly.
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Affiliation(s)
- Ofer Idan
- Department of Biomedical Engineering, Columbia University, New York, New York, USA
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17
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Abstract
The self-organization of actin filaments is a topic that links cell biology with condensed matter physics. In vitro assays allow precise manipulation of component mechanical and chemical properties, needed for rigorous tests of theoretical models. We review recent work on in vitro motility assays that documented emergence of ordered actin filament microdomains powered by myosin motor proteins at high filament densities. Motor and filament surface density and mechanochemical cycle kinetics are additional parameters under current investigation. Individual filament collisions have been studied in order to elucidate the emergent population behavior. Apolar, weak interactions evidenced by local filament deformations during crossover events are attenuated at high motor densities. Theoretical analysis requires refinement of rigid rod filament models. In intact cells, accessory proteins modulate actin filament length, bundling or sliding and this gives rise to complex emergent structures and behaviors such as cell motility and chemotaxis. The development of generic, mechanical and biochemical frameworks with predictive power that link molecular properties with micro- and macroscopic phenomena seen in living cells requires dialogue between theoreticians and experimentalists.
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Affiliation(s)
- Shahid M. Khan
- Lifesciences, LUMS School of Science & Engineering; Lahore, Pakistan
| | - Rehan Ali
- Lifesciences, LUMS School of Science & Engineering; Lahore, Pakistan
| | - Nimra Asi
- Lifesciences, LUMS School of Science & Engineering; Lahore, Pakistan
| | - Justin E. Molloy
- Physical Biochemistry, MRC National Institute for Medical Research; The Ridgeway, Mill Hill, UK
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18
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Smith D. The interaction energy of charged filaments in an electrolyte: Results for all filament spacings. J Theor Biol 2011; 276:8-15. [DOI: 10.1016/j.jtbi.2011.01.046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2010] [Revised: 12/17/2010] [Accepted: 01/29/2011] [Indexed: 10/18/2022]
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Persson M, Albet-Torres N, Ionov L, Sundberg M, Höök F, Diez S, Månsson A, Balaz M. Heavy meromyosin molecules extending more than 50 nm above adsorbing electronegative surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:9927-9936. [PMID: 20337414 DOI: 10.1021/la100395a] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
In the in vitro motility assay, actin filaments are propelled by surface-adsorbed myosin motors, or rather, myosin motor fragments such as heavy meromyosin (HMM). Recently, efforts have been made to develop actomyosin powered nanodevices on the basis of this assay but such developments are hampered by limited understanding of the HMM adsorption geometry. Therefore, we here investigate the HMM adsorption geometries on trimethylchlorosilane- [TMCS-] derivatized hydrophobic surfaces and on hydrophilic negatively charged surfaces (SiO(2)). The TMCS surface is of great relevance in fundamental studies of actomyosin and both surface substrates are important for the development of motor powered nanodevices. Whereas both the TMCS and SiO(2) surfaces were nearly saturated with HMM (incubation at 120 microg mL(-1)) there was little actin binding on SiO(2) in the absence of ATP and no filament sliding in the presence of ATP. This contrasts with excellent actin-binding and motility on TMCS. Quartz crystal microbalance with dissipation (QCM-D) studies demonstrate a HMM layer with substantial protein mass up to 40 nm above the TMCS surface, considerably more than observed for myosin subfragment 1 (S1; 6 nm). Together with the excellent actin transportation on TMCS, this strongly suggests that HMM adsorbs to TMCS mainly via its most C-terminal tail part. Consistent with this idea, fluorescence interference contrast (FLIC) microscopy showed that actin filaments are held by HMM 38 +/- 2 nm above the TMCS-surface with the catalytic site, on average, 20-30 nm above the surface. Viewed in a context with FLIC, QCM-D and TIRF results, the lack of actin motility and the limited actin binding on SiO(2) shows that HMM adsorbs largely via the actin-binding region on this surface with the C-terminal coiled-coil tails extending >50 nm into solution. The results and new insights from this study are of value, not only for the development of motor powered nanodevices but also for the interpretation of fundamental biophysical studies of actomyosin function and for the understanding of surface-protein interactions in general.
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Affiliation(s)
- Malin Persson
- School of Natural Sciences, The Linnaeus University SE-391 82 Kalmar, Sweden
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Korten T, Månsson A, Diez S. Towards the application of cytoskeletal motor proteins in molecular detection and diagnostic devices. Curr Opin Biotechnol 2010; 21:477-88. [PMID: 20860918 DOI: 10.1016/j.copbio.2010.05.001] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2010] [Revised: 04/30/2010] [Accepted: 05/06/2010] [Indexed: 01/12/2023]
Abstract
Over the past ten years, great advancements have been made towards using biomolecular motors for nanotechnological applications. In particular, devices using cytoskeletal motor proteins for molecular transport are maturing. First efforts towards designing such devices used motor proteins attached to micro-structured substrates for the directed transport of microtubules and actin filaments. Soon thereafter, the specific capture, transport and detection of target analytes like viruses were demonstrated. Recently, spatial guiding of the gliding filaments was added to increase the sensitivity of detection and allow parallelization. Whereas molecular motor powered devices have not yet demonstrated performance beyond the level of existing detection techniques, the potential is great: Replacing microfluidics with transport powered by molecular motors allows integration of the energy source (ATP) into the assay solution. This opens up the opportunity to design highly integrated, miniaturized, autonomous detection devices. Such devices, in turn, may allow fast and cheap on-site diagnosis of diseases and detection of environmental pathogens and toxins.
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Affiliation(s)
- Till Korten
- Max-Planck-Institute for Molecular Cell Biology and Genetics, Dresden, Germany
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Katira P, Hess H. Two-stage capture employing active transport enables sensitive and fast biosensors. NANO LETTERS 2010; 10:567-72. [PMID: 20055432 PMCID: PMC2819759 DOI: 10.1021/nl903468p] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2009] [Revised: 12/28/2009] [Indexed: 05/20/2023]
Abstract
Nanoscale sensors enable the detection of analytes with improved signal-to-noise ratio but suffer from mass transport limitations. Molecular shuttles, assembled from, e.g., antibody-functionalized microtubules and kinesin motor proteins, can selectively capture analytes from solution and deliver the analytes to a sensor patch. This two-stage process can accelerate mass transport to nanoscale biosensors and facilitate the rapid detection of analytes. Here, the possible increase of the signal-to-noise ratio is calculated, and the optimal layout of a system which integrates active transport is determined.
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Affiliation(s)
- Parag Katira
- Department of Materials Science and Engineering, University of Florida, Gainesville, Florida 32611-6400
| | - Henry Hess
- Department of Materials Science and Engineering, University of Florida, Gainesville, Florida 32611-6400
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Zhang S, You B, Gu G, Wu L. A simple approach to fabricate morphological gradient on polymer surfaces. POLYMER 2009. [DOI: 10.1016/j.polymer.2009.11.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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