Mechanical unfolding of biomolecular structures has been exclusively performed at the single-molecule level by single-molecule force spectroscopy (SMFS) techniques. Here we transformed sophisticated mechanical investigations on individual molecules into a simple platform suitable for molecular ensembles. By using shear flow inside a homogenizer tip, DNA secondary structures such as i-motifs are unfolded by shear force up to 50 pN at a 77 796 s −1 shear rate. We found that the larger the molecules, the higher the exerted shear forces. This shear force approach revealed affinity between ligands and i-motif structures. It also demonstrated a mechano-click reaction in which a Cu( i ) catalyzed azide–alkyne cycloaddition was modulated by shear force. We anticipate that this ensemble force spectroscopy method can investigate intra- and inter-molecular interactions with the throughput, accuracy, and robustness unparalleled to those of SMFS methods.
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A nanoscale DNA force spectrometer capable of applying tension and compression on biomolecules
Abstract Single molecule force spectroscopy is a powerful approach to probe the structure, conformational changes, and kinetic properties of biological and synthetic macromolecules. However, common approaches to apply forces to biomolecules require expensive and cumbersome equipment and relatively large probes such as beads or cantilevers, which limits their use for many environments and makes integrating with other methods challenging. Furthermore, existing methods have key limitations such as an inability to apply compressive forces on single molecules. We report a nanoscale DNA force spectrometer (nDFS), which is based on a DNA origami hinge with tunable mechanical and dynamic properties. The angular free energy landscape of the nDFS can be engineered across a wide range through substitution of less than 5% of the strand components. We further incorporate a removable strut that enables reversible toggling of the nDFS between open and closed states to allow for actuated application of tensile and compressive forces. We demonstrate the ability to apply compressive forces by inducing a large bend in a 249bp DNA molecule, and tensile forces by inducing DNA unwrapping of a nucleosome sample. These results establish a versatile tool for force spectroscopy and robust methods for designing nanoscale mechanical devices with tunable force application.
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- Award ID(s):
- 1715321
- PAR ID:
- 10290046
- Date Published:
- Journal Name:
- Nucleic Acids Research
- ISSN:
- 0305-1048
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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null (Ed.)DNA nanotechnology has reported a wide range of structurally tunable scaffolds with precise control over their size, shape and mechanical properties. One promising application of these nanodevices is as probes for protein function or determination of protein structure. In this perspective we cover several recent examples in this field, including determining the effect of ligand spacing and multivalency on cell activation, applying forces at the nanoscale, and helping to solve protein structure by cryo-EM. We also highlight some future directions in the chemistry necessary for integrating proteins with DNA nanoscaffolds, as well as opportunities for computational modeling of hybrid protein-DNA nanomaterials.more » « less
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Abstract Characterizing the mechanical properties of single cells is important for developing descriptive models of tissue mechanics and improving the understanding of mechanically driven cell processes. Standard methods for measuring single‐cell mechanical properties typically provide isotropic mechanical descriptions. However, many cells exhibit specialized geometries
in vivo , with anisotropic cytoskeletal architectures reflective of their function, and are exposed to dynamic multiaxial loads, raising the need for more complete descriptions of their anisotropic mechanical properties under complex deformations. Here, we describe the cellular microbiaxial stretching (CμBS) assay in which controlled deformations are applied to micropatterned cells while simultaneously measuring cell stress. CμBS utilizes a set of linear actuators to apply tensile or compressive, short‐ or long‐term deformations to cells micropatterned on a fluorescent bead‐doped polyacrylamide gel. Using traction force microscopy principles and the known geometry of the cell and the mechanical properties of the underlying gel, we calculate the stress within the cell to formulate stress‐strain curves that can be further used to create mechanical descriptions of the cells, such as strain energy density functions. © 2022 Wiley Periodicals LLC.Basic Protocol 1 : Assembly of CμBS stretching constructsBasic Protocol 2 : Polymerization of micropatterned, bead‐doped polyacrylamide gel on an elastomer membraneSupport Protocol : Cell culture and seeding onto CμBS constructsBasic Protocol 3 : Implementing CμBS stretching protocols and traction force microscopyBasic Protocol 4 : Data analysis and cell stress measurements -
null (Ed.)Dynamically crosslinked polymers and their composites have tremendous potential in the development of the next round of advanced materials for aerospace, sensing, and tribological applications. These materials have self-healing properties, or the ability to recover from scratches and cuts. Applied forces can have a significant impact on the mechanical properties of non-dynamic systems. However, the impacts of forces on the self-healing ability of dynamically bonded systems are still poorly understood. Here, we used a combined computational and experimental approach to study the impact of mechanical forces on the self-healing of a model dynamic covalent crosslinked polymer system. Surprisingly, the mechanical history of the materials has a distinct impact on the observed recovery of the mechanical properties after the material is damaged. Higher compressive forces and sustained forces lead to greater self-healing, indicating that mechanical forces can promote dynamic chemistry. The atomistic details provided in molecular dynamics simulations are used to understand the mechanism with both non-covalent and dynamic covalent linkage responses to the external loading. Finite element analysis is performed to bridge the gap between experiments and simulations and to further explore the underlying mechanisms. The self-healing behavior of the crosslinked polymers is explained using reaction rate theory, with the applied force proposed to lower the energy barrier to bond exchange. Overall, our study provides fundamental understanding of how and why the self-healing of cross-linked polymers is affected by a compressive force and the force application time.more » « less
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Abstract Introduction Mechanical forces provide critical biological signals to cells. Within the distal lung, tensile forces act across the basement membrane and epithelial cells atop. Stretching devices have supported studies of mechanical forces in distal lung epithelium to gain mechanistic insights into pulmonary diseases. However, the integration of curvature into devices applying mechanical forces onto lung epithelial cell monolayers has remained challenging. To address this, we developed a hammock-shaped platform that offers desired curvature and mechanical forces to lung epithelial monolayers.
Methods We developed hammocks using polyethylene terephthalate (PET)-based membranes and magnetic-particle modified silicone elastomer films within a 48-well plate that mimic the alveolar curvature and tensile forces during breathing. These hammocks were engineered and characterized for mechanical and cell-adhesive properties to facilitate cell culture. Using human small airway epithelial cells (SAECs), we measured monolayer formation and mechanosensing using F-Actin staining and immunofluorescence for cytokeratin to visualize intermediate filaments.
Results We demonstrate a multi-functional design that facilitates a range of curvatures along with the incorporation of magnetic elements for dynamic actuation to induce mechanical forces. Using this system, we then showed that SAECs remain viable, proliferate, and form an epithelial cell monolayer across the entire hammock. By further applying mechanical stimulation via magnetic actuation, we observed an increase in proliferation and strengthening of the cytoskeleton, suggesting an increase in mechanosensing.
Conclusion This hammock strategy provides an easily accessible and tunable cell culture platform for mimicking distal lung mechanical forces in vitro. We anticipate the promise of this culture platform for mechanistic studies, multi-modal stimulation, and drug or small molecule testing, extendable to other cell types and organ systems.
- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1093/nar/gkab656
