Kinetics and Thermodynamics of Watson–Crick Base Pairing Driven DNA Origami Dimerization

We investigate the kinetics and thermodynamics
of DNA origami dimerization
using flat rectangle origami components and different architectures
of Watson–Crick complementary single-stranded DNA (“sticky
end”) linking strategies. We systematically vary the number
of linkers, the length of the sticky ends on the linker, and linker
architecture and measure the corresponding yields as well as forward
and reverse reaction rate constants through fluorescence quenching
assays. Yields were further verified using atomic force microscopy.
We calculate values of H° and ΔS° for various interface designs and find nonlinear
van’t Hoff behavior, best described by two linear equations,
suggesting distinct regimes of dimerization between those with and
those without well-formed interfaces. We find that self-assembly reactions
can be tuned by manipulating the interface architecture without suffering
a loss in yield, even when yield is high, ∼75–80%. We
show that the second-order forward reaction rate constant (kon) depends on both linker architecture and
number of linkers used, with typical values on the order of 105–106 (M·s)−1, values
that are similar to those of bimolecular association of small, complementary
DNA strands. The kon values are generally
non-Arrhenius, tending to increase with decreasing temperature. Finally,
we use kinetic and thermodynamic information about the optimal linking
architecture to extend the system to an infinite, two-component repeating
lattice system and show that we can form micron-sized lattices, with
well-formed structures up to 8 μm2.