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Research

Our research focuses on understanding the physical properties and mechanical design of biological systems ranging from the single molecule scale to the macroscopic scale (kind of... we study ants!).  At the molecular and cellular scale our group uses a combination of DNA nanotechnology, single molecule and single cell fluorescence imaging, force spectroscopy, and mechanical modeling to investigate a variety of physiological problems.  We utilize a recently developed nanotechnology called scaffolded DNA origami to design and fabricate devices and sensors that have similar dimensions to typical biomolecular machinery (~1-100nm). 

Areas of research interest:

DNA-based nanomachine and nanorobot design (collaboration with Dr. Haijun Su):  

Structural DNA nanotechnology is an emerging field with applications in areas including drug delivery, biosensing, material templating, and molecular computing. This field was established in the 1980s largely with the pioneering work of Nadrian Seeman. Since then, structural DNA nanotechnology, in particular the development of scaffolded DNA origamihas enabled the fabrication of nanometer scale objects with geometric complexity approaching that of natural biomolecules.  For recent reviews of structural DNA nanotechnology and applications click here or here. Dr. Castro worked in the lab of Prof. Hendrik Dietz at the Technische Universität München designing DNA nanostructures and establishing methods for DNA self-assembly.

Our lab in the MAE department at The Ohio State University is interested in developing novel approaches to design dynamic and controllable DNA nanostructures. We seek to apply engineering approaches used to make macroscopic machines to the world of DNA-based design. We are building modular mechanically functional components with constrained motion and controllable mechanical properties. The table below summarizes one of our approaches to build joints that can ultimately combined to make complex mechanisms and machines like the stewart platform shown.

Ongoing lab projects in this area:

 

Drug Delivery Devices:

We use DNA nanostructures to circumvent daunorubicin drug resistance at clinically relevant doses in a leukemia cell line model. The fabrication of a rod-like DNA origami drug carrier is reported that can be controllably loaded with daunorubicin. It is further directly verified that nanostructure-mediated daunorubicin delivery leads to increased drug entry and retention in cells relative to free daunorubicin at equal concentrations, which yields significantly enhanced drug efficacy. Our results indicate that DNA origami nanostructures can circumvent efflux-pump-mediated drug resistance in leukemia cells at clinically relevant drug concentrations and provide a robust DNA nanostructure design that could be implemented in a wide range of cellular applications due to its remarkably fast self-assembly (≈5 min) and excellent stability in cell culture conditions.

Force Spectroscopy:

Single molecule force spectroscopy has become a widely used approach to probe the mechanical properties, stability, and kinetics of single biomolecules and bimolecular interactions. The most widely used approaches for force spectroscopy are optical trapping, magnetic tweezers, and atomic force microscopy. For a nice review of these methods click here. Dr. Castro spent several years exploring the physical properties of biological cells and biopolymers using optical trapping combined with single molecule fluorescence techniques. The movie below depicts an optical trapping experiments on fluorescently labeled amyloid protein fibrils (the bead is ~1um diameter). Further details of this study can be found here.

Amyloid fiber force-extension experiment with optical trapping. The bead is ~1um in diameter.

These experiments are similar to macroscopic tensile tests used to measure the mechanical properties of materials. While these experiments can be very insightful into properties and behaviors of cells and molecules, the instrumentation required is generally expensive and cumbersome, and the experiments are generally low-throughput (one at a time). Our lab is currently interested in developing novel approaches to force spectroscopy using DNA nanotechnology that exploit tunable entropic forces of flexible polymers to apply forces to bimolecular interactions. Our main goal is to enable force spectroscopy measurements in single molecule fluorescence assays where data can be collected on ~100 devices simultaneously.

Ongoing lab projects in this area:

High-throughput fluorescence-based force spectroscopy with DNA nanotechnology. (coming soon)

 

Designing responsive nanodevices for biophysical measurements

A key goal of our lab is to develop measurement devices that can expand, complement or exploit existing biophysical tools to enable probing or manipulating molecular and cellular scale biophysical interactions, processes, or properties in real time. We exploit our ability to design DNA nanodevices with three key characteristics: 1) precise geometry, 2) tunable mechanical or dynamic properties, and 3) programmable and specific molecular interactions with target biomolecules. These three functional characteristics enable the design of nanomechanical DNA devices where dynamic behavior or deformation of the device provides a readout of physical interactions with the local environment or with specific target molecules. We are currently pursuing multiple projects in this direction.

DNA origami tools to study chromatin structure and dynamics (collaboration with Poirier Lab)

Engineering DNA nanodynamics for ultrasensitive detection of the local environment (collaboration with Poirier Lab)

Assembly and mechanics of DNA origami filaments

Reverse Engineering Ant Neck Joint Material and Structural Design: 

At the macroscale our group is also interested in reverse engineering the structural and material design of ants.  Ants are capable of very impressive mechanical functions. See for example the photo of an ant holding 100x its own weight hanging upside down from bare glass taken by Thomas Endlein at Cambridge University for a photo competition. This mechanical functionality is enabled by the material and structural design that integrated multiple hard and soft components into a functional mechanical system. A close look at ants reveals that amazing complexity as shown in the scanning electron microscopy images below.

Photo taken by Thomas Endlein at Cambridge University for a Photo competition (http://www.bbsrc.ac.uk/news/people-skills-training/2010/100219-pr-scient...). SEM image of an Allegheny Mound Ant.


We are using engineering approaches to try to understand how the complex material and structural design enables the amazing function of ants. For some examples see the videos below.

Ongoing lab projects in this area:

Reverse engineering the mechanical design of an ant neck joint

 

Nanoscale force measurement:

Nanoscale Molecular Force SensorThis project aims to develop a device to measure biomolecular forces at the single molecule scale.  Ultimately we will implement this force sensor to measure the physical forces applied by biological cells during physiological processes such as migration.  As part of this project, we are collaborating with Dr. Michael Poirer's lab in Physics, Dr. John Lannutti's lab in Materials Science and Engineering, Dr. Sooryakumar's lab in Physics, and Dr. Samir Ghadiali's lab in Biomedical Engineering.  Click on the project title for more info.

Research Team - Michael Hudoba (Ph.D. student, NBL), Paula Vivas Basto (Post-doc, Poirier Lab), Tyler Nelson (Ph.D. student, Lannutti Lab)

Support - NSF Nanoscale Science and Engineering Center (NSEC)

 

 

Co-stimulatory Growth Signaling in B Cell Malignancies:

(under construction)

Research Team - Chris Lucas (PhD, School of Biomedical Science, post-doc, NBL), Emily Briggs (M.S., NBL)

Support - Ohio State University Comprehensive Cancer Center (CCC) Leukemia SPORE Career Development Program