All-Covalent Nuclease-Resistant and Hydrogel-Tethered DNA Hairpin Probes Map pN Cell Traction Forces

A portable and sensitive DNA-based electrochemical sensor for detecting piconewton-scale cellular forces

BACKGROUND

Cell-generated forces are a key player in cell biology, especially during cellular shape formation, migration, cancer development, and immune response. The measurement of forces exerted and experienced by cells is fundamental in understanding these mechanosensitive cellular behaviors. While cell-generated forces can now be detected based on techniques like fluorescence microscopy, atomic force microscopy, optical/magnetic tweezers, however, most of these approaches rely on complicated instruments or materials, as well as skilled operators, which could limit their potential broad applications in regular biological laboratories.

RESULTS

A new type of smartphone-based electrochemical sensor is developed here for cellular force measurement. In this system, a double-stranded DNA-based force probe, known as tension gauge tether, is attached to the surface of a gold screen-printed electrode, which is then incorporated into a portable smartphone-based electrochemical device. Cellular force-induced DNA detachment on the sensor surface results in multiple redox reporters to reach the surface of the electrode and generate enhanced electrochemical signals. To further improve the sensitivity, a CRISPR-Cas12a system has also been incorporated to cleave the remaining surface-attached anchor DNA strand. Using integrin-mediated tension as an example, piconewton-scale adhesion forces generated by ≤ 10 HeLa cells could now be reliably detected. Meanwhile, the threshold forces of these electrochemical sensors can also be modularly tuned to detect different levels of cellular forces.

SIGNIFICANCE

These novel DNA-based highly sensitive, portable, cost-efficient, and easy-to-use electrochemical sensors can be potentially powerful tools for detecting different cell-generated molecular forces. Functioning as complementary tools with traction force microscopy and fluorescent probes, these electrochemical sensors can be straightforwardly applied in regular biological laboratories for understanding the basic mechanical principles of cell signaling and for developing novel strategies and materials in tissue engineering, regenerative medicine, and cell therapy.

Unravelling molecular mechanobiology using DNA-based fluorogenic tension sensors

Investigations of the biological system have revealed many principles that govern regular life processes. Recently, the analysis of tiny mechanical forces associated with many biological processes revealed their significance in understanding biological functions. Consequently, this piqued the interest of researchers, and a series of technologies have been developed to understand biomechanical cues at the molecular level. Notable techniques include single-molecule force spectroscopy, traction force microscopy, and molecular tension sensors. Well-defined double-stranded DNA structures could possess programmable mechanical characteristics, and hence, they have become one of the central molecules in molecular tension sensor technology. With the advancement of DNA technology, DNA or nucleic acid-based robust tension sensors offer the possibility of understanding mechanobiology in the bulk to single-molecule level range with desired spatiotemporal resolution. This review presents a comprehensive account of molecular tension sensors with a special emphasis on DNA-based fluorogenic tension sensors. Along with a detailed discussion on irreversible and reversible DNA-based tension sensors and their application in super-resolution microscopy, a discussion on biomolecules associated with cellular mechanotransduction and key findings in the field are included. This review ends with an elaborate discussion on the current challenges and future prospects of molecular tension sensors.

Nuclease-Resistant L-DNA Tension Probes Enable Long-Term Force Mapping of Single Cells and Cell Consortia

DNA-based tension probes with precisely programmable force responses provide important insights into cellular mechanosensing. However, their degradability in cell culture limits their use for long-term imaging, for instance, when cells migrate, divide, and differentiate. This is a critical limitation for providing insights into mechanobiology for these longer-term processes. Here, we present DNA-based tension probes that are entirely designed based on the stereoisomer of biological D-DNA, i.e., L-DNA. We demonstrate that L-DNA tension probes are essentially indestructible by nucleases and provide days-long imaging without significant loss in image quality. We also show their superiority already for short imaging times commonly used for classical D-DNA tension probes. We showcase the potential of these resilient probes to image minute movements, and for generating long term force maps of single cells and of collectively migrating cell populations.

Measuring Integrin Force Loading Rates Using a Two-Step DNA Tension Sensor

Cells apply forces to extracellular matrix (ECM) ligands through transmembrane integrin receptors: an interaction which is intimately involved in cell motility, wound healing, cancer invasion and metastasis. These small (piconewton) integrin-ECM forces have been studied by molecular tension fluorescence microscopy (MTFM), which utilizes a force-induced conformational change of a probe to detect mechanical events. MTFM has revealed the force magnitude for integrin receptors in a variety of cell models including primary cells. However, force dynamics and specifically the force loading rate (LR) have important implications in receptor signaling and adhesion formation and remain poorly characterized. Here, we develop an LR probe composed of an engineered DNA structure that undergoes two mechanical transitions at distinct force thresholds: a low force threshold at 4.7 pN (hairpin unfolding) and a high force threshold at 47 pN (duplex shearing). These transitions yield distinct fluorescence signatures observed through single-molecule fluorescence microscopy in live cells. Automated analysis of tens of thousands of events from eight cells showed that the bond lifetime of integrins that engage their ligands and transmit a force >4.7 pN decays exponentially with a τ of 45.6 s. A subset of these events mature in magnitude to >47 pN with a median loading rate of 1.1 pN s-1 and primarily localize at the periphery of the cell-substrate junction. The LR probe design is modular and can be adapted to measure force ramp rates for a broad range of mechanoreceptors and cell models, thus aiding in the study of molecular mechanotransduction in living systems.

Novel tools to study cell-ECM interactions, cell adhesion dynamics and migration

Integrin-mediated cell adhesion is essential for cell migration, mechanotransduction and tissue integrity. In vivo, these processes are regulated by complex physicochemical signals from the extracellular matrix (ECM). These nuanced cues, including molecular composition, rigidity and topology, call for sophisticated systems to faithfully explore cell behaviour. Here, we discuss recent methodological advances in cell-ECM adhesion research and compile a toolbox of techniques that we expect to shape this field in future. We outline methodological breakthroughs facilitating the transition from rigid 2D substrates to more complex and dynamic 3D systems, as well as advances in super-resolution imaging for an in-depth understanding of adhesion nanostructure. Selected methods are exemplified with relevant biological findings to underscore their applicability in cell adhesion research. We expect this new "toolbox" of methods will allow for a closer approximation of in vitro experimental setups to in vivo conditions, providing deeper insights into physiological and pathophysiological processes associated with cell-ECM adhesion.

Electrochemical DNA-based sensors for measuring cell-generated forces

Mechanical forces play an important role in cellular communication and signaling. We developed in this study novel electrochemical DNA-based force sensors for measuring cell-generated adhesion forces. Two types of DNA probes, i.e., tension gauge tether and DNA hairpin, were constructed on the surface of a smartphone-based electrochemical device to detect piconewton-scale cellular forces at tunable levels. Upon experiencing cellular tension, the unfolding of DNA probes induces the separation of redox reporters from the surface of the electrode, which results in detectable electrochemical signals. Using integrin-mediated cell adhesion as an example, our results indicated that these electrochemical sensors can be used for highly sensitive, robust, simple, and portable measurements of cell-generated forces.

A portable electrochemical DNA sensor for sensitive and tunable detection of piconewton-scale cellular forces

Cell-generated forces are a key player in cell biology, especially during cellular shape formation, migration, cancer development, and immune response. A new type of label-free smartphone-based electrochemical DNA sensor is developed here for cellular force measurement. When cells apply tension forces to the DNA sensors, the rapid rupture of DNA duplexes allows multiple redox reporters to reach the electrode and generate highly sensitive electrochemical signals. The sensitivity of these portable sensors can be further enhanced by incorporating a CRISPR-Cas12a system. Meanwhile, the threshold force values of these DNA-based sensors can be rationally tuned based on the force application geometries and also DNA intercalating agents. Overall, these highly sensitive, portable, cost-efficient, and easy-to-use electrochemical sensors can be powerful tools for detecting different cell-generated molecular forces.

Measuring integrin force loading rates using a two-step DNA tension sensor

Cells apply forces to extracellular matrix (ECM) ligands through transmembrane integrin receptors: an interaction which is intimately involved in cell motility, wound healing, cancer invasion and metastasis. These small (pN) forces exerted by cells have been studied by molecular tension fluorescence microscopy (MTFM), which utilizes a force-induced conformational change of a probe to detect mechanical events. MTFM has revealed the force magnitude for integrins receptors in a variety of cell models including primary cells. However, force dynamics and specifically the force loading rate (LR) have important implications in receptor signaling and adhesion formation and remain poorly characterized. Here, we develop a LR probe which is comprised of an engineered DNA structures that undergoes two mechanical transitions at distinct force thresholds: a low force threshold at 4.7 pN corresponding to hairpin unfolding and a high force threshold at 56 pN triggered through duplex shearing. These transitions yield distinct fluorescence signatures observed through single-molecule fluorescence microscopy in live-cells. Automated analysis of tens of thousands of events from 8 cells showed that the bond lifetime of integrins that engage their ligands and transmit a force >4.7 pN decays exponentially with a τ of 45.6 sec. A small subset of these events (<10%) mature in magnitude to >56pN with a median loading rate of 1.3 pNs-1 with these mechanical ramp events localizing at the periphery of the cell-substrate junction. Importantly, the LR probe design is modular and can be adapted to measure force ramp rates for a broad range of mechanoreceptors and cell models, thus aiding in the study of mechanotransduction.

A Nano-Electroporation-DNA Tensioner Platform Enhances Intracellular Delivery and Mechanical Analysis Toward Rapid Drug Assessment

In vitro, drug assessment holds tremendous potential to success in novel drug development and precision medicine. Traditional techniques for drug assessment, however, face remarkable challenges to achieve high speed, as limited by incubation-based drug delivery (>several hours) and cell viability measurements (>1 d), which significantly compromise the efficacy in clinical trials. In this work, a nano-electroporation-DNA tensioner platform is reported that shortens the time of drug delivery to less than 3 s, and that of cellular mechanical force analysis to 30 min. The platform adopts a nanochannel structure to localize a safe electric field for cell perforation, while enhancing delivery speed by 103 times for intracellular delivery, as compared to molecular diffusion in coculture methods. The platform is further equipped with a DNA tensioner to detect cellular mechanical force for quantifying cell viability after drug treatment. Systematic head-to-head comparison, by analyzing FDA (food and drug administration)-approved drugs (paclitaxel, doxorubicin), demonstrated the platform with high speed, efficiency, and safety, showing a simple yet powerful tool for clinical drug screening and development.