Figure 1
From: Programmable DNA Nanosystem for Molecular Interrogation
OPTIMuS operational principles.
(a) A schematic illustrating the key mechanical components of OPTIMuS. A movable ring surrounds a cylindrical core that is anchored at both ends by “dumbbell” shaped frame elements. The ring is pushed and/or pulled away from frameR by user-controlled ssDNA to dsDNA transitions, whereas “resistance” at the interface can obstruct ring movement. (b) A three-dimensional rendering of OPTIMuS showing the 24 helix bundle in the honeycomb lattice arrangement (Supplementary Figs 2 and 4). (c) A cross-sectional view of the ring/frameR interface shows active sites, loops and the FRET reporter pair. (d) The idealized overall reconfiguration that can be elicited in OPTIMuS. On the left is the ground state (G) that has all force domains in single-stranded form (EC, Ch, L). Upon adding staples corresponding to them (ECS, ChS, LS) the nanosystem reconfigures with a displaced ring position. Hybridization on the left-side (at EC and Ch) and the right-side (L) of the ring is reported by via FRET. (e) Depiction of the mechanism of force-induced motion by an ssDNA to dsDNA transition. The three force domains, EC, Ch and L are based upon the following scenarios. In scenario 1, hybridization of randomly coiled ssDNA creates a pushing force that increases the separation between attached substrates. In Scenario 2, pulling forces are created when a stretched ssDNA collapses into a short double helix upon hybridization, thereby bringing the substrates closer together. In scenario 3, which occurs when EC is formed before or simultaneously with Ch duplexes, the mechanically stretched ssDNA cannot form a duplex with its complement despite the favorable ΔG for the same molecules when stereochemically unconstrained. (f) A schematic of the blunt end and non-blunt end interactions between the coaxial helices of ring and frameR. Non-blunt ends are created by leaving eight scaffold bases at the crossover unhybridized. The resultant single-stranded region prevents base stacking and minimizes adhesive interaction between the duplexes. (g) Illustration of a toehold-mediated DNA strand displacement reaction.
