Biophysical Approaches for Applying and Measuring Biological Forces

Single-molecule detection and super-resolution imaging with a portable and adaptable 3D-printed microscopy platform (Brick-MIC)

Over the past decades, single-molecule and super-resolution microscopy have advanced and represent essential tools for life science research. There is, however, a growing gap between the state of the art and what is accessible to biologists, biochemists, medical researchers, or labs with financial constraints. To bridge this gap, we introduce Brick-MIC, a versatile and affordable open-source 3D-printed microspectroscopy and imaging platform. Brick-MIC enables the integration of various fluorescence imaging techniques with single-molecule resolution within a single platform and exchange between different modalities within minutes. We here present variants of Brick-MIC that facilitate single-molecule fluorescence detection, fluorescence correlation spectroscopy, time-correlated single-photon counting and super-resolution imaging (STORM and PAINT). Detailed descriptions of the hardware and software components, as well as data analysis routines, are provided, to allow non-optics specialists to operate their own Brick-MIC with minimal effort and investments. We foresee that our affordable, flexible, and open-source Brick-MIC platform will be a valuable tool for many laboratories worldwide.

Single-molecule detection and super-resolution imaging with a portable and adaptable 3D-printed microscopy platform (Brick-MIC)

Over the past decades, single-molecule and super-resolution microscopy have advanced and represent essential tools for life science research. There is,however, a growing gap between the state-of-the-art and what is accessible to biologists, biochemists, medical researchers or labs with financial constraints. To bridge this gap, we introduce Brick-MIC, a versatile and affordable open-source 3D-printed micro-spectroscopy and imaging platform. Brick-MIC enables the integration of various fluorescence imaging techniques with single-molecule resolution within a single platform and exchange between different modalities within minutes. We here present variants of Brick-MIC that facilitate single-molecule fluorescence detection, fluorescence correlation spectroscopy and super-resolution imaging (STORM and PAINT). Detailed descriptions of the hardware and software components, as well as data analysis routines are provided, to allow non-optics specialist to operate their own Brick-MIC with minimal effort and investments. We foresee that our affordable, flexible, and opensource Brick-MIC platform will be a valuable tool for many laboratories worldwide.

Molecular Force Sensors for Biological Application

The mechanical forces exerted by cells on their surrounding microenvironment are known as cellular traction forces. These forces play crucial roles in various biological processes, such as tissue development, wound healing and cell functions. However, it is hard for traditional techniques to measure cellular traction forces accurately because their magnitude (from pN to nN) and the length scales over which they occur (from nm to μm) are extremely small. In order to fully understand mechanotransduction, highly sensitive tools for measuring cellular forces are needed. Current powerful techniques for measuring traction forces include traction force microscopy (TFM) and fluorescent molecular force sensors (FMFS). In this review, we elucidate the force imaging principles of TFM and FMFS. Then we highlight the application of FMFS in a variety of biological processes and offer our perspectives and insights into the potential applications of FMFS.

Decoding Biomechanical Cues Based on DNA Sensors

Biological systems perceive and respond to mechanical forces, generating mechanical cues to regulate life processes. Analyzing biomechanical forces has profound significance for understanding biological functions. Therefore, a series of molecular mechanical techniques have been developed, mainly including single-molecule force spectroscopy, traction force microscopy, and molecular tension sensor systems, which provide indispensable tools for advancing the field of mechanobiology. DNA molecules with a programmable structure and well-defined mechanical characteristics have attached much attention to molecular tension sensors as sensing elements, and are designed for the study of biomechanical forces to present biomechanical information with high sensitivity and resolution. In this work, a comprehensive overview of molecular mechanical technology is presented, with a particular focus on molecular tension sensor systems, specifically those based on DNA. Finally, the future development and challenges of DNA-based molecular tension sensor systems are looked upon.

Nanoparticles traversing the extracellular matrix induce biophysical perturbation of fibronectin depicted by surface chemistry

While the filtering and accumulation effects of the extracellular matrix (ECM) on nanoparticles (NPs) have been experimentally observed, the detailed interactions between NPs and specific biomolecules within the ECM remain poorly understood and pose challenges for in vivo molecular-level investigations. Herein, we adopt molecular dynamics simulations to elucidate the impacts of methyl-, hydroxy-, amine-, and carboxyl-modified gold NPs on the cell-binding domains of fibronectin (Fn), an indispensable component of the ECM for cell attachment and signaling. Simulation results show that NPs can specifically bind to distinct Fn domains, and the strength of these interactions depends on the physicochemical properties of NPs. NP-NH3+ exhibits the highest affinity to domains rich in acidic residues, leading to strong electrostatic interactions that induce severe deformation, potentially disrupting the normal functioning of Fn. NP-CH3 and NP-COO- selectively occupy the RGD/PHSRN motifs, which may hinder their recognition by integrins on the cell surface. Additionally, NPs can disrupt the dimerization of Fn through competing for residues at the dimer interface or by diminishing the shape complementarity between dimerized proteins. The mechanical stretching of Fn, crucial for ECM fibrillogenesis, is suppressed by NPs due to their local rigidifying effect. These results provide valuable molecular-level insights into the impacts of various NPs on the ECM, holding significant implications for advancing nanomedicine and nanosafety evaluation.

Mechanotransduction and epigenetic modulations of chromatin: Role of mechanical signals in gene regulation

Mechanical forces may be generated within a cell due to tissue stiffness, cytoskeletal reorganization, and the changes (even subtle) in the cell's physical surroundings. These changes of forces impose a mechanical tension within the intracellular protein network (both cytosolic and nuclear). Mechanical tension could be released by a series of protein-protein interactions often facilitated by membrane lipids, lectins and sugar molecules and thus generate a type of signal to drive cellular processes, including cell differentiation, polarity, growth, adhesion, movement, and survival. Recent experimental data have accentuated the molecular mechanism of this mechanical signal transduction pathway, dubbed mechanotransduction. Mechanosensitive proteins in the cell's plasma membrane discern the physical forces and channel the information to the cell interior. Cells respond to the message by altering their cytoskeletal arrangement and directly transmitting the signal to the nucleus through the connection of the cytoskeleton and nucleoskeleton before the information despatched to the nucleus by biochemical signaling pathways. Nuclear transmission of the force leads to the activation of chromatin modifiers and modulation of the epigenetic landscape, inducing chromatin reorganization and gene expression regulation; by the time chemical messengers (transcription factors) arrive into the nucleus. While significant research has been done on the role of mechanotransduction in tumor development and cancer progression/metastasis, the mechanistic basis of force-activated carcinogenesis is still enigmatic. Here, in this review, we have discussed the various cues and molecular connections to better comprehend the cellular mechanotransduction pathway, and we also explored the detailed role of some of the multiple players (proteins and macromolecular complexes) involved in mechanotransduction. Thus, we have described an avenue: how mechanical stress directs the epigenetic modifiers to modulate the epigenome of the cells and how aberrant stress leads to the cancer phenotype.

Imaging of Accumulated Mechanical Stresses Using Self-Assembled Layered Conjugated Polymer

When mechanical stresses, such as tensile, compressive, and frictional stresses, are applied to objects by various motions, they are accumulated in materials. Conventional mechanoresponsive materials and sensors detect one-time applied stress. However, the accumulated stresses are not visualized or measured in previous works. The present study demonstrated imaging and sensing of not only one-time but also accumulated tensile, compressive, and frictional stresses. Polyurethane (PU) film was combined with 2D layered polydiacetylene (PDA), a stimuli-responsive color-changing polymer. PDA generally exhibits no color changes with the application of tensile and compression stresses because the molecular motion leading to the color change is not induced by such mechanical stresses. Here the versatile mechanoresponsiveness was achieved using a block copolymer guest partially intercalated in the layered PDA. As the interlayer and outerlayer segments interact with PDA and PU, respectively, the applied stresses to the film are transferred from PU to PDA via the block copolymer guest. The color changes of the film imaged and quantified the accumulated work depending on the number and strength of the applied multiple stresses such as tensile, compressive, and frictional stresses. The design strategy of materials and methodology of sensing can be applied to the development of new sensors for accumulated mechanical stresses in a wide range of length and strength scales.

Acoustic tweezers for high-throughput single-cell analysis

Acoustic tweezers provide an effective means for manipulating single cells and particles in a high-throughput, precise, selective and contact-free manner. The adoption of acoustic tweezers in next-generation cellular assays may advance our understanding of biological systems. Here we present a comprehensive set of instructions that guide users through device fabrication, instrumentation setup and data acquisition to study single cells with an experimental throughput that surpasses traditional methods, such as atomic force microscopy and micropipette aspiration, by several orders of magnitude. With acoustic tweezers, users can conduct versatile experiments that require the trapping, patterning, pairing and separation of single cells in a myriad of applications ranging across the biological and biomedical sciences. This procedure is widely generalizable and adaptable for investigations in materials and physical sciences, such as the spinning motion of colloids or the development of acoustic-based quantum simulations. Overall, the device fabrication requires ~12 h, the experimental setup of the acoustic tweezers requires 1-2 h and the cell manipulation experiment requires ~30 min to complete. Our protocol is suitable for use by interdisciplinary researchers in biology, medicine, engineering and physics.

Magnetically Actuated Hydrogel Stamping-Assisted Cellular Mechanical Analyzer for Stored Blood Quality Detection

Cellular mechanical property analysis reflecting the physiological and pathological states of cells plays a crucial role in assessing the quality of stored blood. However, its complex equipment needs, operation difficulty, and clogging issues hinder automated and rapid biomechanical testing. Here, we propose a promising biosensor assisted by magnetically actuated hydrogel stamping to fulfill it. The flexible magnetic actuator triggers the collective deformation of multiple cells in the light-cured hydrogel, and it allows for on-demand bioforce stimulation with the advantages of portability, cost-effectiveness, and simplicity of operation. The magnetically manipulated cell deformation processes are captured by the integrated miniaturized optical imaging system, and the cellular mechanical property parameters are extracted from the captured images for real-time analysis and intelligent sensing. In this work, 30 clinical blood samples with different storage durations (<14 days and >14 days) were tested. A deviation of 3.3% in the differentiation of blood storage durations by this system compared to physician annotation demonstrated its feasibility. This system should broaden the application of cellular mechanical assays in diverse clinical settings.

Novel perspective for protein-drug interaction analysis: atomic force microscope

Proteins are major drug targets, and drug-target interaction identification and analysis are important factors for drug discovery. Atomic force microscopy (AFM) is a powerful tool making it possible to image proteins with nanometric resolution and probe intermolecular forces under physiological conditions. We review recent studies conducted in the field of target protein drug discovery using AFM-based analysis technology, including drug-driven changes in nanomechanical properties of protein morphology and interactions. Underlying mechanisms (including thermodynamic and kinetic parameters) of the drug-target interaction and drug-modulating protein-protein interaction (PPI) on the surfaces of models or living cells are discussed. Furthermore, challenges and the outlook for the field are likewise discussed. Overall, this insight into the mechanical properties of protein-drug interactions provides an unprecedented information framework for rational drug discovery in the pharmaceutical field.

COF-Based Electrodes with Vertically Supported Tentacle Array for Ultrahigh Stability Flexible Energy Storage

As an emerging porous crystal polymer, covalent organic frameworks (COFs) possess unique characteristics, such as high porosity, excellent stability, diverse topologies, designable open channels, and functional tunability. However, limited by the solid powder form, most COFs display low active site utilization and weak binding force with the current collector. In this pioneering research, we integrate redox-active COFs onto carbon fiber surfaces (AC-COFs) via strong covalent bridging. The 2,6-diaminoanthraquinone (DAAQ) pillars embedded on the carbon fiber surface are the key to precisely controlling the growth direction of COFs. The obtained tentacle-like array vertically supported on the surface of the carbon fiber can effectively induce charge transfer and prevent COFs from aggregating/collapsing. The strong covalent coupling and increase of accessible active sites contributed to the high specific capacitance of AC-COFs electrode (1034 mF cm^-2). In addition, the COF-based flexible electrode retains an initial capacitance of 98% after 20000 charge-discharge cycles. The flexible all-solid-state symmetric supercapacitor is assembled by PVA/H₂SO₄ gel electrolyte with an areal capacitance of 715 mF cm^-2. Besides, a red LED can be easily powered by three-bending AC-COFs//AC-COFs devices. The innovative synthesis strategy opens up new opportunities to develop high-performance flexible energy storage devices based on COFs.

Directed assembly of genetically engineered eukaryotic cells into living functional materials via ultrahigh-affinity protein interactions

Engineered living materials (ELMs) are gaining traction among synthetic biologists, as their emergent properties and nonequilibrium thermodynamics make them markedly different from traditional materials. However, the aspiration to directly use living cells as building blocks to create higher-order structures or materials, with no need for chemical modification, remains elusive to synthetic biologists. Here, we report a strategy that enables the assembly of engineered Saccharomyces cerevisiae into self-propagating ELMs via ultrahigh-affinity protein/protein interactions. These yeast cells have been genetically engineered to display the protein pairs SpyTag/SpyCatcher or CL7/Im7 on their surfaces, which enable their assembly into multicellular structures capable of further growth and proliferation. The assembly process can be controlled precisely via optical tweezers or microfluidics. Moreover, incorporation of functional motifs such as super uranyl-binding protein and mussel foot proteins via genetic programming rendered these materials suitable for uranium extraction from seawater and bioadhesion, respectively, pointing to their potential in chemical separation and biomedical applications.

The role of cellular traction forces in deciphering nuclear mechanics

Cellular forces exerted on the extracellular matrix (ECM) during adhesion and migration under physiological and pathological conditions regulate not only the overall cell morphology but also nuclear deformation. Nuclear deformation can alter gene expression, integrity of the nuclear envelope, nucleus-cytoskeletal connection, chromatin architecture, and, in some cases, DNA damage responses. Although nuclear deformation is caused by the transfer of forces from the ECM to the nucleus, the role of intracellular organelles in force transfer remains unclear and a challenging area of study. To elucidate nuclear mechanics, various factors such as appropriate biomaterial properties, processing route, cellular force measurement technique, and micromanipulation of nuclear forces must be understood. In the initial phase of this review, we focused on various engineered biomaterials (natural and synthetic extracellular matrices) and their manufacturing routes along with the properties required to mimic the tumor microenvironment. Furthermore, we discussed the principle of tools used to measure the cellular traction force generated during cell adhesion and migration, followed by recently developed techniques to gauge nuclear mechanics. In the last phase of this review, we outlined the principle of traction force microscopy (TFM), challenges in the remodeling of traction forces, microbead displacement tracking algorithm, data transformation from bead movement, and extension of 2-dimensional TFM to multiscale TFM.