Understanding the Mechanical Properties of DNA Origami Tiles and Controlling the Kinetics of Their Folding and Unfolding Reconfiguration

Abstract

DNA origami represents a class of highly programmable macromolecules that can go through conformational changes in response to external signals. Here we show that a two-dimensional origami rectangle can be effectively folded into a short, cylindrical tube by connecting the two opposite edges through the hybridization of linker strands and that this process can be efficiently reversed via toehold-mediated strand displacement. The reconfiguration kinetics was experimentally studied as a function of incubation temperature, initial origami concentration, missing staples, and origami geometry. A kinetic model was developed by introducing the j factor to describe the reaction rates in the cyclization process. We found that the cyclization efficiency (j factor) increases sharply with temperature and depends strongly on the structural flexibility and geometry. A simple mechanical model was used to correlate the observed cyclization efficiency with origami structure details. The mechanical analysis suggests two sources of the energy barrier for DNA origami folding: overcoming global twisting and bending the structure into a circular conformation. It also provides the first semiquantitative estimation of the rigidity of DNA interhelix crossovers, an essential element in structural DNA nanotechnology. This work demonstrates efficient DNA origami reconfiguration, advances our understanding of the dynamics and mechanical properties of self-assembled DNA structures, and should be valuable to the field of DNA nanotechnology.

Rhombic‐Shaped Nanostructures and Mechanical Properties of 2D DNA Origami Constructed with Different Crossover/Nick Designs

“…Thus, the bending rigidity of a crossover B c = 74 pN∙nm 2 was estimated from Equation , using the measured pitches of the rhombic mesh structure fabricated according to the 3‐turn crossover design. The estimated bending rigidity of crossovers is about one‐third of that of the dsDNA ( B = 230 pN∙nm 2 ), which is realistic compared with estimates based on highly rigid or flexible crossover models …”

A Reconfigurable DNA Accordion Rack

“…The self‐assembly‐based synthesis allows the generation of multiple configurations by adding the DNA lock sets with different lengths, either before or after the synthesis of the free‐state structure. Furthermore, by utilizing the strand displacement process, multistep shape reconfigurations can be accomplished by repeating the locking process after detaching the prior DNA locks.…”

Auxetic Two-Dimensional Nanostructures from DNA

“…Despite the structural simplicity, it is still difficult to apply mechanical loads accurately onto nanostructures. 25 Hence, we used chemical loads instead to modulate the jack length through toehold-mediated strand displacement, [26][27][28] thereby resulting in reconfiguration, either expansion or shrinkage. For example, the re-entrant triangle can switch between 30° and 58° as shown in Figure 2b, by modulating the jack length of approximately 45 or 59 nm (6 or 8 full turns), respectively.…”