Branched Kissing Loops for the Construction of Diverse RNA Homooligomeric Nanostructures (original) (raw)
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Nature Chemistry, 2010
DNA has recently been used as a programmable 'smart' building block for the assembly of a wide range of nanostructures. It remains difficult, however, to construct DNA assemblies that are also functional. Incorporating RNA is a promising strategy to circumvent this issue as RNA is structurally related to DNA but exhibits rich chemical, structural and functional diversities. However, only a few examples of rationally designed RNA structures have been reported. Herein, we describe a simple, general strategy for the de novo design of nanostructures in which the selfassembly of RNA strands is programmed by DNA strands. To demonstrate the versatility of this approach, we have designed and constructed three different RNA-DNA hybrid branched nanomotifs (tiles), which readily assemble into one-dimensional nanofibres, extended twodimensional arrays and a discrete three-dimensional object. The current strategy could enable the integration of the precise programmability of DNA with the rich functionality of RNA. Molecular self-assembly holds promise as an effective approach for nanoconstruction 1-4. The use of DNA, in particular, has been extensively explored as smart building blocks 5-9. This has led to the successful assembly of many well-defined nanostructures 10-27 , but the question remains of how to prepare functional DNA assemblies. RNA, in contrast, exhibits rich chemical, structural and functional diversities. For example, mRNAs carry information that directs protein syntheses, and rRNAs fold and assemble into ribosomes. Ribozymes catalyse chemical reactions, aptamers can specifically bind to ligands, and microRNAs and siRNAs regulate gene activities. If RNA could be used as building blocks for nanoconstruction, it would be straightforward to incorporate naturally existing structural and functional RNA modalities into self-assembled nanostructures. However, the rational design and assembly of RNA architectures remains a challenge. Only a few examples have been Users may view, print, copy, download and text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:
Structures of Artificially Designed RNA Nanoarchitectures at Near-Atomic Resolution
2020
Though advances in nanotechnology have enabled the construction of synthetic nucleic acid based nanoarchitectures with ever-increasing complexity for various applications, high-resolution structures are lacking due to the difficulty of obtaining good diffracting crystals. Here we report the design of RNA nanostructures based on homooligomerizable tiles from an RNA single-strand for X-ray determination. Three structures are solved to near-atomic resolution: a 2D parallelogram, an unexpectedly formed 3D nanobracelet, and a 3D nanocage. Structural details of their constituent motifs—such as kissing loops, branched kissing-loops and T-junctions—that resemble natural RNA motifs and resisted X-ray determination are revealed. This work unveils the largely unexplored potential of crystallography in gaining high-resolution feedback for nanostructure design and suggests a novel route to investigate RNA motif structures by configuring them into nanoarchitectures.
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Nature, 2008
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Lecture Notes in Computer Science, 2001
DNA self-assembly is a methodology for the construction of molecular scale structures. In this method, arti cially synthesized single stranded DNA self-assemble into DNA crossover molecules tiles. These DNA tiles have sticky ends that preferentially match the sticky ends of certain other DNA tiles, facilitating the further assembly into tiling lattices. We discuss key theoretical and practical challenges of DNA selfassembly, a s w ell as numerous potential applications. The self-assembly of large 2D lattices consisting of up to thousands of tiles have been recently demonstrated, and 3D DNA lattices may s o o n b e feasible to construct. We describe various novel DNA tiles with properties that facilitate self-assembly and their visualization by imaging devices such as atomic force microscope. We discuss bounds on the speed and error rates of the various types of self-assembly reactions, as well as methods that may minimize errors in self-assembly. W e brie y discuss the ongoing development of attachment chemistry from DNA lattices to various types of molecules, and consider application of DNA lattices assuming the development of such appropriate attachment chemistry from DNA lattices to these objects as a substrate for: a layout of molecular electronic circuit components, b surface chemistry, for example ultra compact annealing arrays, c molecular robotics; for manipulation of molecules using molecular motor devices. DNA self-assembly can, using only a small number of component tiles, provide arbitrarily complex assemblies. It can be used to execute computation, using tiles that specify individual steps of the computation. In this emerging new methodology for computation:-input is provided by sets of single stranded DNA that serve a s n ucleation sites for assemblies, and
Organic & Biomolecular Chemistry, 2006
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In recent years, a number of research groups have begun developing nanofabrication methods based on DNA self-assembly. Here we review our recent experimental progress to utilize novel DNA nanostructures for self-assembly as well as for templates in the fabrication of functional nano-patterned materials. We have prototyped a new DNA nanostructure known as a cross structure. This nanostructure has a 4-fold
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Structural DNA Nanotechnology: From Design to Applications
International Journal of Molecular Sciences, 2012
The exploitation of DNA for the production of nanoscale architectures presents a young yet paradigm breaking approach, which addresses many of the barriers to the self-assembly of small molecules into highly-ordered nanostructures via construct addressability. There are two major methods to construct DNA nanostructures, and in the current review we will discuss the principles and some examples of applications of both the tile-based and DNA origami methods. The tile-based approach is an older method that provides a good tool to construct small and simple structures, usually with multiply repeated domains. In contrast, the origami method, at this time, would appear to be more appropriate for the construction of bigger, more sophisticated and exactly defined structures.