Engineering DNA origami through microscopic simulations

The DNA origami method permits folding of long single-stranded DNA into complex three-dimensional structures with sub-nanometer precision. To ensure that such DNA origami objects behave exactly as designed, their structural, mechanical, and kinetic properties must be characterized at both macroscopic and microscopic scales. Transmission electron microscopy, atomic force microscopy and recently cryo-EM tomography have been used to characterize the properties of DNA origami objects, however their microscopic structures and dynamics have remained unknown. In this lecture, I will describe the results of all-atom molecular dynamics simulations that characterized the structural, mechanical and transport properties of DNA origami objects in unprecedented microscopic detail. Our work demonstrates the potential of all-atom molecular dynamics simulations to play a considerable role in future development of the DNA origami field by providing accurate, quantitative assessment of structural, mechanical and transport properties of DNA origami objects.

About Oleksii Aksimentiev

Oleksii Aksimentiev is an associate professor in physics at the University of Illinois at Urbana-Champaign. Dr. Aksimentiev has a background in soft matter physics and now deploys computational methods to investigate physical phenomena at the interface of solid-state nanodevices and biological macromolecules.

See website: http://bionano.physics.illinois.edu/