Structural Transformation of Wireframe DNA Origami <i>via</i> DNA Polymerase Assisted Gap-Filling

The
programmability of DNA enables constructing nanostructures
with almost any arbitrary shape, which can be decorated with many
functional materials. Moreover, dynamic structures can be realized
such as molecular motors and walkers. In this work, we have explored
the possibility to synthesize the complementary sequences to single-stranded
gap regions in the DNA origami scaffold cost effectively by a DNA
polymerase rather than by a DNA synthesizer. For this purpose, four
different wireframe DNA origami structures were designed to have single-stranded
gap regions. This reduced the number of staple strands needed to determine
the shape and size of the final structure after gap filling. For this,
several DNA polymerases and single-stranded binding (SSB) proteins
were tested, with T4 DNA polymerase being the best fit. The structures
could be folded in as little as 6 min, and the subsequent optimized
gap-filling reaction was completed in less than 3 min. The introduction
of flexible gap regions results in fully collapsed or partially bent
structures due to entropic spring effects. Finally, we demonstrated
structural transformations of such deformed wireframe DNA origami
structures with DNA polymerases including the expansion of collapsed
structures and the straightening of curved tubes. We anticipate that
this approach will become a powerful tool to build DNA wireframe structures
more material-efficiently, and to quickly prototype and test new wireframe
designs that can be expanded, rigidified, or mechanically switched.
Mechanical force generation and structural transitions will enable
applications in structural DNA nanotechnology, plasmonics, or single-molecule
biophysics.