RNA

Overview

publication venue for

• Small molecule telomerase inhibitors are also potent inhibitors of telomeric C-strand synthesis. 2024
• Transcription factors ERα and Sox2 have differing multiphasic DNA- and RNA-binding mechanisms. 2024
• DNMT1 inhibition by pUG-fold quadruplex RNA 2023
• DNMT1 inhibition by pUG-fold quadruplex RNA 2023
• DNMT1 inhibition by pUG-fold quadruplex RNA 2023
• DNMT1 inhibition by pUG-fold quadruplex RNA. 2023
• Evolutionary divergence of Firre localization and expression 2022
• Are stress granules the RNA analogs of misfolded protein aggregates? 2022
• RNA in biological condensates INTRODUCTION 2022
• SARS-CoV-2 infection triggers widespread host mRNA decay leading to an mRNA export block 2021
• RNA partitioning into stress granules is based on the summation of multiple interactions 2021
• PAR-TERRA is the main contributor to telomeric repeat-containing RNA transcripts in normal and cancer mouse cells. 2021
• RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers 2020
• Integrated analysis of directly captured microRNA targets reveals the impact of microRNAs on mammalian transcriptome 2020
• The landscape of eukaryotic mRNPs 2020
• C9orf72 and triplet repeat disorder RNAs: G-quadruplex formation, binding to PRC2 and implications for disease mechanisms 2019
• EIF2B2 mutations in vanishing white matter disease hypersuppress translation and delay recovery during the integrated stress response 2018
• RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme 2017
• Defects in THO/TREX-2 function cause accumulation of novel cytoplasmic mRNP granules that can be cleared by autophagy 2016
• Ubiquitous accumulation of 3′ mRNA decay fragments in Saccharomyces cerevisiae mRNAs with chromosomally integrated MS2 arrays 2016
• The recruitment of chromatin modifiers by long noncoding RNAs: lessons from PRC2 2015
• Differential effects of Ydj1 and Sis1 on Hsp70-mediated clearance of stress granules in Saccharomyces cerevisiae 2015
• MS2 coat proteins bound to yeast mRNAs block 5′ to 3′ degradation and trap mRNA decay products: implications for the localization of mRNAs by MS2-MCP system 2015
• RNA World research-still evolving 2015
• Riboswitches: still a lot of undiscovered country 2015
• Circular RNAs: diversity of form and function 2014
• RNA recognition by the DNA end-binding Ku heterodimer 2013
• tRNA residues evolved to promote translational accuracy. 2013
• Genome-wide maps of polyadenylation reveal dynamic mRNA 3′-end formation in mammalian cell lineages 2013
• Functional consequences of T-stem mutations in E. coli tRNAThrUGU in vitro and in vivo. 2011
• Solution structure of RNase P RNA 2011
• Stm1 modulates translation after 80S formation inSaccharomyces cerevisiae 2011
• Distinct regulatory programs establish widespread sex-specific alternative splicing in Drosophila melanogaster 2011
• Identification of transcription start sites of trans-spliced genes: Uncovering unusual operon arrangements 2011
• Ku can contribute to telomere lengthening in yeast at multiple positions in the telomerase RNP 2011
• Chiral histidine selection by D-ribose RNA 2010
• Structural basis for recognition of S-adenosylhomocysteine by riboswitches 2010
• Natural and artificial RNAs occupy the same restricted region of sequence space 2010
• Multiple independent domains of dGW182 function in miRNA-mediated repression in Drosophila 2009
• Mapping metal-binding sites in the catalytic domain of bacterial RNase P RNA 2009
• Metal ion specificities for folding and cleavage activity in the Schistosoma hammerhead ribozyme 2008
• Toward predicting self-splicing and protein-facilitated splicing of group I introns 2008
• tRNA cleavage is a conserved response to oxidative stress in eukaryotes 2008
• Computational analysis of miRNA-mediated repression of translation: Implications for models of translation initiation inhibition 2008
• Hammerhead redux: does the new structure fit the old biochemical data? 2008
• Ligand-dependent folding of the three-way junction in the purine riboswitch 2008
• Myo2p, a class V myosin in budding yeast, associates with a large ribonucleic acid-protein complex that contains mRNAs and subunits of the RNA-processing body 2008
• The Cech Symposium: A celebration of 25 years of ribozymes, 10 years of TERT, and 60 years of Tom 2008
• Minimal and extended hammerheads utilize a similar dynamic reaction mechanism for catalysis. 2008
• C. elegans sequences that control trans-splicing and operon pre-mRNA processing 2007
• Improved native affinity purification of RNA 2007
• The 51-63 base pair of tRNA confers specificity for binding by EF-Tu. 2007
• A novel family of C. elegans snRNPs contains proteins associated with trans-splicing 2007
• Characterization of the structure, function, and mechanism of B2 RNA, an ncRNA repressor of RNA polymerase II transcription 2007
• Local RNA structural changes induced by crystallization are revealed by SHAPE 2007
• Translation-independent inhibition of mRNA deadenylation during stress in Saccharomyces cerevisiae 2006
• Low abundance of telomerase in yeast: Implications for telomerase haploinsufficiency 2006
• Conventional 3′ end formation is not required for NMD substrate recognition in Saccharomyces cerevisiae 2006
• The domain of the Bacillus subtilis DEAD-box helicase YxiN that is responsible for specific binding of 23S rRNA has an RNA recognition motif fold. 2006
• Comparison of crystal structure interactions and thermodynamics for stabilizing mutations in the Tetrahymena ribozyme 2006
• Virus-like particles of the Ty3 retrotransposon assemble in association with P-body components 2006
• Binding of misacylated tRNAs to the ribosomal A site. 2005
• Crystal structure and functional analysis of DEAD-box protein Dhh1p 2005
• Structural implications of novel diversity in eucaryal RNase P RNA 2005
• Processing bodies require RNA for assembly and contain nontranslating mRNAs 2005
• U2AF binding selects for the high conservation of the C. elegans 3′ splice site 2005
• Overexpression of Exportin 5 enhances RNA interference mediated by short hairpin RNAs and microRNAs 2005
• The yeast Apq12 protein affects nucleocytoplasmic mRNA transport 2004
• The Euplotes telomerase subunit p43 stimulates enzymatic activity and processivity in vitro 2004
• A general method for rapid and nondenaturing purification of RNAs 2004
• The conserved RNA recognition motif 3 of U2 snRNA auxiliary factor (U2AF⁶⁵) is essential in vivo but dispensable for activity in vitro 2004
• Less isn't always more. 2003
• A template-proximal RNA paired element contributes to Saccharomyces cerevisiae telomerase activity 2003
• Quantitation of free energy profiles in RNA-ligand interactions by nucleotide analog interference mapping 2003
• UAP56 levels affect viability and mRNA export in Caenorhabditis elegans 2003
• An uncapped RNA suggests a model for Caenorhabditis elegans polycistronic pre-mRNA processing. 2003
• Stop codon suppression via inhibition of eRF1 expression 2003
• Analysis of recombinant yeast decapping enzyme 2003
• The enhancer of decapping proteins, Edc1p and Edc2p, bind RNA and stimulate the activity of the decapping enzyme 2003
• Sex lethal and U2 small nuclear ribonucleoprotein auxiliary factor (U2AF(65)) recognize polypyrimidine tracts using multiple modes of binding 2003
• Phylogenetic analysis of the structure of RNase MRP RNA in yeasts 2002
• In vivo selection of better self-splicing introns in Escherichia coli:: The role of the P1 extension helix of the Tetrahymena intron 2002
• Both Ran and importins have the ability to function as nuclear mRNA export factors 2002
• The DEAD box helicase, Dhh1p, functions in mRNA decapping and interacts with both the decapping and deadenylase complexes 2001
• Chemical and enzymatic synthesis of tRNAs for high-throughput crystallization 2001
• Computational modeling of eukaryotic mRNA turnover 2001
• Evaluation and refinement of tmRNA structure using gene sequences from natural microbial communities 2001
• Defects in the mRNA export factors Rat7p, Gle1p, Mex67p, and Rat8p cause hyperadenylation during 3′-end formation of nascent transcripts 2001
• The Escherichia coli DEAD protein DbpA recognizes a small RNA hairpin in 23S rRNA 2001
• Comparison of the hammerhead cleavage reactions stimulated by monovalent and divalent cations 2001
• Evaluation of methylphosphonates as analogs for detecting phosphate contacts in RNA-protein complexes 2001
• An early transition state for folding of the P4-P6 RNA domain 2001
• Interplay between AAUAAA and the trans-splice site in processing of a Caenorhabditis elegans operon pre-mRNA. 2001
• Phylogenetic-comparative analysis of the eukaryal ribonuclease P RNA 2000
• Suppression of eukaryotic translation termination by selected RNAs 2000
• Differential recognition of the polypyrimidine-tract by the general splicing factor U2AF⁶⁵ and the splicing repressor sex-lethal 2000
• Enhanced detection of tRNA isoacceptors by combinatorial oligonucleotide hybridization 2000
• Molecular interactions and metal binding in the theophylline-binding core of an RNA aptamer 2000
• Quantifying the energetic interplay of RNA tertiary and secondary structure interactions 1999
• Aberrant mRNAs with extended 3′ UTRs are substrates for rapid degradation by mRNA surveillance 1999
• High-performance liquid chromatography purification of homogenous-length RNA produced by trans cleavage with a hammerhead ribozyme 1999
• Identification and characterization of a novel high affinity metal-binding site in the hammerhead ribozyme 1999
• In vitro selection of RNAs with increased tertiary structure stability 1999
• U2AF35 is encoded by an essential gene clustered in an operon with RRM/cyclophilin in Caenorhabditis elegans 1999
• mRNA Surveillance in Eukaryotes: Kinetic Proofreading of Proper Translation Termination as assessed by mRNP Domain Organization? 1999
• Enhancer elements activate the weak 3' splice site of alpha-tropomyosin exon 2. 1998
• In vitro selection of the Naegleria GIR1 ribozyme identifies three base changes that dramatically improve activity 1998
• A quantitative study of the flexibility contributed to RNA structures by nicks and single-stranded gaps 1998
• Cryoenzymology of the hammerhead ribozyme 1998
• T7 RNA polymerase produces 5′ end heterogeneity during in vitro transcription from certain templates 1998
• A new assay for tRNA aminoacylation kinetics 1998
• Effects of polyvalent cations on the folding of an rRNA three-way junction and binding of ribosomal protein S15 1998
• Hammerhead ribozyme kinetics 1998
• Polyadenylation of telomerase RNA in budding yeast 1997
• Functional groups on the cleavage site pyrimidine nucleotide are required for stabilization of the hammerhead transition state 1997
• Mutagenesis and comparative sequence analysis of a base triple joining the two domains of group I ribozymes 1997
• An RNA internal loop acts as a hinge to facilitate ribozyme folding and catalysis 1997
• X-ray crystallography of large RNAs: Heavy-atom derivatives by RNA engineering 1996
• In vitro selection of a novel catalytic RNA: Characterization of a sulfur alkylation reaction and interaction with a small peptide 1996
• Kinetic pathway for folding of the Tetrahymena ribozyme revealed by three UV-inducible crosslinks 1996
• Selecting apt RNAs for NMR 1996
• Kinetic characterization of two I/II format hammerhead ribozymes 1996
• Activity and thermostability of the small self-splicing group I intron in the pre-tRNA(IIe) of the purple bacterium Azoarcus 1996
• IDENTIFICATION OF RIBOZYMES WITHIN A RIBOZYME LIBRARY THAT EFFICIENTLY CLEAVE A LONG SUBSTRATE RNA 1995
• AN IMPORTANT RNA TERTIARY INTERACTION OF GROUP-I AND GROUP-II INTRONS IS IMPLICATED IN GRAM-POSITIVE RNASE-P RNAS 1995
• ANALYSIS OF THE STRUCTURE OF TETRAHYMENA NUCLEAR RNAS IN-VIVO - TELOMERASE RNA, THE SELF-SPLICING RIBOSOMAL-RNA INTRON, AND U2 SNRNA 1995
• GNRA TETRALOOPS MAKE A U-TURN 1995
• INHIBITION OF THE HAMMERHEAD RIBOZYME BY NEOMYCIN 1995
• KEEPING RNA HAPPY 1995
• SELF-ASSEMBLY OF A GROUP-I INTRON ACTIVE-SITE FROM ITS COMPONENT TERTIARY STRUCTURAL DOMAINS 1995

Research

keywords

• 0601 Biochemistry and Cell Biology