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Open Access Publications from the University of California

Molecular-scale Simulations of Dynamic DNA nanostructures

  • Author(s): Shi, Ze
  • Advisor(s): Arya, Gaurav
  • et al.

Structural DNA nanotechnology, the assembly of rigid 3D structures of complex yet precise geometries, has recently been used to design dynamic, mechanically-compliant nanostructures with tunable equilibrium conformations and conformational distributions. Introduction of additional stimuli-responsive behavior in such dynamic nanostructures should further widen the possible applications of DNA nanotechnology. The overarching goal of this dissertation is to explore the potential of coarse-grained molecular modeling and simulations as a design tool for predicting the mechanical properties, the free energy landscape, and stimuli-responsive responsive behavior of dynamic DNA nanostructures. In the first part of this dissertation, coarse-grained molecular dynamics simulations are used to provide insights into the conformational dynamics of a set of mechanically compliant DNA nanostructures, namely, DNA origami hinges. An approach is also proposed for rapidly predicting equilibrium hinge angles from individual force-deformation behaviors of their single- and double-stranded DNA components. In the second part, molecular basis for the mechanism of salt-actuation of such DNA hinges is provided by computing their free energy landscape with respect to the hinge angle using a novel methodology. A simple analytical statistical-mechanical model is also introduced to model the actuation response curves obtained experimentally. This work provides some of the first molecular-scale insights into the conformational dynamics and ion-activated actuation of mechanically compliant DNA nanostructures, which should help guide the design and optimization of new nanodevices.

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