RNA–DNA Hybrid Nanoshape Synthesis by Facile Module Exchange

The preparation of nucleic acid nanostructures has relied predominantly on procedures of additive fabrication in which complex architectures are assembled by concerted self-assembly and sequential addition of building blocks. We had previously established RNA–DNA hybrid nanoshapes with modular architectures that enable multistep synthetic approaches inspired by organic molecular synthesis where additive and transformative steps are used to prepare complex molecular architectures. We report the establishment of module replacement and strand exchange as synthetic transformations in nucleic acid hybrid nanoshapes, which are enabled by minimally destabilizing sequence elements such as a single unpaired overhang nucleotide or a mismatch base pair. Module exchange facilitated by thermodynamic lability triggers adds a powerful transformative approach to the repertoire of additive and transformative synthetic methods for the preparation of complex composite materials

Ligand Optimization by Improving Shape Complementarity at a Hepatitis C Virus RNA Target

Crystal structure analysis revealed key interactions of a 2-amino-benzimidazole viral translation inhibitor that captures an elongated conformation of an RNA switch target in the internal ribosome entry site (IRES) of hepatitis C virus (HCV). Here, we have designed and synthesized quinazoline derivatives with improved shape complementarity at the ligand binding site of the viral RNA target. A spiro-cyclopropyl modification aimed at filling a pocket in the back of the RNA binding site led to a 5-fold increase of ligand affinity while a slightly more voluminous dimethyl substitution at the same position did not improve binding. We demonstrate that precise shape complementarity based solely on hydrophobic interactions contributes significantly to ligand binding even at a hydrophilic RNA target site such as the HCV IRES conformational switch

Conformational Constraint as a Means for Understanding RNA-Aminoglycoside Specificity

The lack of high RNA target selectivity displayed by aminoglycoside antibiotics results from both their electrostatically driven binding mode and their conformational adaptability. The inherent flexibility around their glycosidic bonds allows them to easily assume a variety of conformations, permitting them to structurally adapt to diverse RNA targets. This structural promiscuity results in the formation of aminoglycoside complexes with diverse RNA targets in which the antibiotics assume distinct conformations. Such differences suggest that covalently linking individual rings in an aminoglycoside could reduce its available conformations, thereby altering target selectivity. To explore this possibility, conformationally constrained neomycin and paromomycin analogues designed to mimic the A-site bound aminoglycoside structure have been synthesized and their affinities to the TAR and A-site, two therapeutically relevant RNA targets, have been evaluated. As per design, this constraint has minimal deleterious effect on binding to the A-site. Surprisingly, however, preorganizing these neomycin-class antibiotics into a TAR-disfavored structure has no deleterious effect on binding to this HIV-1 RNA sequence. We rationalize these observations by suggesting that the A-site and HIV TAR possess inherently different selectivities toward aminoglycosides. The inherent plasticity of the TAR RNA, coupled to the remaining flexibility within the conformationally constrained analogues, makes this RNA site an accommodating target for such polycationic ligands. In contrast, the deeply encapsulating A-site is a more discriminating RNA target. These observations suggest that future design of novel target selective RNA-based therapeutics will have to consider the inherent “structural” selectivity of the RNA target and not only the selectivity patterns displayed by the low molecular weight ligands

Mediated attention with multimodal augmented reality

We present an Augmented Reality (AR) system to supportcollaborative tasks in a shared real-world interaction spaceby facilitating joint attention. The users are assisted by information about their interaction partner's field of view both visually and acoustically. In our study, the audiovisual improvements are compared with an AR system without these support mechanisms in terms of the participants' reaction times and error rates. The participants performed a simple object-choice task we call the gaze game to ensure controlled experimental conditions. Additionally, we asked the subjects to fill in a questionnaire to gain subjective feedback from them. We were able to show an improvement for both dependent variables as well as positive feedback for the visual augmentation in the questionnaire.</p

Enhancing human cooperation with multimodal augmented reality

Humans naturally use an impressive variety of ways to com-municate. In this work, we investigate the possibilities of complementing these natural communication channels with articial ones. For this, augmented reality is used as a technique to add synthetic visual and auditory stimuli to people's perception. A system for the mutual displayof the gaze direction of two interactants is presented and its acceptance is shown through a study. Finally, future possibilities of promoting this novel concept of articial communication channels are explored</p

Enhancing human cooperation with multimodal augmented reality

Humans naturally use an impressive variety of ways to com-municate. In this work, we investigate the possibilities of complementing these natural communication channels with articial ones. For this, augmented reality is used as a technique to add synthetic visual and auditory stimuli to people's perception. A system for the mutual displayof the gaze direction of two interactants is presented and its acceptance is shown through a study. Finally, future possibilities of promoting this novel concept of articial communication channels are explored</p

Mediated attention with multimodal augmented reality

We present an Augmented Reality (AR) system to supportcollaborative tasks in a shared real-world interaction spaceby facilitating joint attention. The users are assisted by information about their interaction partner's field of view both visually and acoustically. In our study, the audiovisual improvements are compared with an AR system without these support mechanisms in terms of the participants' reaction times and error rates. The participants performed a simple object-choice task we call the gaze game to ensure controlled experimental conditions. Additionally, we asked the subjects to fill in a questionnaire to gain subjective feedback from them. We were able to show an improvement for both dependent variables as well as positive feedback for the visual augmentation in the questionnaire.</p

1,3-Diazepanes of Natural Product-Like Complexity from Cyanamide-Induced Rearrangement of Epoxy-δ-lactams

A synthetic procedure toward 1,3-diazepane scaffolds of natural product-like complexity was developed for the construction of RNA-directed ligand libraries. A molecular building block was designed that combines the characteristics of RNA-binding natural products, including a high density of hydrogen bond donors and acceptors around a rigid, nonplanar scaffold with straightforward total-synthetic accessibility that permits extensive control over the chemical space. The synthesis of the 1,3-diazepane scaffold was achieved via an unprecedented cyanamide-induced rearrangement of epoxy-δ-lactams

Nanopore-Based Conformational Analysis of a Viral RNA Drug Target

Nanopores are single-molecule sensors that show exceptional promise as a biomolecular analysis tool by enabling label-free detection of small amounts of sample. In this paper, we demonstrate that nanopores are capable of detecting the conformation of an antiviral RNA drug target. The hepatitis C virus uses an internal ribosome entry site (IRES) motif in order to initiate translation by docking to ribosomes in its host cell. The IRES is therefore a viable and important drug target. Drug-induced changes to the conformation of the HCV IRES motif, from a bent to a straight conformation, have been shown to inhibit HCV replication. However, there is presently no straightforward method to analyze the effect of candidate small-molecule drugs on the RNA conformation. In this paper, we show that RNA translocation dynamics through a 3 nm diameter nanopore is conformation-sensitive by demonstrating a difference in transport times between bent and straight conformations of a short viral RNA motif. Detection is possible because bent RNA is stalled in the 3 nm pore, resulting in longer molecular dwell times than straight RNA. Control experiments show that binding of a weaker drug does not produce a conformational change, as consistent with independent fluorescence measurements. Nanopore measurements of RNA conformation can thus be useful for probing the structure of various RNA motifs, as well as structural changes to the RNA upon small-molecule binding