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Malinowska AM, van Mameren J, Peterman EJG, Wuite GJL, Heller I. Introduction to Optical Tweezers: Background, System Designs, and Applications. Methods Mol Biol 2024; 2694:3-28. [PMID: 37823997 DOI: 10.1007/978-1-0716-3377-9_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Optical tweezers are a means to manipulate objects with light. With the technique, microscopically small objects can be held and steered, allowing for accurate measurement of the forces applied to these objects. Optical tweezers can typically obtain a nanometer spatial resolution, a picoNewton force resolution, and a millisecond time resolution, which makes the technique well suited for the study of biological processes from the single-cell down to the single-molecule level. In this chapter, we aim to provide an introduction to the use of optical tweezers for single-molecule analyses. We start from the basic principles and methodology involved in optical trapping, force calibration, and force measurements. Next, we describe the components of an optical tweezers setup and their experimental relevance. Finally, we will provide an overview of the broad applications in context of biological research, with the emphasis on the measurement modes, experimental assays, and possible combinations with fluorescence microscopy techniques.
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Affiliation(s)
- Agata M Malinowska
- LaserLaB Amsterdam and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Joost van Mameren
- Institute of Physics, University of Amsterdam, Amsterdam, The Netherlands
| | - Erwin J G Peterman
- LaserLaB Amsterdam and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Gijs J L Wuite
- LaserLaB Amsterdam and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Iddo Heller
- LaserLaB Amsterdam and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
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Karna D, Mano E, Ji J, Kawamata I, Suzuki Y, Mao H. Chemo-mechanical forces modulate the topology dynamics of mesoscale DNA assemblies. Nat Commun 2023; 14:6459. [PMID: 37833326 PMCID: PMC10575982 DOI: 10.1038/s41467-023-41604-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 09/06/2023] [Indexed: 10/15/2023] Open
Abstract
The intrinsic complexity of many mesoscale (10-100 nm) cellular machineries makes it challenging to elucidate their topological arrangement and transition dynamics. Here, we exploit DNA origami nanospring as a model system to demonstrate that tens of piconewton linear force can modulate higher-order conformation dynamics of mesoscale molecular assemblies. By switching between two chemical structures (i.e., duplex and tetraplex DNA) in the junctions of adjacent origami modules, the corresponding stretching or compressing chemo-mechanical stress reversibly flips the backbone orientations of the DNA nanosprings. Both coarse-grained molecular dynamics simulations and atomic force microscopy measurements reveal that such a backbone conformational switch does not alter the right-handed chirality of the nanospring helix. This result suggests that mesoscale helical handedness may be governed by the torque, rather than the achiral orientation, of nanospring backbones. It offers a topology-based caging/uncaging concept to present chemicals in response to environmental cues in solution.
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Affiliation(s)
- Deepak Karna
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44242, USA
| | - Eriko Mano
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3 Aramaki-aza Aoba, Aoba-ku, Sendai, 980-8578, Japan
| | - Jiahao Ji
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44242, USA
| | - Ibuki Kawamata
- Department of Robotics, Graduate School of Engineering, Tohoku University, 6-6-01 Aramaki-aza Aoba, Aoba-ku, Sendai, 980-8579, Japan.
| | - Yuki Suzuki
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3 Aramaki-aza Aoba, Aoba-ku, Sendai, 980-8578, Japan.
- Department of Chemistry for Materials, Graduate School of Engineering, Mie University, 1577 Kurimamachiya-Cho, Tsu, 514-8507, Japan.
| | - Hanbin Mao
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44242, USA.
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Yu L, Ma Z, He Q. Dynamic DNA Nanostructures for Cell Manipulation. ACS Biomater Sci Eng 2023; 9:562-576. [PMID: 36592368 DOI: 10.1021/acsbiomaterials.2c01204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Dynamic DNA nanostructures are DNA nanostructures with reconfigurable elements that can undergo structural transformations in response to specific stimuli. Thus, anchoring dynamic DNA nanostructures on cell membranes is an attractive and promising strategy for well-controlled cell manipulation. Here, we review the latest progress in dynamic DNA nanostructures for cell manipulation. Commonly used mechanisms for dynamic DNA nanostructures are first introduced. Subsequently, we summarize the anchoring strategies for dynamic DNA nanostructures on cell membranes and list possible applications (including programming cell membrane receptors, controlling ligand activity and drug delivery, capturing and releasing cells, and assembling cells into clusters). Finally, insights into the remaining challenges are presented.
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Affiliation(s)
- Lu Yu
- Department of Endocrinology and Metabolism, The First People's Hospital of Changde City, Renmin Middle Road 818, Changde, Hunan 415000, P. R. China
| | - Zongrui Ma
- Department of Ophthalmology, The First People's Hospital of Changde City, Renmin Middle Road 818, Changde, Hunan 415000, P. R. China
| | - Qunye He
- School of Pharmacy, Shanghai Jiao Tong University, Dongchuan Road 800, Shanghai 200000, P. R. China
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Sethi S, Emura T, Hidaka K, Sugiyama H, Endo M. Photocontrolled DNA nanotubes as stiffness tunable matrices for controlling cellular behavior. NANOSCALE 2023; 15:2904-2910. [PMID: 36691928 DOI: 10.1039/d2nr05202d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Cell behavior is determined by a variety of properties of the extracellular environment like ligand spacing, nanotopography, and matrix stiffness. Matrix stiffness changes occur during many biological processes like wound healing, tumorigenesis, and development. These spatio-temporal dynamic changes in stiffness can cause significant changes in cell morphology, cell signaling, migration, cytoskeleton etc. In this paper, we have created photocontrolled stiffness-tunable DNA nanotubes which can undergo reversible changes in their conformation upon UV and VIS irradiation. When used as a substrate for cell culture, the photocontrolled DNA nanotubes can tune the cell morphology of HeLa cells from a long spindle-shaped morphology with long filopodia protrusions to a round morphology with short filopodia-like extrusions. Such a photocontrolled nanosystem can give us deep insights into the cell-matrix interactions in the native extracellular matrix caused by nanoscopic changes in stiffness.
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Affiliation(s)
- Soumya Sethi
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.
| | - Tomoko Emura
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.
| | - Kumi Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.
- Institute for Integrated Cell-Material Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Masayuki Endo
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.
- Institute for Integrated Cell-Material Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
- Organization for Research and Development of Innovative Science and Technology, Kansai University, Suita, Osaka 564-8680, Japan
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Pokhrel P, Wang J, Selvam S, Jonchhe S, Mandal S, Mao H. Ensemble Force Spectroscopy of a G-Quadruplex Cluster on a Single-Molecule Platform. Biomacromolecules 2022; 23:4795-4803. [PMID: 36322676 PMCID: PMC10347895 DOI: 10.1021/acs.biomac.2c00959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Single-molecule methods offer high sensitivities with precisions superior to bulk assays. However, these methods are low in throughput and cannot repetitively interrogate the same cluster of molecular units. In this work, we investigate a tandem array of G-quadruplexes on a single-molecule DNA template with a throughput of at least two orders of magnitude higher than single-molecule force spectroscopy. During mechanical unfolding by optical tweezers, the array of G-quadruplexes experiences identical force, temperature, and ionic conditions, which not only reduce environmental noise but also render unfolding transitions indistinguishable among individual G-quadruplexes. The resultant ensemble behaviors are analyzed by scanning force diagrams, which reveals accurate F1/2 values, where 50% of G-quadruplexes are unfolded. Independent of the number of G-quadruplexes (n > 15) contained in a cluster, F1/2 can effectively evaluate G-quadruplex ligands in a new method called differential scanning forcemetry. When the same G-quadruplex cluster is subject to a series of constant forces in force-jump experiments, unfolding rate constants of G-quadruplexes can be effectively evaluated as a function of force. The high precision demonstrated in all of these measurements reflects the power of repetitive sampling on the same cluster of single-molecule entities under identical conditions. Since biomolecules such as DNA, RNA, and proteins can be conveniently incorporated in a tandem array, we anticipate that this ensemble assay on single-molecule entities (EASE) provides a generic means of ensemble force spectroscopy to amalgamate the accuracy of ensemble measurements with the precision of single-molecule methods.
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Affiliation(s)
| | | | - Sangeetha Selvam
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Sagun Jonchhe
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Shankar Mandal
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Hanbin Mao
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
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Abstract
Invention of DNA origami has transformed the fabrication and application of biological nanomaterials. In this review, we discuss DNA origami nanoassemblies according to their four fundamental mechanical properties in response to external forces: elasticity, pliability, plasticity and stability. While elasticity and pliability refer to reversible changes in structures and associated properties, plasticity shows irreversible variation in topologies. The irreversible property is also inherent in the disintegration of DNA nanoassemblies, which is manifested by its mechanical stability. Disparate DNA origami devices in the past decade have exploited the mechanical regimes of pliability, elasticity, and plasticity, among which plasticity has shown its dominating potential in biomechanical and physiochemical applications. On the other hand, the mechanical stability of the DNA origami has been used to understand the mechanics of the assembly and disassembly of DNA nano-devices. At the end of this review, we discuss the challenges and future development of DNA origami nanoassemblies, again, from these fundamental mechanical perspectives.
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Affiliation(s)
- Jiahao Ji
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44240, USA.
| | - Deepak Karna
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44240, USA.
| | - Hanbin Mao
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44240, USA.
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