Design Features to Accelerate the Higher-Order Assembly of DNA Origami on Membranes

Nanotechnology often
exploits DNA origami nanostructures assembled
into even larger superstructures up to micrometer sizes with nanometer
shape precision. However, large-scale assembly of such structures
is very time-consuming. Here, we investigated the efficiency of superstructure
assembly on surfaces using indirect cross-linking through low-complexity
connector strands binding staple strand extensions, instead of connector
strands binding to scaffold loops. Using single-molecule imaging techniques,
including fluorescence microscopy and atomic force microscopy, we
show that low sequence complexity connector strands allow formation
of DNA origami superstructures on lipid membranes, with an order-of-magnitude
enhancement in the assembly speed of superstructures. A number of
effects, including suppression of DNA hairpin formation, high local
effective binding site concentration, and multivalency are proposed
to contribute to the acceleration. Thus, the use of low-complexity
sequences for DNA origami higher-order assembly offers a very simple
but efficient way of improving throughput in DNA origami design.