25 Result(s)
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Joseph A. Piccirilli
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Open AccessStructural basis for promiscuity in ligand recognition by yjdF riboswitch
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Sub-3-Å cryo-EM structure of RNA enabled by engineered homomeric self-assembly
High-resolution structural studies are essential for understanding the folding and function of diverse RNAs. Herein, we present a nanoarchitectural engineering strategy for efficient structural determination o...
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Structural basis for substrate binding and catalysis by a self-alkylating ribozyme
Ribozymes that react with small-molecule probes have important applications in transcriptomics and chemical biology, such as RNA labeling and imaging. Understanding the structural basis for these RNA-modifying...
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Branched kissing loops for the construction of diverse RNA homooligomeric nanostructures
In biological systems, large and complex structures are often assembled from multiple simpler identical subunits. This strategy—homooligomerization—allows efficient genetic encoding of structures and avoids th...
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Confluence of theory and experiment reveals the catalytic mechanism of the Varkud satellite ribozyme
The Varkud satellite ribozyme catalyses site-specific RNA cleavage and ligation, and serves as an important model system to understand RNA catalysis. Here, we combine stereospecific phosphorothioate substituti...
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Open AccessA conserved RNA structural motif for organizing topology within picornaviral internal ribosome entry sites
Picornaviral IRES elements are essential for initiating the cap-independent viral translation. However, three-dimensional structures of these elements remain elusive. Here, we report a 2.84-Å resolution crysta...
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Open AccessStructural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif
The DIR2s RNA aptamer, a second-generation, in-vitro selected binder to dimethylindole red (DIR), activates the fluorescence of cyanine dyes, DIR and oxazole thiazole blue (OTB), allowing detection of two well...
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Open AccessSynthesizing topological structures containing RNA
Though knotting and entanglement have been observed in DNA and proteins, their existence in RNA remains an enigma. Synthetic RNA topological structures are significant for understanding the physical and biolog...
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Reverse transcriptases lend a hand in splicing catalysis
The first high-resolution views of group II intron maturases illuminate the architectural and functional roles of these multidomain proteins in splicing and DNA invasion. The maturases show striking structural...
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Crystal structure of the Varkud satellite ribozyme
Crystal structures of the full-length VS ribozyme show a domain-swapped dimer that reveals potential mechanisms for cis and trans processing, and suggest convergent evolution in the active site motifs across mult...
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RNA made in its own mirror image
An RNA enzyme has been generated that can assemble a mirror-image version of itself. The finding helps to answer a long-standing conundrum about how RNA molecules could have proliferated on prebiotic Earth. See L...
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A G-quadruplex–containing RNA activates fluorescence in a GFP-like fluorophore
Spinach is an RNA aptamer analog of GFP that is widely used for fluorescent labeling of cellular RNAs. Crystal structures of Spinach–fluorophore complexes uncover an unusual G-quadruplex RNA fold that is invol...
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Evidence for a group II intron–like catalytic triplex in the spliceosome
It has long been thought that the catalytic RNAs of self-splicing group II introns and the spliceosome function by similar mechanisms. Now, a combination of genetic, cross-linking, and biochemical analyses of ...
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RNA catalyses nuclear pre-mRNA splicing
In nuclear pre-messenger RNA splicing, introns are excised by the spliceosome, a dynamic machine composed of both proteins and small nuclear RNAs (snRNAs). Over thirty years ago, after the discovery of self-sp...
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Prebiotic RNA unstuck
Non-enzymatic copying of an RNA template is appealing as a transition from pre-life to an RNA world, but it has been difficult to demonstrate in the laboratory. Now, two separate studies focusing on RNA's back...
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A portable RNA sequence whose recognition by a synthetic antibody facilitates structural determination
Crystallization of RNA molecules can pose a challenge, and the U1A RNA binding protein has been used to facilitate the process. Now a different portable RNA sequence and a synthetic Fab are presented as tools ...
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'Turning on' riboswitches to their antibacterial potential
Drug-resistant bacteria are a growing challenge to world health, and new approaches to antibiotic development are needed. Riboswitches, regulatory elements of mRNA, are shown to be a potential new target for a...
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The electrostatic character of the ribosomal surface enables extraordinarily rapid target location by ribotoxins
α-sarcin ribotoxins comprise a unique family of ribonucleases that cripple the ribosome by catalyzing endoribonucleolytic cleavage of ribosomal RNA at a specific location in the sarcin/ricin loop (SRL). The SR...
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General acid catalysis by the hepatitis delta virus ribozyme
Recent crystallographic and functional analyses of RNA enzymes have raised the possibility that the purine and pyrimidine nucleobases may function as general acid-base catalysts. However, this mode of nucleoba...
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Metal ion coordination by the AGC triad in domain 5 contributes to group II intron catalysis
Group II introns require numerous divalent metal ions for folding and catalysis. However, because little information about individual metal ions exists, elucidating their ligands, functional roles and relation...
