Quantitative Super-Resolution Microscopy to Assess Adhesion of Neuronal Cells on Single-Layer Graphene Substrates

Single Layer Graphene (SLG) has emerged as a critically important nanomaterial due to its unique optical and electrical properties and has become a potential candidate for biomedical applications, biosensors, and tissue engineering. Due to its intrinsic 2D nature, SLG is an ideal surface for the development of large-area biosensors and, due to its biocompatibility, can be easily exploited as a substrate for cell growth. The cellular response to SLG has been addressed in different studies with high cellular affinity for graphene often detected. Still, little is known about the molecular mechanism that drives/regulates the cellular adhesion and migration on SLG and SLG-coated interfaces with respect to other substrates. Within this scenario, we used quantitative super-resolution microscopy based on single-molecule localization to study the molecular distribution of adhesion proteins at the nanoscale level in cells growing on SLG and glass. In order to reveal the molecular mechanisms underlying the higher affinity of biological samples on SLG, we exploited stochastic optical reconstruction microscopy (STORM) imaging and cluster analysis, quantifying the super-resolution localization of the adhesion protein vinculin in neurons and clearly highlighting substrate-related correlations. Additionally, a comparison with an epithelial cell line (Chinese Hamster Ovary) revealed a cell dependent mechanism of interaction with SLG.

Production of Dynein and Kinesin Motor Ensembles on DNA Origami Nanostructures for Single Molecule Observation

Cytoskeletal motors are responsible for a wide variety of functions in eukaryotic cells, including mitosis, cargo transport, cellular motility, and others. Many of these functions require motors to operate in ensembles. Despite a wealth of knowledge about the mechanisms of individual cytoskeletal motors, comparatively less is known about the mechanisms and emergent behaviors of motor ensembles, examples of which include changes to ensemble processivity and velocity with changing motor number, location, and configuration. Structural DNA nanotechnology, and the specific technique of DNA origami, enables the molecular construction of well-defined architectures of motor ensembles. The shape of cargo structures as well as the type, number and placement of motors on the structure can all be controlled. Here, we provide detailed protocols for producing these ensembles and observing them using total internal reflection fluorescence microscopy. Although these techniques have been specifically applied for cytoskeletal motors, the methods are generalizable to other proteins that assemble in complexes to accomplish their tasks. Overall, the DNA origami method for creating well-defined ensembles of motor proteins provides a powerful tool for dissecting the mechanisms that lead to emergent motile behavior.

A DNA origami platform for quantifying protein copy number in super-resolution

Single-molecule-based super-resolution microscopy offers a unique opportunity for quantifying protein copy-number with nanoscale resolution. However, while fluorescent proteins have been characterized for quantitative imaging using calibration standards, similar calibration tools for immunofluorescence with small organic fluorophores are lacking. Here, we show that DNA origami in combination with GFP antibodies is a versatile platform for calibrating fluorophore and antibody labeling efficiency to quantify protein copy-number in cellular contexts using super-resolution microscopy.

Cargo rigidity affects the sensitivity of dynein ensembles to individual motor pausing

Cytoplasmic dynein is a minus-end directed microtubule-based motor protein that drives intracellular cargo transport in eukaryotic cells. Although many intracellular cargos are propelled by small groups of dynein motors, the biophysical mechanisms governing ensemble motility remain largely unknown. To investigate the emergent motility of motor ensembles, we have designed a programmable DNA origami synthetic cargo "chassis" enabling us to control the number of dynein motors in the ensemble and vary the rigidity of the cargo chassis itself. Using total internal reflection fluorescence microscopy, we have observed dynein ensembles transporting these cargo chassis along microtubules in vitro. We find that ensemble motility depends on cargo rigidity: as the number of motors increases, ensembles transporting flexible cargos move comparatively faster than a single motor, whereas ensembles transporting rigid cargos move slower than a single motor. To explain this, we show that ensembles connected through flexible cargos are less sensitive to the pauses of individual motors within the ensemble. We conclude that cargo rigidity plays an important role in communicating and coordinating the states of motors, and consequently in the subsequent mechanisms of collective motility. The insensitivity of ensemble-driven cargos to the pausing of individual motors may contribute to the robustness and versatility of intracellular cargo transport. © 2016 Wiley Periodicals, Inc.

Engineered, harnessed, and hijacked: synthetic uses for cytoskeletal systems

Synthetic biology re-imagines existing biological systems by designing and constructing new biological parts, devices, and systems. In the arena of cytoskeleton-based transport, synthetic approaches are currently used in two broad ways. First, molecular motors are harnessed for non-physiological functions in cells. Second, transport systems are engineered in vitro to determine the biophysical rules that govern motility. These rules are then applied to synthetic nanotechnological systems. We review recent advances in both of these areas and conclude by discussing future directions in engineering the cytoskeleton and its motors for transport.

Dynein achieves processive motion using both stochastic and coordinated stepping

Processivity, the ability of single molecules to move continuously along a track, is a fundamental requirement of cargo-transporting molecular motors. Here, we investigate how cytoplasmic dynein, a homodimeric, microtubule-based motor, achieves processive motion. To do this, we developed a versatile method for assembling Saccharomyces cerevisiae dynein heterodimers, using complementary DNA oligonucleotides covalently linked to dynein monomers labeled with different organic fluorophores. Using two-color, single-molecule microscopy and high-precision, two-dimensional tracking, we find that dynein has a highly variable stepping pattern that is distinct from all other processive cytoskeletal motors, which use 'hand-over-hand' mechanisms. Uniquely, dynein stepping is stochastic when its two motor domains are close together. However, coordination emerges as the distance between motor domains increases, implying that a tension-based mechanism governs these steps. This plasticity may allow tuning of dynein for its diverse cellular functions.

Imaging single molecules using total internal reflection fluorescence microscopy (TIRFM)

Total internal reflection fluorescence microscopy (TIRFM) allows fluorescent molecules to be visualized with an unparalleled signal-to-noise ratio. This is achieved by illuminating only the molecules that are within a thin volume near the coverslip surface but not those that are deeper in solution. Using this technique, fluorescent molecules within approximately 100 nm of the coverslip can be visualized, and single molecules that are separated by a distance greater than the diffraction limit (approximately 200 nm) can be individually resolved. The application of centroid-tracking methods allows subdiffraction-limited localization precision as low as 1 nm. Additionally, by combining centroid-tracking methods with recent advances in fluorophore technology and imaging methods, even those molecules that are present at high concentrations and closer to one another than the diffraction limit can be individually imaged. TIRF is ideally suited for studying protein dynamics on or near the plasma membrane. Although TIRFM was pioneered in the 1980s, it was not until the mid-1990s that single biological molecules were imaged directly. The explosion of new fluorescent proteins, new organic dyes, and quantum dots (Qdots), along with commercially available TIRFMs, has made this technique increasingly useful and accessible to biologists. In this review, we first describe the theory of TIRFM. We then give a detailed description of important considerations for setting up a TIRFM, based on commercially available systems, and review considerations for purification and labeling of proteins. Finally, we discuss new techniques that allow single molecules to be imaged at cellular concentrations and with super-resolution localization.

Determining single-molecule intensity as a function of power density

When performing analysis using total internal reflection fluorescence microscopy (TIRFM), fluorescence intensity depends linearly on excitation intensity, until the dye spends most of its time in the excited state (i.e., saturation is reached). How much light is seen by the dyes in the sample depends not only on the amount of light exiting the objective but also on the area over which it is spread out. The parameter of interest is the power density, measured in W/cm(2). The highest signal-to-noise ratios will be reached when the illumination power just approaches saturation. To determine at what power density a dye is saturated, one should measure fluorescence intensity as a function of power density, as described in this protocol.

Imaging single molecular motor motility with total internal reflection fluorescence microscopy (TIRFM)

Total internal reflection fluorescence microscopy (TIRFM) allows fluorescent molecules on or near the plasma membrane to be visualized with a very high signal-to-noise ratio. This strategy has been very successful for imaging molecular machines as they move and do work. We provide here a general protocol for imaging single molecular motors as they move along microtubule tracks. Our protocol is designed for the study of cytoplasmic dynein purified from Saccharomyces cerevisiae, but it represents a general framework for any in vitro single-molecule assay.