Poster abstracts
Poster number 93 submitted by Ariel Robbins
Characterizing the force dependent properties of a DNA origami force probe
Ariel Robbins (Ohio State University Department of Physics - Biophysics Program), Peter Beshay (Ohio State University Department of Mechanical and Aerospace Engineering), Carlos E. Castro (Ohio State University Department of Mechanical and Aerospace Engineering), Michael G. Poirier (Ohio State University Department of Physics)
Abstract:
DNA origami nanotechnology is a rapidly developing field that shows promise in scientific applications such as mechanically aided drug delivery, molecular sensing, force sensing, and probing of single molecule dynamics. Complex and dynamic 3-dimensional structures can perform a prescribed function through controlled actuation making their use precise and reproducible. The device in our study, called a nanodyn, acts as a binary force sensor. Consisting of two origami bundles linked by six crossover strands, the device can exist in either an open or closed configuration. With careful design of the crossover strands, the nanodyn can be programed to open at a prescribed force. These nanoprobes can then be used in biological systems where traditional force spectroscopy techniques are more challenging to implement. For instance, shear forces due to fluid flow can be challenging to determine in non-idealized environments, such as in a blood vessel or extracellular matrix.
In order to achieve high resolution data, we have built a magnetic tweezer from an inverted microscope body, achieving a maximum resolution of 3-4 nm in the axial direction and a camera frame rate between 150-250 Hz. This is more than sufficient for measuring the nanodyn opening which has a gap size of around 20 nm and opening/closing rates on the order of seconds to minutes (Hudoba et. al)
Previous experiments by Hudoba et. al. focused on low force detection on the order of 100 fN using Forster Resonance Energy Transfer (FRET) fluctuations due to thermal forces exerted on a nanodyn with a 10 bp zipper. Our ongoing work will expand on these results to include force sensors calibrated to detect forces in the 0.1-20 pN range. We will utilize the axial resolution of our magnetic tweezer to detect the change in length of the nanodyn-tether complex due to the rupture of the embedded zipper. To accommodate zipper rupture over a range of forces, we can alter the length of the DNA zippers as well as the number and orientation in the structure. In combination with constrained and unconstrained loops, we can modify the 6 loops in the nanodyn to fluctuate under a prescribed force. After we have characterized the opening and closing dynamics in a range of devices exhibiting distinct behaviors, we can incorporate them into non-ideal systems for the purpose of force sensing.
References:
Hudoba, M. W., Luo, Y., Zacharias, A., Poirier, M. G. & Castro, C. E. Dynamic DNA Origami Device for Measuring Compressive Depletion Forces. ACS Nano 11, 6566–6573 (2017).
Keywords: DNA Origami, Force Spectroscopy