Verification of Overall Mechanisms in Solution
See also: SPEX Results
Several strands were labeled with fluorophores and quenchers to study there interactions in solution.
Walkers were tagged with quenchers while goals for walkers were tagged with fluorophores. The expected reaction is shown below.
Cargo strands were tagged with fluorophores and goals for cargo were tagged with quenchers. The expected reaction is shown below.
Verification of Random Walking Mechanism on Origami
Fluorescent spectroscopy (SPEX) was used to verify random walk on the origami. We designed a strand named walker goal (WG) which can bind to walkers irreversibly due to its perfect complementarity with walkers. A ROX fluorophore was attached to the 5' end of the probe for the walker goal (PWG) and the corresponding quencher was attached to the 3' end of the walker (Figure 1). When the walker binds to the walker goal, its quencher is directly above the fluorophore of the walker goal, hence quenching it. Thus we can setup experiments where the fluorescent level slowly decreases as more and more walkers reach the walker goal. The overall origami layout was shown in Figure 2.
Three different starting positions were chosen, shown in the figures below. Since it is possible for the walkers to undergo space walking (SW), namely dissociating from the origami, binding to free floating tracks in the solution and rebinding to origami, we added a control group in which only one track at the starting position 10 was planted on the origami. Excess of walker triggers were added in the beginning of the experiment to activate the walkers and excess of walkers with quenchers attached were added in the end to stop the reactions.SEPX Results show that fluorescent signals decreased faster when the walkers were planted nearer to goals.
Light-blue dots: marker to distinguish the orientation of the origami for AFM images
Dark Blue dots: track 1
Red dots: track 2
Yellow star: walker goal
Green dot: biotinylated control staple used for AFM imaging (that staple is not biotinylated in SPEX experiments)