Session: 15-01-01: ASME International Undergraduate Research and Design Exposition

Paper Number: 100634

100634 - Probing Macromolecular Complexes With a Reconfigurable Nanoscale Dna Force Spectrometer 

Single molecule force spectroscopy is a powerful approach to studying the structure of biological materials and their kinetic properties. Nevertheless, the probes limit integration into complex systems, and the cost and complexity of the equipment and assays limit broader use. DNA-based nanodevices are a promising alternative that allows for probing the force response of biomolecules such as nucleosomes. Here, we build on these prior works to develop a nanoscale DNA force spectrometer (nDFS). Specifically, the nDFS allows for enhanced control over forces and especially the application of compression forces. Moreover, the readout from electron microscopy can provide a unique chance to observe the detailed sample structure conformation under force instead of end-to-end distance at an ensemble level. We envision that nDFS can be a complementary solution for understanding the mechanical properties of macromolecular complexes in a range of 10-100 nm.

The hinge-like structure nDFS is fabricated by scaffold DNA origami, and it consists of two arms connected by several single-stranded DNA scaffold linkers. The device behaves like a torsional spring where the arms are stiff, and the mechanical properties are determined by the design of the hinge vertex. We demonstrated the ability to control both the equilibrium angle and stiffness by modifying the detailed vertex architecture, which provides a passive approach to modulating forces applied by the nDFS. We also developed an active approach to the nDFS open or closed by forming or disrupting a DNA duplex strut between the arms, controlled via strand displacement. We experimentally demonstrated these features by 1) applying compressive forces to a 249 bp double-stranded DNA (dsDNA) 2) and applying tensile forces to a mono-nucleosome or tetra-nucleosome array. Specifically, we designed and assembled a set of DNA origami nDFS by carefully selecting DNA strands on the hinge vertex. The structures were visualized by transmission electron microscopy. We applied Boltzmann statistics for solving the nDFS system energy and forces. As a result, we found nDFS can provide up to 5 pN tensile force and 3 pN compression force to test objects. For demonstrations, the experiment showed that nDFS can compress a 249 bp dsDNA in a highly bent state with 0.3 pN and nDFS can unwrap nucleosome 22 basepair or 40 basepair by different nDFS torsional stiffness setups. For future work, we seek to expand the applicability of nDFS to a broader experimental environment by enhancing the structural stability in physiological conditions and increasing the force measurement range.

Presenting Author: YUCHEN WANG Ohio State University

Presenting Author Biography: Yuchen Wang is a mechanical engineering Ph.D. candidate from Ohio State University. He is currently working with professor Carlos Castro in Nanoengineering and Biodesign Lab. He focuses on the development of dynamic structures based on scaffold DNA origami for probing and measuring biomolecules in the mesoscale. He is also interested in image processing with neural networks.

Authors:

YUCHEN WANG Ohio State University
Carlos Castro Ohio State University