A switchable DNA origami/plasmonic hybrid device with a precisely tuneable DNA-free interparticle gap.

We here show a reconfigurable DNA/plasmonic nanodevice with a precisely tunable and DNA-free interparticle gap. The nanodevice comprises two DNA boxes for the size-selective incorporation of nanoparticles in a face-to-face orientation and an underlying switchable DNA platform for the controlled and reversible adjustment of the interparticle distance.

The role of DNA nanostructures in the catalytic properties of an allosterically regulated protease.

DNA-scaffolded enzymes typically show altered kinetic properties; however, the mechanism behind this phenomenon is still poorly understood. We address this question using thrombin, a model of allosterically regulated serine proteases, encaged into DNA origami cavities with distinct structural and electrostatic features. We compare the hydrolysis of substrates that differ only in their net charge due to a terminal residue far from the cleavage site and presumably involved in the allosteric activation of thrombin. Our data show that the reaction rate is affected by DNA/substrate electrostatic interactions, proportionally to the degree of DNA/enzyme tethering. For substrates of opposite net charge, this leads to an inversion of the catalytic response of the DNA-scaffolded thrombin when compared to its freely diffusing counterpart. Hence, by altering the electrostatic environment nearby the encaged enzyme, DNA nanostructures interfere with charge-dependent mechanisms of enzyme-substrate recognition and may offer an alternative tool to regulate allosteric processes through spatial confinement.

Site-specific facet protection of gold nanoparticles inside a 3D DNA origami box: a tool for molecular plasmonics.

Bare gold nanocubes and nanospheres with different sizes are incorporated into a rationally designed 3D DNA origami box. The encaged particles expose a gold surface accessible for subsequent site-specific functionalization, for example, for applications in molecular plasmonics such as SERS or SEF.

Sites of high local frustration in DNA origami.

The self-assembly of a DNA origami structure, although mostly feasible, represents indeed a rather complex folding problem. Entropy-driven folding and nucleation seeds formation may provide possible solutions; however, until now, a unified view of the energetic factors in play is missing. Here, by analyzing the self-assembly of origami domains with identical structure but different nucleobase composition, in function of variable design and experimental parameters, we identify the role played by sequence-dependent forces at the edges of the structure, where topological constraint is higher. Our data show that the degree of mechanical stress experienced by these regions during initial folding reshapes the energy landscape profile, defining the ratio between two possible global conformations. We thus propose a dynamic model of DNA origami assembly that relies on the capability of the system to escape high structural frustration at nucleation sites, eventually resulting in the emergence of a more favorable but previously hidden state.