Directed Assembly of DNA Origami Mechanisms

This project focuses on manipulating the self-assembly folding process to enable complex DNA origami topologies. Using the DNA origami slider, we explore design strategies to control the order of assembling components and the assembly topology.

The figure above illustrates the assembly landscape for a multi-component DNA origami slider. The raw materials including the scaffold and the staples for each component are single-stranded at high temperatures (left). The initial folding trajectory (initiating folding with the track or the tube) during annealing is determined by the thermodynamics of staple binding, which can be controlled by the staple design. Due to the cooperativity of DNA origami assembly, folding of one component proceeds to completion prior to folding the second component. We force the track to fold first by increasing the local binding energy of its staples. Once the first component is folded, the second component then folds so the structure assembles either in the concentric or non-concentric state. We hypothesize that the complex topology of the concentric state can be achieved by folding the track component first, and exploiting the intermediate state to pre-arrange the tube scaffold around the track in the intermediate state. Once the slider is assembled the energy barrier to excessively extend the slider prevents switching between the concentric and non-concentric states.

Modifying the staple design of a DNA origami component (in this case the black track component) to promote long binding domains will increase the annealing temperature of these sections. In a standard annealing ramp, these staple sections will now bind first and due to the cooperative nature of DNA origami folding, this component will start to fold. These design modifications enable a directed sequence of assembly when folding multi-component DNA origami structures. We successfully used this strategy for concentric organization of the slider and demonstrated that a standard annealing ramp or a design where the tube (white) formed first resulted in nonconcentric topologies.

Thermodynamic approach to directing folding pathways. By modifying staple routing in multi-component DNA origami nanostructures we can control the sequence of component self-assembly. We demonstrate this idea using a DNA origami slider, which requires folding of the track (black) before the tube (grey) for proper assembly. (a) By removing selected staple crossovers we can control the binding energy of staples, programming track staples to bind before tube staples, therefore folding components in the desired sequence during a standard thermal annealing ramp. (b) A slider where the track forms first (figure S7) shows a lower theoretical binding energy for the track staples and a partial folding ramp reveals the track forming first. (c) The case with unmodified staples (figure S10) shows a similar binding energy for both components and results in misassembled (non-concentric) components. (d) Similarly, the case where the tube folds first (figure S11) also produces misassembled sliders. Scale bars = 50 nm.

More information about this work is available below:

Marras, A.E., Zhou, L., Kolliopoulos, V., Su, H.J., Castro, C.E. “Directing folding pathways for multi-component DNA origami nanostructures with complex topology.” New Journal of Physics. 18:055005 (2016) — link — pdf