production-dynein-kinesin-motor-ensembles-on-dna-origami

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 ...

Smith College

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.

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

Cytoskeletal molecular motors provide exciting proof that nanoscale transporters can be highly efficient, moving for microns along filamentous tracks by hydrolyzing ATP to fuel nanometer-size steps. For nanotechnology, such conversion of chemical energy into productive work serves as an enticing platform for re-purposing and re-engineering. It also provides a roadmap for successful molecular mechanisms that can be mimicked to create de novo molecular motors for nanotechnology applications. Here we focus specifically on how the mechanisms of molecular motors are being re-engineered for greater control over their transport parameters. We then discuss mechanistic work to create fully synthetic motors de novo and conclude with future directions in creating novel motor systems.

Exploiting molecular motors as nanomachines: the mechanisms of de novo and re-engineered cytoskeletal motors.

The predictable chemistry of Watson-Crick base-pairing imparts a unique structural programmability to DNA, enabling the facile design of molecular reactions that perform computations. However, many of the current architectures limit devices to a single operational cycle. Herein, we introduce the design of the "regenerator", a device based on coupled enthalpic and entropic reactions that permits the regeneration of molecular circuit components.

A Molecular Circuit Regenerator to Implement Iterative Strand Displacement Operations.

Single-molecule-based super-resolution microscopy offers researchers a unique opportunity to quantify 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.

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

The use of super-resolution microscopy in recent years has revealed that proteins often form small assemblies inside cells and are organized in nanoclusters. However, determining the copy number of proteins within these nanoclusters constitutes a major challenge because of unknown labeling stoichiometries and complex fluorophore photophysics. We previously developed a DNA-origami-based calibration approach to extract protein copy number from super-resolution images. However, the applicability of this approach is limited by the fact that the calibration is dependent on the specific labeling and imaging conditions used in each experiment. Hence, the calibration must be repeated for each experimental condition, which is a formidable task. Here, using cells stably expressing dynein intermediate chain fused to green fluorescent protein (HeLa IC74 cells) as a reference sample, we demonstrate that the DNA-origami-based calibration data we previously generated can be extended to super-resolution images taken under different experimental conditions, enabling the quantification of any green-fluorescent-protein-fused protein of interest. To do so, we first quantified the copy number of dynein motors within nanoclusters in the cytosol and along the microtubules. Interestingly, this quantification showed that dynein motors form assemblies consisting of more than one motor, especially along microtubules. This quantification enabled us to use the HeLa IC74 cells as a reference sample to calibrate and quantify protein copy number independently of labeling and imaging conditions, dramatically improving the versatility and applicability of our approach.

Article	Year
Cargo rigidity affects the sensitivity of dynein ensembles to individual motor pausing. Cytoskeleton (Hoboken, N.J.)\| PubMed ID: 27718534	2016
Exploiting molecular motors as nanomachines: the mechanisms of de novo and re-engineered cytoskeletal motors. Current opinion in biotechnology\| PubMed ID: 28088100	2017
A Molecular Circuit Regenerator to Implement Iterative Strand Displacement Operations. Angewandte Chemie (International ed. in English)\| PubMed ID: 28322486	2017
A DNA origami platform for quantifying protein copy number in super-resolution. Nature methods\| PubMed ID: 28650478	2017
Quantifying Protein Copy Number in Super Resolution Using an Imaging-Invariant Calibration. Biophysical journal\| PubMed ID: 31103226	2019

Nathan D. Derr

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