Nanoengineering and Biodesign Laboratory: Research
Accordions
Scaffolded DNA origami has enabled the fabrication of nanoscale objects with unprecedented geometric complexity via programmed molecular self-assembly with DNA. For an overview of the scaffolded DNA origami approach see Dr. Castro's paper. While this approach has been used to develop nanostructures for drug delivery, biosensing, and material templating applications, research to date has largely focused on fabrication of static (no motion) structures. In collaboration with the lab of Dr. Haijun Su, our lab is combining DNA-based design with macroscopic engineering approaches to make DNA origami machines and mechanisms. Similar to macroscopic machines, systems with complex motion can be constructed by combining joints and links into precisely designed mechanisms. We are first developing individual joints with constrained degrees of freedom. We have currently built revolute joints (hinges) with a single angular degree of freedom and prismatic joints (linear joints) with a single translational degree of freedom.
Using the joint designs from above, we have developed prototype mechanisms combining multiple joints for more complex motion. We created a mechanism with four hinges and four links, called a Bennett Linkage, that moves through a well-defined 3D motion path between a closed bundle and open frame configuration. In the absence of actuation, the mechanism passively fluctuates along the constrained motion path due to thermal fluctuation. The videos below shows a series of transmission electron microscopy (TEM) snapshots of the joints and mechanisms in several configurations along the motion path illustrating the motion. We also created a crank slider mechanism coupling linear and rotational motion using hinges and linear joints. This mechanism moves freely in 2D and is demonstrated below.
We have further developed a method to actively control the motion of the mechanisms. Using single-stranded DNA overhangs (black) distributed across the mechanism, we add "closing" strands (green) to bind the overhangs and close the mechanism. We can open the mechanism again by adding "opening" strands (orange), which will remove the closing strands via strand displacement. Using a fluorescence quenching assay, we measured actuation times on ~minute timescales. Our work is establishing a foundation for the design of complex nanoscale machines with controllable motion that could be implemented for example in nanomanufacturing systems to assemble nanoscale objects.
Research Team: Alex Marras, Lifeng Zhou, collaboration with Dr. Haijun Su
For more info see:
Marras, A., Zhou, L., Su, H., and Castro, C.E. Programmable motion of DNA origami mechanisms in PNAS 2015 link. (pdf)
Castro, C.E., Su, H., Marras, A.E., Zhou, L., Johnson, J. "Mechanical Design of DNA nanostructures." Nanoscale 2015. link.
Marras, A.E., Zhou, L., Kolliopoulos, V., Su, H., Castro, C.E., "Directing folding pathways for multi-component DNA origami nanostructures with complex topology." New Journal of Physics. link.
Support - NSF Engineering and Systems Design (ESD) program
Also check out our related work on designing DNA origami compliant mechanisms (below).
Compliant DNA Origami Mechanisms (Collaboration with Dr. Haijun Su)
The concept of compliant mechanism design provides a promising strategy for the fabrication of machines at the nano and micro scale.In compliant mechanisms, specified motion is obtained by the strategic arrangment of components of varying stiffness. This allows motion without the need for very flexible joints. This approach has been established for a range of macroscopic systems. In collaboration with Dr. Haijun Su, our lab is pioneering the development of nanoscale compliant mechanisms. The ability to achieve controlled motion with the use of flexible components is particularly promising for nanomachines because of the potential to overcome Brownian motion (thermal fluctuations). Thermal fluctuations are the consistent random motions imparted by the energy of the surrounding solution. An example of thermal fluctuations is shown here for a DNA origami filament consisting of 6 bundled helices of DNA imaged in our lab by total internal reflection fluorescence microscopy. The filament is approximately 7 μm long. Overcoming this random motion is a critical challenge to enable nanomachines with controllable motion.
We are developing a novel approach to create nanoscale moving systems based on a compliant mechanism design approach. Compliant mechanisms require the ability to create components of varying stiffness. We have built DNA origami nanostructures that function as compliant joints with tunable stiffness. The structures are comprised of comprised of double-stranded DNA (dsDNA) and single-stranded DNA (ssDNA) elements. In the design, the two arms on either side are highly stiff and can be considered as essential rigid. The central portion consists of a layer of dsDNA helices and several ssDNA connections. The entropic tension in the ssDNA balances the bending energy in the dsDNA layer to create a compliant joint where the angle, , and the stiffness can be tuned by adjusting the length of the ssDNA connections. We introduced a ssDNA loop in the structure for straightforward changing of the structure properties. The scale bars in the images are 20 nm.
For more info see:
- Zhou, L., Marras, A.E., Su, H., Castro, C.E. DNA origami compliant nanostructures with tunable mechanical properties. ACS Nano, 2013.
- Zhou, L., Marras, A.E., Su, h., Castro, C.E. Direct Design of an Energy Landscape with Bistable DNA Origami Mechanisms. Nano Letters, 2015.
Compliant components like the one shown above will for the basis of our future efforts to make compliant machines such as the nanoscale manipulator shown here that functions similar to a macroscopic robot arm.
Research team: Lifeng Zhou, Alex Marras
This project is based on work that was supported by: NSF Engineering and Systems Design (ESD) program
Also check out our related work on designing DNA origami machines and mechanisms (above).
Many cancers show primary or acquired drug resistance due to the overexpression of efflux pumps. A novel mechanism to circumvent this is to integrate drugs, such as anthracycline antibiotics, with nanoparticle delivery vehicles that can bypass intrinsic tumor drug-resistance mechanisms. DNA nanoparticles serve as an efficient binding platform for intercalating drugs (e.g., anthracyclines doxorubicin and daunorubicin, which are widely used to treat acute leukemias) and enable precise structure design and chemical modifications, for example, for incorporating targeting capabilities. Here, DNA nanostructures are utilized 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.
See our work here:
The mechanical properties of biopolymers are often characterized in terms of a persistence length. The persistence length of a biopolymer describes the length over which it can appreciably bend due to thermal energy. A more practical way to think of this is to consider a polymer or filament whose fully extended length (contour length) is much larger than the persistence length. Since the polymer contains many persistence length units where it can undergo significant bending, it will coil up into a so-called 'random coil.' On the other hand, a polymer or filament whose contour length is much smaller than the persistence length will remain essentially straight, or in other words not deform, when subject to thermal energy. Take the examples of fluctuations shown here for a dna double-helix (persistence length of ~50nm and contour length of 15 um, this movie was taken from Cohen et al.), a DNA origami bundled filament consisting of 6 dsDNA helices (we have measured persistence lengths of ~1um and this filament has a contour length of ~ 10um), and an amyloid fiber (persistence length of ~5um and this example has a contour length of ~7um).
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Double-stranded DNA has a persistence length of ~50nm. DNA origami nanostructures generally incorporate many dsDNA helices and hence are much stiffer. 6 helix-bundles have been measured to exhibit persistence length of ~1-2 μm (Liedl et al., Kauert et al.), which agrees with our measurements. In general, most DNA origami nanostructures incorporate many (>6) helices. The mechanical properties of these stiffer nanostructures have not been characterized. Furthermore, it is currently not understood how to predict the mechanical behavior of DNA nanostructures based on cross-sectional geometry (i.e. number and arrangement of dsDNA helices). We are characterizing the mechanical properties of several DNA origami nanostrucures with varying cross-sections to understand how the mechanical properties scale with geometry. Typical dimensions of DNA origami nanostructures are generally 10-100nm. Even relatively flexible 6-helix bundle DNA origami nanostructures would appear to be nearly rigid at this lengthscale. Therefore to measure thermal deformations, we are fabricating DNA origami filaments through hierarchical self-assembly that are long enough to experience measureable thermal deformations. An example of a filament containing 18 bundles helices is shown in the TEM image below.
By measuring the conformation of many filaments using TEM imaging, we can creat conformational distributions that can be analyzed to determine the filament bending stiffness. The videos below show simulated conformational distributions for several different persistence length (Lp) filaments. All simulated filaments are 1μm long.
For more info see:
Support - Ohio State University Institute for Materials Research (IMR)
Laboratory
Our lab is located in the Mechanical and Aerospace Engineering Department in Scott Laboratory.
