  DNA origami is a widely used method to construct nanostructures by
self-assembling designed DNA strands. These structures are often used as
"breadboards" for templated assembly of proteins, gold nanoparticles, aptamers,
and other molecules, with applications ranging from therapeutics and
diagnostics to plasmonics and photonics. Imaging these structures using AFM or
TEM is not capable to capture their full conformation ensemble as they only
show their structure flattened on a surface. However, certain conformations of
the nanostructure can position guest molecules into distances unaccounted for
in their intended design, thus leading to spurious interactions between guest
molecules that are designed to be separated. Here, we use molecular dynamics
simulations to capture conformational ensemble of 2D DNA origami tiles and show
that introducing single-stranded overhangs, which are typically used for
functionalization of the origami with guest molecules, induces a curvature of
the tile structure in the bulk. We show that the shape deformation is of
entropic origin, with implications for design of robust DNA origami breadboards
as well as potential approach to modulate structure shape by introducing
overhangs. We then verify experimentally that the overhangs introduce curvature
into the DNA origami tiles.
