A cargo-sorting DNA robot.

Two critical challenges in the design and synthesis of molecular robots are modularity and algorithm simplicity. We demonstrate three modular building blocks for a DNA robot that performs cargo sorting at the molecular level. A simple algorithm encoding recognition between cargos and their destinations allows for a simple robot design: a single-stranded DNA with one leg and two foot domains for walking, and one arm and one hand domain for picking up and dropping off cargos. The robot explores a two-dimensional testing ground on the surface of DNA origami, picks up multiple cargos of two types that are initially at unordered locations, and delivers them to specified destinations until all molecules are sorted into two distinct piles. The robot is designed to perform a random walk without any energy supply. Exploiting this feature, a single robot can repeatedly sort multiple cargos. Localization on DNA origami allows for distinct cargo-sorting tasks to take place simultaneously in one test tube or for multiple robots to collectively perform the same task.

Compiler-aided systematic construction of large-scale DNA strand displacement circuits using unpurified components.

Biochemical circuits made of rationally designed DNA molecules are proofs of concept for embedding control within complex molecular environments. They hold promise for transforming the current technologies in chemistry, biology, medicine and material science by introducing programmable and responsive behaviour to diverse molecular systems. As the transformative power of a technology depends on its accessibility, two main challenges are an automated design process and simple experimental procedures. Here we demonstrate the use of circuit design software, combined with the use of unpurified strands and simplified experimental procedures, for creating a complex DNA strand displacement circuit that consists of 78 distinct species. We develop a systematic procedure for overcoming the challenges involved in using unpurified DNA strands. We also develop a model that takes synthesis errors into consideration and semi-quantitatively reproduces the experimental data. Our methods now enable even novice researchers to successfully design and construct complex DNA strand displacement circuits.

Nanoparticle-induced apoptosis propagates through hydrogen-peroxide-mediated bystander killing: insights from a human intestinal epithelium in vitro model.

The ability to assess the risks of human exposure to engineered nanomaterials requires fundamental understanding of the fate and potential cytotoxicity of nonbiodegradable nanoparticles, for instance, after oral uptake. In this study, we quantify the impact of nanoparticles with low chemical toxicity on the intestinal membrane in a human intestinal in vitro model. Differentiated human colorectal adenocarcinoma cells, Caco-2, were cultured on a permeable support where they form an epithelial monolayer separating an apical and basal compartment. This model system allows a systematic characterization of the effect of nanoparticles on the cell viability as a function of size, surface chemistry, concentration, and incubation time. We used polystyrene (PS) nanoparticles (20 and 40 nm diameter) with two different surface chemistries (carboxylic acid and amines). The experiments performed show a strong decrease in cell viability as a response to nanoparticle exposure. Incubation times of

Engineered SERS substrates with multiscale signal enhancement: nanoparticle cluster arrays.

Defined nanoparticle cluster arrays (NCAs) with total lateral dimensions of up to 25.4 microm x 25.4 microm have been fabricated on top of a 10 nm thin gold film using template-guided self-assembly. This approach provides precise control of the structural parameters in the arrays, allowing a systematic variation of the average number of nanoparticles in the clusters (n) and the edge-to-edge separation (Lambda) between 1 < n < 20 and 50 nm < or = Lambda < or = 1000 nm, respectively. Investigations of the Rayleigh scattering spectra and surface-enhanced Raman scattering (SERS) signal intensities as a function of n and Lambda reveal direct near-field coupling between the particles within individual clusters, whose strength increases with the cluster size (n) until it saturates at around n = 4. Our analysis shows that strong near-field interactions between individual clusters significantly affect the SERS signal enhancement for edge-to-edge separations Lambda < 200 nm. The observed dependencies of the Raman signals on n and Lambda indicate that NCAs support a multiscale signal enhancement which originates from simultaneous inter- and intracluster coupling and |E|-field enhancement. The NCAs provide strong and reproducible SERS signals not only from small molecules but also from whole bacterial cells, which enabled a rapid spectral discrimination between three tested bacteria species: Escherichia coli, Bacillus cereus, and Staphylococcus aureus.