Artificial DNA and RNA structures have been used as scaffolds for a variety of nanoscale devices. In comparison to structures, limited in size, but they also advantages: can fold during transcription thus be genetically encoded expressed cells. We introduce an architecture designing artificial that from single strand, which arrays antiparallel helices are precisely organized by tertiary motifs new type crossover pattern. constructed tiles assemble into hexagonal lattices demonstrated made...

The structural information encoding specific conformations of natural RNAs can be implemented within artificial RNA sequences to control both three-dimensional (3D) shape and self-assembling interfaces for nanotechnology synthetic biology applications. We have identified three motifs known direct helical topology into approximately 90 degrees bends: a five-way tRNA junction, three-way two-helix bend. These motifs, embedded rationally designed (tectoRNA), were chosen generating square-shaped...

Natural stable RNAs fold and assemble into complex three-dimensional architectures by relying on the hierarchical formation of intricate, recurrent networks noncovalent tertiary interactions. These sequence-dependent specify RNA structural modules enabling orientational topological control helical struts to form larger self-folding domains. Borrowing concepts from linguistics, we defined an extended syntax for programming strands complex, responsive nanostructures under both thermodynamic...

RNA nanotechnology aims to use as a programmable material create self-assembling nanodevices for application in medicine and synthetic biology. The main challenge is develop advanced robotic devices that both sense, compute, actuate obtain enhanced control over molecular processes. Here, we the origami method prototype an device, named "Traptamer," mechanically traps fluorescent aptamer, iSpinach. Traptamer shown sense two key strands, acts Boolean AND gate, reversibly controls fluorescence...

Specific recognitions of GNRA tetraloops by small helical receptors are among the most widespread long-range packing interactions in large ribozymes. However, contrast to GYRA and GAAA tetraloops, very few GNRA/receptor have yet been identified involve GGAA nature. A novel vitro selection scheme based on a rigid self-assembling tectoRNA scaffold designed for isolation intermolecular with A-minor motifs has yielded new tetraloop-binding affinity nanomolar range. One selected is 12 nt RNA...

Stable RNAs are modular and hierarchical 3D architectures taking advantage of recurrent structural motifs to form extensive non-covalent tertiary interactions. Sequence atomic structure analysis has revealed a novel submotif involving minimal set five nucleotides, termed the UA_handle motif (5'XU/AN(n)X3'). It consists U:A Watson-Crick: Hoogsteen trans base pair stacked over classic Watson-Crick pair, bulge one or more nucleotides that can act as handle for making different types long-range...

RNA molecules take advantage of prevalent structural motifs to fold and assemble into well-defined 3D architectures. The A-minor junction is a class that specifically controls coaxial stacking helices in natural RNAs. A sensitive self-assembling supra-molecular system was used as an assay compare several previously unidentified junctions by native polyacrylamide gel electrophoresis atomic force microscopy. This modular follows topological rule can accommodate variety interchangeable...

Large-scale and continuous conformational changes in the RNA self-folding process present significant challenges for structural studies, often requiring trade-offs between resolution observational scope. Here, we utilize individual-particle cryo-electron tomography (IPET) to examine post-transcriptional of designed origami 6-helix bundle with a clasp helix (6HBC). By avoiding selection, classification, averaging, or chemical fixation optimizing cryo-ET data acquisition parameters,...

RNA is a functionally rich and diverse biomaterial responsible for regulating several cellular processes. This functionality has been harnessed to build predominately small nanoscale structures drug delivery the treatment of disease. The understanding design principles large will allow further control stoichiometry spatial arrangement drugs ligands. We present characterization nanotubes that self-assemble from programmable monomers, or tiles, formed by five distinct strands. Tiles include...

Magnesium-ion-mediated RNA−RNA loop−receptor interactions, in conjunction with gold nanoparticles derivatized DNA, have been used to make self-assembled nanowires. A wire located between lithographically fabricated nanoelectrodes is demonstrated that exhibits activated conduction by electron hopping at temperatures the 150−300 K range. These techniques ability link particles devices and future may be assemble practical circuits.

We introduce and study the computational power of Oritatami, a theoretical model to explore greedy molecular folding, by which molecule begins fold before awaiting end its production. This is inspired recent experimental work demonstrating construction shapes at nanoscale folding an RNA during transcription from engineered sequence synthetic DNA. An important challenge this model, also encountered in experiments, get single into different shapes, depending on surrounding molecules....

Abstract RNA nanotechnology takes advantage of structural modularity to build self‐assembling nano‐architectures with applications in medicine and synthetic biology. The use paranemic motifs, that form without unfolding existing secondary structure, allows for the creation nanostructures are compatible cotranscriptional folding vitro vivo. In previous work, kissing‐loop (KL) motifs have been widely used design fold cotranscriptionally. However, crossover (PX) motif has not yet explored...

We introduce and study the computational power of Oritatami, a theoretical model that explores greedy molecular folding, whereby strand begins to fold before its production is complete. This inspired by our recent experimental work demonstrating construction shapes at nanoscale from RNA, where strands RNA into programmable during their transcription an engineered sequence synthetic DNA. In we explore process folding single-strand bit in such way final emerges as space-time diagram...

Abstract The folding of RNA and protein molecules during their synthesis is a crucial self-assembly process that nature employs to convert genetic information into the complex molecular machinery supports life. Misfolding events are cause several diseases, pathway central biomolecules, such as ribosome, strictly regulated by programmed maturation processes chaperones. However, dynamic challenging study because current structure determination methods heavily rely on averaging, existing...

The structure of bonds in biomolecules, such as base pairs RNA chains or native interactions proteins, can be presented the form a chord diagram. A given biomolecule is then characterized by genus an auxiliary two-dimensional surface associated to In this work we introduce notion trace, which describes dependence on choice subchain backbone chain. We find that trace encodes interesting physical and biological information about its three dimensional structural complexity; particular it gives...

Stable RNAs rely on a vast repertoire of long-range interactions to assist in the folding complex cellular machineries such as ribosome. The universally conserved L39/H89 interaction is GNRA-like/receptor localized proximity peptidyl transferase center large subunit Because its central location, likely originated at an early evolutionary stage ribosome and played significant role function. However, self-assembly impaired outside ribosomal context. Herein, we demonstrate that structural...