Search Results - "Piccirilli, Joseph A"

Synthesis, Properties, and Applications of Oligonucleotides Containing an RNA Dinucleotide Phosphorothiolate Linkage by Li, Nan-Sheng, Frederiksen, John K, Piccirilli, Joseph A

“…RNA represents a prominent class of biomolecules. Present in all living systems, RNA plays many essential roles in gene expression, regulation, and…”
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Sub-3-Å cryo-EM structure of RNA enabled by engineered homomeric self-assembly by Liu, Di, Thélot, François A., Piccirilli, Joseph A., Liao, Maofu, Yin, Peng

“…High-resolution structural studies are essential for understanding the folding and function of diverse RNAs. Herein, we present a nanoarchitectural engineering…”
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Crystal structure of a cap-independent translation enhancer RNA by Lewicka, Anna, Roman, Christina, Jones, Stacey, Disare, Michael, Rice, Phoebe A, Piccirilli, Joseph A

“…Abstract In eukaryotic messenger RNAs, the 5′ cap structure binds to the translation initiation factor 4E to facilitate early stages of translation. Although…”
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The hammerhead self-cleaving motif as a precursor to complex endonucleolytic ribozymes by DasGupta, Saurja, Nykiel, Kamila, Piccirilli, Joseph A.

“…Connections between distinct catalytic RNA motifs through networks of mutations that retain catalytic function (neutral networks) were likely central to the…”
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Branched kissing loops for the construction of diverse RNA homooligomeric nanostructures by Liu, Di, Geary, Cody W., Chen, Gang, Shao, Yaming, Li, Mo, Mao, Chengde, Andersen, Ebbe S., Piccirilli, Joseph A., Rothemund, Paul W. K., Weizmann, Yossi

“…In biological systems, large and complex structures are often assembled from multiple simpler identical subunits. This strategy—homooligomerization—allows…”
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Crystal structure of the Varkud satellite ribozyme by Suslov, Nikolai B, DasGupta, Saurja, Huang, Hao, Fuller, James R, Lilley, David M J, Rice, Phoebe A, Piccirilli, Joseph A

“…Crystal structures of the full-length VS ribozyme show a domain-swapped dimer that reveals potential mechanisms for cis and trans processing, and suggest…”
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Structural Basis for Substrate Helix Remodeling and Cleavage Loop Activation in the Varkud Satellite Ribozyme by DasGupta, Saurja, Suslov, Nikolai B, Piccirilli, Joseph A

“…The Varkud satellite (VS) ribozyme catalyzes site-specific RNA cleavage and ligation reactions. Recognition of the substrate involves a kissing loop…”
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Post-transcriptional methylation of mitochondrial-tRNA differentially contributes to mitochondrial pathology by Maharjan, Sunita, Gamper, Howard, Yamaki, Yuka, Christian, Thomas, Henley, Robert Y., Li, Nan-Sheng, Suzuki, Takeo, Suzuki, Tsutomu, Piccirilli, Joseph A., Wanunu, Meni, Seifert, Erin, Wallace, Douglas C., Hou, Ya-Ming

“…Human mitochondrial tRNAs (mt-tRNAs), critical for mitochondrial biogenesis, are frequently associated with pathogenic mutations. These mt-tRNAs have unusual…”
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The DEAH Box ATPases Prp16 and Prp43 Cooperate to Proofread 5′ Splice Site Cleavage during Pre-mRNA Splicing by Koodathingal, Prakash, Novak, Thaddeus, Piccirilli, Joseph A., Staley, Jonathan P.

“…To investigate the mechanisms underlying accurate pre-mRNA splicing, we developed an in vitro assay sensitive to proofreading of 5′ splice site cleavage. We…”
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Synthesizing topological structures containing RNA by Liu, Di, Shao, Yaming, Chen, Gang, Tse-Dinh, Yuk-Ching, Piccirilli, Joseph A., Weizmann, Yossi

“…Though knotting and entanglement have been observed in DNA and proteins, their existence in RNA remains an enigma. Synthetic RNA topological structures are…”
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Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif by Shelke, Sandip A., Shao, Yaming, Laski, Artur, Koirala, Deepak, Weissman, Benjamin P., Fuller, James R., Tan, Xiaohong, Constantin, Tudor P., Waggoner, Alan S., Bruchez, Marcel P., Armitage, Bruce A., Piccirilli, Joseph A.

“…The DIR2s RNA aptamer, a second-generation, in-vitro selected binder to dimethylindole red (DIR), activates the fluorescence of cyanine dyes, DIR and oxazole…”
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A conserved RNA structural motif for organizing topology within picornaviral internal ribosome entry sites by Koirala, Deepak, Shao, Yaming, Koldobskaya, Yelena, Fuller, James R., Watkins, Andrew M., Shelke, Sandip A., Pilipenko, Evgeny V., Das, Rhiju, Rice, Phoebe A., Piccirilli, Joseph A.

“…Picornaviral IRES elements are essential for initiating the cap-independent viral translation. However, three-dimensional structures of these elements remain…”
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General acid catalysis by the hepatitis delta virus ribozyme by Piccirilli, Joseph A, Das, Subha R

“…Recent crystallographic and functional analyses of RNA enzymes have raised the possibility that the purine and pyrimidine nucleobases may function as general…”
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Molecular basis of mycobacterial lipid antigen presentation by CD1c and its recognition by αβ T cells by Roy, Sobhan, Ly, Dalam, Li, Nan-Sheng, Altman, John D, Piccirilli, Joseph A, Moody, D Branch, Adams, Erin J

“…CD1c is a member of the group 1 CD1 family of proteins that are specialized for lipid antigen presentation. Despite high cell surface expression of CD1c on key…”
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Structural basis for promiscuity in ligand recognition by yjdF riboswitch by Krochmal, Daniel, Roman, Christina, Lewicka, Anna, Shao, Yaming, Piccirilli, Joseph A.

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A general and efficient approach to synthesize the phosphoramidites of 5′-18O labeled purine nucleosides by Nan-Sheng, Li, Dai, Qing, Weissman, Benjamin, Harris, Michael E, Piccirilli, Joseph A

“…5′-18O labeled RNA oligos are important probes to investigate the mechanism of 2′-O-transphosphorylation reactions. Here we describe a general and efficient…”
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Experimental and computational analysis of the transition state for ribonuclease A-catalyzed RNA 2′-O-transphosphorylation by Gu, Hong, Zhang, Shuming, Wong, Kin-Yiu, Radak, Brian K., Dissanayake, Thakshila, Kellerman, Daniel L., Dai, Qing, Miyagi, Masaru, Anderson, Vernon E., York, Darrin M., Piccirilli, Joseph A., Harris, Michael E.

“…Enzymes function by stabilizing reaction transition states; therefore, comparison of the transition states of enzymatic and nonenzymatic model reactions can…”
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Identification of catalytic metal ion ligands in ribozymes by Frederiksen, John K., Piccirilli, Joseph A.

“…Site-bound metal ions participate in the catalytic mechanisms of many ribozymes. Understanding these mechanisms therefore requires knowledge of the specific…”
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Reinvestigating the Synthesis and Characterization of Ethyl 3‑[5-(2-Ethoxycarbonyl-1-methylvinyloxy)-1-methyl‑1H‑indol-3-yl]-but-2-enoate by Li, Nan-Sheng, Piccirilli, Joseph A., Greene, Geoffrey L.

“…We reinvestigated the reported method for the synthesis of ethyl 3-[5-(2-ethoxycarbonyl-1-methylvinyloxy)-1-methyl-1H-indol-3-yl]-but-2-enoate (MIBE), which…”
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Crystal Structure of the Catalytic Core of an RNA-Polymerase Ribozyme by Shechner, David M, Grant, Robert A, Bagby, Sarah C, Koldobskaya, Yelena, Piccirilli, Joseph A, Bartel, David P

“…Primordial organisms of the putative RNA world would have required polymerase ribozymes able to replicate RNA. Known ribozymes with polymerase activity best…”
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