Mechanics and Dynamic Behaviors of DNA Origami

Haorong Chen, Purdue University

Abstract

DNA origami represents a class of highly programmable macromolecules. Their moderate mechanical rigidity allows them to undergo conformational changes in response to external signals. Such capability is promising for sensing and actuating applications at the nanoscale. In this work, we present our progress in understanding the mechanical properties of DNA origami by probing their structural reconfiguration kinetics. By fitting the evolution of species population into a set of chemical reaction equations and relating the kinetic rates to the mechanical rigidity of the DNA origami design, we determined the rigidity of DNA crossovers, an essential structural motif in DNA origami, for the first time. The results enable us to build a complete mechanical model that characterizes the dynamic behavior of a DNA origami model system. By taking advantage of the intrinsic flexibility of DNA, we demonstrated several new structural reconfiguration schemes. Single-layered DNA origami tiles are shown to cyclize and open up with high yield in response to the addition of linker and releaser DNA. Progressive fine-tuning of DNA origami structures are demonstrated by modulating their internal stress with the binding of chemical adducts. By enrolling photo-responsive molecules whose DNA binding affinity is switchable, photo-control over DNA origami conformation can be achieved conveniently. Direct DNA photo-damage by short and medium-wavelength UV light is also shown to affect DNA origami conformation by relieving internal stresses. Finally, a "Lego" approach is developed. By choosing the correct linkers, preformed DNA origami building-blocks are demonstrated to assemble into different supra-structures. Reversible assembly and reconfiguration are then demonstrated with such supra-structures.

Degree

Ph.D.

Advisors

Choi, Purdue University.

Subject Area

Nanoscience|Nanotechnology

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