Design
Our design took inspiration from a child’s toy with which everyone is familiar—the Hoberman sphere. The Hoberman sphere has a unique property which matches perfectly to the needs of our aim and design goal.
This unique property of the Hoberman sphere is that it can switch between two states (Figure 0). The first state is an expanded form, or the opened state, in which the vertices in the structure are at their furthest apart. By contrast, in the closed state, the vertices are at their closest together. Due to this property, the Hoberman sphere will allow us to play with the distance between points as it changes between the two states. Therefore, this property can fulfill our goal since we would like to manipulate the distance between CpG motifs. In this scenario, we could envision that CpG motifs are at the vertex points of the Hoberman sphere.
Figure 0. The Hubble Bubble
The structure of our DNA origami only resembles one of the 2D units of the Hoberman sphere due to the complex 3D structure of the total Hoberman sphere being difficult to achieve by DNA origami. The 2D DNA origami unit we recreated was introduced by Li et al. (2021) as the flight ring (Figure 1). However, its basic foundation still maintains the same property as the real life Hoberman sphere in the sense of how it transitions between two states.
Figure 1: Illustration diagram of flight ring structure switching. Two layers of triangles pivot in opposite directions, causing the flight ring structure to switch between closed state (triangle) and opened state (hexagon).
Structure
For the simplicity of understanding, imagine the structure consists of two sets of three triangles on top of each other, creating two layers (Figure 1). When the two layers of triangles are perfectly aligned with each other, it forms a closed state, resulting in the overall shape of the DNA origami to be in a triangular shape. In this closed state, the mobile vertex points are close to one another. In order to reconfigure from a closed state to an opened state, the two layers of triangles pivot in opposite directions, causing the triangles to no longer perfectly align and make the overall shape expand to be hexagonal—the opened state. The opened state is when the mobile vertex points are furthest apart from one another.
Moving Mechanism
There are three units of two triangles sliding on top of each other in flight ring structure (Figure 2).The moving mechanism is two triangles within one unit that are sliding on top of each other in opposite directions. The crucial components to make two triangles slide in opposite directions are the DNA strands attached to the vertices between two triangles, called jacks (Figure 3). There are solid jacks and dashed jacks, with the difference between the two types being how they control the movement of the two triangles in opposite directions. Two units of the flight ring structure have two solid jacks in each unit to control the movement, whilst the remaining unit uses one dashed jack for its movement. When the solid jacks are shortened and the dashed jack is separated, they become shrunk solid jacks and disengaged dashed jack, respectively. The shrunken and disengaged states of the jacks result in the perfect alignment between two triangles, making the closed state (triangle) of the DNA origami. In contrast, when the solid jacks are lengthened and the dashed jack is connected, as extended solid jacks and engaged dashed jack respectively, the two triangles within each unit rotate in opposite directions to make the opened state (hexagon) of the DNA origami.
Figure 2: Illustration diagram of triangle unit. Triangles highlighted by the saturated colouring represent one unit in flight ring structure in both closed state (triangle) and open state (hexagon).
Figure 3: Illustration diagram showing the distribution and attachment of jacks in the origami structure, in both the closed state (triangle) and the opened state (hexagon). The solid line represents the solid jacks and the dashed line represents the dashed jack. In the closed state, the dashed jack separates, which results in the disengaged dashed jack, and the solid jacks are shortened, which results in shrunk solid jacks. In the open state, the dashed jack connects, which results in the engaged dashed jack, and the solid jacks are lengthened which results in extended solid jacks.
The transition between states for the jacks is feasible by strand displacement. The states of the solid jacks and the dashed jack which correspond to the opened state of the flight ring structure—the extended solid jacks and the engaged dashed jack—are controlled by one set of short ssDNA sequences (staples). By contrast, the states of the jacks which correspond to the closed state of the flight ring—the shrunk solid jack and the disengaged dashed jack—are controlled by a second set of staples (Figure 4). Only one of these two sets of staples are present at a time, and to transition between the closed state and the opened state, the currently present staples need to be removed from the DNA origami, which is done by a set of complementary staples, denoted as releaser strands. The staples which anneal the scaffold to form the jacks have a higher affinity for annealing these releaser strands, which is what drives them to be displaced from the DNA origami structure. Once the staples controlling the jacks have been displaced, the flight ring structure is left in an undefined state—which is loosely held together without defined vertex locations—and can be made to form either closed state or opened state with the addition of the appropriate set of staples (Figure 4).
Figure 4: Summary of how the structure transitions from closed state to undefined state to open state and vice versa by the changes on the solid jack and dashed jack. (scaffold in red)
Images adapted fromby Li et al. (2021)
Visualization of the origami structure on caDNAano and oxView/oxDNA
Figure 5: caDNAno schematic of the DNA origami structure in the opened state (hexagon). The long blue line is the scaffold which forms the shape by the binding of the staples. The staples are represented as the short lines forming rectangular boxes over the scaffold. Green rectangles are staples to form the lengthened solid jacks and engaged dashed jacks. The other coloured rectangles are coded in pairs (yellow, pink, orange and red) for the staples which would be the target location for the CpG motif attachment.
Figure 6: oxView of the origami flight ring structure in the opened state (hexagon). The green DNA strands are the jacks. The small section of the DNA strand at each end of the jacks, which are color coded in pairs (yellow, pink, orange and red), denote the staples which would be the target location for the CpG motif attachment.
Figure 7: oxDNA of the flight ring structure in open state (hexagon) illustrates the stability and dynamics of the structure over time.
Figure 8: oxDNA of the flight ring structure in closed state (triangle) illustrates the stability and dynamics of the structure over time.
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